Psyllid ID: psy200

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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-------430-------440-------450-------460-------470-------480-------490
Protein Sequence
MVLHPNEPITTVEEVPRSPRVTRSCSQLPQTPKSQRPNTCRTPTSHQPITPKTPSTLLSDLHLGSPRTPSSLLRSLKLDSPKRKIDTALEFASPKRVFKDADATSSGAASAVDATSTSDAVRSVSGSRSSAKADCLRPLSPIKNIILDKKSPFKAFIRDDEDLIKRSPAKLCSPRKLLFSEDKPKVEEKAKDSCELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITNHLIDLTYDNVKENGEVTGIGLKEVLGVISSVYCTSQSLHCSKDEDSFPLQQKLALASLLLLKSRPNVKDVTLGK
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHccccccccccHHHHHHHHHHHHHHHHcccccccEEEEcccccHHHHHHHHHHHHHHHccccEEEEEcccccccHHHHHHHHHHHHccccccccHHHHHHHHHHHHcccccEEEEEEEcccccccccHHHHHHHHccccccccEEEEEEEEcccccHHHHcccccccccccccEEEEccccHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHcccccccccccccccHHHHHHHHHHHHHHcccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccccccccccccccccccccccccccccccccHHHccccccccccccccccccccccccccccccccccccccccccHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHcccccccccccccHHHHHHHHHHHHHHHHcccccEEEEEccccccHHHHHHHHHHHHHHccccEEEEEEccEcccHHHHHHHHHHHHccccccccHHHHHHHHHHcccccccEEEEEEcHHHHHHcccccEEEEEcccccccccEEEEEEEEcccccHHHHHHHHHHHcccccEEEEcccccHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHcccccccccccHHHHHHHHHHHHccHHHHHHHHHHHcccHHHHHHHHHHHHHHHHccccEEcccc
Coil and Loop (DISEMBL)
mvlhpnepittveevprsprvtrscsqlpqtpksqrpntcrtptshqpitpktpstllsdlhlgsprtpssllrslkldspkrkIDTAlefaspkrvfkdadatssgaasavdatstsdavrsvsgsrssakadclrplspikniildkkspfkafirddedlikrspaklcsprkllfsedkpkveekakdscelpgrevQLEGIRQFLLGHvnnetsgsmyisgppgtgksasLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNElklkpggkserHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTifewpsipgsklVLVGVANALDLTDRMLPRLqanvtlqptlmnfapysREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITNHLIdltydnvkengevtGIGLKEVLGVISSVyctsqslhcskdedsfpLQQKLALASLLLlksrpnvkdvtlgk
Flexible Loop (DISEMBL)
mvlhpnepittveevprsprvtrscsqlpqtpksqrpntcrtptshqpitpktpstllsdlhlgSPRTPSsllrslkldspkRKIDtalefaspkrvfkdadatssgaasavdatstsdavrsvsgsrssakadclrplspikniildkkspfkAFIRddedlikrspaklcsprkllfsedkpkveekakdscelpgreVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNElklkpggkserHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIfewpsipgsKLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITNHLIDLTYDNVKENGEVTGIGLKEVLGVISSVYCTSQSLHCSKDEDSFPLQQKLALASllllksrpnvkdvtlgk
Low Complexity Region (SEG)
MVLHPNEPITTVEEVPRSPRVTRSCSQLPQTPKSQRPNTCRTPTSHQPITPKTPSTLLSDLHlgsprtpssllrslKLDSPKRKIDTALEFASPKRVFKdadatssgaasavdatstsdavrsvsgsrssaKADCLRPLSPIKNIILDKKSPFKAFIRDDEDLIKRSPAKLCSPRKLLFSEDKPKVEEKAKDSCELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFDTKHKSillildeidaleSRKQTILYTIFEWPSIPGSKLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITNHLIDLTYDNVKENGEVTGIGLKEVLGVISSVYCTSQSLHCSKDEDSFPlqqklalasllllksRPNVKDVTLGK
Disordered region (IsUnstruct)
******************************************************************************************************************************************LSPIKNIILDKKSPFKAFIRD*****************************************VQLEGIRQFLLGHVNN******************SLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITNHLIDLTYDNVKENGEVTGIGLKEVLGVISSVYCTSQSLHCSKD**SFPLQQKLALASLLLL*************
Disordered Region (DISOPRED)
******************************************************************************************************************************************************************************************EEKAKDSCELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITNHLIDL****************KEVLGVISSVYC**********EDSFPLQQKLALASLLLLKSRP*********
Disordered Region (DISEMBL)
MVLHPNEPITTVEE**********************************ITPKTPSTLLSDLHLGSPRTPSSLLRSLKLDSPKRKIDTALEFASPKRVF***********************************DCLRPLSPIKNIILDKKSPFKAFIRDDEDLIKRSPAKLCSPRKLLFSEDK***********ELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITNHLIDLTYDNVKENGEVTGIGLKEVLGVISSVYCTSQSLHCSKDEDSFPLQQKLALASLLLLKSRPNVKDVTLGK
Disordered Region (DISPRO)
*******************************************************************************************************************************************************************************KLLFSEDKPKVEEKAKDSCELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITNHLIDLTYDNVKENGEVTGIGLKEVLGVISSVYCTSQSLHCSKDEDSFPLQQKLALASLLLLKSRPNV*******
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MVLHPNEPITTVEEVPRSPRVTRSCSQLPQTPKSQRPNTCRTPTSHQPITPKTPSTLLSDLHLGSPRTPSSLLRSLKLDSPKRKIDTALEFASPKRVFKDADATSSGAASAVDATSTSDAVRSVSGSRSSAKADCLRPLSPIKNIILDKKSPFKAFIRDDEDLIKRSPAKLCSPRKLLFSEDKPKVEEKAKDSCELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITNHLIDLTYDNVKENGEVTGIGLKEVLGVISSVYCTSQSLHCSKDEDSFPLQQKLALASLLLLKSRPNVKDVTLGK
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	490	2.2.26 [Sep-21-2011]
O89033	562	Cell division control pro	yes	N/A	0.595	0.519	0.414	2e-61
Q99741	560	Cell division control pro	yes	N/A	0.595	0.521	0.408	2e-60
P41411	577	Cell division control pro	yes	N/A	0.602	0.511	0.315	4e-38
O16810	924	Origin recognition comple	no	N/A	0.442	0.234	0.352	3e-31
Q54RM2	631	Origin recognition comple	yes	N/A	0.438	0.340	0.331	4e-31
O74270	805	Origin recognition comple	N/A	N/A	0.651	0.396	0.289	2e-28
Q9JI69	850	Origin recognition comple	no	N/A	0.530	0.305	0.336	3e-28
Q8I615	1189	Origin recognition comple	yes	N/A	0.428	0.176	0.337	4e-27
Q80Z32	848	Origin recognition comple	no	N/A	0.506	0.292	0.328	1e-25
Q13415	861	Origin recognition comple	no	N/A	0.506	0.288	0.328	2e-25

>sp|O89033|CDC6_MOUSE Cell division control protein 6 homolog OS=Mus musculus GN=Cdc6 PE=2 SV=2

 Score =  236 bits (603), Expect = 2e-61,   Method: Compositional matrix adjust.
 Identities = 131/316 (41%), Positives = 192/316 (60%), Gaps = 24/316 (7%)

Query: 196 LPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVS--RAEIKDAFKTIY 253
           LP RE ++  IR FL  H+  + +GS+Y+SG PGTGK+A L+ ++   + E+K  FK+I 
Sbjct: 174 LPAREQEMGVIRNFLKEHICGKKAGSLYLSGAPGTGKTACLSRILQDFKKEVK-GFKSIL 232

Query: 254 INCNSVRNAASVYETIVNELK----LKPGGKSERHQLGAILKYFDTKHKSILLILDEIDA 309
           +NC S+R+A +V+  I  E+      +P GK    +L   L     K   I+L+LDE+D 
Sbjct: 233 LNCMSLRSAQAVFPAIAQEIGREELCRPAGKDLMRKLEKHLTA--EKGPMIVLVLDEMDQ 290

Query: 310 LESRKQTILYTIFEWPSIPGSKLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSR 369
           L+S+ Q +LYT+FEWP +  S+LVL+G+AN LDLTDR+LPRL+A    +P L+NF PY+R
Sbjct: 291 LDSKGQDVLYTLFEWPWLSNSRLVLIGIANTLDLTDRILPRLEARENCKPQLLNFPPYTR 350

Query: 370 EQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITNHLIDLTYDNVK-- 427
            QI  I+  +L Q  K  + +++A+Q  A KV+AVSGDIRKA+D+    I++   +V+  
Sbjct: 351 NQIAAILQDRLSQVSKDQVLDSAAIQFCARKVSAVSGDIRKALDVCRRAIEIVESDVRSQ 410

Query: 428 -------------ENGEVTGIGLKEVLGVISSVYCTSQSLHCSKDEDSFPLQQKLALASL 474
                        E+     +GL  +  VIS V     +L     +DS PLQQK+ + SL
Sbjct: 411 TVLKPLSECKSPSESPVPKRVGLAHISQVISEVDGNRVTLSQENTQDSLPLQQKILVCSL 470

Query: 475 LLLKSRPNVKDVTLGK 490
           LLL  R  +K+VTLGK
Sbjct: 471 LLLTRRLKIKEVTLGK 486

Involved in the initiation of DNA replication. Also participates in checkpoint controls that ensure DNA replication is completed before mitosis is initiated.
Mus musculus (taxid: 10090)

>sp|Q99741|CDC6_HUMAN Cell division control protein 6 homolog OS=Homo sapiens GN=CDC6 PE=1 SV=1

 Score =  234 bits (596), Expect = 2e-60,   Method: Compositional matrix adjust.
 Identities = 129/316 (40%), Positives = 191/316 (60%), Gaps = 24/316 (7%)

Query: 196 LPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVS--RAEIKDAFKTIY 253
           LP RE +++ IR FL  H+  + +GS+Y+SG PGTGK+A L+ ++   + E+K  FKTI 
Sbjct: 172 LPAREREMDVIRNFLREHICGKKAGSLYLSGAPGTGKTACLSRILQDLKKELK-GFKTIM 230

Query: 254 INCNSVRNAASVYETIVNELKL----KPGGKSERHQLGAILKYFDTKHKSILLILDEIDA 309
           +NC S+R A +V+  I  E+      +P GK    +L   +     K   I+L+LDE+D 
Sbjct: 231 LNCMSLRTAQAVFPAIAQEICQEEVSRPAGKDMMRKLEKHMTA--EKGPMIVLVLDEMDQ 288

Query: 310 LESRKQTILYTIFEWPSIPGSKLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSR 369
           L+S+ Q +LYT+FEWP +  S LVL+G+AN LDLTDR+LPRLQA    +P L+NF PY+R
Sbjct: 289 LDSKGQDVLYTLFEWPWLSNSHLVLIGIANTLDLTDRILPRLQAREKCKPQLLNFPPYTR 348

Query: 370 EQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITNHLIDLTYDNVKEN 429
            QI+ I+  +L Q  +  + + +A+Q  A KV+AVSGD+RKA+D+    I++   +VK  
Sbjct: 349 NQIVTILQDRLNQVSRDQVLDNAAVQFCARKVSAVSGDVRKALDVCRRAIEIVESDVKSQ 408

Query: 430 GEV---------------TGIGLKEVLGVISSVYCTSQSLHCSKDEDSFPLQQKLALASL 474
             +                 +GL  +  VIS V     +L     +DSFPLQQK+ + SL
Sbjct: 409 TILKPLSECKSPSEPLIPKRVGLIHISQVISEVDGNRMTLSQEGAQDSFPLQQKILVCSL 468

Query: 475 LLLKSRPNVKDVTLGK 490
           +LL  +  +K+VTLGK
Sbjct: 469 MLLIRQLKIKEVTLGK 484

Involved in the initiation of DNA replication. Also participates in checkpoint controls that ensure DNA replication is completed before mitosis is initiated.

Homo sapiens (taxid: 9606)

>sp|P41411|CDC18_SCHPO Cell division control protein 18 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=cdc18 PE=1 SV=1

 Score =  159 bits (403), Expect = 4e-38,   Method: Compositional matrix adjust.
 Identities = 108/342 (31%), Positives = 174/342 (50%), Gaps = 47/342 (13%)

Query: 189 KAKDSCELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASL-NLLVSRAEIKD 247
           K+  S  + GRE +   +  F   H++    G++Y+SG PGTGK+  L N+L        
Sbjct: 162 KSYRSAGVVGRENEKSIVESFFRQHLDANAGGALYVSGAPGTGKTVLLHNVLDHVVSDYP 221

Query: 248 AFKTIYINCNSVRNAASVYETIVNELKLKPGGKSERHQLG---AILKYF----DTKHKSI 300
                YINC ++    +++E I +++  +   ++E H +     +  +F    +  +  +
Sbjct: 222 KVNVCYINCMTINEPKAIFEKIHSKIVKEEILENEDHHINFQCELESHFTQSANELYNPV 281

Query: 301 LLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVANALDLTDRMLPRLQANVTLQPT 360
           +++LDE+D L +R+Q +LYT+FEWPS P S+L+LVG+ANALD+TDR LPRL+    + P 
Sbjct: 282 IIVLDEMDHLIAREQQVLYTLFEWPSRPTSRLILVGIANALDMTDRFLPRLRTK-HITPK 340

Query: 361 LMNFAPYSREQILEIISQKLK-------------------------------QTDKFNMF 389
           L++F PY+ ++I  II  +LK                                 D+    
Sbjct: 341 LLSFTPYTAQEISTIIKARLKTAATTSEKNNPFTPIKSISEVSDDSINVVSQHADETPFI 400

Query: 390 NASALQLLAGKVAAVSGDIRKAIDITNHLIDLTYDNVKENGEVT----GIGLKEVLGVIS 445
           + +A++L A KVAA SGD+RKA+DI  H I+L     K   + T     I    +  V+ 
Sbjct: 401 HPAAIELCARKVAASSGDLRKALDICRHAIELAEREWKAQHDNTLSSVDIPRASIAHVVR 460

Query: 446 SVYCTSQSLHCSKDEDSFPLQQKLALASLLLL-KSRPNVKDV 486
           +    SQS   S    +  LQQK  L +L++  K+  +V DV
Sbjct: 461 ATSAMSQS--ASARLKNLGLQQKAILCTLVVCEKTSLSVADV 500

Part of the checkpoint control that prevents mitosis from occurring until S phase is completed. Plays a key role in coupling S phase to start and mitosis. Acts at the initiation of DNA replication and plays a major role in controlling the onset of S-phase. Together with orp1, involved in the maintenance of replication forks and activation of cds1-dependent S-phase checkpoint.

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

>sp|O16810|ORC1_DROME Origin recognition complex subunit 1 OS=Drosophila melanogaster GN=Orc1 PE=1 SV=2

 Score =  136 bits (343), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 84/238 (35%), Positives = 133/238 (55%), Gaps = 21/238 (8%)

Query: 196 LPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSAS-------LNLLVSRAEIKDA 248
           LP RE + E I  FL G + ++  G MY+SG PGTGK+A+       L  +  + E+  A
Sbjct: 568 LPCREREFENIYAFLEGKIQDQCGGCMYVSGVPGTGKTATVTGVIRTLQRMAKQNELP-A 626

Query: 249 FKTIYINCNSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFDT---KHKSILLILD 305
           F+ + IN   +      Y  I  +L  K     + H L  + K F T   +  + +L++D
Sbjct: 627 FEYLEINGMRLTEPRQAYVQIYKQLTGKTVSWEQAHAL--LEKRFTTPAPRRVTTVLLVD 684

Query: 306 EIDALESRKQTILYTIFEWPSIPGSKLVLVGVANALDLTDRMLPRLQANVT--LQPTLMN 363
           E+D L +R+Q ++Y + +WP+   +KLV+V +AN +DL +R+   L   VT  L  T + 
Sbjct: 685 ELDILCNRRQDVVYNLLDWPTKSAAKLVVVTIANTMDLPERL---LMGKVTSRLGLTRLT 741

Query: 364 FAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITNHLIDL 421
           F PYS +Q+ EI++ +L  ++    F   A+QL+A KVAAVSGD R+A+DI     ++
Sbjct: 742 FQPYSHKQLQEIVTARLGGSE---TFKGEAVQLVARKVAAVSGDARRALDICRRATEI 796

Component of the origin recognition complex (ORC) that binds origins of replication. DNA-binding is ATP-dependent, however specific DNA sequences that define origins of replication have not been identified so far. ORC is required to assemble the pre-replication complex necessary to initiate DNA replication.

Drosophila melanogaster (taxid: 7227)

>sp|Q54RM2|ORC1_DICDI Origin recognition complex subunit 1 OS=Dictyostelium discoideum GN=orcA PE=3 SV=1

 Score =  136 bits (343), Expect = 4e-31,   Method: Compositional matrix adjust.
 Identities = 79/238 (33%), Positives = 141/238 (59%), Gaps = 23/238 (9%)

Query: 195 ELPGREVQLEGIRQFLLGHVN-NETSGSMYISGPPGTGKSASLNLLVSRAEIKDA----- 248
           +LPGRE +   I  F+   +  NE+ G +YI+G PGTGK+A++  ++   + K       
Sbjct: 233 KLPGREKEKATIASFIRAKLKANESGGCLYIAGMPGTGKTATVKEIIKELQAKKKQQGGG 292

Query: 249 ----FKTIYINCNSVRNAASVYETIVNELK-----LKPGGKSERHQLGAILKYFDTKHKS 299
               F+ I IN   + +   +Y  + N+++     L+P   S +  L  I + F+ K+K 
Sbjct: 293 GGLNFQFIEINGMQLSDPHQLYHILYNKMQKTRKSLEPKKISSQDALRLIQRNFELKNKK 352

Query: 300 I---LLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVANALDLTDRMLPRLQANVT 356
               ++++DE D+L ++KQT++Y +FEWP+ P SKL+++ +AN ++L D +LPR+++ + 
Sbjct: 353 KQFRVILVDEFDSLITKKQTVIYNLFEWPNKPNSKLIIIAIANTMNLPDTLLPRVKSRMG 412

Query: 357 LQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDI 414
           LQ   + F PY+ EQ+  II  +L+  D    F+  ++Q+ + +VAAV GD R+A++I
Sbjct: 413 LQK--VPFTPYNIEQLETIIKYRLQDLD---AFDEESIQICSKRVAAVCGDARRALEI 465

Component of the origin recognition complex (ORC) that binds origins of replication. DNA-binding is ATP-dependent, however specific DNA sequences that define origins of replication have not been identified so far. ORC is required to assemble the pre-replication complex necessary to initiate DNA replication.

Dictyostelium discoideum (taxid: 44689)

>sp|O74270|ORC1_CANAX Origin recognition complex subunit 1 OS=Candida albicans GN=ORC1 PE=2 SV=1

 Score =  127 bits (320), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 99/342 (28%), Positives = 169/342 (49%), Gaps = 23/342 (6%)

Query: 165 KRSPAKLCSPRKLLFSEDKPKVEEKAKDSCELPGREVQLEGIRQFLLGHVNNETSGSMYI 224
           K  P++   P+ + F E K ++    K +  LPGRE +   I       VN +T   +Y+
Sbjct: 368 KSVPSEFTDPKSVAFKEVKQRLHTSQKLNA-LPGREDEFAMIYMNHESAVNEKTGCCVYV 426

Query: 225 SGPPGTGKSASLNLLVS-------RAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKP 277
            G PG GK+A++  +V        R E+ + F  + +N   + +    YE + + +    
Sbjct: 427 CGLPGMGKTATIKDVVEQMTYSSERGEM-EQFSYLELNGLKLLSPTVAYEALWHHI---S 482

Query: 278 GGKSERHQLGAILK-YF---DTKHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLV 333
           G K        +L+ YF   D K K +++++DE D + ++KQ ++Y  F WP+   SKL+
Sbjct: 483 GDKVSASNAALLLEEYFKREDHKRKPLVILMDEFDQIATKKQNVMYNFFNWPTYSTSKLI 542

Query: 334 LVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFN----MF 389
           ++ VAN +DL +RML    A+  L    + F  Y+ +Q+ +II+ +L+   K N    + 
Sbjct: 543 VIAVANTMDLPERMLTNKIAS-RLGLRRIQFRGYTFQQLGDIITHRLEMITKNNRRKVVI 601

Query: 390 NASALQLLAGKVAAVSGDIRKAIDITNHLIDLTYDNVKEN--GEVTGIGLKEVLGVISSV 447
            + A+   + KVA+VSGD R+A+ I    +++      EN  GE      + ++  IS+ 
Sbjct: 602 TSDAIGFASRKVASVSGDARRALTICRRAVEIAEKEYLENKKGEDDSEPYQVLISHISTA 661

Query: 448 YCTSQSLHCSKDEDSFPLQQKLALASLLLLKSRPNVKDVTLG 489
              + +   SK   S P   KL LASLL    R  + + +LG
Sbjct: 662 INETVNSPLSKYIASLPFASKLVLASLLRRSRRTGLAENSLG 703

Component of the origin recognition complex (ORC) that binds origins of replication. It has a role in both chromosomal replication and mating type transcriptional silencing. Binds to the ARS consensus sequence (ACS) of origins of replication in an ATP-dependent manner.

Candida albicans (taxid: 5476)

>sp|Q9JI69|ORC1_CRIGR Origin recognition complex subunit 1 OS=Cricetulus griseus GN=ORC1 PE=2 SV=1

 Score =  126 bits (317), Expect = 3e-28,   Method: Compositional matrix adjust.
 Identities = 95/282 (33%), Positives = 157/282 (55%), Gaps = 22/282 (7%)

Query: 196 LPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLN----LLVSRAEIKDA--F 249
           LP RE + + I  F+   + + T G MYISG PGTGK+A++N     L   A+  D   F
Sbjct: 493 LPCREQEFQDIYSFVESKLLDGTGGCMYISGVPGTGKTATVNEVIRCLQQAAQTNDVPPF 552

Query: 250 KTIYINCNSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYF---DTKHKSILLILDE 306
           + + +N   +     VY  I+ +L  +    +   QL A  K F    ++ ++ +L++DE
Sbjct: 553 EYVDVNGMKLTEPHQVYVQILQKLTGQKATANHAAQLLA--KRFCSQGSQQETTVLLVDE 610

Query: 307 IDALESRKQTILYTIFEWPSIPGSKLVLVGVANALDLTDR-MLPRLQANVTLQPTLMNFA 365
           +D L + KQ ++Y +F+WP+  G++L+++ +AN +DL +R M+ R+ + + L  T M+F 
Sbjct: 611 LDLLWTSKQDVMYNLFDWPTHKGARLIVLAIANTMDLPERIMMNRVSSRLGL--TRMSFQ 668

Query: 366 PYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDI---TNHLIDLT 422
           PYS  Q+ EI+  +LK       F   A+QL+A KVAA+SGD R+ +DI      + +L+
Sbjct: 669 PYSHNQLKEILVSRLKH---LKAFEDDAIQLVARKVAALSGDARRCLDICRRATEICELS 725

Query: 423 YDNVKENGEVTGIGLKEVLG-VISSVYCTSQSLHCSKDEDSF 463
           +++    G VT   L E +  + SS Y T+   +CS  E  F
Sbjct: 726 HNHGNSLGPVTVSHLMEAIDEMFSSSYITAIK-NCSLLEQGF 766

Component of the origin recognition complex (ORC) that binds origins of replication. DNA-binding is ATP-dependent, however specific DNA sequences that define origins of replication have not been identified so far. ORC is required to assemble the pre-replication complex necessary to initiate DNA replication.

Cricetulus griseus (taxid: 10029)

>sp|Q8I615|ORC1_PLAF7 Origin recognition complex subunit 1 OS=Plasmodium falciparum (isolate 3D7) GN=orc1 PE=2 SV=1

 Score =  123 bits (308), Expect = 4e-27,   Method: Compositional matrix adjust.
 Identities = 79/234 (33%), Positives = 134/234 (57%), Gaps = 24/234 (10%)

Query: 196  LPGREVQLEGIRQFLLGHVNNETSGS---MYISGPPGTGKSASLNLLVSRAEIKD----- 247
            LP RE +++ +  FL   +  + SGS   +YISG PGTGK+A++  ++   +IK      
Sbjct: 784  LPCREKEIKEVHGFLESGI--KQSGSNQILYISGMPGTGKTATVYSVIQLLQIKSRKKLL 841

Query: 248  -AFKTIYINCNSVRNAASVYETIVNEL--KLKPGGKSERHQLGAILKYFDTKHKS----I 300
             +F    IN  +V +  + Y+    +L  K  P      +    I + F+   K      
Sbjct: 842  PSFNVFEINGMNVVHPNAAYQVFYKQLFNKKPPNA---LNSFKIIDRLFNKSQKDNRDVS 898

Query: 301  LLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVANALDLTDRMLPRLQANVTLQPT 360
            +LI+DEID L ++ Q +L+T+F+WP+   SKL+L+ ++N +DL DR++PR ++ +     
Sbjct: 899  ILIIDEIDYLITKTQKVLFTLFDWPTKINSKLILIAISNTMDLPDRLIPRCRSRLAFGRL 958

Query: 361  LMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDI 414
            +  F+PY  ++I +II ++L+   +  + + +A+QL A KVA VSGDIRKA+ I
Sbjct: 959  V--FSPYKGDEIEKIIKERLENCKE--IIDHTAIQLCARKVANVSGDIRKALQI 1008

Component of the origin recognition complex (ORC) that binds origins of replication. DNA-binding is ATP-dependent, however specific DNA sequences that define origins of replication have not been identified so far. ORC is required to assemble the pre-replication complex necessary to initiate DNA replication.

Plasmodium falciparum (isolate 3D7) (taxid: 36329)

>sp|Q80Z32|ORC1_RAT Origin recognition complex subunit 1 OS=Rattus norvegicus GN=Orc1 PE=2 SV=1

 Score =  118 bits (296), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 89/271 (32%), Positives = 150/271 (55%), Gaps = 23/271 (8%)

Query: 196 LPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLN----LLVSRAEIKDA--F 249
           LP RE + + I  F+   + + T G MYISG PGTGK+A+++     L   A+  D   F
Sbjct: 491 LPCREQEFQDIYSFVESKLLDGTGGCMYISGVPGTGKTATVHEVIRCLQQAAQTNDVPPF 550

Query: 250 KTIYINCNSVRNAASVYETIVNELKLKPGGKSERHQLGAIL-KYF---DTKHKSILLILD 305
           + + +N   +     VY  I+ +L    G K+  +    +L K F    ++ ++ +L++D
Sbjct: 551 EYVEVNGMKLTEPHQVYVQILQKLT---GQKATANHAAELLAKQFCSRGSQKETTVLLVD 607

Query: 306 EIDALESRKQTILYTIFEWPSIPGSKLVLVGVANALDLTDR-MLPRLQANVTLQPTLMNF 364
           E+D L + KQ +LY +F+WP+  G++LV++ +AN +DL +R M+ R+ + + L  T M+F
Sbjct: 608 ELDLLWTHKQDVLYNLFDWPTHKGARLVVLTIANTMDLPERIMMNRVASRLGL--TRMSF 665

Query: 365 APYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDI---TNHLIDL 421
            PYS  Q+ +I+  +LK       F   A+QL+A KVAA+SGD R+ +DI      + ++
Sbjct: 666 QPYSHSQLKQILVSRLKH---LKAFEDDAVQLVARKVAALSGDARRCLDICRRATEICEV 722

Query: 422 TYDNVKENGEVTGIGLKEVLG-VISSVYCTS 451
           ++        VT   L E +  + SS Y T+
Sbjct: 723 SHQRGDSQCLVTVAHLMEAIDEMFSSSYITA 753

Component of the origin recognition complex (ORC) that binds origins of replication. DNA-binding is ATP-dependent, however specific DNA sequences that define origins of replication have not been identified so far. ORC is required to assemble the pre-replication complex necessary to initiate DNA replication.

Rattus norvegicus (taxid: 10116)

>sp|Q13415|ORC1_HUMAN Origin recognition complex subunit 1 OS=Homo sapiens GN=ORC1 PE=1 SV=2

 Score =  117 bits (294), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 89/271 (32%), Positives = 147/271 (54%), Gaps = 23/271 (8%)

Query: 196 LPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLN----LLVSRAEIKDA--F 249
           LP RE + + I  F+   + + T G MYISG PGTGK+A+++     L   A+  D   F
Sbjct: 504 LPCREQEFQDIYNFVESKLLDHTGGCMYISGVPGTGKTATVHEVIRCLQQAAQANDVPPF 563

Query: 250 KTIYINCNSVRNAASVYETIVNELKLKPGGKSERHQLGAIL-KYFDTK---HKSILLILD 305
           + I +N   +     VY  I+ +L    G K+  +    +L K F T+    ++ +L++D
Sbjct: 564 QYIEVNGMKLTEPHQVYVQILQKLT---GQKATANHAAELLAKQFCTRGSPQETTVLLVD 620

Query: 306 EIDALESRKQTILYTIFEWPSIPGSKLVLVGVANALDLTDR-MLPRLQANVTLQPTLMNF 364
           E+D L + KQ I+Y +F+WP+   ++LV++ +AN +DL +R M+ R+ + + L  T M F
Sbjct: 621 ELDLLWTHKQDIMYNLFDWPTHKEARLVVLAIANTMDLPERIMMNRVSSRLGL--TRMCF 678

Query: 365 APYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDI---TNHLIDL 421
            PY+  Q+ +I+  +LK       F   A+QL+A KVAA+SGD R+ +DI      + + 
Sbjct: 679 QPYTYSQLQQILRSRLKH---LKAFEDDAIQLVARKVAALSGDARRCLDICRRATEICEF 735

Query: 422 TYDNVKENGEVT-GIGLKEVLGVISSVYCTS 451
           +       G VT    ++ V  + SS Y T+
Sbjct: 736 SQQKPDSPGLVTIAHSMEAVDEMFSSSYITA 766

Component of the origin recognition complex (ORC) that binds origins of replication. DNA-binding is ATP-dependent, however specific DNA sequences that define origins of replication have not been identified so far. ORC is required to assemble the pre-replication complex necessary to initiate DNA replication.

Homo sapiens (taxid: 9606)

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	490
189238005	525	PREDICTED: similar to Cdc6 [Tribolium ca	0.642	0.6	0.466	3e-84
322785578	559	hypothetical protein SINV_00317 [Solenop	0.6	0.525	0.509	5e-81
307196035	543	Cell division control protein 6-like pro	0.595	0.537	0.490	1e-77
332025295	562	Cell division control protein 6-like pro	0.693	0.604	0.450	6e-77
350404657	548	PREDICTED: cell division control protein	0.638	0.571	0.471	1e-75
345495580	550	PREDICTED: cell division control protein	0.640	0.570	0.438	2e-75
345495578	542	PREDICTED: cell division control protein	0.640	0.579	0.445	5e-75
340720985	548	PREDICTED: cell division control protein	0.638	0.571	0.466	1e-74
307181462	586	Cell division control protein 6-like pro	0.706	0.590	0.445	6e-74
383847203	550	PREDICTED: cell division control protein	0.640	0.570	0.466	4e-73

>gi|189238005|ref|XP_001813224.1| PREDICTED: similar to Cdc6 [Tribolium castaneum] gi|270006647|gb|EFA03095.1| hypothetical protein TcasGA2_TC013003 [Tribolium castaneum]

 Score =  318 bits (816), Expect = 3e-84,   Method: Compositional matrix adjust.
 Identities = 158/339 (46%), Positives = 235/339 (69%), Gaps = 24/339 (7%)

Query: 173 SPRKLLFSEDK--PKVEEKAKDSC--ELPGREVQLEGIRQFLLGHVNNETSGSMYISGPP 228
           S RK LF ED            SC   LPGRE +L  ++QF+L H++  TSG++YISGPP
Sbjct: 110 SNRKKLFQEDDLYQNARRALHSSCPTNLPGREKELGDLKQFILQHLDEGTSGTLYISGPP 169

Query: 229 GTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKPGGKSERHQLGA 288
           GTGK+ASLNL++   +I    + +Y+NC S++++ S++  I  +L +K  GKSE+  +GA
Sbjct: 170 GTGKTASLNLVLEDPQISSGIEHVYVNCTSIKSSGSIFSRIAKDLGIKASGKSEKDYVGA 229

Query: 289 ILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVANALDLTDRML 348
           I K+    H++ILL+LDEID LES+KQ++LYTIFEWP+ P S+L+L+G+ANALDLTDR+L
Sbjct: 230 IEKFLQKGHRTILLVLDEIDQLESKKQSVLYTIFEWPANPNSRLILIGIANALDLTDRIL 289

Query: 349 PRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDI 408
           PRLQA   L+P LM+FAPY+++QI+EI + +LK  +  ++F+  ALQ+LAGKVAA+SGD+
Sbjct: 290 PRLQARCELKPQLMHFAPYTKQQIVEIFTNRLKNANVLDIFSPIALQMLAGKVAAISGDV 349

Query: 409 RKAIDITNHLIDLTYDNVKENGE-----------------VTGIGLKEVLGVISSVYCTS 451
           R+A+DI   +I+++  + K+ GE                 +  + +++V+ V++ VY T+
Sbjct: 350 RRALDIGRRVIEMS--DKKKRGECVLKSVENLATELEEKKLESVDMRQVVQVLNRVYGTT 407

Query: 452 QSLHCSKDEDSFPLQQKLALASLLLLKSRPNVKDVTLGK 490
           QSL   + EDSFPLQQK+ + SLLL+  +   KDVT+G+
Sbjct: 408 QSLD-EEVEDSFPLQQKIIVCSLLLILKKAKNKDVTIGR 445

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|322785578|gb|EFZ12233.1| hypothetical protein SINV_00317 [Solenopsis invicta]

 Score =  308 bits (789), Expect = 5e-81,   Method: Compositional matrix adjust.
 Identities = 161/316 (50%), Positives = 226/316 (71%), Gaps = 22/316 (6%)

Query: 195 ELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYI 254
           +LPGRE +L  ++++LL H++ E SGS+YISGPPGTGK+A L  ++  +++K  FK +YI
Sbjct: 169 DLPGREEELMKLQKYLLDHLDQEMSGSLYISGPPGTGKTACLFKIMQHSDVKSKFKVVYI 228

Query: 255 NCNSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRK 314
           NC S+++AA++Y  I  EL L    KS ++    I KY  +KHK++LL+LDEID L+SRK
Sbjct: 229 NCTSMKSAAAIYAKIAQELSLLGTTKSGKNSKAVIEKYLKSKHKTLLLVLDEIDQLDSRK 288

Query: 315 QTILYTIFEWPSIPGSKLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILE 374
           Q++LY+IFEWPSIP SKL+LVG+ANALDLTDR+LPRLQA   L+PTLM++APYS++QI +
Sbjct: 289 QSVLYSIFEWPSIPNSKLILVGIANALDLTDRILPRLQARCELKPTLMHYAPYSKQQIFD 348

Query: 375 IISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITNHLIDL------------T 422
           IIS +L + D  N+F   A+Q LAGKVAA+SGDIRKA+DI+  +I+L            T
Sbjct: 349 IISARLNEADATNVFTPPAIQFLAGKVAAISGDIRKALDISRRVIELAESHQVAQILRPT 408

Query: 423 YDN-------VKENGEVTG-IGLKEVLGVISSVYCTSQSLHCSKDEDSFPLQQKLALASL 474
            DN        KE   V   + LKEV+ V++ VY  SQ+L+  + +D+FPLQQKL + SL
Sbjct: 409 NDNDMNIEPSKKETEAVDKPVDLKEVVTVLNGVYGGSQNLN--EQQDTFPLQQKLLICSL 466

Query: 475 LLLKSRPNVKDVTLGK 490
           LL+ ++   KD+T+G+
Sbjct: 467 LLILNKGRNKDITVGR 482

Source: Solenopsis invicta

Species: Solenopsis invicta

Genus: Solenopsis

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307196035|gb|EFN77760.1| Cell division control protein 6-like protein [Harpegnathos saltator]

 Score =  297 bits (760), Expect = 1e-77,   Method: Compositional matrix adjust.
 Identities = 155/316 (49%), Positives = 219/316 (69%), Gaps = 24/316 (7%)

Query: 195 ELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYI 254
           ELPGRE +L  +++F   H+  ETS S+YISGPPGTGK+ASL+ ++ + E K  FK +YI
Sbjct: 155 ELPGRENELNKLQEFFQEHLEKETSSSLYISGPPGTGKTASLSKIMQQPEFKSQFKCVYI 214

Query: 255 NCNSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRK 314
           NC ++++AA++Y  I+ EL +    KS ++    I KY  +KHK + L+LDEID LES+K
Sbjct: 215 NCTTMKSAAAIYAKIIQELSISSSTKSGKNNKAIIEKYLMSKHKMLFLVLDEIDQLESKK 274

Query: 315 QTILYTIFEWPSIPGSKLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILE 374
           Q++LY+IFEWPS+  SKL+LVG+ANALDLTDR+LPRLQA   L+PTLM+FA Y+++QI  
Sbjct: 275 QSVLYSIFEWPSLLNSKLILVGIANALDLTDRILPRLQARCELKPTLMHFASYTKQQISN 334

Query: 375 IISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITNHLIDL------------- 421
           IIS +L Q +  N+F  SA+QLLAGKVAAVSGDIR+A+DI+  +I+L             
Sbjct: 335 IISTRLSQANASNIFTPSAIQLLAGKVAAVSGDIRRALDISRRVIELAESEKIATVLCPT 394

Query: 422 -----TYDNVKENGEVTG--IGLKEVLGVISSVYCTSQSLHCSKDEDSFPLQQKLALASL 474
                  +N  +  E+T   + LKEVL V++ VY ++Q+     ++D FP+QQKL L SL
Sbjct: 395 NDNDTNTENSTKQMEITEKPVELKEVLAVLNGVYGSTQNF----NKDMFPIQQKLLLCSL 450

Query: 475 LLLKSRPNVKDVTLGK 490
           LL+ ++   KD+T G+
Sbjct: 451 LLILNKGRNKDITAGR 466

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332025295|gb|EGI65466.1| Cell division control protein 6-like protein [Acromyrmex echinatior]

 Score =  294 bits (753), Expect = 6e-77,   Method: Compositional matrix adjust.
 Identities = 169/375 (45%), Positives = 243/375 (64%), Gaps = 35/375 (9%)

Query: 139 LSPIKNIILDKKSPFKAFIRDDEDLIKRSPA---KLCSPRKLLFSEDKPKVEEKAKDSCE 195
           LSP K   L  K  F + + ++ED I   P    K  + RK L              +  
Sbjct: 123 LSPKKEGRLAPKQLFDSCLSEEEDEIISKPIGSNKYQNARKSLH----------GSITDN 172

Query: 196 LPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYIN 255
           LPGRE +L  ++++LL H++ ETSGS+YISGPPGTGK+A L  ++ +++++  FK +YIN
Sbjct: 173 LPGREEELTKLQKYLLEHLDQETSGSLYISGPPGTGKTACLFKIMQQSDVRSKFKMVYIN 232

Query: 256 CNSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQ 315
           C S+++A ++Y  I+ EL +    KS ++    I KY  +KHK++LL+LDEID LES+KQ
Sbjct: 233 CTSMKSATAIYAKIIQELSIPGMTKSGKNSKAIIEKYLVSKHKTLLLVLDEIDQLESKKQ 292

Query: 316 TILYTIFEWPSIPGSKLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEI 375
           ++LY+IFEWPS P SKL+L+G+AN+LDLTDR+LPRLQA   L+P LM+FAPYS++QI  I
Sbjct: 293 SVLYSIFEWPSKPNSKLILIGIANSLDLTDRILPRLQARCELKPALMHFAPYSKQQIFNI 352

Query: 376 ISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITNHLIDL------------TY 423
           IS +L + +  N+F   A+Q LA KVAA+SGDIRKA+DI+  +I+L            T 
Sbjct: 353 ISTRLNEANATNVFTPPAIQFLASKVAAISGDIRKALDISRRVIELASSHQVAQVLRPTI 412

Query: 424 DN-------VKENGEVTG-IGLKEVLGVISSVYCTSQSLHCSKDEDSFPLQQKLALASLL 475
           DN        KE   V   + LKEV+ V++ VY   Q+L  S ++D+FPLQQKL + SLL
Sbjct: 413 DNDTNIEPSKKETEAVEKPVDLKEVITVLNGVYGGIQNL--SNEQDTFPLQQKLLICSLL 470

Query: 476 LLKSRPNVKDVTLGK 490
           L+ ++   KD+T+G+
Sbjct: 471 LILNKGKNKDITVGR 485

Source: Acromyrmex echinatior

Species: Acromyrmex echinatior

Genus: Acromyrmex

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|350404657|ref|XP_003487176.1| PREDICTED: cell division control protein 6 homolog [Bombus impatiens]

 Score =  290 bits (741), Expect = 1e-75,   Method: Compositional matrix adjust.
 Identities = 160/339 (47%), Positives = 234/339 (69%), Gaps = 26/339 (7%)

Query: 176 KLLFSEDKPKVEEKAKDSC---ELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGK 232
           K LF  ++ +   KA  S     LPGRE +L+ +++F+  H+ NETSGS+Y+SGPPGTGK
Sbjct: 135 KRLFGTERYRNARKALHSSVPDTLPGRENELQELQEFMEEHLKNETSGSLYVSGPPGTGK 194

Query: 233 SASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKP---GGKSERHQLGAI 289
           +A L+ L+ + E K  FK IY+NC ++++AA++YE I+ +L L P     KS ++  G I
Sbjct: 195 TACLSKLILKTEFKSKFKVIYVNCTTMKSAATIYEKIIQKLGLPPILAERKSGKYSKGVI 254

Query: 290 LKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVANALDLTDRMLP 349
            KY  + HK +LLILDEID LES+KQ++LY+IFEWPSI  SKL+LVG+ANALDLTDR+LP
Sbjct: 255 EKYLGSNHKMLLLILDEIDQLESKKQSVLYSIFEWPSIHNSKLILVGIANALDLTDRILP 314

Query: 350 RLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIR 409
           RLQA   L+P LM+F+PY++++I  IIS++L + +  ++F  +A+Q+L+GKVAA+SGDIR
Sbjct: 315 RLQARCELKPKLMHFSPYTKQEICNIISERLSEANVSDLFTKTAIQMLSGKVAAISGDIR 374

Query: 410 KAIDITNHLIDLTYDNV-------KENGEVT-----------GIGLKEVLGVISSVYCTS 451
           +A+DI+  +I+L   +          N E+             + LKEV+ V++ +Y  S
Sbjct: 375 RALDISRRVIELAESHKLAQVLQPTNNNEINIPKKQQSAVDQPVDLKEVITVLNGIYGGS 434

Query: 452 QSLHCSKDEDSFPLQQKLALASLLLLKSRPNVKDVTLGK 490
           Q++   K+E +FPLQQKL L SLLL+ ++   KDVT+GK
Sbjct: 435 QNIE--KEESTFPLQQKLLLCSLLLILNKGRNKDVTVGK 471

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|345495580|ref|XP_003427533.1| PREDICTED: cell division control protein 6 homolog isoform 2 [Nasonia vitripennis]

 Score =  289 bits (740), Expect = 2e-75,   Method: Compositional matrix adjust.
 Identities = 153/349 (43%), Positives = 226/349 (64%), Gaps = 35/349 (10%)

Query: 173 SPRKLLFSEDKPKVEEKAKDSC---ELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPG 229
           +P+KL F   K     KA  S     L GRE +L  + +++  H++NETSGS+Y+SGPPG
Sbjct: 127 APKKL-FPSSKYSEARKALHSALPENLVGREAELCKLEEYIQFHLDNETSGSLYVSGPPG 185

Query: 230 TGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKPGGKSERHQLGAI 289
           TGK+ASL+ ++ + + K AF+ +Y+NC ++++A+S+Y  I+ EL LK   KS R    AI
Sbjct: 186 TGKTASLSKIMLKPKFKKAFQIVYVNCTTMKSASSIYSKIIQELGLKTT-KSARGSKTAI 244

Query: 290 LKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVANALDLTDRMLP 349
            KY    HK +LL+LDE+D LE++ Q +LY+IFEWPSIP SKLVLVG+ANAL+LTD +LP
Sbjct: 245 EKYLAQSHKMLLLVLDEMDQLETKNQAVLYSIFEWPSIPESKLVLVGLANALNLTDTILP 304

Query: 350 RLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIR 409
           RLQA   L+PTL++F  Y+++QI++II+++LK+ +  ++F  +A+QLLAGKVAAVSGDIR
Sbjct: 305 RLQARCELKPTLLHFQSYTKQQIMDIITERLKEANVLDIFTGTAMQLLAGKVAAVSGDIR 364

Query: 410 KAIDITNHLIDLTYDN--------VKENGEVTG--------------------IGLKEVL 441
           +A+DI   ++++              ENGE                       +  KEV 
Sbjct: 365 RALDIGRRVVEIAESQKMMQVLQPTNENGEFVTSKIFQVINSASTAESANEKPVDFKEVR 424

Query: 442 GVISSVYCTSQSLHCSKDEDSFPLQQKLALASLLLLKSRPNVKDVTLGK 490
            V++ VY  S+  +   +E SFP+QQK+ L SL+L+ ++   KDV +GK
Sbjct: 425 SVLNKVYGGSE--NADSEESSFPVQQKILLCSLMLILNKSKNKDVNMGK 471

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|345495578|ref|XP_001605030.2| PREDICTED: cell division control protein 6 homolog isoform 1 [Nasonia vitripennis]

 Score =  288 bits (737), Expect = 5e-75,   Method: Compositional matrix adjust.
 Identities = 152/341 (44%), Positives = 227/341 (66%), Gaps = 27/341 (7%)

Query: 173 SPRKLLFSEDKPKVEEKAKDSC---ELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPG 229
           +P+KL F   K     KA  S     L GRE +L  + +++  H++NETSGS+Y+SGPPG
Sbjct: 127 APKKL-FPSSKYSEARKALHSALPENLVGREAELCKLEEYIQFHLDNETSGSLYVSGPPG 185

Query: 230 TGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKPGGKSERHQLGAI 289
           TGK+ASL+ ++ + + K AF+ +Y+NC ++++A+S+Y  I+ EL LK   KS R    AI
Sbjct: 186 TGKTASLSKIMLKPKFKKAFQIVYVNCTTMKSASSIYSKIIQELGLKTT-KSARGSKTAI 244

Query: 290 LKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVANALDLTDRMLP 349
            KY    HK +LL+LDE+D LE++ Q +LY+IFEWPSIP SKLVLVG+ANAL+LTD +LP
Sbjct: 245 EKYLAQSHKMLLLVLDEMDQLETKNQAVLYSIFEWPSIPESKLVLVGLANALNLTDTILP 304

Query: 350 RLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIR 409
           RLQA   L+PTL++F  Y+++QI++II+++LK+ +  ++F  +A+QLLAGKVAAVSGDIR
Sbjct: 305 RLQARCELKPTLLHFQSYTKQQIMDIITERLKEANVLDIFTGTAMQLLAGKVAAVSGDIR 364

Query: 410 KAIDITNHLIDL------------TYDN--------VKENGEVTGIGLKEVLGVISSVYC 449
           +A+DI   ++++            T +N          E+     +  KEV  V++ VY 
Sbjct: 365 RALDIGRRVVEIAESQKMMQVLQPTNENDANPDSASTAESANEKPVDFKEVRSVLNKVYG 424

Query: 450 TSQSLHCSKDEDSFPLQQKLALASLLLLKSRPNVKDVTLGK 490
            S+  +   +E SFP+QQK+ L SL+L+ ++   KDV +GK
Sbjct: 425 GSE--NADSEESSFPVQQKILLCSLMLILNKSKNKDVNMGK 463

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340720985|ref|XP_003398908.1| PREDICTED: cell division control protein 6 homolog [Bombus terrestris]

 Score =  287 bits (734), Expect = 1e-74,   Method: Compositional matrix adjust.
 Identities = 158/339 (46%), Positives = 232/339 (68%), Gaps = 26/339 (7%)

Query: 176 KLLFSEDKPKVEEKAKDSC---ELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGK 232
           K LF  ++ +   KA  S     LPGRE +L+ + +F+  H+ NETSGS+Y+SGPPGTGK
Sbjct: 135 KRLFGTERYRNARKALHSSIPDTLPGRENELQKLEEFMEEHLKNETSGSLYVSGPPGTGK 194

Query: 233 SASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKP---GGKSERHQLGAI 289
           +A L+ L+ + E K  FK IY+NC ++++AA++Y  I+ +L L P     KS ++  G I
Sbjct: 195 TACLSKLILKTEFKSKFKVIYVNCTTMKSAATIYAKIIQKLGLPPILAERKSGKYSKGVI 254

Query: 290 LKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVANALDLTDRMLP 349
            KY  + HK +LLILDEID LES+KQ++LY++FEWPSI  SKL+LVG+ANALDLTDR+LP
Sbjct: 255 EKYLSSNHKMLLLILDEIDQLESKKQSVLYSVFEWPSIHNSKLILVGIANALDLTDRILP 314

Query: 350 RLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIR 409
           RLQA   L+P LM+F+PY++++I  IIS++L + +  ++F  +A+Q+L+GKVAA+SGDIR
Sbjct: 315 RLQARCELKPKLMHFSPYTKQEICNIISERLSEANVSDLFTKTAIQMLSGKVAAISGDIR 374

Query: 410 KAIDITNHLIDLTYDNV-------KENGEVT-----------GIGLKEVLGVISSVYCTS 451
           +A+DI+  +I+L   +          N E+             + LKEV+ V++ +Y  S
Sbjct: 375 RALDISRRVIELAESHKLAQVLQPTNNNEINLPKKQQSAVDQPVDLKEVITVLNGIYGGS 434

Query: 452 QSLHCSKDEDSFPLQQKLALASLLLLKSRPNVKDVTLGK 490
           Q++   K+E +FPLQQKL L SLLL+ ++   KDVT+GK
Sbjct: 435 QNIE--KEESTFPLQQKLLLCSLLLILNKGRNKDVTVGK 471

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307181462|gb|EFN69054.1| Cell division control protein 6-like protein [Camponotus floridanus]

 Score =  284 bits (727), Expect = 6e-74,   Method: Compositional matrix adjust.
 Identities = 167/375 (44%), Positives = 250/375 (66%), Gaps = 29/375 (7%)

Query: 139 LSPIKNIILDKKSPFKAFIRDDEDLIKRSPAKLCSPRKLLFSEDKPKVEEKAKDSCE--- 195
           LS  K   L+ K  FK+  ++++D +  +     S    LF  +K +   KA  S E   
Sbjct: 141 LSTAKENRLNPKQLFKSHSKEEKDELNCNSLLFNS----LFGLNKYQNARKALHSSETEE 196

Query: 196 LPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYIN 255
           LPGRE +L  +++F   H+   TSGS+Y+SGPPGTGK+ASL  ++ ++++K   K +YIN
Sbjct: 197 LPGREKELAKLQEFFQRHLERGTSGSLYVSGPPGTGKTASLFKIMRQSDLKSKLKIVYIN 256

Query: 256 CNSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQ 315
           C S+++AA++Y  I+ EL +    KS ++    I +Y  +K   +LL+LDEID LES+KQ
Sbjct: 257 CTSMKSAAAIYAKIIQELAITSATKSGKNGKAIIERYLTSKKSMLLLVLDEIDQLESKKQ 316

Query: 316 TILYTIFEWPSIPGSKLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEI 375
           ++LY+IFEWPSI  SKL+L+G+ANALDLTDR+LPRLQA   L+P LM+FAPY+++QI +I
Sbjct: 317 SVLYSIFEWPSISNSKLILIGIANALDLTDRILPRLQARCELKPMLMHFAPYTKQQISDI 376

Query: 376 ISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITNHLIDL------------TY 423
           IS +L Q +   +F +SA+QLLAGKVAA+SGDIR+A+DI+  +++L            T 
Sbjct: 377 ISSRLNQVNANGVFTSSAIQLLAGKVAAISGDIRRALDISRRVVELAESHQVAQVLRPTN 436

Query: 424 DN------VKENGEVTG--IGLKEVLGVISSVYCTSQSLHCSKDEDSFPLQQKLALASLL 475
           DN      +K+  EVT   + LKEV+ +++ VY  +Q++   +++++FPLQQKL L SLL
Sbjct: 437 DNDTNIEPLKQEMEVTEKPVDLKEVVTILNGVYGGTQNI--DQEQETFPLQQKLLLCSLL 494

Query: 476 LLKSRPNVKDVTLGK 490
           L+ ++   KDVT+GK
Sbjct: 495 LILNKGRNKDVTVGK 509

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383847203|ref|XP_003699244.1| PREDICTED: cell division control protein 6 homolog [Megachile rotundata]

 Score =  281 bits (720), Expect = 4e-73,   Method: Compositional matrix adjust.
 Identities = 159/341 (46%), Positives = 236/341 (69%), Gaps = 27/341 (7%)

Query: 173 SPRKLLFSEDKPKVEEKAKDSC---ELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPG 229
           +P+KL FS +K +   KA  S     LPGRE++L+ ++ F+  H+ NE SGS+Y+SGPPG
Sbjct: 137 APKKL-FSFEKYRNARKALHSSVPENLPGREMELQQLQDFMTEHLKNERSGSLYVSGPPG 195

Query: 230 TGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKPGGKSERHQLGAI 289
           TGK+A L+ L+ + E K  FK +Y+NC ++++A ++Y  I+ EL L    K+ + +  AI
Sbjct: 196 TGKTACLSKLMLKPEFKSQFKVVYVNCTTMKSATTIYAKIIQELGLS-TPKTVKDKKLAI 254

Query: 290 LKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVANALDLTDRMLP 349
            KY  +KHK +L+ILDEID LES+ Q++LY+IFEWPSI  SKL+LVG+ANALDLTDR+LP
Sbjct: 255 EKYLISKHKMLLMILDEIDQLESKNQSVLYSIFEWPSICNSKLILVGIANALDLTDRILP 314

Query: 350 RLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIR 409
           RLQA   L+P LM+F+PY+++QI  IIS++L +    ++F   A+Q+L+GKVAA+SGDIR
Sbjct: 315 RLQARCELKPKLMHFSPYTKQQICNIISERLSEAKVSDLFTGPAIQMLSGKVAAISGDIR 374

Query: 410 KAIDITNHLIDLTYDNVKE------NGEV-TGIG-------------LKEVLGVISSVYC 449
           +A+DI+  +I+    +  E      N ++ TG+G             LKE++ V++ VY 
Sbjct: 375 RALDISRRVIEFAESHKLEQVLQPTNNKIETGMGSPKKQPPGDKPVDLKEIITVLNDVYG 434

Query: 450 TSQSLHCSKDEDSFPLQQKLALASLLLLKSRPNVKDVTLGK 490
            SQ++   K+E +FPLQQKL L SLLL+ ++  +KDVT+G+
Sbjct: 435 GSQNIE--KEESTFPLQQKLLLCSLLLILNKGRIKDVTVGR 473

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	490
FB|FBgn0035918	662	Cdc6 "Cdc6" [Drosophila melano	0.512	0.379	0.419	5.9e-60
RGD|1309157	561	Cdc6 "cell division cycle 6" [	0.595	0.520	0.370	3.7e-48
UNIPROTKB|F1RXE3	560	CDC6 "Uncharacterized protein"	0.691	0.605	0.329	6e-48
MGI|MGI:1345150	562	Cdc6 "cell division cycle 6" [	0.595	0.519	0.367	7.7e-48
ZFIN|ZDB-GENE-050506-131	588	cdc6 "cell division cycle 6 ho	0.693	0.578	0.337	7.6e-46
UNIPROTKB|E1BAQ1	560	CDC6 "Uncharacterized protein"	0.597	0.523	0.365	5.6e-45
UNIPROTKB|E2R6N1	559	CDC6 "Uncharacterized protein"	0.6	0.525	0.359	1.2e-44
UNIPROTKB|Q99741	560	CDC6 "Cell division control pr	0.593	0.519	0.365	1.9e-44
UNIPROTKB|G4MTZ7	598	MGG_01614 "Cell division contr	0.491	0.403	0.337	1.8e-33
POMBASE|SPBC14C8.07c	577	cdc18 "MCM loader" [Schizosacc	0.389	0.331	0.326	3.3e-32

FB|FBgn0035918 Cdc6 "Cdc6" [Drosophila melanogaster (taxid:7227)]

 Score = 553 (199.7 bits), Expect = 5.9e-60, Sum P(3) = 5.9e-60
 Identities = 107/255 (41%), Positives = 167/255 (65%)

Query:   180 SEDKPKVEEKAKDSCE---LPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASL 236
             S +K +   +  +S E   LPGRE QL+ +R+F   H+ ++TSGS+Y+SG PGTGK+A L
Sbjct:   248 SRNKYQNARRVLNSAETQNLPGRESQLQELREFFSNHLESQTSGSLYVSGQPGTGKTACL 307

Query:   237 NLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFDTK 296
             +LL+   +     + +YINC S+ +  +VY+ +  EL+LK  G++ER  L AI ++  T 
Sbjct:   308 SLLLRDPDFSKRLQRVYINCTSIASVGAVYKKLCTELQLKVSGRTERDHLEAIQRHLKTA 367

Query:   297 HKSXXXXXXXXXXXXSRKQTILYTIFEWPSIPGSKLVLVGVANALDLTDRMLPRLQANVT 356
              +             + +Q +LYTIFEWP++PGS+++LVG+AN+LDLTDR L RL A   
Sbjct:   368 KRMLLLVLDEIDQLCTSRQEVLYTIFEWPALPGSRILLVGIANSLDLTDRALMRLNARCE 427

Query:   357 LQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITN 416
             L+P LM+F PYS++QI+EI   +L + +  ++F    LQLLA KV+A+SGD+R+A+DI  
Sbjct:   428 LKPRLMHFPPYSKQQIVEIFKSRLAEAEVLDVFPPVTLQLLAAKVSAISGDVRRALDIGR 487

Query:   417 HLIDLTYDNVKENGE 431
              ++++  +  K +GE
Sbjct:   488 RVVEIA-EQQKRDGE 501

GO:0003689 "DNA clamp loader activity" evidence=ISS

GO:0006267 "pre-replicative complex assembly" evidence=ISS

GO:0005656 "pre-replicative complex" evidence=ISS

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005634 "nucleus" evidence=IDA

RGD|1309157 Cdc6 "cell division cycle 6" [Rattus norvegicus (taxid:10116)]

 Score = 473 (171.6 bits), Expect = 3.7e-48, Sum P(2) = 3.7e-48
 Identities = 117/316 (37%), Positives = 171/316 (54%)

Query:   196 LPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVS--RAEIKDAFKTIY 253
             LP RE ++  IR FL  H+  + +GS+Y+SG PGTGK+A L+ ++   + E+K  FKTI 
Sbjct:   173 LPAREQEMGVIRDFLKEHICGKKAGSLYLSGAPGTGKTACLSRILQDFKKEVK-GFKTIV 231

Query:   254 INCNSVRNAASVYETIVNEL---KL-KPGGKSERHQLGAILKYFDTKHKSXXXXXXXXXX 309
             +NC S+RNA +V+  I  E+   +L +P GK    +L   L     +             
Sbjct:   232 LNCMSLRNAQAVFPAIAQEIGREELCRPTGKDLMRKLEKHLTA--ERGPMIVLVLDEMDQ 289

Query:   310 XXSRKQTILYTIFEWPSIPGSKLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSR 369
               S+ Q +LYT+FEWP +  S+LVL+G+AN LDLTDR+LPRL+A    +P L+NF PY+R
Sbjct:   290 LDSKGQDVLYTLFEWPWLSNSRLVLIGIANTLDLTDRILPRLEAREGCKPKLLNFPPYTR 349

Query:   370 EQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITNHLIDLTYDNVKEN 429
              QI  I+  +L Q  K  + +++A+Q  A KV+AVSGDIRKA+D+    I++   +V+  
Sbjct:   350 NQIAAILQDRLSQVSKDQVLDSAAIQFCARKVSAVSGDIRKALDVCRRAIEIVESDVRSQ 409

Query:   430 ------GEVTG---------IGLKEVLGVISSVYCTSQSLHCSKDEDSFPXXXXXXXXXX 474
                    E            +GL  +  VIS V     +L     +DS P          
Sbjct:   410 TVLKPLSECKSPCESLVPKRVGLAHISQVISGVDGNRVTLSQENTQDSLPLQQKILVCSL 469

Query:   475 XXXXXRPNVKDVTLGK 490
                  R  +K+VTLGK
Sbjct:   470 LLLTKRLKIKEVTLGK 485

GO:0000922 "spindle pole" evidence=IEA;ISO

GO:0003682 "chromatin binding" evidence=IEA;ISO

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA;ISO

GO:0005737 "cytoplasm" evidence=IEA;ISO

GO:0005819 "spindle" evidence=ISO

GO:0017111 "nucleoside-triphosphatase activity" evidence=IEA

GO:0019900 "kinase binding" evidence=IEA;ISO

GO:0051233 "spindle midzone" evidence=IEA;ISO

GO:0051301 "cell division" evidence=IEA

GO:0051984 "positive regulation of chromosome segregation" evidence=IEA;ISO

GO:0071777 "positive regulation of cell cycle cytokinesis" evidence=IEA;ISO

GO:0090007 "regulation of mitotic anaphase" evidence=IEA;ISO

UNIPROTKB|F1RXE3 CDC6 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 464 (168.4 bits), Expect = 6.0e-48, Sum P(2) = 6.0e-48
 Identities = 122/370 (32%), Positives = 191/370 (51%)

Query:   150 KSPFKAFIRDDEDLI----KRSPAKLCSPRKLLFSEDKPKVEEKAKDSC------ELPGR 199
             +S  ++ IR D ++     +R P +  S R  LF ++    ++ AK         +LP R
Sbjct:   117 QSKTRSSIRKDAEVTTSSEQRCPLEKESARMRLFKQEGTCYQQ-AKQVLTTAVPDQLPAR 175

Query:   200 EVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVS--RAEIKDAFKTIYINCN 257
             E +++ +R FL  H+  E +GS+Y+SG PGTGK+A L+ ++   + E+K  FKT+ +NC 
Sbjct:   176 EKEMDVLRNFLREHICGEKAGSLYLSGAPGTGKTACLSRILQDLKKELK-GFKTVMLNCM 234

Query:   258 SVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFDTKHKS--XXXXXXXXXXXXSRKQ 315
             S+R+A +V+  I  E+  +   +     L   L+   T  K               S+ Q
Sbjct:   235 SLRSAQAVFPAIAQEICQEEVSRPAGKDLMRKLENHMTAEKGPMIVLVLDEMDQLDSKGQ 294

Query:   316 TILYTIFEWPSIPGSKLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEI 375
              +LYT+FEWP +  S+LVL+G+AN LDLTDR+LPRLQA    +P L+NF PY++ QI  I
Sbjct:   295 DVLYTLFEWPWLSSSRLVLIGIANTLDLTDRILPRLQAREKCKPRLLNFPPYTKNQIATI 354

Query:   376 ISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITNHLIDLTYDNVKEN------ 429
             +  +L Q  K  + +++A+Q  A KV+AVSGD+RKA+D+    I++   +VK        
Sbjct:   355 LQDRLNQASKDQVLDSAAVQFCARKVSAVSGDVRKALDVCRRAIEIVESDVKSQTLLKPL 414

Query:   430 GEVTG---------IGLKEVLGVISSVYCTSQSLHCSKDEDSFPXXXXXXXXXXXXXXXR 480
              E            +G+  +  V+S V     +L     +D FP                
Sbjct:   415 SECKSPSESLVPKRVGVIHISQVLSEVDGNRMALSQEGAQDCFPLQQKILVCSLLLLTRH 474

Query:   481 PNVKDVTLGK 490
                K+VTLGK
Sbjct:   475 LKTKEVTLGK 484

GO:0090007 "regulation of mitotic anaphase" evidence=IEA

GO:0071777 "positive regulation of cell cycle cytokinesis" evidence=IEA

GO:0051984 "positive regulation of chromosome segregation" evidence=IEA

GO:0051233 "spindle midzone" evidence=IEA

GO:0019900 "kinase binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0003682 "chromatin binding" evidence=IEA

GO:0000922 "spindle pole" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0017111 "nucleoside-triphosphatase activity" evidence=IEA

MGI|MGI:1345150 Cdc6 "cell division cycle 6" [Mus musculus (taxid:10090)]

 Score = 472 (171.2 bits), Expect = 7.7e-48, Sum P(2) = 7.7e-48
 Identities = 116/316 (36%), Positives = 172/316 (54%)

Query:   196 LPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVS--RAEIKDAFKTIY 253
             LP RE ++  IR FL  H+  + +GS+Y+SG PGTGK+A L+ ++   + E+K  FK+I 
Sbjct:   174 LPAREQEMGVIRNFLKEHICGKKAGSLYLSGAPGTGKTACLSRILQDFKKEVK-GFKSIL 232

Query:   254 INCNSVRNAASVYETIVNEL---KL-KPGGKSERHQLGAILKYFDTKHKSXXXXXXXXXX 309
             +NC S+R+A +V+  I  E+   +L +P GK    +L   L     K             
Sbjct:   233 LNCMSLRSAQAVFPAIAQEIGREELCRPAGKDLMRKLEKHLTA--EKGPMIVLVLDEMDQ 290

Query:   310 XXSRKQTILYTIFEWPSIPGSKLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSR 369
               S+ Q +LYT+FEWP +  S+LVL+G+AN LDLTDR+LPRL+A    +P L+NF PY+R
Sbjct:   291 LDSKGQDVLYTLFEWPWLSNSRLVLIGIANTLDLTDRILPRLEARENCKPQLLNFPPYTR 350

Query:   370 EQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITNHLIDLTYDNVK-- 427
              QI  I+  +L Q  K  + +++A+Q  A KV+AVSGDIRKA+D+    I++   +V+  
Sbjct:   351 NQIAAILQDRLSQVSKDQVLDSAAIQFCARKVSAVSGDIRKALDVCRRAIEIVESDVRSQ 410

Query:   428 -------------ENGEVTGIGLKEVLGVISSVYCTSQSLHCSKDEDSFPXXXXXXXXXX 474
                          E+     +GL  +  VIS V     +L     +DS P          
Sbjct:   411 TVLKPLSECKSPSESPVPKRVGLAHISQVISEVDGNRVTLSQENTQDSLPLQQKILVCSL 470

Query:   475 XXXXXRPNVKDVTLGK 490
                  R  +K+VTLGK
Sbjct:   471 LLLTRRLKIKEVTLGK 486

GO:0000166 "nucleotide binding" evidence=IEA

GO:0000922 "spindle pole" evidence=ISO

GO:0003682 "chromatin binding" evidence=IDA

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISO

GO:0005737 "cytoplasm" evidence=IDA

GO:0005819 "spindle" evidence=IDA

GO:0006260 "DNA replication" evidence=IEA

GO:0007049 "cell cycle" evidence=IEA

GO:0007067 "mitosis" evidence=IEA

GO:0017111 "nucleoside-triphosphatase activity" evidence=IEA

GO:0019900 "kinase binding" evidence=ISO

GO:0051233 "spindle midzone" evidence=ISO

GO:0051301 "cell division" evidence=IEA

GO:0051984 "positive regulation of chromosome segregation" evidence=ISO

GO:0071777 "positive regulation of cell cycle cytokinesis" evidence=ISO

GO:0090007 "regulation of mitotic anaphase" evidence=ISO

ZFIN|ZDB-GENE-050506-131 cdc6 "cell division cycle 6 homolog (S. cerevisiae)" [Danio rerio (taxid:7955)]

 Score = 452 (164.2 bits), Expect = 7.6e-46, Sum P(2) = 7.6e-46
 Identities = 124/367 (33%), Positives = 187/367 (50%)

Query:   138 PLSPIKNIILDKKSPFKAFIRDDEDLIKRSPAKLCSPRKLLFSEDKPKVE--EKAKDSC- 194
             PLSPI      + SP +       ++I R+  K  SP   LF   K   +  ++A  +  
Sbjct:   159 PLSPIS-----RPSPTRLNETSCTNIIPRTEGK--SPVMRLFPMKKSGFQSVKQALHTAV 211

Query:   195 --ELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLN-LLVSRAEIKDAFKT 251
                L  RE +   I  FL  HV  E   S+YISG PGTGK+A LN +L  +  +    +T
Sbjct:   212 PERLLSREAERAAIVSFLQNHVVAEKPSSLYISGAPGTGKTACLNCVLQEQKALLKGIQT 271

Query:   252 IYINCNSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFDTKHKSXXXXXXXXXXXX 311
             + INC ++R++ +++  +  +L++ P G S+      + KY  +   +            
Sbjct:   272 VVINCMNLRSSHAIFPLLGEQLEV-PKGNSQAR----LEKYLTSSGPTVLLVLDEMDQLD 326

Query:   312 SRKQTILYTIFEWPSIPGSKLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQ 371
             S+ Q +LYTIFEWP +P S++ L+G+ANALDLTDR+LPRLQA    +P L+NF PYS E+
Sbjct:   327 SKSQEVLYTIFEWPYLPKSRVCLIGIANALDLTDRILPRLQAKPHCRPKLLNFPPYSHEE 386

Query:   372 ILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITNHLIDLTY--DNVKEN 429
             +  I+  +L Q     + +A+A+Q  A KV+AVSGD RKA+DI    +++    D  K  
Sbjct:   387 LNAIVQDRLTQVSGEGVLDAAAVQFCARKVSAVSGDARKALDICRRAVEIVEAGDRSKMA 446

Query:   430 GEVTG------IGLKEVLGVISSVYCTSQSLHCSKDEDSFPXXXXXXXXXXXXXXXRPNV 483
              E T       + + +V  V+S VY   +    S D +SFP                   
Sbjct:   447 SEPTASSKVSRVSVPQVARVLSEVY-GDRMASSSGDGESFPLQQKLLVCCLLLIIRNGKS 505

Query:   484 KDVTLGK 490
             K++ LGK
Sbjct:   506 KEIQLGK 512

GO:0005524 "ATP binding" evidence=IEA

GO:0017111 "nucleoside-triphosphatase activity" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

UNIPROTKB|E1BAQ1 CDC6 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 473 (171.6 bits), Expect = 5.6e-45, P = 5.6e-45
 Identities = 116/317 (36%), Positives = 170/317 (53%)

Query:   195 ELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVS--RAEIKDAFKTI 252
             +LP RE +++ IR FL  H+  + +GS+Y+SG PGTGK+A L+ ++   + E+K  FKTI
Sbjct:   171 QLPAREKEMDVIRNFLREHIYGKKAGSLYLSGAPGTGKTACLSRILQDLKKELK-GFKTI 229

Query:   253 YINCNSVRNAASVYETIVNEL----KLKPGGKSERHQLGAILKYFDTKHKSXXXXXXXXX 308
              +NC S+R+A +V+  I  E+      +P GK    +L   +     K            
Sbjct:   230 VLNCMSLRSAQAVFPAIAQEICQEEVSRPAGKDMMRRLENHMTA--EKGPMIVLVLDEMD 287

Query:   309 XXXSRKQTILYTIFEWPSIPGSKLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYS 368
                SR Q +LYT+FEWP +  S+LVL+G+AN LDLTDR+LPRLQA    +P L+NF PY+
Sbjct:   288 QLDSRGQDVLYTLFEWPWLSNSRLVLIGIANTLDLTDRILPRLQAREKCKPQLLNFPPYT 347

Query:   369 REQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITNHLIDLTYDNVKE 428
             + QI  I+  +L Q     + + +A+Q  A KV+AVSGD+RKA+DI    I++   +VK 
Sbjct:   348 KNQIATILQDRLNQASNDQVLDNAAIQFCARKVSAVSGDVRKALDICRRAIEVVESDVKS 407

Query:   429 N------GEVTG---------IGLKEVLGVISSVYCTSQSLHCSKDEDSFPXXXXXXXXX 473
                     E            +G+  +  VIS V     +L     +DSFP         
Sbjct:   408 QTILKPLSECKSPSESLVPKRVGVIHISQVISEVDGNRMTLSQEGAQDSFPLQQKILVCS 467

Query:   474 XXXXXXRPNVKDVTLGK 490
                   R  +K+VTLGK
Sbjct:   468 LLLLTRRLKIKEVTLGK 484

GO:0090007 "regulation of mitotic anaphase" evidence=IEA

GO:0071777 "positive regulation of cell cycle cytokinesis" evidence=IEA

GO:0051984 "positive regulation of chromosome segregation" evidence=IEA

GO:0051233 "spindle midzone" evidence=IEA

GO:0019900 "kinase binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0003682 "chromatin binding" evidence=IEA

GO:0000922 "spindle pole" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0017111 "nucleoside-triphosphatase activity" evidence=IEA

UNIPROTKB|E2R6N1 CDC6 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 470 (170.5 bits), Expect = 1.2e-44, P = 1.2e-44
 Identities = 113/314 (35%), Positives = 169/314 (53%)

Query:   196 LPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVS--RAEIKDAFKTIY 253
             LP RE ++  IR FL  H+  + +GS+Y+SG PGTGK+A L+ ++     E+KD FKTI 
Sbjct:   171 LPAREKEMNVIRNFLREHICGKKAGSLYLSGAPGTGKTACLSRILQDLEKELKD-FKTIM 229

Query:   254 INCNSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFDTKHKS--XXXXXXXXXXXX 311
             +NC S+RNA +V+  I  E+  +   +     +   L+   T  K               
Sbjct:   230 LNCMSLRNAQAVFPAIAQEICQEEVSRPAGRDMMKKLENHMTAEKGPMIVLVLDEVDQLD 289

Query:   312 SRKQTILYTIFEWPSIPGSKLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQ 371
             S+ Q +LYT+FEWP +  S+LVL+G+AN LDLTDR+LPRLQA    +P L+NF PY++ Q
Sbjct:   290 SKGQDVLYTLFEWPWLSNSRLVLIGIANTLDLTDRILPRLQAREKCKPQLLNFPPYTKNQ 349

Query:   372 ILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITNHLIDLTYDNVKEN-- 429
             I  I+ ++L    +  + + +A+Q  A KV+A+SGD+RKA+D+    I++   +VK    
Sbjct:   350 IATILQERLDLVSRAQVLDNAAIQFCARKVSALSGDVRKALDVCRRAIEIVESDVKSQTV 409

Query:   430 ----GEVTG---------IGLKEVLGVISSVYCTSQSLHCSKDEDSFPXXXXXXXXXXXX 476
                  E T          +GL  +  VIS V     +L     +DSFP            
Sbjct:   410 LKPLSECTSPSESLVPKRVGLIHISQVISEVDGNRMTLSKEGAQDSFPLQQKILVCSLLL 469

Query:   477 XXXRPNVKDVTLGK 490
                +  +K+VTLGK
Sbjct:   470 LIRQLKIKEVTLGK 483

GO:0090007 "regulation of mitotic anaphase" evidence=IEA

GO:0071777 "positive regulation of cell cycle cytokinesis" evidence=IEA

GO:0051984 "positive regulation of chromosome segregation" evidence=IEA

GO:0051233 "spindle midzone" evidence=IEA

GO:0019900 "kinase binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0003682 "chromatin binding" evidence=IEA

GO:0000922 "spindle pole" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0017111 "nucleoside-triphosphatase activity" evidence=IEA

UNIPROTKB|Q99741 CDC6 "Cell division control protein 6 homolog" [Homo sapiens (taxid:9606)]

 Score = 468 (169.8 bits), Expect = 1.9e-44, P = 1.9e-44
 Identities = 116/317 (36%), Positives = 170/317 (53%)

Query:   196 LPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVS--RAEIKDAFKTIY 253
             LP RE +++ IR FL  H+  + +GS+Y+SG PGTGK+A L+ ++   + E+K  FKTI 
Sbjct:   172 LPAREREMDVIRNFLREHICGKKAGSLYLSGAPGTGKTACLSRILQDLKKELK-GFKTIM 230

Query:   254 INCNSVRNAASVYETIVNEL----KLKPGGKSERHQLGAILKYFDT-KHKSXXXXXXXXX 308
             +NC S+R A +V+  I  E+      +P GK    +L    K+    K            
Sbjct:   231 LNCMSLRTAQAVFPAIAQEICQEEVSRPAGKDMMRKLE---KHMTAEKGPMIVLVLDEMD 287

Query:   309 XXXSRKQTILYTIFEWPSIPGSKLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYS 368
                S+ Q +LYT+FEWP +  S LVL+G+AN LDLTDR+LPRLQA    +P L+NF PY+
Sbjct:   288 QLDSKGQDVLYTLFEWPWLSNSHLVLIGIANTLDLTDRILPRLQAREKCKPQLLNFPPYT 347

Query:   369 REQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITNHLIDLTYDNVKE 428
             R QI+ I+  +L Q  +  + + +A+Q  A KV+AVSGD+RKA+D+    I++   +VK 
Sbjct:   348 RNQIVTILQDRLNQVSRDQVLDNAAVQFCARKVSAVSGDVRKALDVCRRAIEIVESDVKS 407

Query:   429 N------GEVTG---------IGLKEVLGVISSVYCTSQSLHCSKDEDSFPXXXXXXXXX 473
                     E            +GL  +  VIS V     +L     +DSFP         
Sbjct:   408 QTILKPLSECKSPSEPLIPKRVGLIHISQVISEVDGNRMTLSQEGAQDSFPLQQKILVCS 467

Query:   474 XXXXXXRPNVKDVTLGK 490
                   +  +K+VTLGK
Sbjct:   468 LMLLIRQLKIKEVTLGK 484

GO:0017111 "nucleoside-triphosphatase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0007067 "mitosis" evidence=IEA

GO:0051301 "cell division" evidence=IEA

GO:0003682 "chromatin binding" evidence=IEA

GO:0000076 "DNA replication checkpoint" evidence=TAS

GO:0000079 "regulation of cyclin-dependent protein serine/threonine kinase activity" evidence=TAS

GO:0000166 "nucleotide binding" evidence=TAS

GO:0005737 "cytoplasm" evidence=TAS

GO:0007089 "traversing start control point of mitotic cell cycle" evidence=TAS

GO:0008156 "negative regulation of DNA replication" evidence=TAS

GO:0008285 "negative regulation of cell proliferation" evidence=TAS

GO:0000075 "cell cycle checkpoint" evidence=TAS

GO:0000082 "G1/S transition of mitotic cell cycle" evidence=TAS

GO:0000083 "regulation of transcription involved in G1/S phase of mitotic cell cycle" evidence=TAS

GO:0000084 "S phase of mitotic cell cycle" evidence=TAS

GO:0000216 "M/G1 transition of mitotic cell cycle" evidence=TAS

GO:0000278 "mitotic cell cycle" evidence=TAS

GO:0005654 "nucleoplasm" evidence=TAS

GO:0005829 "cytosol" evidence=TAS

GO:0006260 "DNA replication" evidence=TAS

GO:0005515 "protein binding" evidence=IPI

GO:0019900 "kinase binding" evidence=IPI

GO:0090007 "regulation of mitotic anaphase" evidence=IMP

GO:0071777 "positive regulation of cell cycle cytokinesis" evidence=IMP

GO:0005634 "nucleus" evidence=IDA

GO:0000922 "spindle pole" evidence=IDA

GO:0051233 "spindle midzone" evidence=IDA

GO:0051984 "positive regulation of chromosome segregation" evidence=IDA

UNIPROTKB|G4MTZ7 MGG_01614 "Cell division control protein 18" [Magnaporthe oryzae 70-15 (taxid:242507)]

 Score = 324 (119.1 bits), Expect = 1.8e-33, Sum P(2) = 1.8e-33
 Identities = 86/255 (33%), Positives = 131/255 (51%)

Query:   189 KAKDSCELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKD- 247
             +  D   L GR+ +   +  FL    ++  +G +Y+SGPPGTGKSA +N +      K  
Sbjct:   125 RGNDPGRLIGRDGERASLETFLAKCTSSTPNGCLYVSGPPGTGKSAMVNAVTDELVSKTP 184

Query:   248 AFKTIYINCNSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFDTKHK---SXXXXX 304
             + +  YINC SV+++  +Y T++ +L  +     E     A+ + F  K K   +     
Sbjct:   185 SVRKAYINCMSVKSSNDLYVTLLEQLGDEIN-ILESEPAAALQQVFIPKRKVAGAFLVVL 243

Query:   305 XXXXXXXSRKQTILYTIFEWPSIPGSKLVLVGVANALDLTDRMLPRLQANVTLQPTLMNF 364
                    S     LY IFEW     S++ LVG+ANALDLTDR LPRL++   L+P L+ F
Sbjct:   244 DEIDHILSLDLESLYKIFEWSMQKSSRVSLVGIANALDLTDRFLPRLKSR-NLKPELLPF 302

Query:   365 APYSREQILEIISQKLKQ---TDKFN-----MFNASALQLLAGKVAAVSGDIRKAIDITN 416
              PYS  QI  I++ +LK        N      F+ +A++L + KV++ +GD+RKA +I  
Sbjct:   303 LPYSAPQIKAIVTDRLKSLMPAGSTNAGFIPFFHPAAIELCSRKVSSQTGDLRKAYEILR 362

Query:   417 HLIDLTYDNVKENGE 431
               +DL     K   E
Sbjct:   363 RALDLVEAETKRKLE 377

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

POMBASE|SPBC14C8.07c cdc18 "MCM loader" [Schizosaccharomyces pombe (taxid:4896)]

 Score = 288 (106.4 bits), Expect = 3.3e-32, Sum P(3) = 3.3e-32
 Identities = 66/202 (32%), Positives = 111/202 (54%)

Query:   189 KAKDSCELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDA 248
             K+  S  + GRE +   +  F   H++    G++Y+SG PGTGK+  L+ ++    + D 
Sbjct:   162 KSYRSAGVVGRENEKSIVESFFRQHLDANAGGALYVSGAPGTGKTVLLHNVLDHV-VSDY 220

Query:   249 FKT--IYINCNSVRNAASVYETIVNELKLKPGGKSERHQLG---AILKYFDTK----HKS 299
              K    YINC ++    +++E I +++  +   ++E H +     +  +F       +  
Sbjct:   221 PKVNVCYINCMTINEPKAIFEKIHSKIVKEEILENEDHHINFQCELESHFTQSANELYNP 280

Query:   300 XXXXXXXXXXXXSRKQTILYTIFEWPSIPGSKLVLVGVANALDLTDRMLPRLQANVTLQP 359
                         +R+Q +LYT+FEWPS P S+L+LVG+ANALD+TDR LPRL+    + P
Sbjct:   281 VIIVLDEMDHLIAREQQVLYTLFEWPSRPTSRLILVGIANALDMTDRFLPRLRTK-HITP 339

Query:   360 TLMNFAPYSREQILEIISQKLK 381
              L++F PY+ ++I  II  +LK
Sbjct:   340 KLLSFTPYTAQEISTIIKARLK 361

GO:0003689 "DNA clamp loader activity" evidence=ISO

GO:0005524 "ATP binding" evidence=ISM

GO:0005656 "pre-replicative complex" evidence=ISO

GO:0006267 "pre-replicative complex assembly" evidence=ISO

GO:0006270 "DNA replication initiation" evidence=IMP

GO:0033314 "mitotic DNA replication checkpoint" evidence=IMP

GO:0043596 "nuclear replication fork" evidence=IC

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	490
COG1474	366	COG1474, CDC6, Cdc6-related protein, AAA superfami	6e-43
TIGR02928	365	TIGR02928, TIGR02928, orc1/cdc6 family replication	4e-27
PTZ00112	1164	PTZ00112, PTZ00112, origin recognition complex 1 p	1e-26
PRK00411	394	PRK00411, cdc6, cell division control protein 6; R	8e-24
pfam13401	124	pfam13401, AAA_22, AAA domain	1e-14
pfam00004	131	pfam00004, AAA, ATPase family associated with vari	1e-09
cd00009	151	cd00009, AAA, The AAA+ (ATPases Associated with a	3e-09
smart00382	148	smart00382, AAA, ATPases associated with a variety	2e-08
pfam13191	154	pfam13191, AAA_16, AAA ATPase domain	3e-08
smart00487	201	smart00487, DEXDc, DEAD-like helicases superfamily	0.001
COG2256	436	COG2256, MGS1, ATPase related to the helicase subu	0.004

>gnl|CDD|224391 COG1474, CDC6, Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]

 Score =  155 bits (394), Expect = 6e-43
 Identities = 81/298 (27%), Positives = 143/298 (47%), Gaps = 21/298 (7%)

Query: 195 ELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDA-FKTIY 253
           ELP RE ++  +  FL   +  E   ++ I GP GTGK+A++  ++   E   A  + +Y
Sbjct: 18  ELPHREEEINQLASFLAPALRGERPSNIIIYGPTGTGKTATVKFVMEELEESSANVEVVY 77

Query: 254 INCNSVRNAASVYETIVNELKLKP--GGKSERHQLGAILKYFDTKHKSILLILDEIDALE 311
           INC  +R    V   I+N+L   P  G  S    L  +      K K++++ILDE+DAL 
Sbjct: 78  INCLELRTPYQVLSKILNKLGKVPLTGDSSLEI-LKRLYDNLSKKGKTVIVILDEVDALV 136

Query: 312 SRKQTILYTIFEWPSIPGSKLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQ 371
            +   +LY++   P     K+ ++ V+N     D + PR++++  L P+ + F PY+ E+
Sbjct: 137 DKDGEVLYSLLRAPGENKVKVSIIAVSNDDKFLDYLDPRVKSS--LGPSEIVFPPYTAEE 194

Query: 372 ILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITNHLIDLTYDNVKENGE 431
           + +I+ +++++     + +   L+L+A  VAA SGD RKAIDI             E  E
Sbjct: 195 LYDILRERVEEGFSAGVIDDDVLKLIAALVAAESGDARKAIDILRR--------AGEIAE 246

Query: 432 VTG---IGLKEVLGVISSVYCTSQSLHCSKDEDSFPLQQKLALASLLLLKSRPNVKDV 486
             G   +    V      +          +   + PL QK+ L +++ L    +  ++
Sbjct: 247 REGSRKVSEDHVREAQEEIE----RDVLEEVLKTLPLHQKIVLLAIVELTVEISTGEL 300

Length = 366

>gnl|CDD|234063 TIGR02928, TIGR02928, orc1/cdc6 family replication initiation protein

 Score =  111 bits (281), Expect = 4e-27
 Identities = 56/233 (24%), Positives = 108/233 (46%), Gaps = 15/233 (6%)

Query: 195 ELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSAS----LNLLVSRAEIKDA-F 249
            +  R+ Q+E + + L   +      +++I G  GTGK+A     +  L   AE +D   
Sbjct: 16  RIVHRDEQIEELAKALRPILRGSRPSNVFIYGKTGTGKTAVTKYVMKELEEAAEDRDVRV 75

Query: 250 KTIYINCNSVRNAASVYETIVNELKLKPG-----GKSERHQLGAILKYFDTKHKSILLIL 304
            T+Y+NC  +     V   + N+L+         G S       + K  + +  S++++L
Sbjct: 76  VTVYVNCQILDTLYQVLVELANQLRGSGEEVPTTGLSTSEVFRRLYKELNERGDSLIIVL 135

Query: 305 DEIDALESRKQTILYTI---FEWPSIPGSKLVLVGVANALDLTDRMLPRLQANVTLQPTL 361
           DEID L      +LY +        +  +K+ ++G++N L   + + PR+++  +L    
Sbjct: 136 DEIDYLVGDDDDLLYQLSRARSNGDLDNAKVGVIGISNDLKFRENLDPRVKS--SLCEEE 193

Query: 362 MNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDI 414
           + F PY  E++ +I+  + ++     + +   + L A   A   GD RKAID+
Sbjct: 194 IIFPPYDAEELRDILENRAEKAFYDGVLDDGVIPLCAALAAQEHGDARKAIDL 246

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 [DNA metabolism, DNA replication, recombination, and repair]. Length = 365

>gnl|CDD|240274 PTZ00112, PTZ00112, origin recognition complex 1 protein; Provisional

 Score =  114 bits (286), Expect = 1e-26
 Identities = 102/359 (28%), Positives = 175/359 (48%), Gaps = 35/359 (9%)

Query: 74  RSLKLDSPKRKIDTA--LEFASPKRVFKDADATSSGAASAVDATSTSDAVRSVSGSRSSA 131
           +SLKL   K KI+     +  S K     A  T+S  A     T         S ++  +
Sbjct: 640 KSLKLIIEKLKINEQGGQKKNSKKEYMNPAQTTTSSKAKTHSKTKNDHNKSKTSKNKEPS 699

Query: 132 KADCLRPLSPIKNIILDKKSPFKAFIRDDED-----LIKRSPAKLCSPRKLLFSEDKPKV 186
                  L  +K         FK+FI+ D++     L++          +++  +  PK 
Sbjct: 700 ST---SFLQDVKKKSDPHNVDFKSFIKQDQENYYVNLLRNITDPTDKAIRMMQLDVVPKY 756

Query: 187 EEKAKDSCELPGREVQLEGIRQFLLGHVNNETSGS-MYISGPPGTGKSASLNLLVSRAEI 245
                    LP RE +++ +  FL   +    S   +YISG PGTGK+A++  ++   + 
Sbjct: 757 ---------LPCREKEIKEVHGFLESGIKQSGSNQILYISGMPGTGKTATVYSVIQLLQH 807

Query: 246 KD------AFKTIYINCNSVRNAASVYETIVNEL--KLKPGGKSERHQLGAILKYF--DT 295
           K       +F    IN  +V +  + Y+ +  +L  K  P   +    L  +      D 
Sbjct: 808 KTKQKLLPSFNVFEINGMNVVHPNAAYQVLYKQLFNKKPPNALNSFKILDRLFNQNKKDN 867

Query: 296 KHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVANALDLTDRMLPRLQANV 355
           ++ SIL+I DEID L ++ Q +L+T+F+WP+   SKLVL+ ++N +DL +R++PR ++ +
Sbjct: 868 RNVSILII-DEIDYLITKTQKVLFTLFDWPTKINSKLVLIAISNTMDLPERLIPRCRSRL 926

Query: 356 TLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDI 414
                +  F+PY  ++I +II ++L+   +  + + +A+QL A KVA VSGDIRKA+ I
Sbjct: 927 AFGRLV--FSPYKGDEIEKIIKERLENCKE--IIDHTAIQLCARKVANVSGDIRKALQI 981

Length = 1164

>gnl|CDD|234751 PRK00411, cdc6, cell division control protein 6; Reviewed

 Score =  102 bits (257), Expect = 8e-24
 Identities = 59/226 (26%), Positives = 111/226 (49%), Gaps = 8/226 (3%)

Query: 195 ELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAE-IKDAFKTIY 253
            LP RE Q+E +   L   +      ++ I GPPGTGK+ ++  +    E I      +Y
Sbjct: 31  NLPHREEQIEELAFALRPALRGSRPLNVLIYGPPGTGKTTTVKKVFEELEEIAVKVVYVY 90

Query: 254 INCNSVRNAASVYETIVNELKLKP---GGKSERHQLGAILKYFDTKHKSILLILDEIDAL 310
           INC   R   +++  I  +L   P    G S       I +Y D + + +++ LD+I+ L
Sbjct: 91  INCQIDRTRYAIFSEIARQLFGHPPPSSGLSFDELFDKIAEYLDERDRVLIVALDDINYL 150

Query: 311 -ESRKQTILYTIFEWP-SIPGSKLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYS 368
            E     +LY++       PG+++ ++G+++ L     + PR+++    +P  + F PY+
Sbjct: 151 FEKEGNDVLYSLLRAHEEYPGARIGVIGISSDLTFLYILDPRVKS--VFRPEEIYFPPYT 208

Query: 369 REQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDI 414
            ++I +I+  ++++     + +   L L+A   A   GD R AID+
Sbjct: 209 ADEIFDILKDRVEEGFYPGVVDDEVLDLIADLTAREHGDARVAIDL 254

Length = 394

>gnl|CDD|222104 pfam13401, AAA_22, AAA domain

 Score = 70.0 bits (172), Expect = 1e-14
 Identities = 28/127 (22%), Positives = 47/127 (37%), Gaps = 5/127 (3%)

Query: 217 ETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLK 276
             +G   ++G  G+GK+  L  L  +       + +Y+   S+     +   I+  L L 
Sbjct: 2   RGAGIGVLTGESGSGKTTLLRRLARQL---PNRRVVYVEAPSLGTPKDLLRKILRALGLP 58

Query: 277 PGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVG 336
             G +    L AIL          LLI+DE   L       L  +++        ++LVG
Sbjct: 59  LSGGTTAELLEAILDALKR-RGRPLLIIDEAQHLSLEALEELRDLYDLSEKGIQ-VILVG 116

Query: 337 VANALDL 343
                 L
Sbjct: 117 TPELRKL 123

Length = 124

>gnl|CDD|215649 pfam00004, AAA, ATPase family associated with various cellular activities (AAA)

 Score = 56.1 bits (136), Expect = 1e-09
 Identities = 35/140 (25%), Positives = 59/140 (42%), Gaps = 31/140 (22%)

Query: 222 MYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKPGGKS 281
           + + GPPGTGK+ +L   V++ E+   F  I I+ + + +              K  G+S
Sbjct: 1   LLLYGPPGTGKT-TLAKAVAK-ELGAPF--IEISGSELVS--------------KYVGES 42

Query: 282 ERHQLGAILKYFDTKHKSILLILDEIDAL-----------ESRKQTILYTIFEWPSIPGS 330
           E+ +L  + +        ++ I DEIDAL             R    L T  +  +   S
Sbjct: 43  EK-RLRELFEAAKKLAPCVIFI-DEIDALAGSRGSGGDSESRRVVNQLLTELDGFTSSLS 100

Query: 331 KLVLVGVANALDLTDRMLPR 350
           K++++   N  D  D  L R
Sbjct: 101 KVIVIAATNRPDKLDPALLR 120

AAA family proteins often perform chaperone-like functions that assist in the assembly, operation, or disassembly of protein complexes. Length = 131

>gnl|CDD|99707 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

 Score = 55.6 bits (134), Expect = 3e-09
 Identities = 30/155 (19%), Positives = 55/155 (35%), Gaps = 19/155 (12%)

Query: 201 VQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVR 260
           V  E   + L   +      ++ + GPPGTGK+     + +          +Y+N + + 
Sbjct: 1   VGQEEAIEALREALELPPPKNLLLYGPPGTGKTTLARAIANELFRPG-APFLYLNASDLL 59

Query: 261 NAASVYETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQT---- 316
               V E   + L       +E+ + G             +L +DEID+L    Q     
Sbjct: 60  EGLVVAELFGHFLVRLLFELAEKAKPG-------------VLFIDEIDSLSRGAQNALLR 106

Query: 317 ILYTIFEWPSIPGSKLVLVGVANALDLTDRMLPRL 351
           +L T+ +        + ++G  N   L D      
Sbjct: 107 VLETLNDLRIDRE-NVRVIGATNRPLLGDLDRALY 140

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. Length = 151

>gnl|CDD|214640 smart00382, AAA, ATPases associated with a variety of cellular activities

 Score = 53.1 bits (127), Expect = 2e-08
 Identities = 31/139 (22%), Positives = 45/139 (32%), Gaps = 8/139 (5%)

Query: 218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKP 277
               + I GPPG+GK+     L +R         IYI+   +         ++     K 
Sbjct: 1   PGEVILIVGPPGSGKTTLARAL-ARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKA 59

Query: 278 GGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQTILY-----TIFEWPSIPGSKL 332
            G  E     A+      K K  +LILDEI +L   +Q  L                  L
Sbjct: 60  SGSGELRLRLALALAR--KLKPDVLILDEITSLLDAEQEALLLLLEELRLLLLLKSEKNL 117

Query: 333 VLVGVANALDLTDRMLPRL 351
            ++   N        L R 
Sbjct: 118 TVILTTNDEKDLGPALLRR 136

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. Length = 148

>gnl|CDD|221970 pfam13191, AAA_16, AAA ATPase domain

 Score = 52.6 bits (126), Expect = 3e-08
 Identities = 26/158 (16%), Positives = 55/158 (34%), Gaps = 21/158 (13%)

Query: 195 ELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYI 254
            L GRE +LE +    L    +    S+ ++GP GTGK++ L  L+       A K    
Sbjct: 1   RLVGREEELERLLD-ALRRARSGGPPSVLLTGPSGTGKTSLLRELLEGLL-VAAGKCDQA 58

Query: 255 NCNSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFD-----------------TKH 297
             N     +     ++ +L  +   +    +   +                       + 
Sbjct: 59  ERNPPYAFSQALRELLRQLLRELAAELLLLREALLAALGAELIEGLQDLVELLERLLARA 118

Query: 298 KSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLV 335
           + ++L+LD++   +     +L  +          L++V
Sbjct: 119 RPLVLVLDDLQWADEESLDLLAALLRRL--ERLPLLVV 154

This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Length = 154

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

 Score = 39.4 bits (92), Expect = 0.001
 Identities = 33/163 (20%), Positives = 54/163 (33%), Gaps = 32/163 (19%)

Query: 199 REVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKS-ASLNLLVSRAEIKDAFKTIYINCN 257
           R  Q E I   L G         + ++ P G+GK+ A+L   +   +     + + +   
Sbjct: 10  RPYQKEAIEALLSGL------RDVILAAPTGSGKTLAALLPALEALKRGKGGRVLVLVPT 63

Query: 258 S--VRNAASVYETIVNELKLKP----GGKSERHQL---------------GAILKYFDTK 296
                  A   + +   L LK     GG S+R QL               G +L   +  
Sbjct: 64  RELAEQWAEELKKLGPSLGLKVVGLYGGDSKREQLRKLESGKTDILVTTPGRLLDLLEND 123

Query: 297 HKSI----LLILDEIDALESRKQTILYTIFEWPSIPGSKLVLV 335
             S+    L+ILDE   L                    +L+L+
Sbjct: 124 KLSLSNVDLVILDEAHRLLDGGFGDQLEKLLKLLPKNVQLLLL 166

Length = 201

>gnl|CDD|225165 COG2256, MGS1, ATPase related to the helicase subunit of the Holliday junction resolvase [DNA replication, recombination, and repair]

 Score = 39.1 bits (92), Expect = 0.004
 Identities = 52/259 (20%), Positives = 96/259 (37%), Gaps = 73/259 (28%)

Query: 220 GSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKPGG 279
            SM + GPPGTGK+ +L  L++      AF+ +    + V++   + E       L    
Sbjct: 49  HSMILWGPPGTGKT-TLARLIAG-TTNAAFEALSAVTSGVKDLREIIEEARKNRLLG--- 103

Query: 280 KSERHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVG--- 336
                             +  +L LDEI      +Q  L      P +    ++L+G   
Sbjct: 104 ------------------RRTILFLDEIHRFNKAQQDALL-----PHVENGTIILIGATT 140

Query: 337 ------VANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNM-- 388
                 +  AL      L R +        +    P S E I +++ + L   ++  +  
Sbjct: 141 ENPSFELNPAL------LSRAR--------VFELKPLSSEDIKKLLKRAL-LDEERGLGG 185

Query: 389 ----FNASALQLLAGKVAAVSGDIRKAIDITNHLIDLTYDNVKENGEVTGIGLKEVLGVI 444
                +  AL  L   V   +GD R+A++    L++L   + + +  +    L+E+L   
Sbjct: 186 QIIVLDEEALDYL---VRLSNGDARRALN----LLELAALSAEPDEVLILELLEEILQRR 238

Query: 445 SSVYCTSQSLHCSKDEDSF 463
           S+ +         KD D+ 
Sbjct: 239 SARF--------DKDGDAH 249

Length = 436

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	490
PTZ00112	1164	origin recognition complex 1 protein; Provisional	100.0
KOG2227|consensus	529		100.0
COG1474	366	CDC6 Cdc6-related protein, AAA superfamily ATPase	100.0
KOG1514|consensus	767		100.0
TIGR02928	365	orc1/cdc6 family replication initiation protein. M	100.0
PRK00411	394	cdc6 cell division control protein 6; Reviewed	100.0
COG2256	436	MGS1 ATPase related to the helicase subunit of the	99.91
COG2255	332	RuvB Holliday junction resolvasome, helicase subun	99.89
COG1222	406	RPT1 ATP-dependent 26S proteasome regulatory subun	99.88
PRK00080	328	ruvB Holliday junction DNA helicase RuvB; Reviewed	99.88
TIGR00635	305	ruvB Holliday junction DNA helicase, RuvB subunit.	99.88
PF05496	233	RuvB_N: Holliday junction DNA helicase ruvB N-term	99.87
PRK14956	484	DNA polymerase III subunits gamma and tau; Provisi	99.87
KOG0989|consensus	346		99.87
PRK07003	830	DNA polymerase III subunits gamma and tau; Validat	99.86
PLN03025	319	replication factor C subunit; Provisional	99.85
KOG0991|consensus	333		99.85
KOG2028|consensus	554		99.85
PRK12323	700	DNA polymerase III subunits gamma and tau; Provisi	99.85
PRK14949	944	DNA polymerase III subunits gamma and tau; Provisi	99.84
KOG0730|consensus	693		99.84
PRK14960	702	DNA polymerase III subunits gamma and tau; Provisi	99.84
PRK06645	507	DNA polymerase III subunits gamma and tau; Validat	99.83
COG1223	368	Predicted ATPase (AAA+ superfamily) [General funct	99.83
PRK14958	509	DNA polymerase III subunits gamma and tau; Provisi	99.83
PRK04195	482	replication factor C large subunit; Provisional	99.83
KOG0738|consensus	491		99.83
PRK13342	413	recombination factor protein RarA; Reviewed	99.83
PRK14962	472	DNA polymerase III subunits gamma and tau; Provisi	99.83
PRK14952	584	DNA polymerase III subunits gamma and tau; Provisi	99.82
KOG0734|consensus	752		99.82
PRK07764	824	DNA polymerase III subunits gamma and tau; Validat	99.82
PRK07994	647	DNA polymerase III subunits gamma and tau; Validat	99.82
PRK14959	624	DNA polymerase III subunits gamma and tau; Provisi	99.82
PRK14951	618	DNA polymerase III subunits gamma and tau; Provisi	99.82
PRK08691	709	DNA polymerase III subunits gamma and tau; Validat	99.81
PRK14964	491	DNA polymerase III subunits gamma and tau; Provisi	99.81
PRK13341	725	recombination factor protein RarA/unknown domain f	99.81
PRK14961	363	DNA polymerase III subunits gamma and tau; Provisi	99.81
PRK14957	546	DNA polymerase III subunits gamma and tau; Provisi	99.81
PRK03992	389	proteasome-activating nucleotidase; Provisional	99.8
PRK14087	450	dnaA chromosomal replication initiation protein; P	99.8
PRK00440	319	rfc replication factor C small subunit; Reviewed	99.79
KOG0733|consensus	802		99.79
PRK08451	535	DNA polymerase III subunits gamma and tau; Validat	99.79
TIGR00602	637	rad24 checkpoint protein rad24. This family is bas	99.79
PTZ00454	398	26S protease regulatory subunit 6B-like protein; P	99.79
CHL00195	489	ycf46 Ycf46; Provisional	99.79
PRK12402	337	replication factor C small subunit 2; Reviewed	99.78
CHL00176	638	ftsH cell division protein; Validated	99.78
PRK05563	559	DNA polymerase III subunits gamma and tau; Validat	99.78
PTZ00361	438	26 proteosome regulatory subunit 4-like protein; P	99.78
PRK14963	504	DNA polymerase III subunits gamma and tau; Provisi	99.78
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	99.78
PRK06893	229	DNA replication initiation factor; Validated	99.78
TIGR03015	269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	99.78
PRK14969	527	DNA polymerase III subunits gamma and tau; Provisi	99.77
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	99.77
PRK05896	605	DNA polymerase III subunits gamma and tau; Validat	99.77
PRK07133	725	DNA polymerase III subunits gamma and tau; Validat	99.77
PRK09111	598	DNA polymerase III subunits gamma and tau; Validat	99.76
PRK14965	576	DNA polymerase III subunits gamma and tau; Provisi	99.76
PRK14088	440	dnaA chromosomal replication initiation protein; P	99.76
TIGR02880	284	cbbX_cfxQ probable Rubsico expression protein CbbX	99.76
TIGR01241	495	FtsH_fam ATP-dependent metalloprotease FtsH. HflB(	99.76
PRK08084	235	DNA replication initiation factor; Provisional	99.76
TIGR02397	355	dnaX_nterm DNA polymerase III, subunit gamma and t	99.75
TIGR02902	531	spore_lonB ATP-dependent protease LonB. Members of	99.75
PRK14955	397	DNA polymerase III subunits gamma and tau; Provisi	99.75
PRK00149	450	dnaA chromosomal replication initiation protein; R	99.75
PRK14086	617	dnaA chromosomal replication initiation protein; P	99.75
KOG0733|consensus	802		99.75
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	99.75
PRK14953	486	DNA polymerase III subunits gamma and tau; Provisi	99.74
TIGR01242	364	26Sp45 26S proteasome subunit P45 family. Many pro	99.74
KOG1970|consensus	634		99.74
PRK14954	620	DNA polymerase III subunits gamma and tau; Provisi	99.74
KOG0728|consensus	404		99.74
PRK06305	451	DNA polymerase III subunits gamma and tau; Validat	99.74
PRK06647	563	DNA polymerase III subunits gamma and tau; Validat	99.74
CHL00181	287	cbbX CbbX; Provisional	99.74
KOG0739|consensus	439		99.74
PRK14948	620	DNA polymerase III subunits gamma and tau; Provisi	99.73
PRK14950	585	DNA polymerase III subunits gamma and tau; Provisi	99.73
PRK08727	233	hypothetical protein; Validated	99.73
PRK14970	367	DNA polymerase III subunits gamma and tau; Provisi	99.72
COG2812	515	DnaX DNA polymerase III, gamma/tau subunits [DNA r	99.72
KOG1969|consensus	877		99.72
PHA02544	316	44 clamp loader, small subunit; Provisional	99.72
KOG0731|consensus	774		99.72
PRK12422	445	chromosomal replication initiation protein; Provis	99.72
KOG0736|consensus	953		99.72
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	99.71
PRK08903	227	DnaA regulatory inactivator Hda; Validated	99.71
TIGR03689	512	pup_AAA proteasome ATPase. In the Actinobacteria,	99.71
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	99.7
COG0464	494	SpoVK ATPases of the AAA+ class [Posttranslational	99.7
PRK14971	614	DNA polymerase III subunits gamma and tau; Provisi	99.7
COG0593	408	DnaA ATPase involved in DNA replication initiation	99.7
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	99.7
KOG0652|consensus	424		99.7
PF03215	519	Rad17: Rad17 cell cycle checkpoint protein	99.7
PRK05642	234	DNA replication initiation factor; Validated	99.69
CHL00095	821	clpC Clp protease ATP binding subunit	99.68
PLN00020	413	ribulose bisphosphate carboxylase/oxygenase activa	99.68
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	99.67
PF00308	219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	99.67
KOG0727|consensus	408		99.67
KOG2228|consensus	408		99.66
PRK06620	214	hypothetical protein; Validated	99.66
KOG0740|consensus	428		99.66
CHL00206	2281	ycf2 Ycf2; Provisional	99.65
PRK09087	226	hypothetical protein; Validated	99.64
PRK10733	644	hflB ATP-dependent metalloprotease; Reviewed	99.64
KOG0737|consensus	386		99.64
COG1224	450	TIP49 DNA helicase TIP49, TBP-interacting protein	99.63
COG0465	596	HflB ATP-dependent Zn proteases [Posttranslational	99.63
PF05621	302	TniB: Bacterial TniB protein; InterPro: IPR008868	99.63
TIGR02903	615	spore_lon_C ATP-dependent protease, Lon family. Me	99.62
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	99.61
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	99.61
KOG0990|consensus	360		99.61
PRK09112	351	DNA polymerase III subunit delta'; Validated	99.6
KOG0726|consensus	440		99.6
PRK10865	857	protein disaggregation chaperone; Provisional	99.6
KOG0729|consensus	435		99.58
TIGR00763	775	lon ATP-dependent protease La. This protein is ind	99.58
COG0466	782	Lon ATP-dependent Lon protease, bacterial type [Po	99.58
PRK07940	394	DNA polymerase III subunit delta'; Validated	99.58
PF00931	287	NB-ARC: NB-ARC domain; InterPro: IPR002182 This is	99.57
PF00004	132	AAA: ATPase family associated with various cellula	99.57
PRK10787	784	DNA-binding ATP-dependent protease La; Provisional	99.57
PF01637	234	Arch_ATPase: Archaeal ATPase; InterPro: IPR011579	99.56
TIGR02974	329	phageshock_pspF psp operon transcriptional activat	99.56
KOG2035|consensus	351		99.56
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	99.54
PF05673	249	DUF815: Protein of unknown function (DUF815); Inte	99.54
PRK04132	846	replication factor C small subunit; Provisional	99.53
KOG2004|consensus	906		99.53
COG2204	464	AtoC Response regulator containing CheY-like recei	99.53
TIGR02640	262	gas_vesic_GvpN gas vesicle protein GvpN. Members o	99.52
KOG0735|consensus	952		99.52
KOG0730|consensus	693		99.52
PRK11608	326	pspF phage shock protein operon transcriptional ac	99.51
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	99.5
COG3829	560	RocR Transcriptional regulator containing PAS, AAA	99.5
TIGR02329	526	propionate_PrpR propionate catabolism operon regul	99.5
COG1221	403	PspF Transcriptional regulators containing an AAA-	99.5
PRK05342	412	clpX ATP-dependent protease ATP-binding subunit Cl	99.49
TIGR01817	534	nifA Nif-specific regulatory protein. This model r	99.49
PRK13531	498	regulatory ATPase RavA; Provisional	99.48
PRK05022	509	anaerobic nitric oxide reductase transcription reg	99.48
COG3267	269	ExeA Type II secretory pathway, component ExeA (pr	99.48
PRK07471	365	DNA polymerase III subunit delta'; Validated	99.48
PRK05201	443	hslU ATP-dependent protease ATP-binding subunit Hs	99.47
PRK15424	538	propionate catabolism operon regulatory protein Pr	99.47
KOG0651|consensus	388		99.47
TIGR00390	441	hslU ATP-dependent protease HslVU, ATPase subunit.	99.47
TIGR00678	188	holB DNA polymerase III, delta' subunit. At positi	99.46
PF06068	398	TIP49: TIP49 C-terminus; InterPro: IPR010339 This	99.45
KOG0732|consensus	1080		99.45
PRK10820	520	DNA-binding transcriptional regulator TyrR; Provis	99.44
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	99.44
PRK13407	334	bchI magnesium chelatase subunit I; Provisional	99.42
PRK15429	686	formate hydrogenlyase transcriptional activator Fh	99.42
PRK07399	314	DNA polymerase III subunit delta'; Validated	99.42
COG0470	325	HolB ATPase involved in DNA replication [DNA repli	99.41
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	99.41
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	99.41
CHL00081	350	chlI Mg-protoporyphyrin IX chelatase	99.41
COG3604	550	FhlA Transcriptional regulator containing GAF, AAA	99.41
TIGR00382	413	clpX endopeptidase Clp ATP-binding regulatory subu	99.41
PRK11388	638	DNA-binding transcriptional regulator DhaR; Provis	99.4
PRK05564	313	DNA polymerase III subunit delta'; Validated	99.39
KOG0742|consensus	630		99.39
KOG0744|consensus	423		99.38
KOG0735|consensus	952		99.38
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	99.38
TIGR02030	337	BchI-ChlI magnesium chelatase ATPase subunit I. Th	99.38
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	99.38
PRK10865	857	protein disaggregation chaperone; Provisional	99.38
KOG2680|consensus	454		99.37
KOG4658|consensus	889		99.36
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	99.35
TIGR02442	633	Cob-chelat-sub cobaltochelatase subunit. A number	99.35
PRK08058	329	DNA polymerase III subunit delta'; Validated	99.34
TIGR00764	608	lon_rel lon-related putative ATP-dependent proteas	99.34
KOG0741|consensus	744		99.33
KOG2543|consensus	438		99.33
KOG1942|consensus	456		99.32
CHL00095	821	clpC Clp protease ATP binding subunit	99.32
COG2607	287	Predicted ATPase (AAA+ superfamily) [General funct	99.32
TIGR01650	327	PD_CobS cobaltochelatase, CobS subunit. This model	99.29
PRK05707	328	DNA polymerase III subunit delta'; Validated	99.28
PRK10923	469	glnG nitrogen regulation protein NR(I); Provisiona	99.28
PF13191	185	AAA_16: AAA ATPase domain; PDB: 2V1U_A.	99.26
TIGR02915	445	PEP_resp_reg putative PEP-CTERM system response re	99.26
TIGR01818	463	ntrC nitrogen regulation protein NR(I). This model	99.24
PRK11331	459	5-methylcytosine-specific restriction enzyme subun	99.22
PRK15115	444	response regulator GlrR; Provisional	99.21
TIGR02031	589	BchD-ChlD magnesium chelatase ATPase subunit D. Th	99.21
COG0714	329	MoxR-like ATPases [General function prediction onl	99.21
TIGR00368	499	Mg chelatase-related protein. The N-terminal end m	99.21
PRK13765	637	ATP-dependent protease Lon; Provisional	99.2
COG1239	423	ChlI Mg-chelatase subunit ChlI [Coenzyme metabolis	99.19
PRK06871	325	DNA polymerase III subunit delta'; Validated	99.18
PRK07993	334	DNA polymerase III subunit delta'; Validated	99.18
PF13177	162	DNA_pol3_delta2: DNA polymerase III, delta subunit	99.18
COG1220	444	HslU ATP-dependent protease HslVU (ClpYQ), ATPase	99.16
PF00158	168	Sigma54_activat: Sigma-54 interaction domain; Inte	99.15
smart00350	509	MCM minichromosome maintenance proteins.	99.15
PLN03210	1153	Resistant to P. syringae 6; Provisional	99.14
PRK11361	457	acetoacetate metabolism regulatory protein AtoC; P	99.14
PRK08769	319	DNA polymerase III subunit delta'; Validated	99.13
KOG1968|consensus	871		99.13
KOG0743|consensus	457		99.1
PF07728	139	AAA_5: AAA domain (dynein-related subfamily); Inte	99.09
PF05729	166	NACHT: NACHT domain	99.08
PRK08116	268	hypothetical protein; Validated	99.06
COG1219	408	ClpX ATP-dependent protease Clp, ATPase subunit [P	99.04
PRK10365	441	transcriptional regulatory protein ZraR; Provision	99.04
PRK09862	506	putative ATP-dependent protease; Provisional	99.03
COG3283	511	TyrR Transcriptional regulator of aromatic amino a	99.02
PHA02244	383	ATPase-like protein	99.0
KOG0745|consensus	564		99.0
PRK06090	319	DNA polymerase III subunit delta'; Validated	99.0
PRK06964	342	DNA polymerase III subunit delta'; Validated	98.99
KOG0736|consensus	953		98.97
PF14516	331	AAA_35: AAA-like domain	98.97
PRK12377	248	putative replication protein; Provisional	98.96
COG3284	606	AcoR Transcriptional activator of acetoin/glycerol	98.95
PF14532	138	Sigma54_activ_2: Sigma-54 interaction domain; PDB:	98.95
PF13173	128	AAA_14: AAA domain	98.92
COG0606	490	Predicted ATPase with chaperone activity [Posttran	98.92
PRK06835	329	DNA replication protein DnaC; Validated	98.9
PF07693	325	KAP_NTPase: KAP family P-loop domain; InterPro: IP	98.9
PRK13406	584	bchD magnesium chelatase subunit D; Provisional	98.89
PRK07952	244	DNA replication protein DnaC; Validated	98.87
PF01078	206	Mg_chelatase: Magnesium chelatase, subunit ChlI; I	98.86
smart00382	148	AAA ATPases associated with a variety of cellular	98.86
PRK07132	299	DNA polymerase III subunit delta'; Validated	98.85
PRK06921	266	hypothetical protein; Provisional	98.83
PRK04841	903	transcriptional regulator MalT; Provisional	98.8
PTZ00111	915	DNA replication licensing factor MCM4; Provisional	98.77
PRK08699	325	DNA polymerase III subunit delta'; Validated	98.77
PRK07276	290	DNA polymerase III subunit delta'; Validated	98.76
KOG1051|consensus	898		98.76
PTZ00202	550	tuzin; Provisional	98.75
PF12775	272	AAA_7: P-loop containing dynein motor region D3; P	98.74
PRK05917	290	DNA polymerase III subunit delta'; Validated	98.73
PRK08181	269	transposase; Validated	98.73
KOG0741|consensus	744		98.73
COG3899	849	Predicted ATPase [General function prediction only	98.73
PRK05818	261	DNA polymerase III subunit delta'; Validated	98.72
PF07724	171	AAA_2: AAA domain (Cdc48 subfamily); InterPro: IPR	98.71
COG1484	254	DnaC DNA replication protein [DNA replication, rec	98.71
PF07726	131	AAA_3: ATPase family associated with various cellu	98.69
PRK06526	254	transposase; Provisional	98.65
PF10923	416	DUF2791: P-loop Domain of unknown function (DUF279	98.64
smart00763	361	AAA_PrkA PrkA AAA domain. This is a family of PrkA	98.61
PRK08939	306	primosomal protein DnaI; Reviewed	98.61
COG2909	894	MalT ATP-dependent transcriptional regulator [Tran	98.57
COG1241	682	MCM2 Predicted ATPase involved in replication cont	98.52
COG4650	531	RtcR Sigma54-dependent transcription regulator con	98.52
PHA00729	226	NTP-binding motif containing protein	98.49
PF10443	431	RNA12: RNA12 protein; InterPro: IPR018850 Mitochon	98.48
PF01695	178	IstB_IS21: IstB-like ATP binding protein; InterPro	98.48
COG1373	398	Predicted ATPase (AAA+ superfamily) [General funct	98.45
PRK09183	259	transposase/IS protein; Provisional	98.42
PRK14700	300	recombination factor protein RarA; Provisional	98.41
PF10236	309	DAP3: Mitochondrial ribosomal death-associated pro	98.39
PRK00771	437	signal recognition particle protein Srp54; Provisi	98.39
PF03969	362	AFG1_ATPase: AFG1-like ATPase; InterPro: IPR005654	98.37
KOG1051|consensus	898		98.37
cd01128	249	rho_factor Transcription termination factor rho is	98.35
COG1618	179	Predicted nucleotide kinase [Nucleotide transport	98.33
PRK10536	262	hypothetical protein; Provisional	98.33
cd01120	165	RecA-like_NTPases RecA-like NTPases. This family i	98.29
PRK12723	388	flagellar biosynthesis regulator FlhF; Provisional	98.28
KOG0480|consensus	764		98.27
PF12780	268	AAA_8: P-loop containing dynein motor region D4; I	98.24
PF13604	196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	98.24
KOG0478|consensus	804		98.24
PRK12608	380	transcription termination factor Rho; Provisional	98.23
TIGR00767	415	rho transcription termination factor Rho. Members	98.16
PF00493	331	MCM: MCM2/3/5 family This family extends the MCM d	98.16
PRK09376	416	rho transcription termination factor Rho; Provisio	98.15
KOG0482|consensus	721		98.14
PRK04296	190	thymidine kinase; Provisional	98.13
COG2842	297	Uncharacterized ATPase, putative transposase [Gene	98.12
PRK08485	206	DNA polymerase III subunit delta'; Validated	98.04
PRK06581	263	DNA polymerase III subunit delta'; Validated	98.0
PRK14722	374	flhF flagellar biosynthesis regulator FlhF; Provis	97.98
PRK05703	424	flhF flagellar biosynthesis regulator FlhF; Valida	97.94
cd00046	144	DEXDc DEAD-like helicases superfamily. A diverse f	97.93
PRK14974	336	cell division protein FtsY; Provisional	97.92
PF04665	241	Pox_A32: Poxvirus A32 protein; InterPro: IPR006758	97.91
KOG2170|consensus	344		97.91
PF00448	196	SRP54: SRP54-type protein, GTPase domain; InterPro	97.9
COG1066	456	Sms Predicted ATP-dependent serine protease [Postt	97.89
PF02562	205	PhoH: PhoH-like protein; InterPro: IPR003714 PhoH	97.87
PF03266	168	NTPase_1: NTPase; InterPro: IPR004948 This entry r	97.86
) 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	97.86
PF09848	352	DUF2075: Uncharacterized conserved protein (DUF207	97.84
PF05970	364	PIF1: PIF1-like helicase; InterPro: IPR010285 This	97.83
COG5271	4600	MDN1 AAA ATPase containing von Willebrand factor t	97.81
PRK10867	433	signal recognition particle protein; Provisional	97.81
PRK13695	174	putative NTPase; Provisional	97.81
TIGR00959	428	ffh signal recognition particle protein. This mode	97.8
cd01124	187	KaiC KaiC is a circadian clock protein primarily f	97.8
COG5271	4600	MDN1 AAA ATPase containing von Willebrand factor t	97.79
COG1419	407	FlhF Flagellar GTP-binding protein [Cell motility	97.78
PF08298	358	AAA_PrkA: PrkA AAA domain; InterPro: IPR013153 Thi	97.77
PF00910	107	RNA_helicase: RNA helicase; InterPro: IPR000605 He	97.73
TIGR01448	720	recD_rel helicase, putative, RecD/TraA family. Thi	97.72
TIGR03877	237	thermo_KaiC_1 KaiC domain protein, Ph0284 family.	97.71
COG0464	494	SpoVK ATPases of the AAA+ class [Posttranslational	97.71
TIGR03499	282	FlhF flagellar biosynthetic protein FlhF.	97.7
PRK09361	225	radB DNA repair and recombination protein RadB; Pr	97.7
KOG3347|consensus	176		97.7
PRK11889	436	flhF flagellar biosynthesis regulator FlhF; Provis	97.69
TIGR02768	744	TraA_Ti Ti-type conjugative transfer relaxase TraA	97.69
PLN02674	244	adenylate kinase	97.69
TIGR01425	429	SRP54_euk signal recognition particle protein SRP5	97.68
TIGR01618	220	phage_P_loop phage nucleotide-binding protein. Thi	97.67
PRK11823	446	DNA repair protein RadA; Provisional	97.67
cd01121	372	Sms Sms (bacterial radA) DNA repair protein. This	97.66
PF07034	330	ORC3_N: Origin recognition complex (ORC) subunit 3	97.65
cd03115	173	SRP The signal recognition particle (SRP) mediates	97.65
KOG0477|consensus	854		97.64
cd03281	213	ABC_MSH5_euk MutS5 homolog in eukaryotes. The MutS	97.64
cd01131	198	PilT Pilus retraction ATPase PilT. PilT is a nucle	97.63
KOG2383|consensus	467		97.62
PRK12724	432	flagellar biosynthesis regulator FlhF; Provisional	97.62
TIGR02237	209	recomb_radB DNA repair and recombination protein R	97.61
smart00487	201	DEXDc DEAD-like helicases superfamily.	97.6
PRK12727	559	flagellar biosynthesis regulator FlhF; Provisional	97.6
COG4088	261	Predicted nucleotide kinase [Nucleotide transport	97.59
cd01122	271	GP4d_helicase GP4d_helicase is a homohexameric 5'-	97.59
cd00984	242	DnaB_C DnaB helicase C terminal domain. The hexame	97.57
PHA02774	613	E1; Provisional	97.54
PF12774	231	AAA_6: Hydrolytic ATP binding site of dynein motor	97.54
cd01123	235	Rad51_DMC1_radA Rad51_DMC1_radA,B. This group of r	97.54
COG1485	367	Predicted ATPase [General function prediction only	97.52
PRK15455	644	PrkA family serine protein kinase; Provisional	97.51
PRK05574	340	holA DNA polymerase III subunit delta; Reviewed	97.51
TIGR02012	321	tigrfam_recA protein RecA. This model describes or	97.49
TIGR01447	586	recD exodeoxyribonuclease V, alpha subunit. This f	97.49
TIGR03881	229	KaiC_arch_4 KaiC domain protein, PAE1156 family. M	97.49
PF13207	121	AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6	97.49
TIGR01359	183	UMP_CMP_kin_fam UMP-CMP kinase family. This subfam	97.49
PRK10875	615	recD exonuclease V subunit alpha; Provisional	97.49
PRK13889	988	conjugal transfer relaxase TraA; Provisional	97.48
PRK05800	170	cobU adenosylcobinamide kinase/adenosylcobinamide-	97.48
COG0541	451	Ffh Signal recognition particle GTPase [Intracellu	97.48
PRK06067	234	flagellar accessory protein FlaH; Validated	97.45
TIGR02688	449	conserved hypothetical protein TIGR02688. Members	97.45
PRK05973	237	replicative DNA helicase; Provisional	97.44
PRK14532	188	adenylate kinase; Provisional	97.44
TIGR03878	259	thermo_KaiC_2 KaiC domain protein, AF_0795 family.	97.43
PTZ00494	664	tuzin-like protein; Provisional	97.41
PF04851	184	ResIII: Type III restriction enzyme, res subunit;	97.41
PRK14723	767	flhF flagellar biosynthesis regulator FlhF; Provis	97.4
PRK00279	215	adk adenylate kinase; Reviewed	97.39
cd00983	325	recA RecA is a bacterial enzyme which has roles in	97.38
KOG0481|consensus	729		97.36
COG4608	268	AppF ABC-type oligopeptide transport system, ATPas	97.35
PRK08533	230	flagellar accessory protein FlaH; Reviewed	97.35
PRK04328	249	hypothetical protein; Provisional	97.34
cd01393	226	recA_like RecA is a bacterial enzyme which has rol	97.34
PRK09354	349	recA recombinase A; Provisional	97.33
PRK08118	167	topology modulation protein; Reviewed	97.33
PF13481	193	AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C.	97.33
PRK06762	166	hypothetical protein; Provisional	97.33
PRK12726	407	flagellar biosynthesis regulator FlhF; Provisional	97.32
TIGR01128	302	holA DNA polymerase III, delta subunit. subunit ar	97.32
PRK06995	484	flhF flagellar biosynthesis regulator FlhF; Valida	97.31
COG2805	353	PilT Tfp pilus assembly protein, pilus retraction	97.3
TIGR01420	343	pilT_fam pilus retraction protein PilT. This model	97.28
PF06745	226	KaiC: KaiC; InterPro: IPR014774 This entry represe	97.26
TIGR00416	454	sms DNA repair protein RadA. The gene protuct code	97.26
PRK14528	186	adenylate kinase; Provisional	97.24
COG0194	191	Gmk Guanylate kinase [Nucleotide transport and met	97.24
PRK13808	333	adenylate kinase; Provisional	97.24
PRK10416	318	signal recognition particle-docking protein FtsY;	97.23
PF08433	270	KTI12: Chromatin associated protein KTI12 ; InterP	97.23
PRK07261	171	topology modulation protein; Provisional	97.21
COG3854	308	SpoIIIAA ncharacterized protein conserved in bacte	97.2
cd00544	169	CobU Adenosylcobinamide kinase / adenosylcobinamid	97.2
PRK13826	1102	Dtr system oriT relaxase; Provisional	97.2
COG1124	252	DppF ABC-type dipeptide/oligopeptide/nickel transp	97.2
PRK14531	183	adenylate kinase; Provisional	97.19
PRK14527	191	adenylate kinase; Provisional	97.19
TIGR00064	272	ftsY signal recognition particle-docking protein F	97.18
COG4619	223	ABC-type uncharacterized transport system, ATPase	97.17
PRK14721	420	flhF flagellar biosynthesis regulator FlhF; Provis	97.17
PF03796	259	DnaB_C: DnaB-like helicase C terminal domain; Inte	97.16
PRK02496	184	adk adenylate kinase; Provisional	97.16
cd01129	264	PulE-GspE PulE/GspE The type II secretory pathway	97.15
cd01394	218	radB RadB. The archaeal protein radB shares simila	97.14
TIGR02238	313	recomb_DMC1 meiotic recombinase Dmc1. This model d	97.14
PRK13900	332	type IV secretion system ATPase VirB11; Provisiona	97.14
cd03216	163	ABC_Carb_Monos_I This family represents the domain	97.13
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	97.12
PRK08233	182	hypothetical protein; Provisional	97.12
PF13086	236	AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV	97.11
COG4178	604	ABC-type uncharacterized transport system, permeas	97.11
TIGR01351	210	adk adenylate kinases. Adenylate kinase (EC 2.7.4.	97.1
COG1102	179	Cmk Cytidylate kinase [Nucleotide transport and me	97.1
cd03214	180	ABC_Iron-Siderophores_B12_Hemin ABC transporters,	97.09
TIGR00150	133	HI0065_YjeE ATPase, YjeE family. Members of this f	97.08
TIGR02782	299	TrbB_P P-type conjugative transfer ATPase TrbB. Th	97.07
PRK07452	326	DNA polymerase III subunit delta; Validated	97.06
PF13479	213	AAA_24: AAA domain	97.06
cd03283	199	ABC_MutS-like MutS-like homolog in eukaryotes. The	97.06
TIGR02858	270	spore_III_AA stage III sporulation protein AA. Mem	97.05
KOG0479|consensus	818		97.05
PF00270	169	DEAD: DEAD/DEAH box helicase; InterPro: IPR011545	97.04
PF13245	76	AAA_19: Part of AAA domain	97.04
PRK06585	343	holA DNA polymerase III subunit delta; Reviewed	97.04
cd01428	194	ADK Adenylate kinase (ADK) catalyzes the reversibl	97.03
PF07088	484	GvpD: GvpD gas vesicle protein; InterPro: IPR00978	97.02
TIGR03574	249	selen_PSTK L-seryl-tRNA(Sec) kinase, archaeal. Mem	97.02
cd03243	202	ABC_MutS_homologs The MutS protein initiates DNA m	97.01
PRK04040	188	adenylate kinase; Provisional	97.01
cd00267	157	ABC_ATPase ABC (ATP-binding cassette) transporter	97.01
PRK13709	1747	conjugal transfer nickase/helicase TraI; Provision	97.01
PF05272	198	VirE: Virulence-associated protein E; InterPro: IP	97.0
cd03287	222	ABC_MSH3_euk MutS3 homolog in eukaryotes. The MutS	97.0
PRK04301	317	radA DNA repair and recombination protein RadA; Va	96.99
PRK14529	223	adenylate kinase; Provisional	96.99
PF01443	234	Viral_helicase1: Viral (Superfamily 1) RNA helicas	96.99
TIGR02788	308	VirB11 P-type DNA transfer ATPase VirB11. The VirB	96.98
PTZ00035	337	Rad51 protein; Provisional	96.97
TIGR02236	310	recomb_radA DNA repair and recombination protein R	96.97
PLN03187	344	meiotic recombination protein DMC1 homolog; Provis	96.97
PRK06696	223	uridine kinase; Validated	96.94
PRK06731	270	flhF flagellar biosynthesis regulator FlhF; Valida	96.94
PRK09270	229	nucleoside triphosphate hydrolase domain-containin	96.93
PLN02200	234	adenylate kinase family protein	96.91
PRK12678	672	transcription termination factor Rho; Provisional	96.91
cd03238	176	ABC_UvrA The excision repair protein UvrA; Nucleot	96.9
COG0563	178	Adk Adenylate kinase and related kinases [Nucleoti	96.89
TIGR03600	421	phage_DnaB phage replicative helicase, DnaB family	96.87
PRK00131	175	aroK shikimate kinase; Reviewed	96.87
TIGR03575	340	selen_PSTK_euk L-seryl-tRNA(Sec) kinase, eukaryoti	96.87
PRK06547	172	hypothetical protein; Provisional	96.86
cd02027	149	APSK Adenosine 5'-phosphosulfate kinase (APSK) cat	96.86
COG1121	254	ZnuC ABC-type Mn/Zn transport systems, ATPase comp	96.85
PRK14712	1623	conjugal transfer nickase/helicase TraI; Provision	96.85
PF00006	215	ATP-synt_ab: ATP synthase alpha/beta family, nucle	96.84
PF13671	143	AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1	96.84
PRK09302	509	circadian clock protein KaiC; Reviewed	96.84
PRK13894	319	conjugal transfer ATPase TrbB; Provisional	96.84
TIGR01587	358	cas3_core CRISPR-associated helicase Cas3. This mo	96.84
PRK09694	878	helicase Cas3; Provisional	96.83
cd03221	144	ABCF_EF-3 ABCF_EF-3 Elongation factor 3 (EF-3) is	96.83
cd03280	200	ABC_MutS2 MutS2 homologs in bacteria and eukaryote	96.82
TIGR02760	1960	TraI_TIGR conjugative transfer relaxase protein Tr	96.81
cd03247	178	ABCC_cytochrome_bd The CYD subfamily implicated in	96.8
PTZ00293	211	thymidine kinase; Provisional	96.79
KOG3928|consensus	461		96.79
PF13238	129	AAA_18: AAA domain; PDB: 3IIK_A 3IIJ_A 3IIL_A 1RKB	96.79
cd03246	173	ABCC_Protease_Secretion This family represents the	96.79
smart00534	185	MUTSac ATPase domain of DNA mismatch repair MUTS f	96.78
TIGR00665	434	DnaB replicative DNA helicase. This model describe	96.78
PTZ00088	229	adenylate kinase 1; Provisional	96.77
PLN02459	261	probable adenylate kinase	96.75
PRK14737	186	gmk guanylate kinase; Provisional	96.75
PRK10646	153	ADP-binding protein; Provisional	96.75
KOG0058|consensus	716		96.75
cd01133	274	F1-ATPase_beta F1 ATP synthase beta subunit, nucle	96.74
cd03282	204	ABC_MSH4_euk MutS4 homolog in eukaryotes. The MutS	96.74
PRK03839	180	putative kinase; Provisional	96.73
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	96.72
KOG1808|consensus	1856		96.72
PF00406	151	ADK: Adenylate kinase; InterPro: IPR000850 Adenyla	96.71
COG2804	500	PulE Type II secretory pathway, ATPase PulE/Tfp pi	96.71
PRK07594	433	type III secretion system ATPase SsaN; Validated	96.71
cd03222	177	ABC_RNaseL_inhibitor The ABC ATPase RNase L inhibi	96.7
cd01878	204	HflX HflX subfamily. A distinct conserved domain w	96.69
cd03223	166	ABCD_peroxisomal_ALDP Peroxisomal ATP-binding cass	96.69
cd02019	69	NK Nucleoside/nucleotide kinase (NK) is a protein	96.68
KOG0922|consensus	674		96.68
COG1936	180	Predicted nucleotide kinase (related to CMP and AM	96.67
COG1136	226	SalX ABC-type antimicrobial peptide transport syst	96.66
PRK00625	173	shikimate kinase; Provisional	96.66
COG0467	260	RAD55 RecA-superfamily ATPases implicated in signa	96.65
PF05707	193	Zot: Zonular occludens toxin (Zot); InterPro: IPR0	96.64
cd04160	167	Arfrp1 Arfrp1 subfamily. Arfrp1 (Arf-related prote	96.64
cd01852	196	AIG1 AIG1 (avrRpt2-induced gene 1). This represent	96.62
cd01853	249	Toc34_like Toc34-like (Translocon at the Outer-env	96.62
TIGR03880	224	KaiC_arch_3 KaiC domain protein, AF_0351 family. T	96.62
TIGR02525	372	plasmid_TraJ plasmid transfer ATPase TraJ. Members	96.61
PRK05748	448	replicative DNA helicase; Provisional	96.61
PF02367	123	UPF0079: Uncharacterised P-loop hydrolase UPF0079;	96.6
TIGR02239	316	recomb_RAD51 DNA repair protein RAD51. This eukary	96.6
PRK08972	444	fliI flagellum-specific ATP synthase; Validated	96.57
TIGR00041	195	DTMP_kinase thymidylate kinase. Function: phosphor	96.56
PF00437	270	T2SE: Type II/IV secretion system protein; InterPr	96.56

>PTZ00112 origin recognition complex 1 protein; Provisional

Probab=100.00  E-value=1.9e-35  Score=308.45  Aligned_cols=293  Identities=28%  Similarity=0.454  Sum_probs=242.9

Q ss_pred             CCcchHHHhhcCC----CCCCChHHHHHHHHHHHHhhhccCCC-CeEEEECCCCCcHHHHHHHHHHHhhhc------CCc
Q psy200          181 EDKPKVEEKAKDS----CELPGREVQLEGIRQFLLGHVNNETS-GSMYISGPPGTGKSASLNLLVSRAEIK------DAF  249 (490)
Q Consensus       181 ~~~~~~~~~~l~~----~~lvgre~~~~~l~~~L~~~~~~~~~-~~ill~GppGtGKTtla~~l~~~l~~~------~~~  249 (490)
                      ...+..+...|+.    +.|+||++++++|..+|...+.+..+ .+++|+|+||||||++++.|++++...      ..+
T Consensus       738 ~~p~~~A~rvL~~DYVPD~LPhREeEIeeLasfL~paIkgsgpnnvLYIyG~PGTGKTATVK~VLrELqeeaeqk~lp~f  817 (1164)
T PTZ00112        738 TDPTDKAIRMMQLDVVPKYLPCREKEIKEVHGFLESGIKQSGSNQILYISGMPGTGKTATVYSVIQLLQHKTKQKLLPSF  817 (1164)
T ss_pred             CChHHHHHHHcCcccCCCcCCChHHHHHHHHHHHHHHHhcCCCCceEEEECCCCCCHHHHHHHHHHHHHHHHhhccCCCc
Confidence            4456667776766    89999999999999999998875544 456799999999999999999988521      247


Q ss_pred             eEEEEeccCCCCHHHHHHHHHHHhcCC--CCCCcHHHHHHHHHHHH-hcCCCeEEEEEecCccccccCHHHHHHhHhCCC
Q psy200          250 KTIYINCNSVRNAASVYETIVNELKLK--PGGKSERHQLGAILKYF-DTKHKSILLILDEIDALESRKQTILYTIFEWPS  326 (490)
Q Consensus       250 ~~~~v~~~~~~~~~~l~~~i~~~l~~~--~~~~s~~~~~~~l~~~l-~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~  326 (490)
                      .++++||..+.+...++..|+.+|...  ..+....++++.+...+ ...+...||||||||.|....++.|+.+++|..
T Consensus       818 ~vVYINCm~Lstp~sIYqvI~qqL~g~~P~~GlsS~evLerLF~~L~k~~r~v~IIILDEID~L~kK~QDVLYnLFR~~~  897 (1164)
T PTZ00112        818 NVFEINGMNVVHPNAAYQVLYKQLFNKKPPNALNSFKILDRLFNQNKKDNRNVSILIIDEIDYLITKTQKVLFTLFDWPT  897 (1164)
T ss_pred             eEEEEeCCccCCHHHHHHHHHHHHcCCCCCccccHHHHHHHHHhhhhcccccceEEEeehHhhhCccHHHHHHHHHHHhh
Confidence            889999999999999999999998542  22333333333333333 333456799999999999888999999999987


Q ss_pred             CCCCcEEEEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhC
Q psy200          327 IPGSKLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSG  406 (490)
Q Consensus       327 ~~~~~vilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~G  406 (490)
                      ..+++++|||++|..++.+++++++++||+.  ..+.|.||+.+|+.+||..++...  ...++++++++|+++++...|
T Consensus       898 ~s~SKLiLIGISNdlDLperLdPRLRSRLg~--eeIvF~PYTaEQL~dILk~RAe~A--~gVLdDdAIELIArkVAq~SG  973 (1164)
T PTZ00112        898 KINSKLVLIAISNTMDLPERLIPRCRSRLAF--GRLVFSPYKGDEIEKIIKERLENC--KEIIDHTAIQLCARKVANVSG  973 (1164)
T ss_pred             ccCCeEEEEEecCchhcchhhhhhhhhcccc--ccccCCCCCHHHHHHHHHHHHHhC--CCCCCHHHHHHHHHhhhhcCC
Confidence            7788999999999999999999999999975  369999999999999999999865  356899999999999999999


Q ss_pred             CHHHHHHHHHHHHHHHHhccccCCcccccCHHHHHHHHHHhccCccccccccccCCCChHhHHHHHHHHHHhcCCCCCCc
Q psy200          407 DIRKAIDITNHLIDLTYDNVKENGEVTGIGLKEVLGVISSVYCTSQSLHCSKDEDSFPLQQKLALASLLLLKSRPNVKDV  486 (490)
Q Consensus       407 d~r~ai~ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~~~~~~~~~~~~~~~~l~~L~~~qk~vL~al~~~~~~~~~~~~  486 (490)
                      |+|.||++|+.|++.+  ++      ..|+.+||.+|+..++...+    .+.|..||+|+++||+||+.+.+..+...+
T Consensus       974 DARKALDILRrAgEik--eg------skVT~eHVrkAleeiE~srI----~e~IktLPlHqKLVLlALIlLlk~tg~~~i 1041 (1164)
T PTZ00112        974 DIRKALQICRKAFENK--RG------QKIVPRDITEATNQLFDSPL----TNAINYLPWPFKMFLTCLIVELRMLNDFII 1041 (1164)
T ss_pred             HHHHHHHHHHHHHhhc--CC------CccCHHHHHHHHHHHHhhhH----HHHHHcCCHHHHHHHHHHHHHHhhcCCCce
Confidence            9999999999999863  22      47999999999999988887    788999999999999999988877555456


Q ss_pred             ccC
Q psy200          487 TLG  489 (490)
Q Consensus       487 ~~g  489 (490)
                      +.|
T Consensus      1042 ~TG 1044 (1164)
T PTZ00112       1042 PYK 1044 (1164)
T ss_pred             eHH
Confidence            655

>KOG2227|consensus

Probab=100.00  E-value=1.9e-35  Score=288.53  Aligned_cols=291  Identities=38%  Similarity=0.665  Sum_probs=253.8

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcC-CceEEEEeccCCCCHHHHHHHHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKD-AFKTIYINCNSVRNAASVYETIVNE  272 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~-~~~~~~v~~~~~~~~~~l~~~i~~~  272 (490)
                      ..++||+.+...+.+|+...+....++.++|.|.||+|||.+...++..+.... .+..+|+||..+.....+|..|+..
T Consensus       150 ~~l~gRe~e~~~v~~F~~~hle~~t~gSlYVsG~PGtgkt~~l~rvl~~~~~~~~~~~~v~inc~sl~~~~aiF~kI~~~  229 (529)
T KOG2227|consen  150 GTLKGRELEMDIVREFFSLHLELNTSGSLYVSGQPGTGKTALLSRVLDSLSKSSKSPVTVYINCTSLTEASAIFKKIFSS  229 (529)
T ss_pred             CCccchHHHHHHHHHHHHhhhhcccCcceEeeCCCCcchHHHHHHHHHhhhhhcccceeEEEeeccccchHHHHHHHHHH
Confidence            789999999999999999999999999999999999999999999998876433 3477999999999999999988888


Q ss_pred             hc-CCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEEEecCCCChhHhhhHHh
Q psy200          273 LK-LKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVANALDLTDRMLPRL  351 (490)
Q Consensus       273 l~-~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI~~tn~~~~~~~l~~~l  351 (490)
                      +- .........+....|.........++||++||+|+|....+..|+.+|+|....++++++||++|..|+.++++++|
T Consensus       230 ~~q~~~s~~~~~~~~~~~~~h~~q~k~~~llVlDEmD~L~tr~~~vLy~lFewp~lp~sr~iLiGiANslDlTdR~LprL  309 (529)
T KOG2227|consen  230 LLQDLVSPGTGMQHLEKFEKHTKQSKFMLLLVLDEMDHLITRSQTVLYTLFEWPKLPNSRIILIGIANSLDLTDRFLPRL  309 (529)
T ss_pred             HHHHhcCCchhHHHHHHHHHHHhcccceEEEEechhhHHhhcccceeeeehhcccCCcceeeeeeehhhhhHHHHHhhhh
Confidence            72 22222223566677777776666799999999999999999999999999999999999999999999999999999


Q ss_pred             hhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHhccccC--
Q psy200          352 QANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITNHLIDLTYDNVKEN--  429 (490)
Q Consensus       352 ~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll~~a~~~a~~~~~~~--  429 (490)
                      ..++++.+..+.|.||+.+++.+||..++..+ ....+-+.+++.+|+++++.+||+|.|+++|++|+++++.++...  
T Consensus       310 ~~~~~~~P~~l~F~PYTk~qI~~Il~~rl~~~-~t~~~~~~Aie~~ArKvaa~SGDlRkaLdv~R~aiEI~E~e~r~~~~  388 (529)
T KOG2227|consen  310 NLDLTIKPKLLVFPPYTKDQIVEILQQRLSEE-STSIFLNAAIELCARKVAAPSGDLRKALDVCRRAIEIAEIEKRKILD  388 (529)
T ss_pred             hhccCCCCceeeecCCCHHHHHHHHHHHHhcc-cccccchHHHHHHHHHhccCchhHHHHHHHHHHHHHHHHHHHhhccc
Confidence            99999999999999999999999999999987 344566789999999999999999999999999999998876543  


Q ss_pred             ---------CcccccCHHHHHHHHHHhccCccccccccccCCCChHhHHHHHHHHHHhcCCCCCCcccCC
Q psy200          430 ---------GEVTGIGLKEVLGVISSVYCTSQSLHCSKDEDSFPLQQKLALASLLLLKSRPNVKDVTLGK  490 (490)
Q Consensus       430 ---------~~~~~It~~~v~~a~~~~~~~~~~~~~~~~l~~L~~~qk~vL~al~~~~~~~~~~~~~~g~  490 (490)
                               .....|.++++..+++.+.+.+.    .....+||+||+++||.++.+++... +++++|+
T Consensus       389 ~~l~~~~~p~~~~~v~~~~va~viSk~~~s~~----~~s~~slplqqkiilctl~~l~r~~k-kd~s~~e  453 (529)
T KOG2227|consen  389 DPLSPGTSPEKKKKVGVEHVAAVISKVDGSPS----ARSRESLPLQQKIILCTLVLLIRGNK-KDVSIAE  453 (529)
T ss_pred             cCCCCCCCcccccccchHHHHHHhhhhccChh----hhhhhhcCcccchhHHHHHHHHhccc-ccccHHH
Confidence                     11257889999999999998888    44445999999999999999998887 8888763

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

Probab=100.00  E-value=1.1e-32  Score=274.49  Aligned_cols=274  Identities=27%  Similarity=0.454  Sum_probs=250.7

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcC-CceEEEEeccCCCCHHHHHHHHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKD-AFKTIYINCNSVRNAASVYETIVNE  272 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~-~~~~~~v~~~~~~~~~~l~~~i~~~  272 (490)
                      +.+.+|+.+++++..+|...+.++.+.+++|||++|||||++++.+++++.... ...++|+||....+...++..|++.
T Consensus        17 ~~l~~Re~ei~~l~~~l~~~~~~~~p~n~~iyG~~GTGKT~~~~~v~~~l~~~~~~~~~~yINc~~~~t~~~i~~~i~~~   96 (366)
T COG1474          17 EELPHREEEINQLASFLAPALRGERPSNIIIYGPTGTGKTATVKFVMEELEESSANVEVVYINCLELRTPYQVLSKILNK   96 (366)
T ss_pred             ccccccHHHHHHHHHHHHHHhcCCCCccEEEECCCCCCHhHHHHHHHHHHHhhhccCceEEEeeeeCCCHHHHHHHHHHH
Confidence            669999999999999999999999888999999999999999999999997543 3348999999999999999999999


Q ss_pred             hc-CCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEEEecCCCChhHhhhHHh
Q psy200          273 LK-LKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVANALDLTDRMLPRL  351 (490)
Q Consensus       273 l~-~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI~~tn~~~~~~~l~~~l  351 (490)
                      ++ .+..|.+..++.+.+.+.+...++.+||+|||+|.|....++.|+.++.+......++++|+++|..++.+.+++++
T Consensus        97 ~~~~p~~g~~~~~~~~~l~~~~~~~~~~~IvvLDEid~L~~~~~~~LY~L~r~~~~~~~~v~vi~i~n~~~~~~~ld~rv  176 (366)
T COG1474          97 LGKVPLTGDSSLEILKRLYDNLSKKGKTVIVILDEVDALVDKDGEVLYSLLRAPGENKVKVSIIAVSNDDKFLDYLDPRV  176 (366)
T ss_pred             cCCCCCCCCchHHHHHHHHHHHHhcCCeEEEEEcchhhhccccchHHHHHHhhccccceeEEEEEEeccHHHHHHhhhhh
Confidence            94 46778889999999999998888899999999999999988999999998876688999999999998889999999


Q ss_pred             hhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHhccccCCc
Q psy200          352 QANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITNHLIDLTYDNVKENGE  431 (490)
Q Consensus       352 ~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll~~a~~~a~~~~~~~~~  431 (490)
                      +++++.  ..|.|+||+.+|+..||..+.........+++++++.++...+..+||.|.+|++|+.|.++|+.++     
T Consensus       177 ~s~l~~--~~I~F~pY~a~el~~Il~~R~~~~~~~~~~~~~vl~lia~~~a~~~GDAR~aidilr~A~eiAe~~~-----  249 (366)
T COG1474         177 KSSLGP--SEIVFPPYTAEELYDILRERVEEGFSAGVIDDDVLKLIAALVAAESGDARKAIDILRRAGEIAEREG-----  249 (366)
T ss_pred             hhccCc--ceeeeCCCCHHHHHHHHHHHHHhhccCCCcCccHHHHHHHHHHHcCccHHHHHHHHHHHHHHHHhhC-----
Confidence            998875  4699999999999999999998765677899999999999999999999999999999999999999     


Q ss_pred             ccccCHHHHHHHHHHhccCccccccccccCCCChHhHHHHHHHHHHh
Q psy200          432 VTGIGLKEVLGVISSVYCTSQSLHCSKDEDSFPLQQKLALASLLLLK  478 (490)
Q Consensus       432 ~~~It~~~v~~a~~~~~~~~~~~~~~~~l~~L~~~qk~vL~al~~~~  478 (490)
                      ..+|+.+++..|..++.....    .+.+..|+.||+++|++++.+.
T Consensus       250 ~~~v~~~~v~~a~~~~~~~~~----~~~~~~L~~~~ki~L~~i~~~~  292 (366)
T COG1474         250 SRKVSEDHVREAQEEIERDVL----EEVLKTLPLHQKIVLLAIVELT  292 (366)
T ss_pred             CCCcCHHHHHHHHHHhhHHHH----HHHHHcCCHhHHHHHHHHHHhc
Confidence            789999999999888877777    6889999999999999999875

>KOG1514|consensus

Probab=100.00  E-value=1.3e-32  Score=280.02  Aligned_cols=284  Identities=32%  Similarity=0.518  Sum_probs=251.0

Q ss_pred             CCCCChHHHHHHHHHHHHhhhcc-CCCCeEEEECCCCCcHHHHHHHHHHHhh------hcCCceEEEEeccCCCCHHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVNN-ETSGSMYISGPPGTGKSASLNLLVSRAE------IKDAFKTIYINCNSVRNAASVY  266 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~-~~~~~ill~GppGtGKTtla~~l~~~l~------~~~~~~~~~v~~~~~~~~~~l~  266 (490)
                      +.|.||+.++.+|..+++..+.. +.+.+++|+|-||||||.+++.|.+.|.      .-+.|.++++|+..+..+.++|
T Consensus       396 ~sLpcRe~E~~~I~~f~~~~i~~~~~g~~mYIsGvPGtGKT~tV~~Vm~~Lq~~s~~~e~p~f~yveINgm~l~~~~~~Y  475 (767)
T KOG1514|consen  396 ESLPCRENEFSEIEDFLRSFISDQGLGSCMYISGVPGTGKTATVLEVMKELQTSSAQKELPKFDYVEINGLRLASPREIY  475 (767)
T ss_pred             ccccchhHHHHHHHHHHHhhcCCCCCceeEEEecCCCCCceehHHHHHHHHHHHHhhcCCCCccEEEEcceeecCHHHHH
Confidence            88999999999999999998877 5566999999999999999999999875      2457899999999999999999


Q ss_pred             HHHHHHhcCCCCCCcHHHHHHHHHHHHh---cCCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEEEecCCCCh
Q psy200          267 ETIVNELKLKPGGKSERHQLGAILKYFD---TKHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVANALDL  343 (490)
Q Consensus       267 ~~i~~~l~~~~~~~s~~~~~~~l~~~l~---~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI~~tn~~~~  343 (490)
                      ..|+..|.+...  ......+.+...+.   ....++||+|||+|.|....|+.|+++|+|....+++++||+++|.+|+
T Consensus       476 ~~I~~~lsg~~~--~~~~al~~L~~~f~~~k~~~~~~VvLiDElD~Lvtr~QdVlYn~fdWpt~~~sKLvvi~IaNTmdl  553 (767)
T KOG1514|consen  476 EKIWEALSGERV--TWDAALEALNFRFTVPKPKRSTTVVLIDELDILVTRSQDVLYNIFDWPTLKNSKLVVIAIANTMDL  553 (767)
T ss_pred             HHHHHhcccCcc--cHHHHHHHHHHhhccCCCCCCCEEEEeccHHHHhcccHHHHHHHhcCCcCCCCceEEEEecccccC
Confidence            999999987543  34444555555554   3467899999999999999999999999999999999999999999999


Q ss_pred             hHhhhH-HhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHH
Q psy200          344 TDRMLP-RLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITNHLIDLT  422 (490)
Q Consensus       344 ~~~l~~-~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll~~a~~~a  422 (490)
                      +++++. ++.+|+|+  .+|.|.||+.+++.+|+..+|...   ..|.++++++++++++..+||.|+++++|.+|.++|
T Consensus       554 PEr~l~nrvsSRlg~--tRi~F~pYth~qLq~Ii~~RL~~~---~~f~~~aielvarkVAavSGDaRraldic~RA~Eia  628 (767)
T KOG1514|consen  554 PERLLMNRVSSRLGL--TRICFQPYTHEQLQEIISARLKGL---DAFENKAIELVARKVAAVSGDARRALDICRRAAEIA  628 (767)
T ss_pred             HHHHhccchhhhccc--eeeecCCCCHHHHHHHHHHhhcch---hhcchhHHHHHHHHHHhccccHHHHHHHHHHHHHHh
Confidence            999875 89999887  699999999999999999999876   568999999999999999999999999999999999


Q ss_pred             Hhccc--cCCcccccCHHHHHHHHHHhccCccccccccccCCCChHhHHHHHHHHHHhcCCCCCCccc
Q psy200          423 YDNVK--ENGEVTGIGLKEVLGVISSVYCTSQSLHCSKDEDSFPLQQKLALASLLLLKSRPNVKDVTL  488 (490)
Q Consensus       423 ~~~~~--~~~~~~~It~~~v~~a~~~~~~~~~~~~~~~~l~~L~~~qk~vL~al~~~~~~~~~~~~~~  488 (490)
                      ..+..  +.+....|++.||.+|+++++....    ...+.+|++.|+.+|+||+...++.+..+.++
T Consensus       629 ~~~~~~~k~~~~q~v~~~~v~~Ai~em~~~~~----~~~i~glS~~~k~fl~ai~~e~~~~g~~e~~~  692 (767)
T KOG1514|consen  629 EERNVKGKLAVSQLVGILHVMEAINEMLASPY----IKALKGLSFLQKIFLTAIVAETEGTGLEEATL  692 (767)
T ss_pred             hhhcccccccccceeehHHHHHHHHHHhhhhH----HHHhcchHHHHHHHHHHHHHHHhhcchHHHHH
Confidence            88774  2223467999999999999999888    78999999999999999999998887666544

>TIGR02928 orc1/cdc6 family replication initiation protein

Probab=100.00  E-value=1.6e-31  Score=271.00  Aligned_cols=284  Identities=21%  Similarity=0.338  Sum_probs=233.9

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhc-C----CceEEEEeccCCCCHHHHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIK-D----AFKTIYINCNSVRNAASVYET  268 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~-~----~~~~~~v~~~~~~~~~~l~~~  268 (490)
                      +.|+||++++++|..+|...+.+..++.++|+||||+|||++++.+++++... .    .+.+++++|....+...++..
T Consensus        15 ~~l~gRe~e~~~l~~~l~~~~~~~~~~~i~I~G~~GtGKT~l~~~~~~~l~~~~~~~~~~~~~v~in~~~~~~~~~~~~~   94 (365)
T TIGR02928        15 DRIVHRDEQIEELAKALRPILRGSRPSNVFIYGKTGTGKTAVTKYVMKELEEAAEDRDVRVVTVYVNCQILDTLYQVLVE   94 (365)
T ss_pred             CCCCCcHHHHHHHHHHHHHHHcCCCCCcEEEECCCCCCHHHHHHHHHHHHHHHhhccCCceEEEEEECCCCCCHHHHHHH
Confidence            67999999999999999987777777899999999999999999999987522 1    278999999999888999999


Q ss_pred             HHHHhc---C--CCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCHHHHHHhHhC---CCCCCCcEEEEEecCC
Q psy200          269 IVNELK---L--KPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEW---PSIPGSKLVLVGVANA  340 (490)
Q Consensus       269 i~~~l~---~--~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~---~~~~~~~vilI~~tn~  340 (490)
                      |+.++.   .  +..+.+..+..+.+.+.+...++++||||||+|.+....++.|+.++.+   ....+.++.+|+++|.
T Consensus        95 i~~~l~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~vlvIDE~d~L~~~~~~~L~~l~~~~~~~~~~~~~v~lI~i~n~  174 (365)
T TIGR02928        95 LANQLRGSGEEVPTTGLSTSEVFRRLYKELNERGDSLIIVLDEIDYLVGDDDDLLYQLSRARSNGDLDNAKVGVIGISND  174 (365)
T ss_pred             HHHHHhhcCCCCCCCCCCHHHHHHHHHHHHHhcCCeEEEEECchhhhccCCcHHHHhHhccccccCCCCCeEEEEEEECC
Confidence            999983   2  2233455666666666665557789999999999986666778888776   2334578999999998


Q ss_pred             CChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHHHHHHHHH
Q psy200          341 LDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITNHLID  420 (490)
Q Consensus       341 ~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll~~a~~  420 (490)
                      .++.+.+.+++.+||..  ..+.|.||+.+|+.+++..++........+++++++.+++......||+|.++++|+.|+.
T Consensus       175 ~~~~~~l~~~~~s~~~~--~~i~f~p~~~~e~~~il~~r~~~~~~~~~~~~~~l~~i~~~~~~~~Gd~R~al~~l~~a~~  252 (365)
T TIGR02928       175 LKFRENLDPRVKSSLCE--EEIIFPPYDAEELRDILENRAEKAFYDGVLDDGVIPLCAALAAQEHGDARKAIDLLRVAGE  252 (365)
T ss_pred             cchHhhcCHHHhccCCc--ceeeeCCCCHHHHHHHHHHHHHhhccCCCCChhHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Confidence            88888888899888852  4799999999999999999987432345688999999988777788999999999999999


Q ss_pred             HHHhccccCCcccccCHHHHHHHHHHhccCccccccccccCCCChHhHHHHHHHHHHhcCCCCCCcccC
Q psy200          421 LTYDNVKENGEVTGIGLKEVLGVISSVYCTSQSLHCSKDEDSFPLQQKLALASLLLLKSRPNVKDVTLG  489 (490)
Q Consensus       421 ~a~~~~~~~~~~~~It~~~v~~a~~~~~~~~~~~~~~~~l~~L~~~qk~vL~al~~~~~~~~~~~~~~g  489 (490)
                      .|..++     ...|+.+||.+|+..+.....    .+.+.+||.+|+.+|+||+.+.+. +...++.|
T Consensus       253 ~a~~~~-----~~~it~~~v~~a~~~~~~~~~----~~~i~~l~~~~~~~l~ai~~~~~~-~~~~~~~~  311 (365)
T TIGR02928       253 IAEREG-----AERVTEDHVEKAQEKIEKDRL----LELIRGLPTHSKLVLLAIANLAAN-DEDPFRTG  311 (365)
T ss_pred             HHHHcC-----CCCCCHHHHHHHHHHHHHHHH----HHHHHcCCHHHHHHHHHHHHHHhc-CCCCccHH
Confidence            998887     678999999999999876655    688999999999999999988765 33445443

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.

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=100.00  E-value=5.7e-31  Score=269.77  Aligned_cols=276  Identities=23%  Similarity=0.376  Sum_probs=233.3

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcC-CceEEEEeccCCCCHHHHHHHHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKD-AFKTIYINCNSVRNAASVYETIVNE  272 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~-~~~~~~v~~~~~~~~~~l~~~i~~~  272 (490)
                      +.|+||++++++|..+|...+.+..+.+++|+|+||+|||++++.+++++.... ++.+++++|....+...++..|+.+
T Consensus        30 ~~l~~Re~e~~~l~~~l~~~~~~~~~~~~lI~G~~GtGKT~l~~~v~~~l~~~~~~~~~v~in~~~~~~~~~~~~~i~~~  109 (394)
T PRK00411         30 ENLPHREEQIEELAFALRPALRGSRPLNVLIYGPPGTGKTTTVKKVFEELEEIAVKVVYVYINCQIDRTRYAIFSEIARQ  109 (394)
T ss_pred             CCCCCHHHHHHHHHHHHHHHhCCCCCCeEEEECCCCCCHHHHHHHHHHHHHHhcCCcEEEEEECCcCCCHHHHHHHHHHH
Confidence            789999999999999998887777778899999999999999999999886443 6789999999998999999999999


Q ss_pred             hcC---CCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCcccc-ccCHHHHHHhHhCC-CCCCCcEEEEEecCCCChhHhh
Q psy200          273 LKL---KPGGKSERHQLGAILKYFDTKHKSILLILDEIDALE-SRKQTILYTIFEWP-SIPGSKLVLVGVANALDLTDRM  347 (490)
Q Consensus       273 l~~---~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~-~~~~~~L~~l~~~~-~~~~~~vilI~~tn~~~~~~~l  347 (490)
                      +..   +..+.+..++.+.+.+.+...++++||+|||+|.+. ...++.|+.++.+. ...+.++.+|+++|..++.+.+
T Consensus       110 l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~viviDE~d~l~~~~~~~~l~~l~~~~~~~~~~~v~vI~i~~~~~~~~~l  189 (394)
T PRK00411        110 LFGHPPPSSGLSFDELFDKIAEYLDERDRVLIVALDDINYLFEKEGNDVLYSLLRAHEEYPGARIGVIGISSDLTFLYIL  189 (394)
T ss_pred             hcCCCCCCCCCCHHHHHHHHHHHHHhcCCEEEEEECCHhHhhccCCchHHHHHHHhhhccCCCeEEEEEEECCcchhhhc
Confidence            865   234456777778887777766788999999999997 44567777777643 2344588899999988888888


Q ss_pred             hHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHhccc
Q psy200          348 LPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITNHLIDLTYDNVK  427 (490)
Q Consensus       348 ~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll~~a~~~a~~~~~  427 (490)
                      .+++.+|+..  ..+.|.||+.+++.+++..++........+++++++.+++.+....||+|.++++|..|+..|..++ 
T Consensus       190 ~~~~~s~~~~--~~i~f~py~~~e~~~il~~r~~~~~~~~~~~~~~l~~i~~~~~~~~Gd~r~a~~ll~~a~~~a~~~~-  266 (394)
T PRK00411        190 DPRVKSVFRP--EEIYFPPYTADEIFDILKDRVEEGFYPGVVDDEVLDLIADLTAREHGDARVAIDLLRRAGLIAEREG-  266 (394)
T ss_pred             CHHHHhcCCc--ceeecCCCCHHHHHHHHHHHHHhhcccCCCCHhHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHcC-
Confidence            8888888753  4799999999999999999987542344689999999999887779999999999999999999888 


Q ss_pred             cCCcccccCHHHHHHHHHHhccCccccccccccCCCChHhHHHHHHHHHHhcC
Q psy200          428 ENGEVTGIGLKEVLGVISSVYCTSQSLHCSKDEDSFPLQQKLALASLLLLKSR  480 (490)
Q Consensus       428 ~~~~~~~It~~~v~~a~~~~~~~~~~~~~~~~l~~L~~~qk~vL~al~~~~~~  480 (490)
                          ...|+.+||..|+..+.....    ...+.+||.+|+.+|+||+.+.+.
T Consensus       267 ----~~~I~~~~v~~a~~~~~~~~~----~~~~~~L~~~~k~~L~ai~~~~~~  311 (394)
T PRK00411        267 ----SRKVTEEDVRKAYEKSEIVHL----SEVLRTLPLHEKLLLRAIVRLLKK  311 (394)
T ss_pred             ----CCCcCHHHHHHHHHHHHHHHH----HHHHhcCCHHHHHHHHHHHHHHhc
Confidence                678999999999999866555    578999999999999999987754

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

Probab=99.91  E-value=1.9e-23  Score=201.80  Aligned_cols=209  Identities=20%  Similarity=0.283  Sum_probs=165.3

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHh
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNEL  273 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l  273 (490)
                      ++++|++..+.. ...|...+..+...+++|||||||||||+|+.|+....    ..|..+++..               
T Consensus        24 de~vGQ~HLlg~-~~~lrr~v~~~~l~SmIl~GPPG~GKTTlA~liA~~~~----~~f~~~sAv~---------------   83 (436)
T COG2256          24 DEVVGQEHLLGE-GKPLRRAVEAGHLHSMILWGPPGTGKTTLARLIAGTTN----AAFEALSAVT---------------   83 (436)
T ss_pred             HHhcChHhhhCC-CchHHHHHhcCCCceeEEECCCCCCHHHHHHHHHHhhC----CceEEecccc---------------
Confidence            889999888755 45566666778899999999999999999999999864    6677776543               


Q ss_pred             cCCCCCCcHHHHHHHHHHHHhc--CCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEEEecCCCChhHhhhHHh
Q psy200          274 KLKPGGKSERHQLGAILKYFDT--KHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVANALDLTDRMLPRL  351 (490)
Q Consensus       274 ~~~~~~~s~~~~~~~l~~~l~~--~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI~~tn~~~~~~~l~~~l  351 (490)
                            .+.+++++.++++.+.  .|+..||||||||++....|+.|     ++...+..+++||+|+..- ...+.+.|
T Consensus        84 ------~gvkdlr~i~e~a~~~~~~gr~tiLflDEIHRfnK~QQD~l-----Lp~vE~G~iilIGATTENP-sF~ln~AL  151 (436)
T COG2256          84 ------SGVKDLREIIEEARKNRLLGRRTILFLDEIHRFNKAQQDAL-----LPHVENGTIILIGATTENP-SFELNPAL  151 (436)
T ss_pred             ------ccHHHHHHHHHHHHHHHhcCCceEEEEehhhhcChhhhhhh-----hhhhcCCeEEEEeccCCCC-CeeecHHH
Confidence                  4577777777776432  36789999999999999999999     5556678899999997432 23457899


Q ss_pred             hhccCCCCeeEEeCCCCHHHHHHHHHHHHhcc-----CCCCCCCHHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHhcc
Q psy200          352 QANVTLQPTLMNFAPYSREQILEIISQKLKQT-----DKFNMFNASALQLLAGKVAAVSGDIRKAIDITNHLIDLTYDNV  426 (490)
Q Consensus       352 ~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~-----~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll~~a~~~a~~~~  426 (490)
                      .+|+.    ++.|.|++.+++.+++.+-+...     +....+++++++.+++   ...||.|.++|+|+.++..+....
T Consensus       152 lSR~~----vf~lk~L~~~di~~~l~ra~~~~~rgl~~~~~~i~~~a~~~l~~---~s~GD~R~aLN~LE~~~~~~~~~~  224 (436)
T COG2256         152 LSRAR----VFELKPLSSEDIKKLLKRALLDEERGLGGQIIVLDEEALDYLVR---LSNGDARRALNLLELAALSAEPDE  224 (436)
T ss_pred             hhhhh----eeeeecCCHHHHHHHHHHHHhhhhcCCCcccccCCHHHHHHHHH---hcCchHHHHHHHHHHHHHhcCCCc
Confidence            99996    89999999999999999854433     1234478999999987   788999999999999987776544


Q ss_pred             ccCCcccccCHHHHHHHHHHhc
Q psy200          427 KENGEVTGIGLKEVLGVISSVY  448 (490)
Q Consensus       427 ~~~~~~~~It~~~v~~a~~~~~  448 (490)
                             .++.+.+.+.+.+..
T Consensus       225 -------~~~~~~l~~~l~~~~  239 (436)
T COG2256         225 -------VLILELLEEILQRRS  239 (436)
T ss_pred             -------ccCHHHHHHHHhhhh
Confidence                   344777777777643

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

Probab=99.89  E-value=1.2e-21  Score=180.97  Aligned_cols=241  Identities=16%  Similarity=0.171  Sum_probs=190.0

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccC-CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNE-TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNE  272 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~-~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~  272 (490)
                      ++++|+++..+.|.-++..+...+ .-.++||+||||.||||||+.++++++  .++  ....++.+             
T Consensus        26 ~efiGQ~~vk~~L~ifI~AAk~r~e~lDHvLl~GPPGlGKTTLA~IIA~Emg--vn~--k~tsGp~l-------------   88 (332)
T COG2255          26 DEFIGQEKVKEQLQIFIKAAKKRGEALDHVLLFGPPGLGKTTLAHIIANELG--VNL--KITSGPAL-------------   88 (332)
T ss_pred             HHhcChHHHHHHHHHHHHHHHhcCCCcCeEEeeCCCCCcHHHHHHHHHHHhc--CCe--Eecccccc-------------
Confidence            889999999999999998764433 557999999999999999999999997  222  22222222             


Q ss_pred             hcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCHHHHHHhHhCCCC---------------CCCcEEEEEe
Q psy200          273 LKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPSI---------------PGSKLVLVGV  337 (490)
Q Consensus       273 l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~---------------~~~~vilI~~  337 (490)
                             ....++...|.. ++   ..-||||||||.+.....+.|+-.|+-...               .-.++.+||+
T Consensus        89 -------eK~gDlaaiLt~-Le---~~DVLFIDEIHrl~~~vEE~LYpaMEDf~lDI~IG~gp~Arsv~ldLppFTLIGA  157 (332)
T COG2255          89 -------EKPGDLAAILTN-LE---EGDVLFIDEIHRLSPAVEEVLYPAMEDFRLDIIIGKGPAARSIRLDLPPFTLIGA  157 (332)
T ss_pred             -------cChhhHHHHHhc-CC---cCCeEEEehhhhcChhHHHHhhhhhhheeEEEEEccCCccceEeccCCCeeEeee
Confidence                   223333333333 22   234999999999999988999887653321               2346789999


Q ss_pred             cCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHHHHHH
Q psy200          338 ANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITNH  417 (490)
Q Consensus       338 tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll~~  417 (490)
                      |++..+   +...++.||++   ..+++.|+.+|+.+|+.+.....  ...+++++...|++   .+.|-+|-|..+|++
T Consensus       158 TTr~G~---lt~PLrdRFGi---~~rlefY~~~eL~~Iv~r~a~~l--~i~i~~~~a~eIA~---rSRGTPRIAnRLLrR  226 (332)
T COG2255         158 TTRAGM---LTNPLRDRFGI---IQRLEFYTVEELEEIVKRSAKIL--GIEIDEEAALEIAR---RSRGTPRIANRLLRR  226 (332)
T ss_pred             cccccc---ccchhHHhcCC---eeeeecCCHHHHHHHHHHHHHHh--CCCCChHHHHHHHH---hccCCcHHHHHHHHH
Confidence            986543   44688999996   89999999999999999877665  56789999999998   888999999999999


Q ss_pred             HHHHHHhccccCCcccccCHHHHHHHHHHhccCccccccccccCCCChHhHHHHHHHHHHhcCCCCCCcc
Q psy200          418 LIDLTYDNVKENGEVTGIGLKEVLGVISSVYCTSQSLHCSKDEDSFPLQQKLALASLLLLKSRPNVKDVT  487 (490)
Q Consensus       418 a~~~a~~~~~~~~~~~~It~~~v~~a~~~~~~~~~~~~~~~~l~~L~~~qk~vL~al~~~~~~~~~~~~~  487 (490)
                      ....|.-.+     ...|+.+...+|+..+.-..         .+|...++.+|.+|+..+.++.+.--+
T Consensus       227 VRDfa~V~~-----~~~I~~~ia~~aL~~L~Vd~---------~GLd~~D~k~L~~li~~f~GgPVGl~t  282 (332)
T COG2255         227 VRDFAQVKG-----DGDIDRDIADKALKMLDVDE---------LGLDEIDRKYLRALIEQFGGGPVGLDT  282 (332)
T ss_pred             HHHHHHHhc-----CCcccHHHHHHHHHHhCccc---------ccccHHHHHHHHHHHHHhCCCCccHHH
Confidence            999999888     67899999999998876443         488899999999999999888876443

>COG1222 RPT1 ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein turnover, chaperones]

Probab=99.88  E-value=1.7e-21  Score=185.41  Aligned_cols=222  Identities=18%  Similarity=0.258  Sum_probs=166.9

Q ss_pred             CCCCChHHHHHHHHHHHHhhhcc---------CCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVNN---------ETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAAS  264 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~---------~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~  264 (490)
                      +++-|.++++++|++.++--+.+         .+++++|||||||||||.||++||++.    +..|+.+.++.      
T Consensus       151 ~dIGGL~~Qi~EirE~VELPL~~PElF~~~GI~PPKGVLLYGPPGTGKTLLAkAVA~~T----~AtFIrvvgSE------  220 (406)
T COG1222         151 EDIGGLDEQIQEIREVVELPLKNPELFEELGIDPPKGVLLYGPPGTGKTLLAKAVANQT----DATFIRVVGSE------  220 (406)
T ss_pred             hhccCHHHHHHHHHHHhcccccCHHHHHHcCCCCCCceEeeCCCCCcHHHHHHHHHhcc----CceEEEeccHH------
Confidence            68999999999999988765443         378999999999999999999999984    47788885543      


Q ss_pred             HHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccC-----------HHHHHHhHhC--CCCCCCc
Q psy200          265 VYETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRK-----------QTILYTIFEW--PSIPGSK  331 (490)
Q Consensus       265 l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~-----------~~~L~~l~~~--~~~~~~~  331 (490)
                      |.+        .+.|....-+++.|.-+..  +.|+||||||||.+...+           |..+.+|+.-  ......+
T Consensus       221 lVq--------KYiGEGaRlVRelF~lAre--kaPsIIFiDEIDAIg~kR~d~~t~gDrEVQRTmleLL~qlDGFD~~~n  290 (406)
T COG1222         221 LVQ--------KYIGEGARLVRELFELARE--KAPSIIFIDEIDAIGAKRFDSGTSGDREVQRTMLELLNQLDGFDPRGN  290 (406)
T ss_pred             HHH--------HHhccchHHHHHHHHHHhh--cCCeEEEEechhhhhcccccCCCCchHHHHHHHHHHHHhccCCCCCCC
Confidence            222        4556777788888875554  679999999999997553           4455555432  2446789


Q ss_pred             EEEEEecCCCChhHhhhHHhhh--ccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHH
Q psy200          332 LVLVGVANALDLTDRMLPRLQA--NVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIR  409 (490)
Q Consensus       332 vilI~~tn~~~~~~~l~~~l~~--R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r  409 (490)
                      +-||++||+.|..+   |+|.+  ||.   ..|.|+.++.+...+||+-+..+-..   -++-.++.|++...+.+|  .
T Consensus       291 vKVI~ATNR~D~LD---PALLRPGR~D---RkIEfplPd~~gR~~Il~IHtrkM~l---~~dvd~e~la~~~~g~sG--A  359 (406)
T COG1222         291 VKVIMATNRPDILD---PALLRPGRFD---RKIEFPLPDEEGRAEILKIHTRKMNL---ADDVDLELLARLTEGFSG--A  359 (406)
T ss_pred             eEEEEecCCccccC---hhhcCCCccc---ceeecCCCCHHHHHHHHHHHhhhccC---ccCcCHHHHHHhcCCCch--H
Confidence            99999999876544   44432  454   58999999999999999988776532   233447777773334443  2


Q ss_pred             HHHHHHHHHHHHHHhccccCCcccccCHHHHHHHHHHhccCc
Q psy200          410 KAIDITNHLIDLTYDNVKENGEVTGIGLKEVLGVISSVYCTS  451 (490)
Q Consensus       410 ~ai~ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~~~~~~~~  451 (490)
                      .+-.+|..|.++|.++.     ...|+++||.+|+.++....
T Consensus       360 dlkaictEAGm~AiR~~-----R~~Vt~~DF~~Av~KV~~~~  396 (406)
T COG1222         360 DLKAICTEAGMFAIRER-----RDEVTMEDFLKAVEKVVKKK  396 (406)
T ss_pred             HHHHHHHHHhHHHHHhc-----cCeecHHHHHHHHHHHHhcc
Confidence            33458999999999998     77999999999999987643

>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed

Probab=99.88  E-value=5.4e-21  Score=190.59  Aligned_cols=248  Identities=16%  Similarity=0.164  Sum_probs=184.2

Q ss_pred             CCCCcchHHHhhcCCCCCCChHHHHHHHHHHHHhhhc-cCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEecc
Q psy200          179 FSEDKPKVEEKAKDSCELPGREVQLEGIRQFLLGHVN-NETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCN  257 (490)
Q Consensus       179 ~~~~~~~~~~~~l~~~~lvgre~~~~~l~~~L~~~~~-~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~  257 (490)
                      .|...|+|...    ++|+|++++++.+..++..... ....++++|+||||+|||++|++++++++    ..+.++++.
T Consensus        14 ~~~~~~rP~~~----~~~vG~~~~~~~l~~~l~~~~~~~~~~~~~ll~GppG~GKT~la~~ia~~l~----~~~~~~~~~   85 (328)
T PRK00080         14 EIERSLRPKSL----DEFIGQEKVKENLKIFIEAAKKRGEALDHVLLYGPPGLGKTTLANIIANEMG----VNIRITSGP   85 (328)
T ss_pred             hhhhhcCcCCH----HHhcCcHHHHHHHHHHHHHHHhcCCCCCcEEEECCCCccHHHHHHHHHHHhC----CCeEEEecc
Confidence            34456666666    8999999999999998876533 34567899999999999999999999986    333444433


Q ss_pred             CCCCHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCHHHHHHhHhCCCC----------
Q psy200          258 SVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPSI----------  327 (490)
Q Consensus       258 ~~~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~----------  327 (490)
                      ....                    ...+...+.    ..+...+|||||||.+....++.|+.+++....          
T Consensus        86 ~~~~--------------------~~~l~~~l~----~l~~~~vl~IDEi~~l~~~~~e~l~~~~e~~~~~~~l~~~~~~  141 (328)
T PRK00080         86 ALEK--------------------PGDLAAILT----NLEEGDVLFIDEIHRLSPVVEEILYPAMEDFRLDIMIGKGPAA  141 (328)
T ss_pred             cccC--------------------hHHHHHHHH----hcccCCEEEEecHhhcchHHHHHHHHHHHhcceeeeeccCccc
Confidence            2211                    112222222    123356999999999987777777766543210          


Q ss_pred             -----CCCcEEEEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHH
Q psy200          328 -----PGSKLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVA  402 (490)
Q Consensus       328 -----~~~~vilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~  402 (490)
                           .-..+++|++|+..   ..+.+.+++||+.   .+.|.+++.+++.++|...+...  ...+++++++.|++   
T Consensus       142 ~~~~~~l~~~~li~at~~~---~~l~~~L~sRf~~---~~~l~~~~~~e~~~il~~~~~~~--~~~~~~~~~~~ia~---  210 (328)
T PRK00080        142 RSIRLDLPPFTLIGATTRA---GLLTSPLRDRFGI---VQRLEFYTVEELEKIVKRSARIL--GVEIDEEGALEIAR---  210 (328)
T ss_pred             cceeecCCCceEEeecCCc---ccCCHHHHHhcCe---eeecCCCCHHHHHHHHHHHHHHc--CCCcCHHHHHHHHH---
Confidence                 11347788888854   3456678899974   79999999999999999988876  56789999999997   


Q ss_pred             HhhCCHHHHHHHHHHHHHHHHhccccCCcccccCHHHHHHHHHHhccCccccccccccCCCChHhHHHHHHHHHHhcCCC
Q psy200          403 AVSGDIRKAIDITNHLIDLTYDNVKENGEVTGIGLKEVLGVISSVYCTSQSLHCSKDEDSFPLQQKLALASLLLLKSRPN  482 (490)
Q Consensus       403 ~~~Gd~r~ai~ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~~~~~~~~~~~~~~~~l~~L~~~qk~vL~al~~~~~~~~  482 (490)
                      .+.|++|.+.++|+++...+...+     ...|+.+++..++..+.         -....|+..++.+|.+++..+..+.
T Consensus       211 ~~~G~pR~a~~~l~~~~~~a~~~~-----~~~I~~~~v~~~l~~~~---------~~~~~l~~~~~~~l~~~~~~~~~~~  276 (328)
T PRK00080        211 RSRGTPRIANRLLRRVRDFAQVKG-----DGVITKEIADKALDMLG---------VDELGLDEMDRKYLRTIIEKFGGGP  276 (328)
T ss_pred             HcCCCchHHHHHHHHHHHHHHHcC-----CCCCCHHHHHHHHHHhC---------CCcCCCCHHHHHHHHHHHHHcCCCc
Confidence            778999999999999988887665     45899999999997642         2236889999999999998877664


Q ss_pred             C
Q psy200          483 V  483 (490)
Q Consensus       483 ~  483 (490)
                      +
T Consensus       277 ~  277 (328)
T PRK00080        277 V  277 (328)
T ss_pred             e
Confidence            3

>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit

Probab=99.88  E-value=9.6e-21  Score=187.33  Aligned_cols=235  Identities=17%  Similarity=0.206  Sum_probs=173.7

Q ss_pred             CCCCChHHHHHHHHHHHHhhhcc-CCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVNN-ETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNE  272 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~-~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~  272 (490)
                      ++|+|++++++.|..++...... ....+++|+||||+|||++++++++++.    ..+..+.+.....           
T Consensus         4 ~~~iG~~~~~~~l~~~l~~~~~~~~~~~~~ll~Gp~G~GKT~la~~ia~~~~----~~~~~~~~~~~~~-----------   68 (305)
T TIGR00635         4 AEFIGQEKVKEQLQLFIEAAKMRQEALDHLLLYGPPGLGKTTLAHIIANEMG----VNLKITSGPALEK-----------   68 (305)
T ss_pred             HHHcCHHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHHHHHhC----CCEEEeccchhcC-----------
Confidence            57999999999999999754432 3457899999999999999999999875    2233333222111           


Q ss_pred             hcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCHHHHHHhHhCCC---------------CCCCcEEEEEe
Q psy200          273 LKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPS---------------IPGSKLVLVGV  337 (490)
Q Consensus       273 l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~---------------~~~~~vilI~~  337 (490)
                               ...+...+..    .+...+|||||+|.+....++.|+.+++...               .....+++|++
T Consensus        69 ---------~~~l~~~l~~----~~~~~vl~iDEi~~l~~~~~e~l~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~li~~  135 (305)
T TIGR00635        69 ---------PGDLAAILTN----LEEGDVLFIDEIHRLSPAVEELLYPAMEDFRLDIVIGKGPSARSVRLDLPPFTLVGA  135 (305)
T ss_pred             ---------chhHHHHHHh----cccCCEEEEehHhhhCHHHHHHhhHHHhhhheeeeeccCccccceeecCCCeEEEEe
Confidence                     1122222221    1335699999999998877777776654211               11234778888


Q ss_pred             cCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHHHHHH
Q psy200          338 ANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITNH  417 (490)
Q Consensus       338 tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll~~  417 (490)
                      |+..   ..+.+.+++||+.   .+.|.+++.+++.+++...+...  ...+++++++.|++   ...|++|.+++++..
T Consensus       136 t~~~---~~l~~~l~sR~~~---~~~l~~l~~~e~~~il~~~~~~~--~~~~~~~al~~ia~---~~~G~pR~~~~ll~~  204 (305)
T TIGR00635       136 TTRA---GMLTSPLRDRFGI---ILRLEFYTVEELAEIVSRSAGLL--NVEIEPEAALEIAR---RSRGTPRIANRLLRR  204 (305)
T ss_pred             cCCc---cccCHHHHhhcce---EEEeCCCCHHHHHHHHHHHHHHh--CCCcCHHHHHHHHH---HhCCCcchHHHHHHH
Confidence            8743   3456778899973   68999999999999999988765  46789999999987   778999999999999


Q ss_pred             HHHHHHhccccCCcccccCHHHHHHHHHHhccCccccccccccCCCChHhHHHHHHHHHHhcCC
Q psy200          418 LIDLTYDNVKENGEVTGIGLKEVLGVISSVYCTSQSLHCSKDEDSFPLQQKLALASLLLLKSRP  481 (490)
Q Consensus       418 a~~~a~~~~~~~~~~~~It~~~v~~a~~~~~~~~~~~~~~~~l~~L~~~qk~vL~al~~~~~~~  481 (490)
                      +...|...+     ...|+.+++..++..+.         -....++..++.+|.||+..+++.
T Consensus       205 ~~~~a~~~~-----~~~it~~~v~~~l~~l~---------~~~~~l~~~~~~~L~al~~~~~~~  254 (305)
T TIGR00635       205 VRDFAQVRG-----QKIINRDIALKALEMLM---------IDELGLDEIDRKLLSVLIEQFQGG  254 (305)
T ss_pred             HHHHHHHcC-----CCCcCHHHHHHHHHHhC---------CCCCCCCHHHHHHHHHHHHHhCCC
Confidence            887876665     45799999999998831         124688999999999998877654

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.

>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=99.87  E-value=1e-21  Score=178.56  Aligned_cols=190  Identities=18%  Similarity=0.270  Sum_probs=131.1

Q ss_pred             CCCCChHHHHHHHHHHHHhhhcc-CCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVNN-ETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNE  272 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~-~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~  272 (490)
                      ++++|+++.++.+.-++...... ....++++|||||+||||||+.++++++    ..+..+++.....           
T Consensus        24 ~efiGQ~~l~~~l~i~i~aa~~r~~~l~h~lf~GPPG~GKTTLA~IIA~e~~----~~~~~~sg~~i~k-----------   88 (233)
T PF05496_consen   24 DEFIGQEHLKGNLKILIRAAKKRGEALDHMLFYGPPGLGKTTLARIIANELG----VNFKITSGPAIEK-----------   88 (233)
T ss_dssp             CCS-S-HHHHHHHHHHHHHHHCTTS---EEEEESSTTSSHHHHHHHHHHHCT------EEEEECCC--S-----------
T ss_pred             HHccCcHHHHhhhHHHHHHHHhcCCCcceEEEECCCccchhHHHHHHHhccC----CCeEeccchhhhh-----------
Confidence            99999999999998888765433 3567999999999999999999999986    4555666544322           


Q ss_pred             hcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCHHHHHHhHhCCCC---------------CCCcEEEEEe
Q psy200          273 LKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPSI---------------PGSKLVLVGV  337 (490)
Q Consensus       273 l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~---------------~~~~vilI~~  337 (490)
                               ..++...+.. +   +...||||||||+|....|+.|+..++-...               .-.++.+||+
T Consensus        89 ---------~~dl~~il~~-l---~~~~ILFIDEIHRlnk~~qe~LlpamEd~~idiiiG~g~~ar~~~~~l~~FTligA  155 (233)
T PF05496_consen   89 ---------AGDLAAILTN-L---KEGDILFIDEIHRLNKAQQEILLPAMEDGKIDIIIGKGPNARSIRINLPPFTLIGA  155 (233)
T ss_dssp             ---------CHHHHHHHHT------TT-EEEECTCCC--HHHHHHHHHHHHCSEEEEEBSSSSS-BEEEEE----EEEEE
T ss_pred             ---------HHHHHHHHHh-c---CCCcEEEEechhhccHHHHHHHHHHhccCeEEEEeccccccceeeccCCCceEeee
Confidence                     2233333322 2   2345999999999999999999998874321               1135789999


Q ss_pred             cCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHHHHHH
Q psy200          338 ANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITNH  417 (490)
Q Consensus       338 tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll~~  417 (490)
                      |++..   .+...+++||++   ..+++.|+.+|+.+|+.+.....  ...+++++...|++   .+.|..|-|.++|++
T Consensus       156 TTr~g---~ls~pLrdRFgi---~~~l~~Y~~~el~~Iv~r~a~~l--~i~i~~~~~~~Ia~---rsrGtPRiAnrll~r  224 (233)
T PF05496_consen  156 TTRAG---LLSSPLRDRFGI---VLRLEFYSEEELAKIVKRSARIL--NIEIDEDAAEEIAR---RSRGTPRIANRLLRR  224 (233)
T ss_dssp             ESSGC---CTSHCCCTTSSE---EEE----THHHHHHHHHHCCHCT--T-EE-HHHHHHHHH---CTTTSHHHHHHHHHH
T ss_pred             ecccc---ccchhHHhhcce---ecchhcCCHHHHHHHHHHHHHHh--CCCcCHHHHHHHHH---hcCCChHHHHHHHHH
Confidence            98653   355789999994   67899999999999999876665  56789999999998   889999999999998


Q ss_pred             HHHHH
Q psy200          418 LIDLT  422 (490)
Q Consensus       418 a~~~a  422 (490)
                      +...|
T Consensus       225 vrD~a  229 (233)
T PF05496_consen  225 VRDFA  229 (233)
T ss_dssp             HCCCC
T ss_pred             HHHHH
Confidence            75443

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.

>PRK14956 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.87  E-value=3.3e-21  Score=195.35  Aligned_cols=234  Identities=13%  Similarity=0.157  Sum_probs=167.7

Q ss_pred             cCCCCcchHHHhhcCCCCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEecc
Q psy200          178 LFSEDKPKVEEKAKDSCELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCN  257 (490)
Q Consensus       178 ~~~~~~~~~~~~~l~~~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~  257 (490)
                      ..|.++|+|...    ++++|++..+..|..++..   +.-++.++|+||+||||||+|+.+++.+......  -...|.
T Consensus         6 ~~L~~KyRP~~f----~dvVGQe~iv~~L~~~i~~---~ri~ha~Lf~GP~GtGKTTlAriLAk~Lnce~~~--~~~pCg   76 (484)
T PRK14956          6 EVLSRKYRPQFF----RDVIHQDLAIGALQNALKS---GKIGHAYIFFGPRGVGKTTIARILAKRLNCENPI--GNEPCN   76 (484)
T ss_pred             chhHHHhCCCCH----HHHhChHHHHHHHHHHHHc---CCCCeEEEEECCCCCCHHHHHHHHHHhcCccccc--CccccC
Confidence            467788998888    9999999999998888864   2334568999999999999999999998632211  112333


Q ss_pred             CCCCHHHHHHHHHHHhcC-CC-CCCcHHHHHHHHHHHHh--cCCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEE
Q psy200          258 SVRNAASVYETIVNELKL-KP-GGKSERHQLGAILKYFD--TKHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLV  333 (490)
Q Consensus       258 ~~~~~~~l~~~i~~~l~~-~~-~~~s~~~~~~~l~~~l~--~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vi  333 (490)
                      .+.+...+...+..++.. .. ...+.+.+++.......  ..++..|+||||+|.|....++.|+..++.   ....++
T Consensus        77 ~C~sC~~i~~g~~~dviEIdaas~~gVd~IReL~e~l~~~p~~g~~KV~IIDEah~Ls~~A~NALLKtLEE---Pp~~vi  153 (484)
T PRK14956         77 ECTSCLEITKGISSDVLEIDAASNRGIENIRELRDNVKFAPMGGKYKVYIIDEVHMLTDQSFNALLKTLEE---PPAHIV  153 (484)
T ss_pred             CCcHHHHHHccCCccceeechhhcccHHHHHHHHHHHHhhhhcCCCEEEEEechhhcCHHHHHHHHHHhhc---CCCceE
Confidence            333333332221111110 10 11234445444333221  235677999999999998888888777753   456788


Q ss_pred             EEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHH
Q psy200          334 LVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAID  413 (490)
Q Consensus       334 lI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~  413 (490)
                      ||.+|+.   ...+.+.+.+||.    .+.|.+++.+++.+++.+.+..+  ...++++++..|++   ...|++|.+++
T Consensus       154 FILaTte---~~kI~~TI~SRCq----~~~f~~ls~~~i~~~L~~i~~~E--gi~~e~eAL~~Ia~---~S~Gd~RdAL~  221 (484)
T PRK14956        154 FILATTE---FHKIPETILSRCQ----DFIFKKVPLSVLQDYSEKLCKIE--NVQYDQEGLFWIAK---KGDGSVRDMLS  221 (484)
T ss_pred             EEeecCC---hhhccHHHHhhhh----eeeecCCCHHHHHHHHHHHHHHc--CCCCCHHHHHHHHH---HcCChHHHHHH
Confidence            8888874   5678899999996    89999999999999999999887  36789999999998   88899999999


Q ss_pred             HHHHHHHHHHhccccCCcccccCHHHHHHHH
Q psy200          414 ITNHLIDLTYDNVKENGEVTGIGLKEVLGVI  444 (490)
Q Consensus       414 ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~  444 (490)
                      +|++++..+  .+       .|+.+.|.+.+
T Consensus       222 lLeq~i~~~--~~-------~it~~~V~~~l  243 (484)
T PRK14956        222 FMEQAIVFT--DS-------KLTGVKIRKMI  243 (484)
T ss_pred             HHHHHHHhC--CC-------CcCHHHHHHHh
Confidence            999987542  22       47777776655

>KOG0989|consensus

Probab=99.87  E-value=2.7e-21  Score=180.56  Aligned_cols=209  Identities=21%  Similarity=0.241  Sum_probs=155.4

Q ss_pred             cccCCCCcchHHHhhcCCCCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCc--eEEE
Q psy200          176 KLLFSEDKPKVEEKAKDSCELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAF--KTIY  253 (490)
Q Consensus       176 ~~~~~~~~~~~~~~~l~~~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~--~~~~  253 (490)
                      +...|.++|.|...    ++++|++..+..|...+..    ....++++|||||||||+++++++.++....-+  .+..
T Consensus        22 ~~~swteKYrPkt~----de~~gQe~vV~~L~~a~~~----~~lp~~LFyGPpGTGKTStalafar~L~~~~~~~~rvl~   93 (346)
T KOG0989|consen   22 KHRSWTEKYRPKTF----DELAGQEHVVQVLKNALLR----RILPHYLFYGPPGTGKTSTALAFARALNCEQLFPCRVLE   93 (346)
T ss_pred             CccchHHHhCCCcH----HhhcchHHHHHHHHHHHhh----cCCceEEeeCCCCCcHhHHHHHHHHHhcCccccccchhh
Confidence            34479999999988    9999999999888887753    567899999999999999999999998642222  3444


Q ss_pred             EeccCCCCHHHHHHHHHHHhcCCCCCCcHHHHHHHHHH---HHhc-CCCeEEEEEecCccccccCHHHHHHhHhCCCCCC
Q psy200          254 INCNSVRNAASVYETIVNELKLKPGGKSERHQLGAILK---YFDT-KHKSILLILDEIDALESRKQTILYTIFEWPSIPG  329 (490)
Q Consensus       254 v~~~~~~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~---~l~~-~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~  329 (490)
                      .|++...... +.            ......+......   .... .....||||||.|.|....|.+|.+.++-. .. 
T Consensus        94 lnaSderGis-vv------------r~Kik~fakl~~~~~~~~~~~~~~fKiiIlDEcdsmtsdaq~aLrr~mE~~-s~-  158 (346)
T KOG0989|consen   94 LNASDERGIS-VV------------REKIKNFAKLTVLLKRSDGYPCPPFKIIILDECDSMTSDAQAALRRTMEDF-SR-  158 (346)
T ss_pred             hccccccccc-ch------------hhhhcCHHHHhhccccccCCCCCcceEEEEechhhhhHHHHHHHHHHHhcc-cc-
Confidence            4444332111 10            0111111111110   0111 122369999999999999999999998852 23 


Q ss_pred             CcEEEEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHH
Q psy200          330 SKLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIR  409 (490)
Q Consensus       330 ~~vilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r  409 (490)
                       ...||.+||   +.+++...+.+||.    .+.|+++..+++...|+.++..+  ...+++++++.|++   .+.||+|
T Consensus       159 -~trFiLIcn---ylsrii~pi~SRC~----KfrFk~L~d~~iv~rL~~Ia~~E--~v~~d~~al~~I~~---~S~GdLR  225 (346)
T KOG0989|consen  159 -TTRFILICN---YLSRIIRPLVSRCQ----KFRFKKLKDEDIVDRLEKIASKE--GVDIDDDALKLIAK---ISDGDLR  225 (346)
T ss_pred             -ceEEEEEcC---ChhhCChHHHhhHH----HhcCCCcchHHHHHHHHHHHHHh--CCCCCHHHHHHHHH---HcCCcHH
Confidence             444555577   57888899999996    79999999999999999999988  46799999999998   7889999


Q ss_pred             HHHHHHHHHHH
Q psy200          410 KAIDITNHLID  420 (490)
Q Consensus       410 ~ai~ll~~a~~  420 (490)
                      .|+.+|+.+..
T Consensus       226 ~Ait~Lqsls~  236 (346)
T KOG0989|consen  226 RAITTLQSLSL  236 (346)
T ss_pred             HHHHHHHHhhc
Confidence            99999998865

>PRK07003 DNA polymerase III subunits gamma and tau; Validated

Probab=99.86  E-value=6e-21  Score=200.06  Aligned_cols=219  Identities=15%  Similarity=0.251  Sum_probs=155.5

Q ss_pred             CCCcchHHHhhcCCCCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCC
Q psy200          180 SEDKPKVEEKAKDSCELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSV  259 (490)
Q Consensus       180 ~~~~~~~~~~~l~~~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~  259 (490)
                      +.++|++...    ++++|+++.++.|..++..   +...+.+||+|++|+||||+++.+++.+.+....  -...|..+
T Consensus         6 LarKYRPqtF----dEVIGQe~Vv~~L~~aL~~---gRL~HAyLFtGPpGvGKTTlAriLAKaLnCe~~~--~~~PCG~C   76 (830)
T PRK07003          6 LARKWRPKDF----ASLVGQEHVVRALTHALDG---GRLHHAYLFTGTRGVGKTTLSRIFAKALNCETGV--TSQPCGVC   76 (830)
T ss_pred             HHHHhCCCcH----HHHcCcHHHHHHHHHHHhc---CCCCeEEEEECCCCCCHHHHHHHHHHHhcCccCC--CCCCCccc
Confidence            4457888777    9999999999999988863   3345667899999999999999999998643221  11223333


Q ss_pred             CCHHHHHHHHHHH-hcCC-CCCCcHHHHHHHHHHHHhc--CCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEE
Q psy200          260 RNAASVYETIVNE-LKLK-PGGKSERHQLGAILKYFDT--KHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLV  335 (490)
Q Consensus       260 ~~~~~l~~~i~~~-l~~~-~~~~s~~~~~~~l~~~l~~--~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI  335 (490)
                      .+...+...-+.+ +... ....+.+++++.+......  .++..||||||+|.|....++.|+++++.   ...+++||
T Consensus        77 ~sCr~I~~G~h~DviEIDAas~rgVDdIReLIe~a~~~P~~gr~KVIIIDEah~LT~~A~NALLKtLEE---PP~~v~FI  153 (830)
T PRK07003         77 RACREIDEGRFVDYVEMDAASNRGVDEMAALLERAVYAPVDARFKVYMIDEVHMLTNHAFNAMLKTLEE---PPPHVKFI  153 (830)
T ss_pred             HHHHHHhcCCCceEEEecccccccHHHHHHHHHHHHhccccCCceEEEEeChhhCCHHHHHHHHHHHHh---cCCCeEEE
Confidence            2222221100000 0111 1113455565555543321  24567999999999988778888887764   33467777


Q ss_pred             EecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHHHH
Q psy200          336 GVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDIT  415 (490)
Q Consensus       336 ~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll  415 (490)
                      .+||.   ..++.+.|++||.    .+.|.+++.+++.++|.+.+..+  ...+++++++.|++   ...|++|.+++++
T Consensus       154 LaTtd---~~KIp~TIrSRCq----~f~Fk~Ls~eeIv~~L~~Il~~E--gI~id~eAL~lIA~---~A~GsmRdALsLL  221 (830)
T PRK07003        154 LATTD---PQKIPVTVLSRCL----QFNLKQMPAGHIVSHLERILGEE--RIAFEPQALRLLAR---AAQGSMRDALSLT  221 (830)
T ss_pred             EEECC---hhhccchhhhheE----EEecCCcCHHHHHHHHHHHHHHc--CCCCCHHHHHHHHH---HcCCCHHHHHHHH
Confidence            77763   5677889999995    89999999999999999999887  45689999999998   7789999999999


Q ss_pred             HHHHHHH
Q psy200          416 NHLIDLT  422 (490)
Q Consensus       416 ~~a~~~a  422 (490)
                      .+++...
T Consensus       222 dQAia~~  228 (830)
T PRK07003        222 DQAIAYS  228 (830)
T ss_pred             HHHHHhc
Confidence            9887543

>PLN03025 replication factor C subunit; Provisional

Probab=99.85  E-value=3.7e-20  Score=183.76  Aligned_cols=198  Identities=19%  Similarity=0.256  Sum_probs=147.5

Q ss_pred             CCCCcchHHHhhcCCCCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcC-CceEEEEecc
Q psy200          179 FSEDKPKVEEKAKDSCELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKD-AFKTIYINCN  257 (490)
Q Consensus       179 ~~~~~~~~~~~~l~~~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~-~~~~~~v~~~  257 (490)
                      +|.++|+|...    ++++|+++.++.|..++..    +...+++|+||||+|||++|+++++++.... ...++.++.+
T Consensus         2 ~w~~kyrP~~l----~~~~g~~~~~~~L~~~~~~----~~~~~lll~Gp~G~GKTtla~~la~~l~~~~~~~~~~eln~s   73 (319)
T PLN03025          2 PWVEKYRPTKL----DDIVGNEDAVSRLQVIARD----GNMPNLILSGPPGTGKTTSILALAHELLGPNYKEAVLELNAS   73 (319)
T ss_pred             ChhhhcCCCCH----HHhcCcHHHHHHHHHHHhc----CCCceEEEECCCCCCHHHHHHHHHHHHhcccCccceeeeccc
Confidence            69999999998    9999999999888887753    5566799999999999999999999974221 1235556554


Q ss_pred             CCCCHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHh-----cCCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcE
Q psy200          258 SVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFD-----TKHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKL  332 (490)
Q Consensus       258 ~~~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~-----~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~v  332 (490)
                      .....                    +.+++.+.....     ..++..||||||+|.|....|+.|...++... ...++
T Consensus        74 d~~~~--------------------~~vr~~i~~~~~~~~~~~~~~~kviiiDE~d~lt~~aq~aL~~~lE~~~-~~t~~  132 (319)
T PLN03025         74 DDRGI--------------------DVVRNKIKMFAQKKVTLPPGRHKIVILDEADSMTSGAQQALRRTMEIYS-NTTRF  132 (319)
T ss_pred             ccccH--------------------HHHHHHHHHHHhccccCCCCCeEEEEEechhhcCHHHHHHHHHHHhccc-CCceE
Confidence            43221                    122222221111     01346799999999999888999988887432 23334


Q ss_pred             EEEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHH
Q psy200          333 VLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAI  412 (490)
Q Consensus       333 ilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai  412 (490)
                      +  .++|.   ...+.+.+++||.    .+.|.+++.+++...+...+..+  ...+++++++.+++   ...||+|.++
T Consensus       133 i--l~~n~---~~~i~~~L~SRc~----~i~f~~l~~~~l~~~L~~i~~~e--gi~i~~~~l~~i~~---~~~gDlR~al  198 (319)
T PLN03025        133 A--LACNT---SSKIIEPIQSRCA----IVRFSRLSDQEILGRLMKVVEAE--KVPYVPEGLEAIIF---TADGDMRQAL  198 (319)
T ss_pred             E--EEeCC---ccccchhHHHhhh----cccCCCCCHHHHHHHHHHHHHHc--CCCCCHHHHHHHHH---HcCCCHHHHH
Confidence            4  44552   3466788999985    79999999999999999999887  45689999999987   7889999999


Q ss_pred             HHHHHHH
Q psy200          413 DITNHLI  419 (490)
Q Consensus       413 ~ll~~a~  419 (490)
                      +.|+.+.
T Consensus       199 n~Lq~~~  205 (319)
T PLN03025        199 NNLQATH  205 (319)
T ss_pred             HHHHHHH
Confidence            9998443

>KOG0991|consensus

Probab=99.85  E-value=6.4e-21  Score=170.90  Aligned_cols=200  Identities=21%  Similarity=0.283  Sum_probs=156.5

Q ss_pred             ccCCCCcchHHHhhcCCCCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcC-CceEEEEe
Q psy200          177 LLFSEDKPKVEEKAKDSCELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKD-AFKTIYIN  255 (490)
Q Consensus       177 ~~~~~~~~~~~~~~l~~~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~-~~~~~~v~  255 (490)
                      ..+|+++|+|...    .++||.++.+++|..+..    .+...+++|.||||+||||.+..+++++-... .-.++++|
T Consensus        14 ~l~wVeKYrP~~l----~dIVGNe~tv~rl~via~----~gnmP~liisGpPG~GKTTsi~~LAr~LLG~~~ke~vLELN   85 (333)
T KOG0991|consen   14 QLPWVEKYRPSVL----QDIVGNEDTVERLSVIAK----EGNMPNLIISGPPGTGKTTSILCLARELLGDSYKEAVLELN   85 (333)
T ss_pred             cchHHHhhCchHH----HHhhCCHHHHHHHHHHHH----cCCCCceEeeCCCCCchhhHHHHHHHHHhChhhhhHhhhcc
Confidence            4469999999999    999999999999988885    47888999999999999999999999985211 11456676


Q ss_pred             ccCCCCHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHhc-----CCCeEEEEEecCccccccCHHHHHHhHhCCCCCCC
Q psy200          256 CNSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFDT-----KHKSILLILDEIDALESRKQTILYTIFEWPSIPGS  330 (490)
Q Consensus       256 ~~~~~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~-----~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~  330 (490)
                      ++..+.                    .+-++..+..+..+     .++..|||+||+|.|....|.+|++.++... ...
T Consensus        86 ASdeRG--------------------IDvVRn~IK~FAQ~kv~lp~grhKIiILDEADSMT~gAQQAlRRtMEiyS-~tt  144 (333)
T KOG0991|consen   86 ASDERG--------------------IDVVRNKIKMFAQKKVTLPPGRHKIIILDEADSMTAGAQQALRRTMEIYS-NTT  144 (333)
T ss_pred             Cccccc--------------------cHHHHHHHHHHHHhhccCCCCceeEEEeeccchhhhHHHHHHHHHHHHHc-ccc
Confidence            665432                    22233333222211     2667799999999999999999999998653 456


Q ss_pred             cEEEEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHH
Q psy200          331 KLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRK  410 (490)
Q Consensus       331 ~vilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~  410 (490)
                      ++.++|  |   ..+.+.+.+.+||.    .+.|..++..++..-+...+..+  +..++++.++.|.-   -..||+|+
T Consensus       145 RFalaC--N---~s~KIiEPIQSRCA----iLRysklsd~qiL~Rl~~v~k~E--kv~yt~dgLeaiif---ta~GDMRQ  210 (333)
T KOG0991|consen  145 RFALAC--N---QSEKIIEPIQSRCA----ILRYSKLSDQQILKRLLEVAKAE--KVNYTDDGLEAIIF---TAQGDMRQ  210 (333)
T ss_pred             hhhhhh--c---chhhhhhhHHhhhH----hhhhcccCHHHHHHHHHHHHHHh--CCCCCcchHHHhhh---hccchHHH
Confidence            666654  4   24677889999998    79999999999999998888876  57789999998875   67899999


Q ss_pred             HHHHHHHHH
Q psy200          411 AIDITNHLI  419 (490)
Q Consensus       411 ai~ll~~a~  419 (490)
                      ++|.|+..+
T Consensus       211 alNnLQst~  219 (333)
T KOG0991|consen  211 ALNNLQSTV  219 (333)
T ss_pred             HHHHHHHHh
Confidence            999987764

>KOG2028|consensus

Probab=99.85  E-value=3e-20  Score=176.53  Aligned_cols=223  Identities=14%  Similarity=0.257  Sum_probs=168.3

Q ss_pred             cchHHHhhcCCCCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCH
Q psy200          183 KPKVEEKAKDSCELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNA  262 (490)
Q Consensus       183 ~~~~~~~~l~~~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~  262 (490)
                      ..++...    +++||+++.+.+ ...|...++.+....++||||||||||+||+.++..-. ...+.|+.+++...   
T Consensus       131 rmRPktL----~dyvGQ~hlv~q-~gllrs~ieq~~ipSmIlWGppG~GKTtlArlia~tsk-~~SyrfvelSAt~a---  201 (554)
T KOG2028|consen  131 RMRPKTL----DDYVGQSHLVGQ-DGLLRSLIEQNRIPSMILWGPPGTGKTTLARLIASTSK-KHSYRFVELSATNA---  201 (554)
T ss_pred             hcCcchH----HHhcchhhhcCc-chHHHHHHHcCCCCceEEecCCCCchHHHHHHHHhhcC-CCceEEEEEecccc---
Confidence            4444444    888999888877 77777888889999999999999999999999988754 23366777765543   


Q ss_pred             HHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHh---cCCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEEEecC
Q psy200          263 ASVYETIVNELKLKPGGKSERHQLGAILKYFD---TKHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVAN  339 (490)
Q Consensus       263 ~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~---~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI~~tn  339 (490)
                                        ...++++.|+++.+   -.+++.||||||||++....|+.+     ++.+..+.|++||+|+
T Consensus       202 ------------------~t~dvR~ife~aq~~~~l~krkTilFiDEiHRFNksQQD~f-----LP~VE~G~I~lIGATT  258 (554)
T KOG2028|consen  202 ------------------KTNDVRDIFEQAQNEKSLTKRKTILFIDEIHRFNKSQQDTF-----LPHVENGDITLIGATT  258 (554)
T ss_pred             ------------------chHHHHHHHHHHHHHHhhhcceeEEEeHHhhhhhhhhhhcc-----cceeccCceEEEeccc
Confidence                              34555555555432   236788999999999999999988     7777888999999997


Q ss_pred             CCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhcc-----------CCCCCCCHHHHHHHHHHHHHhhCCH
Q psy200          340 ALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQT-----------DKFNMFNASALQLLAGKVAAVSGDI  408 (490)
Q Consensus       340 ~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~-----------~~~~~~~~~~i~~i~~~i~~~~Gd~  408 (490)
                      ..- --++...|.+||.    ++.+++++.+.+..||.+-+...           +....+++.+|+.++.   .+.||.
T Consensus       259 ENP-SFqln~aLlSRC~----VfvLekL~~n~v~~iL~raia~l~dser~~~~l~n~s~~ve~siidyla~---lsdGDa  330 (554)
T KOG2028|consen  259 ENP-SFQLNAALLSRCR----VFVLEKLPVNAVVTILMRAIASLGDSERPTDPLPNSSMFVEDSIIDYLAY---LSDGDA  330 (554)
T ss_pred             CCC-ccchhHHHHhccc----eeEeccCCHHHHHHHHHHHHHhhccccccCCCCCCcchhhhHHHHHHHHH---hcCchH
Confidence            432 3345678889996    89999999999999999855422           0112467788888886   788999


Q ss_pred             HHHHHHHHHHHHHH-HhccccCCcccccCHHHHHHHHHHh
Q psy200          409 RKAIDITNHLIDLT-YDNVKENGEVTGIGLKEVLGVISSV  447 (490)
Q Consensus       409 r~ai~ll~~a~~~a-~~~~~~~~~~~~It~~~v~~a~~~~  447 (490)
                      |.++|.|+.++.++ .+.++.  ....++++|+.+++..-
T Consensus       331 R~aLN~Lems~~m~~tr~g~~--~~~~lSidDvke~lq~s  368 (554)
T KOG2028|consen  331 RAALNALEMSLSMFCTRSGQS--SRVLLSIDDVKEGLQRS  368 (554)
T ss_pred             HHHHHHHHHHHHHHHhhcCCc--ccceecHHHHHHHHhhc
Confidence            99999999886544 333422  24579999999988753

>PRK12323 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.85  E-value=1.6e-20  Score=194.64  Aligned_cols=220  Identities=16%  Similarity=0.214  Sum_probs=154.6

Q ss_pred             CCCCcchHHHhhcCCCCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCC---ceEEEEe
Q psy200          179 FSEDKPKVEEKAKDSCELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDA---FKTIYIN  255 (490)
Q Consensus       179 ~~~~~~~~~~~~l~~~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~---~~~~~v~  255 (490)
                      .+.++|++...    ++++|++..++.|..++..   +.-.+.+||+|++|+||||+++.+++.+.+...   .....-.
T Consensus         5 vLarKYRPqtF----ddVIGQe~vv~~L~~al~~---gRLpHA~LFtGP~GvGKTTLAriLAkaLnC~~p~~~~g~~~~P   77 (700)
T PRK12323          5 VLARKWRPRDF----TTLVGQEHVVRALTHALEQ---QRLHHAYLFTGTRGVGKTTLSRILAKSLNCTGADGEGGITAQP   77 (700)
T ss_pred             hHHHHhCCCcH----HHHcCcHHHHHHHHHHHHh---CCCceEEEEECCCCCCHHHHHHHHHHHhcCCCccccccCCCCC
Confidence            34557777777    9999999999999998874   344566799999999999999999999864210   0001112


Q ss_pred             ccCCCCHHHHHHH-HHHHhcCC-CCCCcHHHHHHHHHHHHh--cCCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCc
Q psy200          256 CNSVRNAASVYET-IVNELKLK-PGGKSERHQLGAILKYFD--TKHKSILLILDEIDALESRKQTILYTIFEWPSIPGSK  331 (490)
Q Consensus       256 ~~~~~~~~~l~~~-i~~~l~~~-~~~~s~~~~~~~l~~~l~--~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~  331 (490)
                      |..+.+...+... ..+-+... ....+.+++++.+.....  ..++..|+||||+|.|....++.|++.++.   ...+
T Consensus        78 CG~C~sC~~I~aG~hpDviEIdAas~~gVDdIReLie~~~~~P~~gr~KViIIDEah~Ls~~AaNALLKTLEE---PP~~  154 (700)
T PRK12323         78 CGQCRACTEIDAGRFVDYIEMDAASNRGVDEMAQLLDKAVYAPTAGRFKVYMIDEVHMLTNHAFNAMLKTLEE---PPEH  154 (700)
T ss_pred             CcccHHHHHHHcCCCCcceEecccccCCHHHHHHHHHHHHhchhcCCceEEEEEChHhcCHHHHHHHHHhhcc---CCCC
Confidence            2222221111100 00000001 112345666665554332  235677999999999998888888777764   3456


Q ss_pred             EEEEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHH
Q psy200          332 LVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKA  411 (490)
Q Consensus       332 vilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~a  411 (490)
                      ++||.+||   ...++.+.|++||.    .+.|.+++.+++.+.|.+.+..+  ...+++++++.|++   ...|++|.+
T Consensus       155 v~FILaTt---ep~kLlpTIrSRCq----~f~f~~ls~eei~~~L~~Il~~E--gi~~d~eAL~~IA~---~A~Gs~RdA  222 (700)
T PRK12323        155 VKFILATT---DPQKIPVTVLSRCL----QFNLKQMPPGHIVSHLDAILGEE--GIAHEVNALRLLAQ---AAQGSMRDA  222 (700)
T ss_pred             ceEEEEeC---ChHhhhhHHHHHHH----hcccCCCChHHHHHHHHHHHHHc--CCCCCHHHHHHHHH---HcCCCHHHH
Confidence            67777776   35778899999996    89999999999999999999876  35688999999987   788999999


Q ss_pred             HHHHHHHHH
Q psy200          412 IDITNHLID  420 (490)
Q Consensus       412 i~ll~~a~~  420 (490)
                      ++++.+++.
T Consensus       223 LsLLdQaia  231 (700)
T PRK12323        223 LSLTDQAIA  231 (700)
T ss_pred             HHHHHHHHH
Confidence            999988764

>PRK14949 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.84  E-value=9.4e-20  Score=194.69  Aligned_cols=217  Identities=16%  Similarity=0.219  Sum_probs=150.5

Q ss_pred             CCCCcchHHHhhcCCCCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccC
Q psy200          179 FSEDKPKVEEKAKDSCELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNS  258 (490)
Q Consensus       179 ~~~~~~~~~~~~l~~~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~  258 (490)
                      .+.++|+|...    ++|+|++..++.|..++..   +.-++.++|+||+||||||+|+.+++.+.+.....  ...|..
T Consensus         5 ~LaeKyRP~tF----ddIIGQe~Iv~~LknaI~~---~rl~HAyLFtGPpGtGKTTLARiLAk~Lnce~~~~--~~pCg~   75 (944)
T PRK14949          5 VLARKWRPATF----EQMVGQSHVLHALTNALTQ---QRLHHAYLFTGTRGVGKTSLARLFAKGLNCEQGVT--ATPCGV   75 (944)
T ss_pred             hHHHHhCCCCH----HHhcCcHHHHHHHHHHHHh---CCCCeEEEEECCCCCCHHHHHHHHHHhccCccCCC--CCCCCC
Confidence            34557777777    9999999999998888863   23444568999999999999999999986331110  012222


Q ss_pred             CCCHHHHHHHH---HHHhcCCCCCCcHHHHHHHHHHHHh--cCCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEE
Q psy200          259 VRNAASVYETI---VNELKLKPGGKSERHQLGAILKYFD--TKHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLV  333 (490)
Q Consensus       259 ~~~~~~l~~~i---~~~l~~~~~~~s~~~~~~~l~~~l~--~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vi  333 (490)
                      +.+...+....   +..+... ...+.+.+++.+.....  ..++..||||||+|.|....++.|+..++.   ....++
T Consensus        76 C~sC~~i~~g~~~DviEidAa-s~~kVDdIReLie~v~~~P~~gk~KViIIDEAh~LT~eAqNALLKtLEE---PP~~vr  151 (944)
T PRK14949         76 CSSCVEIAQGRFVDLIEVDAA-SRTKVDDTRELLDNVQYRPSRGRFKVYLIDEVHMLSRSSFNALLKTLEE---PPEHVK  151 (944)
T ss_pred             chHHHHHhcCCCceEEEeccc-cccCHHHHHHHHHHHHhhhhcCCcEEEEEechHhcCHHHHHHHHHHHhc---cCCCeE
Confidence            21111111000   0001100 01234445444433221  125677999999999998888888888874   344566


Q ss_pred             EEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHH
Q psy200          334 LVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAID  413 (490)
Q Consensus       334 lI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~  413 (490)
                      ||++|+.   ...+.+.|++||.    .+.|.+++.+++.++|.+++..+  ...+++++++.|++   ...|++|.+++
T Consensus       152 FILaTTe---~~kLl~TIlSRCq----~f~fkpLs~eEI~~~L~~il~~E--gI~~edeAL~lIA~---~S~Gd~R~ALn  219 (944)
T PRK14949        152 FLLATTD---PQKLPVTVLSRCL----QFNLKSLTQDEIGTQLNHILTQE--QLPFEAEALTLLAK---AANGSMRDALS  219 (944)
T ss_pred             EEEECCC---chhchHHHHHhhe----EEeCCCCCHHHHHHHHHHHHHHc--CCCCCHHHHHHHHH---HcCCCHHHHHH
Confidence            6666653   4457788999995    89999999999999999999876  46789999999998   78899999999


Q ss_pred             HHHHHHH
Q psy200          414 ITNHLID  420 (490)
Q Consensus       414 ll~~a~~  420 (490)
                      +|.+++.
T Consensus       220 LLdQala  226 (944)
T PRK14949        220 LTDQAIA  226 (944)
T ss_pred             HHHHHHH
Confidence            9998873

>KOG0730|consensus

Probab=99.84  E-value=7.1e-20  Score=186.67  Aligned_cols=224  Identities=20%  Similarity=0.236  Sum_probs=173.9

Q ss_pred             CCCCChHHHHHHHHHHHHhhhcc---------CCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVNN---------ETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAAS  264 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~---------~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~  264 (490)
                      +++-|.++...+|.+.+...+..         .++++||+|||||||||++|++++++.+    ..|+.+.+....+   
T Consensus       434 ~dIGGlE~lK~elq~~V~~p~~~pe~F~r~Gi~ppkGVLlyGPPGC~KT~lAkalAne~~----~nFlsvkgpEL~s---  506 (693)
T KOG0730|consen  434 DDIGGLEELKRELQQAVEWPLKHPEKFARFGISPPKGVLLYGPPGCGKTLLAKALANEAG----MNFLSVKGPELFS---  506 (693)
T ss_pred             hhccCHHHHHHHHHHHHhhhhhchHHHHHhcCCCCceEEEECCCCcchHHHHHHHhhhhc----CCeeeccCHHHHH---
Confidence            78889999999999877765432         4789999999999999999999999965    6778887665433   


Q ss_pred             HHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccC-------H-HHHHHhHhC-C-CCCCCcEEE
Q psy200          265 VYETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRK-------Q-TILYTIFEW-P-SIPGSKLVL  334 (490)
Q Consensus       265 l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~-------~-~~L~~l~~~-~-~~~~~~vil  334 (490)
                                 .|.|.++..+++.|.++..  ..|+|||+||||.+...+       + ..|.+++.. . .....+|+|
T Consensus       507 -----------k~vGeSEr~ir~iF~kAR~--~aP~IiFfDEiDsi~~~R~g~~~~v~~RVlsqLLtEmDG~e~~k~V~V  573 (693)
T KOG0730|consen  507 -----------KYVGESERAIREVFRKARQ--VAPCIIFFDEIDALAGSRGGSSSGVTDRVLSQLLTEMDGLEALKNVLV  573 (693)
T ss_pred             -----------HhcCchHHHHHHHHHHHhh--cCCeEEehhhHHhHhhccCCCccchHHHHHHHHHHHcccccccCcEEE
Confidence                       7888999999999998776  457999999999997664       3 334444422 2 234568999


Q ss_pred             EEecCCCChhHhhhHHhhh--ccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCH-HHHHHHHHHHHHhhCCHHHH
Q psy200          335 VGVANALDLTDRMLPRLQA--NVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNA-SALQLLAGKVAAVSGDIRKA  411 (490)
Q Consensus       335 I~~tn~~~~~~~l~~~l~~--R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~-~~i~~i~~~i~~~~Gd~r~a  411 (490)
                      |++||+   ++.+++++.+  ||.   ..|++++++.+...+||+..+++.    .+.+ -.++.|++.+.+++|  ..+
T Consensus       574 iAATNR---pd~ID~ALlRPGRlD---~iiyVplPD~~aR~~Ilk~~~kkm----p~~~~vdl~~La~~T~g~SG--Ael  641 (693)
T KOG0730|consen  574 IAATNR---PDMIDPALLRPGRLD---RIIYVPLPDLEARLEILKQCAKKM----PFSEDVDLEELAQATEGYSG--AEI  641 (693)
T ss_pred             EeccCC---hhhcCHHHcCCcccc---eeEeecCccHHHHHHHHHHHHhcC----CCCccccHHHHHHHhccCCh--HHH
Confidence            999996   4556667766  676   689999999999999999998876    2333 368888885555554  455


Q ss_pred             HHHHHHHHHHHHhccccCCcccccCHHHHHHHHHHhccCcc
Q psy200          412 IDITNHLIDLTYDNVKENGEVTGIGLKEVLGVISSVYCTSQ  452 (490)
Q Consensus       412 i~ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~~~~~~~~~  452 (490)
                      .++|+.|...|.++.-+   ...|..+||.+|+..+.....
T Consensus       642 ~~lCq~A~~~a~~e~i~---a~~i~~~hf~~al~~~r~s~~  679 (693)
T KOG0730|consen  642 VAVCQEAALLALRESIE---ATEITWQHFEEALKAVRPSLT  679 (693)
T ss_pred             HHHHHHHHHHHHHHhcc---cccccHHHHHHHHHhhcccCC
Confidence            67999999999887643   678999999999998875543

>PRK14960 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.84  E-value=8.6e-20  Score=189.72  Aligned_cols=234  Identities=14%  Similarity=0.198  Sum_probs=159.8

Q ss_pred             CCCcchHHHhhcCCCCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCC
Q psy200          180 SEDKPKVEEKAKDSCELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSV  259 (490)
Q Consensus       180 ~~~~~~~~~~~l~~~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~  259 (490)
                      +..+|+|...    ++++|++..++.|..++..   +...+.++|+||+|+||||+|+.+++.+.+.....  ...|..+
T Consensus         5 LarKyRPktF----ddVIGQe~vv~~L~~aI~~---grl~HAyLF~GPpGvGKTTlAriLAK~LnC~~~~~--~~pCg~C   75 (702)
T PRK14960          5 LARKYRPRNF----NELVGQNHVSRALSSALER---GRLHHAYLFTGTRGVGKTTIARILAKCLNCETGVT--STPCEVC   75 (702)
T ss_pred             HHHHhCCCCH----HHhcCcHHHHHHHHHHHHc---CCCCeEEEEECCCCCCHHHHHHHHHHHhCCCcCCC--CCCCccC
Confidence            4457787777    9999999999999888863   34467789999999999999999999986322110  1112222


Q ss_pred             CCHHHHHHHHHHHh-cCC-CCCCcHHHHHHHHHHHHh--cCCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEE
Q psy200          260 RNAASVYETIVNEL-KLK-PGGKSERHQLGAILKYFD--TKHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLV  335 (490)
Q Consensus       260 ~~~~~l~~~i~~~l-~~~-~~~~s~~~~~~~l~~~l~--~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI  335 (490)
                      .+...+-..-.-++ ... ....+.+++++.+.....  ..++..|+||||+|.|....++.|..+++..   ...+.||
T Consensus        76 ~sC~~I~~g~hpDviEIDAAs~~~VddIReli~~~~y~P~~gk~KV~IIDEVh~LS~~A~NALLKtLEEP---P~~v~FI  152 (702)
T PRK14960         76 ATCKAVNEGRFIDLIEIDAASRTKVEDTRELLDNVPYAPTQGRFKVYLIDEVHMLSTHSFNALLKTLEEP---PEHVKFL  152 (702)
T ss_pred             HHHHHHhcCCCCceEEecccccCCHHHHHHHHHHHhhhhhcCCcEEEEEechHhcCHHHHHHHHHHHhcC---CCCcEEE
Confidence            11111110000000 000 011235555555443221  1245679999999999988888888887743   3345555


Q ss_pred             EecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHHHH
Q psy200          336 GVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDIT  415 (490)
Q Consensus       336 ~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll  415 (490)
                      ++++.   ...+...+.+||.    .+.|.+++.+++.+++.+.+..+  ...++++++..|++   ...|++|.++++|
T Consensus       153 LaTtd---~~kIp~TIlSRCq----~feFkpLs~eEI~k~L~~Il~kE--gI~id~eAL~~IA~---~S~GdLRdALnLL  220 (702)
T PRK14960        153 FATTD---PQKLPITVISRCL----QFTLRPLAVDEITKHLGAILEKE--QIAADQDAIWQIAE---SAQGSLRDALSLT  220 (702)
T ss_pred             EEECC---hHhhhHHHHHhhh----eeeccCCCHHHHHHHHHHHHHHc--CCCCCHHHHHHHHH---HcCCCHHHHHHHH
Confidence            55552   3455677889996    89999999999999999999887  46789999999998   7789999999999


Q ss_pred             HHHHHHHHhccccCCcccccCHHHHHHHHHH
Q psy200          416 NHLIDLTYDNVKENGEVTGIGLKEVLGVISS  446 (490)
Q Consensus       416 ~~a~~~a~~~~~~~~~~~~It~~~v~~a~~~  446 (490)
                      .+++..  ..       ..|+.++|...+..
T Consensus       221 DQaIay--g~-------g~IT~edV~~lLG~  242 (702)
T PRK14960        221 DQAIAY--GQ-------GAVHHQDVKEMLGL  242 (702)
T ss_pred             HHHHHh--cC-------CCcCHHHHHHHhcc
Confidence            888643  22       35777777776543

>PRK06645 DNA polymerase III subunits gamma and tau; Validated

Probab=99.83  E-value=2e-19  Score=185.98  Aligned_cols=242  Identities=17%  Similarity=0.222  Sum_probs=169.2

Q ss_pred             cCCCCcchHHHhhcCCCCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCc--eEEEEe
Q psy200          178 LFSEDKPKVEEKAKDSCELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAF--KTIYIN  255 (490)
Q Consensus       178 ~~~~~~~~~~~~~l~~~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~--~~~~v~  255 (490)
                      ..|..+|+|...    ++++|++..+..|...+..   +..++.++|+||+|+||||+|+.+++.+......  ......
T Consensus         9 ~~la~kyRP~~f----~dliGq~~vv~~L~~ai~~---~ri~~a~Lf~Gp~G~GKTT~ArilAk~Lnc~~~~~~~~~~~~   81 (507)
T PRK06645          9 IPFARKYRPSNF----AELQGQEVLVKVLSYTILN---DRLAGGYLLTGIRGVGKTTSARIIAKAVNCSALITENTTIKT   81 (507)
T ss_pred             cchhhhhCCCCH----HHhcCcHHHHHHHHHHHHc---CCCCceEEEECCCCCCHHHHHHHHHHHhcCccccccCcCcCC
Confidence            367778888888    9999999999988887753   3456789999999999999999999998632110  001112


Q ss_pred             ccCCCCHHHHHHHHHH---HhcCCCCCCcHHHHHHHHHHHHhc--CCCeEEEEEecCccccccCHHHHHHhHhCCCCCCC
Q psy200          256 CNSVRNAASVYETIVN---ELKLKPGGKSERHQLGAILKYFDT--KHKSILLILDEIDALESRKQTILYTIFEWPSIPGS  330 (490)
Q Consensus       256 ~~~~~~~~~l~~~i~~---~l~~~~~~~s~~~~~~~l~~~l~~--~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~  330 (490)
                      |..+.+...+......   .+.. ....+.+++.+.+..+...  .++..|+||||+|.|....++.|...++.   ...
T Consensus        82 C~~C~~C~~i~~~~h~Dv~eida-as~~~vd~Ir~iie~a~~~P~~~~~KVvIIDEa~~Ls~~a~naLLk~LEe---pp~  157 (507)
T PRK06645         82 CEQCTNCISFNNHNHPDIIEIDA-ASKTSVDDIRRIIESAEYKPLQGKHKIFIIDEVHMLSKGAFNALLKTLEE---PPP  157 (507)
T ss_pred             CCCChHHHHHhcCCCCcEEEeec-cCCCCHHHHHHHHHHHHhccccCCcEEEEEEChhhcCHHHHHHHHHHHhh---cCC
Confidence            2222222221110000   0111 1123456666665554321  24567999999999988777777777663   345


Q ss_pred             cEEEEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHH
Q psy200          331 KLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRK  410 (490)
Q Consensus       331 ~vilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~  410 (490)
                      .++||.+|+.   .+.+.+.+++||.    .+.|.+++.+++..++..++..+  ...+++++++.|++   ...|++|.
T Consensus       158 ~~vfI~aTte---~~kI~~tI~SRc~----~~ef~~ls~~el~~~L~~i~~~e--gi~ie~eAL~~Ia~---~s~GslR~  225 (507)
T PRK06645        158 HIIFIFATTE---VQKIPATIISRCQ----RYDLRRLSFEEIFKLLEYITKQE--NLKTDIEALRIIAY---KSEGSARD  225 (507)
T ss_pred             CEEEEEEeCC---hHHhhHHHHhcce----EEEccCCCHHHHHHHHHHHHHHc--CCCCCHHHHHHHHH---HcCCCHHH
Confidence            6666666653   4567788999995    79999999999999999999887  45689999999997   77899999


Q ss_pred             HHHHHHHHHHHHHhccccCCcccccCHHHHHHHHHHhc
Q psy200          411 AIDITNHLIDLTYDNVKENGEVTGIGLKEVLGVISSVY  448 (490)
Q Consensus       411 ai~ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~~~~~  448 (490)
                      ++++|+.++.++...+      ..|+.++|.+.+....
T Consensus       226 al~~Ldkai~~~~~~~------~~It~~~V~~llg~~~  257 (507)
T PRK06645        226 AVSILDQAASMSAKSD------NIISPQVINQMLGLVD  257 (507)
T ss_pred             HHHHHHHHHHhhccCC------CCcCHHHHHHHHCCCC
Confidence            9999999987664332      2578888777665443

>COG1223 Predicted ATPase (AAA+ superfamily) [General function prediction only]

Probab=99.83  E-value=1.4e-19  Score=164.77  Aligned_cols=219  Identities=18%  Similarity=0.224  Sum_probs=156.0

Q ss_pred             CCCCChHHHHHHHHHH---HHhhh--ccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHH
Q psy200          194 CELPGREVQLEGIRQF---LLGHV--NNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYET  268 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~---L~~~~--~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~  268 (490)
                      ++++|+++......-+   |++--  ....++++|+|||||||||++|++++++..    .+++.+++..+         
T Consensus       121 ddViGqEeAK~kcrli~~yLenPe~Fg~WAPknVLFyGppGTGKTm~Akalane~k----vp~l~vkat~l---------  187 (368)
T COG1223         121 DDVIGQEEAKRKCRLIMEYLENPERFGDWAPKNVLFYGPPGTGKTMMAKALANEAK----VPLLLVKATEL---------  187 (368)
T ss_pred             hhhhchHHHHHHHHHHHHHhhChHHhcccCcceeEEECCCCccHHHHHHHHhcccC----CceEEechHHH---------
Confidence            8999999888765443   33211  123678999999999999999999999854    77777765433         


Q ss_pred             HHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccC--H----------HHHHHhHhCCCCCCCcEEEEE
Q psy200          269 IVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRK--Q----------TILYTIFEWPSIPGSKLVLVG  336 (490)
Q Consensus       269 i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~--~----------~~L~~l~~~~~~~~~~vilI~  336 (490)
                           -+...|.....+.+.+..+.+  ..|||+||||+|.+.-.+  |          ++|+.-++- -..+-.++.||
T Consensus       188 -----iGehVGdgar~Ihely~rA~~--~aPcivFiDE~DAiaLdRryQelRGDVsEiVNALLTelDg-i~eneGVvtIa  259 (368)
T COG1223         188 -----IGEHVGDGARRIHELYERARK--AAPCIVFIDELDAIALDRRYQELRGDVSEIVNALLTELDG-IKENEGVVTIA  259 (368)
T ss_pred             -----HHHHhhhHHHHHHHHHHHHHh--cCCeEEEehhhhhhhhhhhHHHhcccHHHHHHHHHHhccC-cccCCceEEEe
Confidence                 223344555566666665554  459999999999986332  1          223222221 23567899999


Q ss_pred             ecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHH-HHH
Q psy200          337 VANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAI-DIT  415 (490)
Q Consensus       337 ~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai-~ll  415 (490)
                      +||.   ++.+++.+++||.   ..|.|.-++.+|...|+...+...  ...++.. ++.++.+..+.+|  |.+. .+|
T Consensus       260 aTN~---p~~LD~aiRsRFE---eEIEF~LP~~eEr~~ile~y~k~~--Plpv~~~-~~~~~~~t~g~Sg--Rdikekvl  328 (368)
T COG1223         260 ATNR---PELLDPAIRSRFE---EEIEFKLPNDEERLEILEYYAKKF--PLPVDAD-LRYLAAKTKGMSG--RDIKEKVL  328 (368)
T ss_pred             ecCC---hhhcCHHHHhhhh---heeeeeCCChHHHHHHHHHHHHhC--CCccccC-HHHHHHHhCCCCc--hhHHHHHH
Confidence            9995   4557789999998   589999999999999999999876  3333333 6777763323332  3443 389


Q ss_pred             HHHHHHHHhccccCCcccccCHHHHHHHHHHhcc
Q psy200          416 NHLIDLTYDNVKENGEVTGIGLKEVLGVISSVYC  449 (490)
Q Consensus       416 ~~a~~~a~~~~~~~~~~~~It~~~v~~a~~~~~~  449 (490)
                      +.|+..|..++     ...|+.+|+..|+.+...
T Consensus       329 K~aLh~Ai~ed-----~e~v~~edie~al~k~r~  357 (368)
T COG1223         329 KTALHRAIAED-----REKVEREDIEKALKKERK  357 (368)
T ss_pred             HHHHHHHHHhc-----hhhhhHHHHHHHHHhhcc
Confidence            99999999998     779999999999997443

>PRK14958 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.83  E-value=1.1e-19  Score=189.36  Aligned_cols=237  Identities=17%  Similarity=0.214  Sum_probs=163.2

Q ss_pred             CCCCcchHHHhhcCCCCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccC
Q psy200          179 FSEDKPKVEEKAKDSCELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNS  258 (490)
Q Consensus       179 ~~~~~~~~~~~~l~~~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~  258 (490)
                      .|.++|+|...    ++++|++..++.|..++..   +.-++.++++||+|+|||++|+.+++.+.+.....  .-.|..
T Consensus         5 ~l~~kyRP~~f----~divGq~~v~~~L~~~~~~---~~l~ha~Lf~Gp~G~GKTt~A~~lAk~l~c~~~~~--~~pCg~   75 (509)
T PRK14958          5 VLARKWRPRCF----QEVIGQAPVVRALSNALDQ---QYLHHAYLFTGTRGVGKTTISRILAKCLNCEKGVS--ANPCND   75 (509)
T ss_pred             hHHHHHCCCCH----HHhcCCHHHHHHHHHHHHh---CCCCeeEEEECCCCCCHHHHHHHHHHHhcCCCCCC--cccCCC
Confidence            35567888777    9999999999999998864   34455679999999999999999999986432211  112222


Q ss_pred             CCCHHHHHHHHHHHh-cCC-CCCCcHHHHHHHHHHHH--hcCCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEE
Q psy200          259 VRNAASVYETIVNEL-KLK-PGGKSERHQLGAILKYF--DTKHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVL  334 (490)
Q Consensus       259 ~~~~~~l~~~i~~~l-~~~-~~~~s~~~~~~~l~~~l--~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vil  334 (490)
                      +.+...+-..-.-++ ... ......+++++.+....  ...++..|+||||+|.|....++.|...++.+   ...++|
T Consensus        76 C~~C~~i~~g~~~d~~eidaas~~~v~~iR~l~~~~~~~p~~~~~kV~iIDE~~~ls~~a~naLLk~LEep---p~~~~f  152 (509)
T PRK14958         76 CENCREIDEGRFPDLFEVDAASRTKVEDTRELLDNIPYAPTKGRFKVYLIDEVHMLSGHSFNALLKTLEEP---PSHVKF  152 (509)
T ss_pred             CHHHHHHhcCCCceEEEEcccccCCHHHHHHHHHHHhhccccCCcEEEEEEChHhcCHHHHHHHHHHHhcc---CCCeEE
Confidence            221111100000000 000 11234555555544322  12356679999999999988888888877743   345666


Q ss_pred             EEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHHH
Q psy200          335 VGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDI  414 (490)
Q Consensus       335 I~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~l  414 (490)
                      |.+|+.   ...+...+.+||.    .+.|.+++.+++.+.+.+.+..+  ...+++++++.|++   ...|++|.++++
T Consensus       153 Ilattd---~~kl~~tI~SRc~----~~~f~~l~~~~i~~~l~~il~~e--gi~~~~~al~~ia~---~s~GslR~al~l  220 (509)
T PRK14958        153 ILATTD---HHKLPVTVLSRCL----QFHLAQLPPLQIAAHCQHLLKEE--NVEFENAALDLLAR---AANGSVRDALSL  220 (509)
T ss_pred             EEEECC---hHhchHHHHHHhh----hhhcCCCCHHHHHHHHHHHHHHc--CCCCCHHHHHHHHH---HcCCcHHHHHHH
Confidence            666652   4566778999995    79999999999999999999887  35689999999987   678999999999


Q ss_pred             HHHHHHHHHhccccCCcccccCHHHHHHHHHHhc
Q psy200          415 TNHLIDLTYDNVKENGEVTGIGLKEVLGVISSVY  448 (490)
Q Consensus       415 l~~a~~~a~~~~~~~~~~~~It~~~v~~a~~~~~  448 (490)
                      |++++..  ..       ..|+.++|...+....
T Consensus       221 Ldq~ia~--~~-------~~It~~~V~~~lg~~~  245 (509)
T PRK14958        221 LDQSIAY--GN-------GKVLIADVKTMLGTIE  245 (509)
T ss_pred             HHHHHhc--CC-------CCcCHHHHHHHHCCCC
Confidence            9988643  22       3677777777665443

>PRK04195 replication factor C large subunit; Provisional

Probab=99.83  E-value=2.9e-19  Score=186.91  Aligned_cols=198  Identities=19%  Similarity=0.304  Sum_probs=147.0

Q ss_pred             CCCCcchHHHhhcCCCCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccC
Q psy200          179 FSEDKPKVEEKAKDSCELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNS  258 (490)
Q Consensus       179 ~~~~~~~~~~~~l~~~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~  258 (490)
                      +|.++|+|...    ++++|+++.++.|..|+..+..+...++++|+||||+|||++|++++++++    +.++.+|++.
T Consensus         3 ~W~eKyrP~~l----~dlvg~~~~~~~l~~~l~~~~~g~~~~~lLL~GppG~GKTtla~ala~el~----~~~ielnasd   74 (482)
T PRK04195          3 PWVEKYRPKTL----SDVVGNEKAKEQLREWIESWLKGKPKKALLLYGPPGVGKTSLAHALANDYG----WEVIELNASD   74 (482)
T ss_pred             CchhhcCCCCH----HHhcCCHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHHHHHcC----CCEEEEcccc
Confidence            79999999998    999999999999999999877655688999999999999999999999975    7788898876


Q ss_pred             CCCHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCcccccc----CHHHHHHhHhCCCCCCCcEEE
Q psy200          259 VRNAASVYETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESR----KQTILYTIFEWPSIPGSKLVL  334 (490)
Q Consensus       259 ~~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~----~~~~L~~l~~~~~~~~~~vil  334 (490)
                      ..+... +..++.......             . +. +.+..||||||+|.|...    ....|..+++   .....+|+
T Consensus        75 ~r~~~~-i~~~i~~~~~~~-------------s-l~-~~~~kvIiIDEaD~L~~~~d~~~~~aL~~~l~---~~~~~iIl  135 (482)
T PRK04195         75 QRTADV-IERVAGEAATSG-------------S-LF-GARRKLILLDEVDGIHGNEDRGGARAILELIK---KAKQPIIL  135 (482)
T ss_pred             cccHHH-HHHHHHHhhccC-------------c-cc-CCCCeEEEEecCcccccccchhHHHHHHHHHH---cCCCCEEE
Confidence            543322 222222111000             0 00 124679999999999763    2455555554   23334444


Q ss_pred             EEecCCCChhHhhhH-HhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHH
Q psy200          335 VGVANALDLTDRMLP-RLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAID  413 (490)
Q Consensus       335 I~~tn~~~~~~~l~~-~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~  413 (490)
                        ++|..   ..+.. .+++||.    .+.|.+++..++..++...+...  ...+++++++.|++   ...||+|.+++
T Consensus       136 --i~n~~---~~~~~k~Lrsr~~----~I~f~~~~~~~i~~~L~~i~~~e--gi~i~~eaL~~Ia~---~s~GDlR~ain  201 (482)
T PRK04195        136 --TANDP---YDPSLRELRNACL----MIEFKRLSTRSIVPVLKRICRKE--GIECDDEALKEIAE---RSGGDLRSAIN  201 (482)
T ss_pred             --eccCc---cccchhhHhccce----EEEecCCCHHHHHHHHHHHHHHc--CCCCCHHHHHHHHH---HcCCCHHHHHH
Confidence              45532   12222 6777775    79999999999999999999876  45689999999998   77899999999


Q ss_pred             HHHH
Q psy200          414 ITNH  417 (490)
Q Consensus       414 ll~~  417 (490)
                      .|+.
T Consensus       202 ~Lq~  205 (482)
T PRK04195        202 DLQA  205 (482)
T ss_pred             HHHH
Confidence            8876

>KOG0738|consensus

Probab=99.83  E-value=2.1e-19  Score=172.25  Aligned_cols=228  Identities=13%  Similarity=0.137  Sum_probs=161.9

Q ss_pred             CCCCChHHHHHHHHHHHHhhhc--------cCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVN--------NETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASV  265 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~--------~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l  265 (490)
                      ++++|..+.++-|.+.+.--+.        ..+.++||++||||||||+||++|+.+++    ..|+-|+.+.+      
T Consensus       212 ~DIagl~~AK~lL~EAVvlPi~mPe~F~GirrPWkgvLm~GPPGTGKTlLAKAvATEc~----tTFFNVSsstl------  281 (491)
T KOG0738|consen  212 DDIAGLHEAKKLLKEAVVLPIWMPEFFKGIRRPWKGVLMVGPPGTGKTLLAKAVATECG----TTFFNVSSSTL------  281 (491)
T ss_pred             HhhcchHHHHHHHHHHHhhhhhhHHHHhhcccccceeeeeCCCCCcHHHHHHHHHHhhc----CeEEEechhhh------
Confidence            7899999999888886543221        23678999999999999999999999975    45555554443      


Q ss_pred             HHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccC-------------HHHHHHhHhCC-CCCC-C
Q psy200          266 YETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRK-------------QTILYTIFEWP-SIPG-S  330 (490)
Q Consensus       266 ~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~-------------~~~L~~l~~~~-~~~~-~  330 (490)
                              ..+|.|.+++-++-.|.-+..  ..|.+|||||||.|+..+             .++|.++-... ...+ .
T Consensus       282 --------tSKwRGeSEKlvRlLFemARf--yAPStIFiDEIDslcs~RG~s~EHEaSRRvKsELLvQmDG~~~t~e~~k  351 (491)
T KOG0738|consen  282 --------TSKWRGESEKLVRLLFEMARF--YAPSTIFIDEIDSLCSQRGGSSEHEASRRVKSELLVQMDGVQGTLENSK  351 (491)
T ss_pred             --------hhhhccchHHHHHHHHHHHHH--hCCceeehhhHHHHHhcCCCccchhHHHHHHHHHHHHhhccccccccce
Confidence                    237888888877777765444  558899999999998653             12333322221 1122 3


Q ss_pred             cEEEEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHH
Q psy200          331 KLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRK  410 (490)
Q Consensus       331 ~vilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~  410 (490)
                      .|+|+++||   +++.|++++++||.   ++|.++-++.+....+|+..+...   ...++-.++.|+++..+++|+  .
T Consensus       352 ~VmVLAATN---~PWdiDEAlrRRlE---KRIyIPLP~~~~R~~Li~~~l~~~---~~~~~~~~~~lae~~eGySGa--D  420 (491)
T KOG0738|consen  352 VVMVLAATN---FPWDIDEALRRRLE---KRIYIPLPDAEARSALIKILLRSV---ELDDPVNLEDLAERSEGYSGA--D  420 (491)
T ss_pred             eEEEEeccC---CCcchHHHHHHHHh---hheeeeCCCHHHHHHHHHHhhccc---cCCCCccHHHHHHHhcCCChH--H
Confidence            466677787   67888888999987   689999999999999999888765   344566678888877677774  2


Q ss_pred             HHHHHHHHHHHHHhcccc------------CCcccccCHHHHHHHHHHhccCcc
Q psy200          411 AIDITNHLIDLTYDNVKE------------NGEVTGIGLKEVLGVISSVYCTSQ  452 (490)
Q Consensus       411 ai~ll~~a~~~a~~~~~~------------~~~~~~It~~~v~~a~~~~~~~~~  452 (490)
                      +-++|+.|.+++.++.-.            +.....|+..||+.|+..+.++..
T Consensus       421 I~nvCreAsm~~mRR~i~g~~~~ei~~lakE~~~~pv~~~Dfe~Al~~v~pSvs  474 (491)
T KOG0738|consen  421 ITNVCREASMMAMRRKIAGLTPREIRQLAKEEPKMPVTNEDFEEALRKVRPSVS  474 (491)
T ss_pred             HHHHHHHHHHHHHHHHHhcCCcHHhhhhhhhccccccchhhHHHHHHHcCcCCC
Confidence            335788887777653211            012356999999999999887654

>PRK13342 recombination factor protein RarA; Reviewed

Probab=99.83  E-value=3.9e-19  Score=182.42  Aligned_cols=213  Identities=20%  Similarity=0.287  Sum_probs=157.8

Q ss_pred             CCCCcchHHHhhcCCCCCCChHHHHHH---HHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEe
Q psy200          179 FSEDKPKVEEKAKDSCELPGREVQLEG---IRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYIN  255 (490)
Q Consensus       179 ~~~~~~~~~~~~l~~~~lvgre~~~~~---l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~  255 (490)
                      +|.++|+|...    ++++|+++.+..   |..++.    .+...+++|+|||||||||+|+.+++.+.    ..++.++
T Consensus         1 pla~~~RP~~l----~d~vGq~~~v~~~~~L~~~i~----~~~~~~ilL~GppGtGKTtLA~~ia~~~~----~~~~~l~   68 (413)
T PRK13342          1 PLAERMRPKTL----DEVVGQEHLLGPGKPLRRMIE----AGRLSSMILWGPPGTGKTTLARIIAGATD----APFEALS   68 (413)
T ss_pred             ChhhhhCCCCH----HHhcCcHHHhCcchHHHHHHH----cCCCceEEEECCCCCCHHHHHHHHHHHhC----CCEEEEe
Confidence            35667888777    899999998776   666664    46677899999999999999999999864    4566776


Q ss_pred             ccCCCCHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHh--cCCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEE
Q psy200          256 CNSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFD--TKHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLV  333 (490)
Q Consensus       256 ~~~~~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~--~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vi  333 (490)
                      +... .                    ...+.+.+..+..  ..++..||||||+|.+....++.|...++     ...++
T Consensus        69 a~~~-~--------------------~~~ir~ii~~~~~~~~~g~~~vL~IDEi~~l~~~~q~~LL~~le-----~~~ii  122 (413)
T PRK13342         69 AVTS-G--------------------VKDLREVIEEARQRRSAGRRTILFIDEIHRFNKAQQDALLPHVE-----DGTIT  122 (413)
T ss_pred             cccc-c--------------------HHHHHHHHHHHHHhhhcCCceEEEEechhhhCHHHHHHHHHHhh-----cCcEE
Confidence            5432 1                    1222222222211  12457799999999998888888877665     24577


Q ss_pred             EEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCC-CCCHHHHHHHHHHHHHhhCCHHHHH
Q psy200          334 LVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFN-MFNASALQLLAGKVAAVSGDIRKAI  412 (490)
Q Consensus       334 lI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~-~~~~~~i~~i~~~i~~~~Gd~r~ai  412 (490)
                      +|++++.. ....+.+.+.+||.    .+.|.+++.+++..++.+.+....... .+++++++.+++   ...||+|.++
T Consensus       123 lI~att~n-~~~~l~~aL~SR~~----~~~~~~ls~e~i~~lL~~~l~~~~~~~i~i~~~al~~l~~---~s~Gd~R~al  194 (413)
T PRK13342        123 LIGATTEN-PSFEVNPALLSRAQ----VFELKPLSEEDIEQLLKRALEDKERGLVELDDEALDALAR---LANGDARRAL  194 (413)
T ss_pred             EEEeCCCC-hhhhccHHHhccce----eeEeCCCCHHHHHHHHHHHHHHhhcCCCCCCHHHHHHHHH---hCCCCHHHHH
Confidence            77776532 23456789999995    799999999999999999876532222 689999999987   5689999999


Q ss_pred             HHHHHHHHHHHhccccCCcccccCHHHHHHHHHHh
Q psy200          413 DITNHLIDLTYDNVKENGEVTGIGLKEVLGVISSV  447 (490)
Q Consensus       413 ~ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~~~~  447 (490)
                      ++++.++..    +      ..|+.+++..++...
T Consensus       195 n~Le~~~~~----~------~~It~~~v~~~~~~~  219 (413)
T PRK13342        195 NLLELAALG----V------DSITLELLEEALQKR  219 (413)
T ss_pred             HHHHHHHHc----c------CCCCHHHHHHHHhhh
Confidence            999988754    2      268999998888764

>PRK14962 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.83  E-value=6.1e-19  Score=181.80  Aligned_cols=235  Identities=20%  Similarity=0.231  Sum_probs=157.7

Q ss_pred             CCCCcchHHHhhcCCCCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccC
Q psy200          179 FSEDKPKVEEKAKDSCELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNS  258 (490)
Q Consensus       179 ~~~~~~~~~~~~l~~~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~  258 (490)
                      .|.++|+|...    ++++|++.....|..++..   +..++.++|+|||||||||+|+.+++.+......  .+..|..
T Consensus         3 ~l~~kyRP~~~----~divGq~~i~~~L~~~i~~---~~l~~~~Lf~GPpGtGKTTlA~~lA~~l~~~~~~--~~~pc~~   73 (472)
T PRK14962          3 ALYRKYRPKTF----SEVVGQDHVKKLIINALKK---NSISHAYIFAGPRGTGKTTVARILAKSLNCENRK--GVEPCNE   73 (472)
T ss_pred             hhHHHHCCCCH----HHccCcHHHHHHHHHHHHc---CCCCeEEEEECCCCCCHHHHHHHHHHHhccccCC--CCCCCcc
Confidence            45668888887    9999999998888777753   3344568999999999999999999987532110  0111111


Q ss_pred             CCCHHHHHHH---HHHHhcCCCCCCcHHHHHHHHHHHH--hcCCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEE
Q psy200          259 VRNAASVYET---IVNELKLKPGGKSERHQLGAILKYF--DTKHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLV  333 (490)
Q Consensus       259 ~~~~~~l~~~---i~~~l~~~~~~~s~~~~~~~l~~~l--~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vi  333 (490)
                      +.+...+...   -...+.. ....+.+.+++......  ...++..||||||+|.|....++.|...++.   ....++
T Consensus        74 c~~c~~i~~g~~~dv~el~a-a~~~gid~iR~i~~~~~~~p~~~~~kVvIIDE~h~Lt~~a~~~LLk~LE~---p~~~vv  149 (472)
T PRK14962         74 CRACRSIDEGTFMDVIELDA-ASNRGIDEIRKIRDAVGYRPMEGKYKVYIIDEVHMLTKEAFNALLKTLEE---PPSHVV  149 (472)
T ss_pred             cHHHHHHhcCCCCccEEEeC-cccCCHHHHHHHHHHHhhChhcCCeEEEEEEChHHhHHHHHHHHHHHHHh---CCCcEE
Confidence            1111111000   0000000 01122344443222211  1124567999999999987777777777663   334677


Q ss_pred             EEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHH
Q psy200          334 LVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAID  413 (490)
Q Consensus       334 lI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~  413 (490)
                      +|++++.   ...+.+++.+||.    .+.|.+++.+++..++...+...  ...+++++++.|++   ...||+|.+++
T Consensus       150 ~Ilattn---~~kl~~~L~SR~~----vv~f~~l~~~el~~~L~~i~~~e--gi~i~~eal~~Ia~---~s~GdlR~aln  217 (472)
T PRK14962        150 FVLATTN---LEKVPPTIISRCQ----VIEFRNISDELIIKRLQEVAEAE--GIEIDREALSFIAK---RASGGLRDALT  217 (472)
T ss_pred             EEEEeCC---hHhhhHHHhcCcE----EEEECCccHHHHHHHHHHHHHHc--CCCCCHHHHHHHHH---HhCCCHHHHHH
Confidence            7766652   3467788999995    89999999999999999998776  45789999999997   67899999999


Q ss_pred             HHHHHHHHHHhccccCCcccccCHHHHHHHHHHh
Q psy200          414 ITNHLIDLTYDNVKENGEVTGIGLKEVLGVISSV  447 (490)
Q Consensus       414 ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~~~~  447 (490)
                      .|+.++..+  .+       .|+.+++..++...
T Consensus       218 ~Le~l~~~~--~~-------~It~e~V~~~l~~~  242 (472)
T PRK14962        218 MLEQVWKFS--EG-------KITLETVHEALGLI  242 (472)
T ss_pred             HHHHHHHhc--CC-------CCCHHHHHHHHcCC
Confidence            998876432  22       48888888877544

>PRK14952 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.82  E-value=2.9e-19  Score=187.56  Aligned_cols=233  Identities=16%  Similarity=0.244  Sum_probs=159.6

Q ss_pred             CCCcchHHHhhcCCCCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCC
Q psy200          180 SEDKPKVEEKAKDSCELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSV  259 (490)
Q Consensus       180 ~~~~~~~~~~~l~~~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~  259 (490)
                      |+++|+|...    ++++|++..++.|..++..   +.-++.++|+||+|+||||+|+.+++.+.+.....  ...|..+
T Consensus         3 l~~kyRP~~f----~eivGq~~i~~~L~~~i~~---~r~~ha~Lf~Gp~G~GKTt~A~~lAk~l~c~~~~~--~~pCg~C   73 (584)
T PRK14952          3 LYRKYRPATF----AEVVGQEHVTEPLSSALDA---GRINHAYLFSGPRGCGKTSSARILARSLNCAQGPT--ATPCGVC   73 (584)
T ss_pred             HHHHhCCCcH----HHhcCcHHHHHHHHHHHHc---CCCCeEEEEECCCCCCHHHHHHHHHHHhccccCCC--CCccccc
Confidence            4568888888    9999999999999998864   23445578999999999999999999886321100  0122222


Q ss_pred             CCHHHHHHHH---HHHhcCCC-CCCcHHHHHHHHHHHHh--cCCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEE
Q psy200          260 RNAASVYETI---VNELKLKP-GGKSERHQLGAILKYFD--TKHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLV  333 (490)
Q Consensus       260 ~~~~~l~~~i---~~~l~~~~-~~~s~~~~~~~l~~~l~--~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vi  333 (490)
                      .+...+...-   .+-+.... ...+.+++++.......  ..++..|+||||+|.|....++.|+..++.   ....++
T Consensus        74 ~~C~~i~~~~~~~~dvieidaas~~gvd~iRel~~~~~~~P~~~~~KVvIIDEah~Lt~~A~NALLK~LEE---pp~~~~  150 (584)
T PRK14952         74 ESCVALAPNGPGSIDVVELDAASHGGVDDTRELRDRAFYAPAQSRYRIFIVDEAHMVTTAGFNALLKIVEE---PPEHLI  150 (584)
T ss_pred             HHHHHhhcccCCCceEEEeccccccCHHHHHHHHHHHHhhhhcCCceEEEEECCCcCCHHHHHHHHHHHhc---CCCCeE
Confidence            2211111000   00000000 11234555443333221  124566999999999998888888888874   344677


Q ss_pred             EEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHH
Q psy200          334 LVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAID  413 (490)
Q Consensus       334 lI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~  413 (490)
                      ||++|+.   ...+.+.+++||.    .+.|.+++.+++.++|..++..+  ...++++++..|++   ...|++|.+++
T Consensus       151 fIL~tte---~~kll~TI~SRc~----~~~F~~l~~~~i~~~L~~i~~~e--gi~i~~~al~~Ia~---~s~GdlR~aln  218 (584)
T PRK14952        151 FIFATTE---PEKVLPTIRSRTH----HYPFRLLPPRTMRALIARICEQE--GVVVDDAVYPLVIR---AGGGSPRDTLS  218 (584)
T ss_pred             EEEEeCC---hHhhHHHHHHhce----EEEeeCCCHHHHHHHHHHHHHHc--CCCCCHHHHHHHHH---HcCCCHHHHHH
Confidence            7776753   4678889999985    89999999999999999999887  35689999999987   77899999999


Q ss_pred             HHHHHHHHHHhccccCCcccccCHHHHHHHH
Q psy200          414 ITNHLIDLTYDNVKENGEVTGIGLKEVLGVI  444 (490)
Q Consensus       414 ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~  444 (490)
                      +|+.++.... .       ..|+.+++...+
T Consensus       219 ~Ldql~~~~~-~-------~~It~~~v~~ll  241 (584)
T PRK14952        219 VLDQLLAGAA-D-------THVTYQRALGLL  241 (584)
T ss_pred             HHHHHHhccC-C-------CCcCHHHHHHHH
Confidence            9999865432 1       256666666554

>KOG0734|consensus

Probab=99.82  E-value=3.5e-19  Score=176.55  Aligned_cols=221  Identities=14%  Similarity=0.153  Sum_probs=162.0

Q ss_pred             CCCCChHHHHHHHHHHHHhh--------hccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGH--------VNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASV  265 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~--------~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l  265 (490)
                      +++.|.++..++|.+.+.-.        +.+.-+++|||+||||||||.||++++-+.    +++|++..++++      
T Consensus       304 ~dVkG~DEAK~ELeEiVefLkdP~kftrLGGKLPKGVLLvGPPGTGKTlLARAvAGEA----~VPFF~~sGSEF------  373 (752)
T KOG0734|consen  304 EDVKGVDEAKQELEEIVEFLKDPTKFTRLGGKLPKGVLLVGPPGTGKTLLARAVAGEA----GVPFFYASGSEF------  373 (752)
T ss_pred             ccccChHHHHHHHHHHHHHhcCcHHhhhccCcCCCceEEeCCCCCchhHHHHHhhccc----CCCeEeccccch------
Confidence            67888877666666554422        223467899999999999999999999884    488888877765      


Q ss_pred             HHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccC----H----HHHHHhH-hCC-CCCCCcEEEE
Q psy200          266 YETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRK----Q----TILYTIF-EWP-SIPGSKLVLV  335 (490)
Q Consensus       266 ~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~----~----~~L~~l~-~~~-~~~~~~vilI  335 (490)
                              ...+.|.....+++.|..+.+  ..||||||||||.+...+    +    ..|.+++ ++. ...+..||||
T Consensus       374 --------dEm~VGvGArRVRdLF~aAk~--~APcIIFIDEiDavG~kR~~~~~~y~kqTlNQLLvEmDGF~qNeGiIvi  443 (752)
T KOG0734|consen  374 --------DEMFVGVGARRVRDLFAAAKA--RAPCIIFIDEIDAVGGKRNPSDQHYAKQTLNQLLVEMDGFKQNEGIIVI  443 (752)
T ss_pred             --------hhhhhcccHHHHHHHHHHHHh--cCCeEEEEechhhhcccCCccHHHHHHHHHHHHHHHhcCcCcCCceEEE
Confidence                    224566778889999887766  569999999999997663    1    2233332 332 4457789999


Q ss_pred             EecCCCChhHhhhHHhhh--ccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCC-HHHHH
Q psy200          336 GVANALDLTDRMLPRLQA--NVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGD-IRKAI  412 (490)
Q Consensus       336 ~~tn~~~~~~~l~~~l~~--R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd-~r~ai  412 (490)
                      ++||.   ++.+++.|-+  ||.   .++.++.++..-..+||..++.+......++   ...|++   ++.|- -..+-
T Consensus       444 gATNf---pe~LD~AL~RPGRFD---~~v~Vp~PDv~GR~eIL~~yl~ki~~~~~VD---~~iiAR---GT~GFsGAdLa  511 (752)
T KOG0734|consen  444 GATNF---PEALDKALTRPGRFD---RHVTVPLPDVRGRTEILKLYLSKIPLDEDVD---PKIIAR---GTPGFSGADLA  511 (752)
T ss_pred             eccCC---hhhhhHHhcCCCccc---eeEecCCCCcccHHHHHHHHHhcCCcccCCC---HhHhcc---CCCCCchHHHH
Confidence            99994   5555555542  555   5899999999999999999998763222333   566776   66663 23445


Q ss_pred             HHHHHHHHHHHhccccCCcccccCHHHHHHHHHHhccCc
Q psy200          413 DITNHLIDLTYDNVKENGEVTGIGLKEVLGVISSVYCTS  451 (490)
Q Consensus       413 ~ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~~~~~~~~  451 (490)
                      |++.+|...|..++     ...|+|.+++.|-..+.-.+
T Consensus       512 NlVNqAAlkAa~dg-----a~~VtM~~LE~akDrIlMG~  545 (752)
T KOG0734|consen  512 NLVNQAALKAAVDG-----AEMVTMKHLEFAKDRILMGP  545 (752)
T ss_pred             HHHHHHHHHHHhcC-----cccccHHHHhhhhhheeecc
Confidence            78999999999998     78999999999999876443

>PRK07764 DNA polymerase III subunits gamma and tau; Validated

Probab=99.82  E-value=2.9e-19  Score=194.27  Aligned_cols=217  Identities=15%  Similarity=0.203  Sum_probs=152.4

Q ss_pred             CCCcchHHHhhcCCCCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCC
Q psy200          180 SEDKPKVEEKAKDSCELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSV  259 (490)
Q Consensus       180 ~~~~~~~~~~~l~~~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~  259 (490)
                      |.++|++...    ++|+|++..++.|..++..   +...+.+||+||+|||||++++.|++.+.+.....  .-.|..+
T Consensus         5 l~~KyRP~~f----~eiiGqe~v~~~L~~~i~~---~ri~Ha~Lf~Gp~G~GKTt~A~~lAr~L~C~~~~~--~~pCg~C   75 (824)
T PRK07764          5 LYRRYRPATF----AEVIGQEHVTEPLSTALDS---GRINHAYLFSGPRGCGKTSSARILARSLNCVEGPT--STPCGEC   75 (824)
T ss_pred             HHHHhCCCCH----HHhcCcHHHHHHHHHHHHh---CCCCceEEEECCCCCCHHHHHHHHHHHhCcccCCC--CCCCccc
Confidence            4578888888    9999999999999988864   33445689999999999999999999986422110  0123333


Q ss_pred             CCHHHHHHHHHHH--h-cCCC-CCCcHHHHHHHHHHHHh--cCCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEE
Q psy200          260 RNAASVYETIVNE--L-KLKP-GGKSERHQLGAILKYFD--TKHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLV  333 (490)
Q Consensus       260 ~~~~~l~~~i~~~--l-~~~~-~~~s~~~~~~~l~~~l~--~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vi  333 (490)
                      .+...+...-...  + .... .....+++++.......  ..++..|+||||+|.|....++.|+++++.   ....++
T Consensus        76 ~sC~~~~~g~~~~~dv~eidaas~~~Vd~iR~l~~~~~~~p~~~~~KV~IIDEad~lt~~a~NaLLK~LEE---pP~~~~  152 (824)
T PRK07764         76 DSCVALAPGGPGSLDVTEIDAASHGGVDDARELRERAFFAPAESRYKIFIIDEAHMVTPQGFNALLKIVEE---PPEHLK  152 (824)
T ss_pred             HHHHHHHcCCCCCCcEEEecccccCCHHHHHHHHHHHHhchhcCCceEEEEechhhcCHHHHHHHHHHHhC---CCCCeE
Confidence            2222211100000  0 0000 11235555554333221  124567999999999999888888888874   334666


Q ss_pred             EEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHH
Q psy200          334 LVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAID  413 (490)
Q Consensus       334 lI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~  413 (490)
                      ||++++.   .+.+++.|++||.    .+.|.+++.+++.++|...|..+  ...++++++..|++   ...|++|.+++
T Consensus       153 fIl~tt~---~~kLl~TIrSRc~----~v~F~~l~~~~l~~~L~~il~~E--Gv~id~eal~lLa~---~sgGdlR~Al~  220 (824)
T PRK07764        153 FIFATTE---PDKVIGTIRSRTH----HYPFRLVPPEVMRGYLERICAQE--GVPVEPGVLPLVIR---AGGGSVRDSLS  220 (824)
T ss_pred             EEEEeCC---hhhhhHHHHhhee----EEEeeCCCHHHHHHHHHHHHHHc--CCCCCHHHHHHHHH---HcCCCHHHHHH
Confidence            6666653   4568889999995    89999999999999999999887  35689999999987   67899999999


Q ss_pred             HHHHHHH
Q psy200          414 ITNHLID  420 (490)
Q Consensus       414 ll~~a~~  420 (490)
                      +|++++.
T Consensus       221 eLEKLia  227 (824)
T PRK07764        221 VLDQLLA  227 (824)
T ss_pred             HHHHHHh
Confidence            9998763

>PRK07994 DNA polymerase III subunits gamma and tau; Validated

Probab=99.82  E-value=3.3e-19  Score=188.06  Aligned_cols=230  Identities=18%  Similarity=0.227  Sum_probs=158.1

Q ss_pred             CCcchHHHhhcCCCCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCC
Q psy200          181 EDKPKVEEKAKDSCELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVR  260 (490)
Q Consensus       181 ~~~~~~~~~~l~~~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~  260 (490)
                      .++|+|...    ++++|++..++.|...+..   +.-.+.++|+|++|+||||+|+.+++.+.+...+  ....|..+.
T Consensus         7 a~KyRP~~f----~divGQe~vv~~L~~~l~~---~rl~hAyLf~Gp~GvGKTTlAr~lAk~L~c~~~~--~~~pCg~C~   77 (647)
T PRK07994          7 ARKWRPQTF----AEVVGQEHVLTALANALDL---GRLHHAYLFSGTRGVGKTTIARLLAKGLNCETGI--TATPCGECD   77 (647)
T ss_pred             HHHhCCCCH----HHhcCcHHHHHHHHHHHHc---CCCCeEEEEECCCCCCHHHHHHHHHHhhhhccCC--CCCCCCCCH
Confidence            346666666    8999999999988888863   2344556899999999999999999998643211  111333332


Q ss_pred             CHHHHHHHHH---HHhcCCCCCCcHHHHHHHHHHHHh--cCCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEE
Q psy200          261 NAASVYETIV---NELKLKPGGKSERHQLGAILKYFD--TKHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLV  335 (490)
Q Consensus       261 ~~~~l~~~i~---~~l~~~~~~~s~~~~~~~l~~~l~--~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI  335 (490)
                      ....+...-.   ..+... ...+.+++++.+.....  ..++..|+||||+|.|....++.|+..++.   ....++||
T Consensus        78 ~C~~i~~g~~~D~ieidaa-s~~~VddiR~li~~~~~~p~~g~~KV~IIDEah~Ls~~a~NALLKtLEE---Pp~~v~FI  153 (647)
T PRK07994         78 NCREIEQGRFVDLIEIDAA-SRTKVEDTRELLDNVQYAPARGRFKVYLIDEVHMLSRHSFNALLKTLEE---PPEHVKFL  153 (647)
T ss_pred             HHHHHHcCCCCCceeeccc-ccCCHHHHHHHHHHHHhhhhcCCCEEEEEechHhCCHHHHHHHHHHHHc---CCCCeEEE
Confidence            2111110000   000101 01345556555544321  135677999999999998888999888874   34456666


Q ss_pred             EecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHHHH
Q psy200          336 GVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDIT  415 (490)
Q Consensus       336 ~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll  415 (490)
                      ++|+.   ...+.+.+++||.    .+.|.+++.+++..+|.+++..+  ...++++++..|++   ...|++|.+++++
T Consensus       154 L~Tt~---~~kLl~TI~SRC~----~~~f~~Ls~~ei~~~L~~il~~e--~i~~e~~aL~~Ia~---~s~Gs~R~Al~ll  221 (647)
T PRK07994        154 LATTD---PQKLPVTILSRCL----QFHLKALDVEQIRQQLEHILQAE--QIPFEPRALQLLAR---AADGSMRDALSLT  221 (647)
T ss_pred             EecCC---ccccchHHHhhhe----EeeCCCCCHHHHHHHHHHHHHHc--CCCCCHHHHHHHHH---HcCCCHHHHHHHH
Confidence            66663   4567788999995    89999999999999999999876  35689999999987   7889999999999


Q ss_pred             HHHHHHHHhccccCCcccccCHHHHHHHH
Q psy200          416 NHLIDLTYDNVKENGEVTGIGLKEVLGVI  444 (490)
Q Consensus       416 ~~a~~~a~~~~~~~~~~~~It~~~v~~a~  444 (490)
                      ++++..  ..+       .|+.++|...+
T Consensus       222 dqaia~--~~~-------~it~~~v~~~l  241 (647)
T PRK07994        222 DQAIAS--GNG-------QVTTDDVSAML  241 (647)
T ss_pred             HHHHHh--cCC-------CcCHHHHHHHH
Confidence            988643  222       45665555544

>PRK14959 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.82  E-value=4.3e-19  Score=185.55  Aligned_cols=234  Identities=13%  Similarity=0.217  Sum_probs=158.6

Q ss_pred             CCCCcchHHHhhcCCCCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccC
Q psy200          179 FSEDKPKVEEKAKDSCELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNS  258 (490)
Q Consensus       179 ~~~~~~~~~~~~l~~~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~  258 (490)
                      .|.++|++...    ++++|++..++.|..++..   +.-.+.+||+||+|+|||++|+.+++.+......  ....|..
T Consensus         5 ~la~KyRP~sf----~dIiGQe~v~~~L~~ai~~---~ri~ha~Lf~GPpG~GKTtiArilAk~L~C~~~~--~~~pCg~   75 (624)
T PRK14959          5 SLTARYRPQTF----AEVAGQETVKAILSRAAQE---NRVAPAYLFSGTRGVGKTTIARIFAKALNCETAP--TGEPCNT   75 (624)
T ss_pred             hHHHHhCCCCH----HHhcCCHHHHHHHHHHHHc---CCCCceEEEECCCCCCHHHHHHHHHHhccccCCC--CCCCCcc
Confidence            56778888888    9999999998888888863   2346788899999999999999999998632110  0012222


Q ss_pred             CCCHHHHHHHHHHHhc-CC-CCCCcHHHHHHHHHHHHh---cCCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEE
Q psy200          259 VRNAASVYETIVNELK-LK-PGGKSERHQLGAILKYFD---TKHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLV  333 (490)
Q Consensus       259 ~~~~~~l~~~i~~~l~-~~-~~~~s~~~~~~~l~~~l~---~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vi  333 (490)
                      +.+...+.....-++. .. ......+.+.. +.+.+.   ..++..||||||+|.|....++.|...++.   ....++
T Consensus        76 C~sC~~i~~g~hpDv~eId~a~~~~Id~iR~-L~~~~~~~p~~g~~kVIIIDEad~Lt~~a~naLLk~LEE---P~~~~i  151 (624)
T PRK14959         76 CEQCRKVTQGMHVDVVEIDGASNRGIDDAKR-LKEAIGYAPMEGRYKVFIIDEAHMLTREAFNALLKTLEE---PPARVT  151 (624)
T ss_pred             cHHHHHHhcCCCCceEEEecccccCHHHHHH-HHHHHHhhhhcCCceEEEEEChHhCCHHHHHHHHHHhhc---cCCCEE
Confidence            2222222111000000 00 00122333333 222221   124567999999999988777888777764   334677


Q ss_pred             EEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHH
Q psy200          334 LVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAID  413 (490)
Q Consensus       334 lI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~  413 (490)
                      ||++|+.   ...+...+++||.    .+.|.+++.+++..+|...+..+  ...+++++++.|++   ...|++|.+++
T Consensus       152 fILaTt~---~~kll~TI~SRcq----~i~F~pLs~~eL~~~L~~il~~e--gi~id~eal~lIA~---~s~GdlR~Al~  219 (624)
T PRK14959        152 FVLATTE---PHKFPVTIVSRCQ----HFTFTRLSEAGLEAHLTKVLGRE--GVDYDPAAVRLIAR---RAAGSVRDSMS  219 (624)
T ss_pred             EEEecCC---hhhhhHHHHhhhh----ccccCCCCHHHHHHHHHHHHHHc--CCCCCHHHHHHHHH---HcCCCHHHHHH
Confidence            7777763   4566677889986    79999999999999999988876  35589999999998   67799999999


Q ss_pred             HHHHHHHHHHhccccCCcccccCHHHHHHHHHH
Q psy200          414 ITNHLIDLTYDNVKENGEVTGIGLKEVLGVISS  446 (490)
Q Consensus       414 ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~~~  446 (490)
                      +|++++  +.  +     ...|+.++|..++..
T Consensus       220 lLeqll--~~--g-----~~~It~d~V~~~lg~  243 (624)
T PRK14959        220 LLGQVL--AL--G-----ESRLTIDGARGVLGL  243 (624)
T ss_pred             HHHHHH--Hh--c-----CCCcCHHHHHHHhCC
Confidence            998764  22  2     236888887766543

>PRK14951 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.82  E-value=3.7e-19  Score=187.36  Aligned_cols=235  Identities=16%  Similarity=0.225  Sum_probs=160.2

Q ss_pred             CCCcchHHHhhcCCCCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCc---eEEEEec
Q psy200          180 SEDKPKVEEKAKDSCELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAF---KTIYINC  256 (490)
Q Consensus       180 ~~~~~~~~~~~l~~~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~---~~~~v~~  256 (490)
                      |.++|++...    ++++|++..++.|..++..   +.-++.+||+|++|+||||+++.+++.+.+....   ....-.|
T Consensus         6 la~KyRP~~f----~dviGQe~vv~~L~~~l~~---~rl~ha~Lf~Gp~GvGKTtlAr~lAk~LnC~~~~~~~~~~~~pC   78 (618)
T PRK14951          6 LARKYRPRSF----SEMVGQEHVVQALTNALTQ---QRLHHAYLFTGTRGVGKTTVSRILAKSLNCQGPDGQGGITATPC   78 (618)
T ss_pred             HHHHHCCCCH----HHhcCcHHHHHHHHHHHHc---CCCCeEEEEECCCCCCHHHHHHHHHHHhcCCCcccccCCCCCCC
Confidence            4567887777    9999999999998888864   3345667999999999999999999998632110   0001123


Q ss_pred             cCCCCHHHHHHHHHHHh-cCC-CCCCcHHHHHHHHHHHHhc--CCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcE
Q psy200          257 NSVRNAASVYETIVNEL-KLK-PGGKSERHQLGAILKYFDT--KHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKL  332 (490)
Q Consensus       257 ~~~~~~~~l~~~i~~~l-~~~-~~~~s~~~~~~~l~~~l~~--~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~v  332 (490)
                      ..+.+...+...-.-++ ... ....+.+++++.+......  .++..|+||||+|.|....++.|...++.   ....+
T Consensus        79 g~C~~C~~i~~g~h~D~~eldaas~~~Vd~iReli~~~~~~p~~g~~KV~IIDEvh~Ls~~a~NaLLKtLEE---PP~~~  155 (618)
T PRK14951         79 GVCQACRDIDSGRFVDYTELDAASNRGVDEVQQLLEQAVYKPVQGRFKVFMIDEVHMLTNTAFNAMLKTLEE---PPEYL  155 (618)
T ss_pred             CccHHHHHHHcCCCCceeecCcccccCHHHHHHHHHHHHhCcccCCceEEEEEChhhCCHHHHHHHHHhccc---CCCCe
Confidence            33322222211000000 000 1113455666655543211  24567999999999998888887777663   34456


Q ss_pred             EEEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHH
Q psy200          333 VLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAI  412 (490)
Q Consensus       333 ilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai  412 (490)
                      +||.+|+.   ...+...+.+||.    .+.|.+++.+++.++|.+.+..+  ...+++++++.|++   ...|++|.++
T Consensus       156 ~fIL~Ttd---~~kil~TIlSRc~----~~~f~~Ls~eei~~~L~~i~~~e--gi~ie~~AL~~La~---~s~GslR~al  223 (618)
T PRK14951        156 KFVLATTD---PQKVPVTVLSRCL----QFNLRPMAPETVLEHLTQVLAAE--NVPAEPQALRLLAR---AARGSMRDAL  223 (618)
T ss_pred             EEEEEECC---chhhhHHHHHhce----eeecCCCCHHHHHHHHHHHHHHc--CCCCCHHHHHHHHH---HcCCCHHHHH
Confidence            66666652   4556777999985    89999999999999999999877  35689999999998   7889999999


Q ss_pred             HHHHHHHHHHHhccccCCcccccCHHHHHHHHH
Q psy200          413 DITNHLIDLTYDNVKENGEVTGIGLKEVLGVIS  445 (490)
Q Consensus       413 ~ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~~  445 (490)
                      +++++++...  .       ..|+.++|.+.+.
T Consensus       224 ~lLdq~ia~~--~-------~~It~~~V~~~Lg  247 (618)
T PRK14951        224 SLTDQAIAFG--S-------GQLQEAAVRQMLG  247 (618)
T ss_pred             HHHHHHHHhc--C-------CCcCHHHHHHHHc
Confidence            9998877542  2       2577777766554

>PRK08691 DNA polymerase III subunits gamma and tau; Validated

Probab=99.81  E-value=3.2e-19  Score=187.17  Aligned_cols=235  Identities=16%  Similarity=0.234  Sum_probs=160.3

Q ss_pred             CCCcchHHHhhcCCCCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCC
Q psy200          180 SEDKPKVEEKAKDSCELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSV  259 (490)
Q Consensus       180 ~~~~~~~~~~~l~~~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~  259 (490)
                      +..+|+|...    ++++|++..++.|..++..   +..++.+||+||+|+|||++|+.+++.+.+....  ....|..+
T Consensus         6 LarKYRP~tF----ddIIGQe~vv~~L~~ai~~---~rl~Ha~Lf~GP~GvGKTTlAriLAk~LnC~~~~--~~~pCg~C   76 (709)
T PRK08691          6 LARKWRPKTF----ADLVGQEHVVKALQNALDE---GRLHHAYLLTGTRGVGKTTIARILAKSLNCENAQ--HGEPCGVC   76 (709)
T ss_pred             HHHHhCCCCH----HHHcCcHHHHHHHHHHHHc---CCCCeEEEEECCCCCcHHHHHHHHHHHhcccCCC--CCCCCccc
Confidence            4457777777    9999999999999998874   3446678999999999999999999988633221  11222222


Q ss_pred             CCHHHHHHH-HHHHhcCC-CCCCcHHHHHHHHHHHH--hcCCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEE
Q psy200          260 RNAASVYET-IVNELKLK-PGGKSERHQLGAILKYF--DTKHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLV  335 (490)
Q Consensus       260 ~~~~~l~~~-i~~~l~~~-~~~~s~~~~~~~l~~~l--~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI  335 (490)
                      .....+... ..+-+... ....+.+.+++.+....  -..++..||||||+|.|....++.|+..++..   ...++||
T Consensus        77 ~sCr~i~~g~~~DvlEidaAs~~gVd~IRelle~a~~~P~~gk~KVIIIDEad~Ls~~A~NALLKtLEEP---p~~v~fI  153 (709)
T PRK08691         77 QSCTQIDAGRYVDLLEIDAASNTGIDNIREVLENAQYAPTAGKYKVYIIDEVHMLSKSAFNAMLKTLEEP---PEHVKFI  153 (709)
T ss_pred             HHHHHHhccCccceEEEeccccCCHHHHHHHHHHHHhhhhhCCcEEEEEECccccCHHHHHHHHHHHHhC---CCCcEEE
Confidence            111111100 00000000 11234455555554321  11245679999999999877777787777642   3345556


Q ss_pred             EecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHHHH
Q psy200          336 GVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDIT  415 (490)
Q Consensus       336 ~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll  415 (490)
                      ++++.   ...+...+++||.    .+.|.+++.+++..+|.+++..+  ...+++++++.|++   ...|++|.++++|
T Consensus       154 LaTtd---~~kL~~TIrSRC~----~f~f~~Ls~eeI~~~L~~Il~kE--gi~id~eAL~~Ia~---~A~GslRdAlnLL  221 (709)
T PRK08691        154 LATTD---PHKVPVTVLSRCL----QFVLRNMTAQQVADHLAHVLDSE--KIAYEPPALQLLGR---AAAGSMRDALSLL  221 (709)
T ss_pred             EEeCC---ccccchHHHHHHh----hhhcCCCCHHHHHHHHHHHHHHc--CCCcCHHHHHHHHH---HhCCCHHHHHHHH
Confidence            56652   3456677889995    79999999999999999999987  46689999999998   6789999999999


Q ss_pred             HHHHHHHHhccccCCcccccCHHHHHHHHHHh
Q psy200          416 NHLIDLTYDNVKENGEVTGIGLKEVLGVISSV  447 (490)
Q Consensus       416 ~~a~~~a~~~~~~~~~~~~It~~~v~~a~~~~  447 (490)
                      ++++...  .       ..|+.++|...+...
T Consensus       222 Dqaia~g--~-------g~It~e~V~~lLG~~  244 (709)
T PRK08691        222 DQAIALG--S-------GKVAENDVRQMIGAV  244 (709)
T ss_pred             HHHHHhc--C-------CCcCHHHHHHHHccc
Confidence            9887642  2       257777777665543

>PRK14964 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.81  E-value=1.6e-18  Score=177.95  Aligned_cols=213  Identities=16%  Similarity=0.199  Sum_probs=158.2

Q ss_pred             CCcchHHHhhcCCCCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcC-------------
Q psy200          181 EDKPKVEEKAKDSCELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKD-------------  247 (490)
Q Consensus       181 ~~~~~~~~~~l~~~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~-------------  247 (490)
                      ..+|+|...    ++++|++..++.|..++..   +.-++.++|+||+|+||||+|+.+++.+.+..             
T Consensus         4 a~KyRP~~f----~dliGQe~vv~~L~~a~~~---~ri~ha~Lf~Gp~G~GKTT~ArilAk~LnC~~~~~~~pCg~C~~C   76 (491)
T PRK14964          4 ALKYRPSSF----KDLVGQDVLVRILRNAFTL---NKIPQSILLVGASGVGKTTCARIISLCLNCSNGPTSDPCGTCHNC   76 (491)
T ss_pred             hHHhCCCCH----HHhcCcHHHHHHHHHHHHc---CCCCceEEEECCCCccHHHHHHHHHHHHcCcCCCCCCCccccHHH
Confidence            457888777    9999999999888877753   34567899999999999999999999874221             


Q ss_pred             -------CceEEEEeccCCCCHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHh--cCCCeEEEEEecCccccccCHHHH
Q psy200          248 -------AFKTIYINCNSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFD--TKHKSILLILDEIDALESRKQTIL  318 (490)
Q Consensus       248 -------~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~--~~~~~~vI~IDEid~l~~~~~~~L  318 (490)
                             ...+++++..+                    ..+.+++++.+.....  ..++..|+||||+|.|....++.|
T Consensus        77 ~~i~~~~~~Dv~eidaas--------------------~~~vddIR~Iie~~~~~P~~~~~KVvIIDEah~Ls~~A~NaL  136 (491)
T PRK14964         77 ISIKNSNHPDVIEIDAAS--------------------NTSVDDIKVILENSCYLPISSKFKVYIIDEVHMLSNSAFNAL  136 (491)
T ss_pred             HHHhccCCCCEEEEeccc--------------------CCCHHHHHHHHHHHHhccccCCceEEEEeChHhCCHHHHHHH
Confidence                   11233333321                    1245555554443321  124567999999999988888888


Q ss_pred             HHhHhCCCCCCCcEEEEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHH
Q psy200          319 YTIFEWPSIPGSKLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLA  398 (490)
Q Consensus       319 ~~l~~~~~~~~~~vilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~  398 (490)
                      ...++.+   ...+++|.+++.   .+.+...+++||.    .+.|.+++.+++.+++...+..+  ...+++++++.|+
T Consensus       137 LK~LEeP---p~~v~fIlatte---~~Kl~~tI~SRc~----~~~f~~l~~~el~~~L~~ia~~E--gi~i~~eAL~lIa  204 (491)
T PRK14964        137 LKTLEEP---APHVKFILATTE---VKKIPVTIISRCQ----RFDLQKIPTDKLVEHLVDIAKKE--NIEHDEESLKLIA  204 (491)
T ss_pred             HHHHhCC---CCCeEEEEEeCC---hHHHHHHHHHhhe----eeecccccHHHHHHHHHHHHHHc--CCCCCHHHHHHHH
Confidence            8887743   345666666652   4567788999995    89999999999999999999887  4678999999999


Q ss_pred             HHHHHhhCCHHHHHHHHHHHHHHHHhccccCCcccccCHHHHHHHH
Q psy200          399 GKVAAVSGDIRKAIDITNHLIDLTYDNVKENGEVTGIGLKEVLGVI  444 (490)
Q Consensus       399 ~~i~~~~Gd~r~ai~ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~  444 (490)
                      +   ...|++|.++++|+.++....  +       .|+.++|...+
T Consensus       205 ~---~s~GslR~alslLdqli~y~~--~-------~It~e~V~~ll  238 (491)
T PRK14964        205 E---NSSGSMRNALFLLEQAAIYSN--N-------KISEKSVRDLL  238 (491)
T ss_pred             H---HcCCCHHHHHHHHHHHHHhcC--C-------CCCHHHHHHHH
Confidence            8   678999999999999875432  2       57777777654

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

Probab=99.81  E-value=7.9e-19  Score=188.83  Aligned_cols=222  Identities=18%  Similarity=0.272  Sum_probs=158.3

Q ss_pred             CCCCcchHHHhhcCCCCCCChHHHHHH---HHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEe
Q psy200          179 FSEDKPKVEEKAKDSCELPGREVQLEG---IRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYIN  255 (490)
Q Consensus       179 ~~~~~~~~~~~~l~~~~lvgre~~~~~---l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~  255 (490)
                      +|.++|+|...    ++++|++..+..   |..++    ..+...+++|+|||||||||+|+.+++.+.    ..++.++
T Consensus        17 PLaek~RP~tl----dd~vGQe~ii~~~~~L~~~i----~~~~~~slLL~GPpGtGKTTLA~aIA~~~~----~~f~~ln   84 (725)
T PRK13341         17 PLADRLRPRTL----EEFVGQDHILGEGRLLRRAI----KADRVGSLILYGPPGVGKTTLARIIANHTR----AHFSSLN   84 (725)
T ss_pred             ChHHhcCCCcH----HHhcCcHHHhhhhHHHHHHH----hcCCCceEEEECCCCCCHHHHHHHHHHHhc----Ccceeeh
Confidence            67778888777    899999998853   44444    446677899999999999999999998864    4456666


Q ss_pred             ccCCCCHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEE
Q psy200          256 CNSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLV  335 (490)
Q Consensus       256 ~~~~~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI  335 (490)
                      +... ...+                 ..+..+.+...+...++..+|||||+|.+....|+.|...++     ...+++|
T Consensus        85 a~~~-~i~d-----------------ir~~i~~a~~~l~~~~~~~IL~IDEIh~Ln~~qQdaLL~~lE-----~g~IiLI  141 (725)
T PRK13341         85 AVLA-GVKD-----------------LRAEVDRAKERLERHGKRTILFIDEVHRFNKAQQDALLPWVE-----NGTITLI  141 (725)
T ss_pred             hhhh-hhHH-----------------HHHHHHHHHHHhhhcCCceEEEEeChhhCCHHHHHHHHHHhc-----CceEEEE
Confidence            5421 1000                 111112222222222456799999999998888888876654     3568888


Q ss_pred             EecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhcc-----CCCCCCCHHHHHHHHHHHHHhhCCHHH
Q psy200          336 GVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQT-----DKFNMFNASALQLLAGKVAAVSGDIRK  410 (490)
Q Consensus       336 ~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~-----~~~~~~~~~~i~~i~~~i~~~~Gd~r~  410 (490)
                      ++++.. ....+.+.+.+|+.    .+.|+|++.+++..++.+.+...     .....+++++++.|++   ...||+|.
T Consensus       142 ~aTTen-p~~~l~~aL~SR~~----v~~l~pLs~edi~~IL~~~l~~~~~~~g~~~v~I~deaL~~La~---~s~GD~R~  213 (725)
T PRK13341        142 GATTEN-PYFEVNKALVSRSR----LFRLKSLSDEDLHQLLKRALQDKERGYGDRKVDLEPEAEKHLVD---VANGDARS  213 (725)
T ss_pred             EecCCC-hHhhhhhHhhcccc----ceecCCCCHHHHHHHHHHHHHHHHhhcCCcccCCCHHHHHHHHH---hCCCCHHH
Confidence            877642 23456788889975    79999999999999999988721     1246789999999998   56899999


Q ss_pred             HHHHHHHHHHHHHhccccCCcccccCHHHHHHHHHH
Q psy200          411 AIDITNHLIDLTYDNVKENGEVTGIGLKEVLGVISS  446 (490)
Q Consensus       411 ai~ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~~~  446 (490)
                      ++++|+.++..+......   ...|+.+++.+++.+
T Consensus       214 lln~Le~a~~~~~~~~~~---~i~It~~~~~e~l~~  246 (725)
T PRK13341        214 LLNALELAVESTPPDEDG---LIDITLAIAEESIQQ  246 (725)
T ss_pred             HHHHHHHHHHhcccCCCC---ceeccHHHHHHHHHH
Confidence            999999988544322200   224888888888766

>PRK14961 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.81  E-value=3.6e-19  Score=179.45  Aligned_cols=233  Identities=16%  Similarity=0.212  Sum_probs=157.5

Q ss_pred             CCCcchHHHhhcCCCCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCC
Q psy200          180 SEDKPKVEEKAKDSCELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSV  259 (490)
Q Consensus       180 ~~~~~~~~~~~l~~~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~  259 (490)
                      +.++|+|...    ++++|+++.++.+...+..   +.-++.++|+||+|+||||+|+.+++.+......  ..-.|..+
T Consensus         6 l~~kyrP~~~----~~iiGq~~~~~~l~~~~~~---~~~~h~~L~~Gp~G~GKTtla~~la~~l~c~~~~--~~~pc~~c   76 (363)
T PRK14961          6 LARKWRPQYF----RDIIGQKHIVTAISNGLSL---GRIHHAWLLSGTRGVGKTTIARLLAKSLNCQNGI--TSNPCRKC   76 (363)
T ss_pred             HHHHhCCCch----hhccChHHHHHHHHHHHHc---CCCCeEEEEecCCCCCHHHHHHHHHHHhcCCCCC--CCCCCCCC
Confidence            4457777766    9999999999998888863   3345567999999999999999999998532111  00112222


Q ss_pred             CCHHHHHHHHHHHhcC-C-CCCCcHHHHHHHHHHHHh--cCCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEE
Q psy200          260 RNAASVYETIVNELKL-K-PGGKSERHQLGAILKYFD--TKHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLV  335 (490)
Q Consensus       260 ~~~~~l~~~i~~~l~~-~-~~~~s~~~~~~~l~~~l~--~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI  335 (490)
                      .+...+.....-++.. . ......+.+.+.+.....  ..++..|+||||+|.+....++.|...++..   ...+.+|
T Consensus        77 ~~c~~~~~~~~~d~~~~~~~~~~~v~~ir~i~~~~~~~p~~~~~kviIIDEa~~l~~~a~naLLk~lEe~---~~~~~fI  153 (363)
T PRK14961         77 IICKEIEKGLCLDLIEIDAASRTKVEEMREILDNIYYSPSKSRFKVYLIDEVHMLSRHSFNALLKTLEEP---PQHIKFI  153 (363)
T ss_pred             HHHHHHhcCCCCceEEecccccCCHHHHHHHHHHHhcCcccCCceEEEEEChhhcCHHHHHHHHHHHhcC---CCCeEEE
Confidence            2222221111101100 0 001234444444333211  1244669999999999877777777776643   3355555


Q ss_pred             EecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHHHH
Q psy200          336 GVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDIT  415 (490)
Q Consensus       336 ~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll  415 (490)
                      .+++.   .+.+.+.+.+||.    .+.|.|++.+++.+++..++..+  ...+++++++.+++   ...|++|.++++|
T Consensus       154 l~t~~---~~~l~~tI~SRc~----~~~~~~l~~~el~~~L~~~~~~~--g~~i~~~al~~ia~---~s~G~~R~al~~l  221 (363)
T PRK14961        154 LATTD---VEKIPKTILSRCL----QFKLKIISEEKIFNFLKYILIKE--SIDTDEYALKLIAY---HAHGSMRDALNLL  221 (363)
T ss_pred             EEcCC---hHhhhHHHHhhce----EEeCCCCCHHHHHHHHHHHHHHc--CCCCCHHHHHHHHH---HcCCCHHHHHHHH
Confidence            55653   4567788999985    89999999999999999999886  35689999999987   6779999999999


Q ss_pred             HHHHHHHHhccccCCcccccCHHHHHHHHH
Q psy200          416 NHLIDLTYDNVKENGEVTGIGLKEVLGVIS  445 (490)
Q Consensus       416 ~~a~~~a~~~~~~~~~~~~It~~~v~~a~~  445 (490)
                      +.++..    +     ...|+.++|.+++.
T Consensus       222 ~~~~~~----~-----~~~It~~~v~~~l~  242 (363)
T PRK14961        222 EHAINL----G-----KGNINIKNVTDMLG  242 (363)
T ss_pred             HHHHHh----c-----CCCCCHHHHHHHHC
Confidence            988754    2     23688888877665

>PRK14957 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.81  E-value=8.5e-19  Score=182.38  Aligned_cols=234  Identities=13%  Similarity=0.194  Sum_probs=156.2

Q ss_pred             CCCCcchHHHhhcCCCCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccC
Q psy200          179 FSEDKPKVEEKAKDSCELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNS  258 (490)
Q Consensus       179 ~~~~~~~~~~~~l~~~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~  258 (490)
                      .+.++|+|...    ++++|++..++.|..++..   +...+.++|+||+|+|||++|+.+++.+.+.....  .-.|..
T Consensus         5 ~La~KyRP~~f----~diiGq~~~v~~L~~~i~~---~rl~ha~Lf~Gp~GvGKTTlAr~lAk~L~c~~~~~--~~pCg~   75 (546)
T PRK14957          5 ALARKYRPQSF----AEVAGQQHALNSLVHALET---QKVHHAYLFTGTRGVGKTTLGRLLAKCLNCKTGVT--AEPCNK   75 (546)
T ss_pred             hHHHHHCcCcH----HHhcCcHHHHHHHHHHHHc---CCCCeEEEEECCCCCCHHHHHHHHHHHhCCCCCCC--CCCCcc
Confidence            45567777777    8999999999998888863   23445688999999999999999999886321110  001211


Q ss_pred             CCCHHHHHHHHHHHh-cCCC-CCCcHHHHHHHHHHHH--hcCCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEE
Q psy200          259 VRNAASVYETIVNEL-KLKP-GGKSERHQLGAILKYF--DTKHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVL  334 (490)
Q Consensus       259 ~~~~~~l~~~i~~~l-~~~~-~~~s~~~~~~~l~~~l--~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vil  334 (490)
                      +.+...+-..-..++ .... .....+++.+.+..+.  ...++..|+||||+|.|....++.|+..++.   ....++|
T Consensus        76 C~sC~~i~~~~~~dlieidaas~~gvd~ir~ii~~~~~~p~~g~~kViIIDEa~~ls~~a~naLLK~LEe---pp~~v~f  152 (546)
T PRK14957         76 CENCVAINNNSFIDLIEIDAASRTGVEETKEILDNIQYMPSQGRYKVYLIDEVHMLSKQSFNALLKTLEE---PPEYVKF  152 (546)
T ss_pred             cHHHHHHhcCCCCceEEeecccccCHHHHHHHHHHHHhhhhcCCcEEEEEechhhccHHHHHHHHHHHhc---CCCCceE
Confidence            111111100000000 0000 1122333333333221  1224567999999999998888888888874   3345556


Q ss_pred             EEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHHH
Q psy200          335 VGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDI  414 (490)
Q Consensus       335 I~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~l  414 (490)
                      |++|+.   ...+.+.+++||.    .+.|.+++.+++..++...+..+  ...+++++++.|++   ...||+|.++++
T Consensus       153 IL~Ttd---~~kil~tI~SRc~----~~~f~~Ls~~eI~~~L~~il~~e--gi~~e~~Al~~Ia~---~s~GdlR~alnl  220 (546)
T PRK14957        153 ILATTD---YHKIPVTILSRCI----QLHLKHISQADIKDQLKIILAKE--NINSDEQSLEYIAY---HAKGSLRDALSL  220 (546)
T ss_pred             EEEECC---hhhhhhhHHHhee----eEEeCCCCHHHHHHHHHHHHHHc--CCCCCHHHHHHHHH---HcCCCHHHHHHH
Confidence            655652   4666777999995    89999999999999999998887  36789999999997   778999999999


Q ss_pred             HHHHHHHHHhccccCCcccccCHHHHHHHHH
Q psy200          415 TNHLIDLTYDNVKENGEVTGIGLKEVLGVIS  445 (490)
Q Consensus       415 l~~a~~~a~~~~~~~~~~~~It~~~v~~a~~  445 (490)
                      |+.++....  +       .|+.+++..++.
T Consensus       221 Lek~i~~~~--~-------~It~~~V~~~l~  242 (546)
T PRK14957        221 LDQAISFCG--G-------ELKQAQIKQMLG  242 (546)
T ss_pred             HHHHHHhcc--C-------CCCHHHHHHHHc
Confidence            999875432  2       466766666443

>PRK03992 proteasome-activating nucleotidase; Provisional

Probab=99.80  E-value=3.8e-18  Score=173.31  Aligned_cols=222  Identities=18%  Similarity=0.237  Sum_probs=154.5

Q ss_pred             CCCCChHHHHHHHHHHHHhhhcc---------CCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVNN---------ETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAAS  264 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~---------~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~  264 (490)
                      +++.|+++++++|.+++...+..         ..+++++|+||||||||++|+++++++.    ..++.++|..+.    
T Consensus       131 ~di~Gl~~~~~~l~~~i~~pl~~~~~~~~~g~~~p~gvLL~GppGtGKT~lAkaia~~~~----~~~i~v~~~~l~----  202 (389)
T PRK03992        131 EDIGGLEEQIREVREAVELPLKKPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAHETN----ATFIRVVGSELV----  202 (389)
T ss_pred             HHhCCcHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCceEEECCCCCChHHHHHHHHHHhC----CCEEEeehHHHh----
Confidence            67999999999999987654332         3577899999999999999999999875    556777664431    


Q ss_pred             HHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccC-----------HHHHHHhHhCC--CCCCCc
Q psy200          265 VYETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRK-----------QTILYTIFEWP--SIPGSK  331 (490)
Q Consensus       265 l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~-----------~~~L~~l~~~~--~~~~~~  331 (490)
                        .        .+.|.....+...|..+..  ..++||||||+|.+....           +..+..++...  .....+
T Consensus       203 --~--------~~~g~~~~~i~~~f~~a~~--~~p~IlfiDEiD~l~~~r~~~~~~~~~~~~~~l~~lL~~ld~~~~~~~  270 (389)
T PRK03992        203 --Q--------KFIGEGARLVRELFELARE--KAPSIIFIDEIDAIAAKRTDSGTSGDREVQRTLMQLLAEMDGFDPRGN  270 (389)
T ss_pred             --H--------hhccchHHHHHHHHHHHHh--cCCeEEEEechhhhhcccccCCCCccHHHHHHHHHHHHhccccCCCCC
Confidence              1        2233344444445544333  458899999999995331           23445554322  123457


Q ss_pred             EEEEEecCCCChhHhhhHHhhh--ccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCC-H
Q psy200          332 LVLVGVANALDLTDRMLPRLQA--NVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGD-I  408 (490)
Q Consensus       332 vilI~~tn~~~~~~~l~~~l~~--R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd-~  408 (490)
                      ++||++||..   +.+++.+.+  ||.   ..|.|++|+.++..+|++.++......   .+..+..+++.   +.|- .
T Consensus       271 v~VI~aTn~~---~~ld~allRpgRfd---~~I~v~~P~~~~R~~Il~~~~~~~~~~---~~~~~~~la~~---t~g~sg  338 (389)
T PRK03992        271 VKIIAATNRI---DILDPAILRPGRFD---RIIEVPLPDEEGRLEILKIHTRKMNLA---DDVDLEELAEL---TEGASG  338 (389)
T ss_pred             EEEEEecCCh---hhCCHHHcCCccCc---eEEEECCCCHHHHHHHHHHHhccCCCC---CcCCHHHHHHH---cCCCCH
Confidence            8999999964   455666654  666   479999999999999999887664211   12335666662   3332 3


Q ss_pred             HHHHHHHHHHHHHHHhccccCCcccccCHHHHHHHHHHhccCcc
Q psy200          409 RKAIDITNHLIDLTYDNVKENGEVTGIGLKEVLGVISSVYCTSQ  452 (490)
Q Consensus       409 r~ai~ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~~~~~~~~~  452 (490)
                      ..+-.+|..|...|..++     ...|+.+||.+|+..+.....
T Consensus       339 adl~~l~~eA~~~a~~~~-----~~~i~~~d~~~A~~~~~~~~~  377 (389)
T PRK03992        339 ADLKAICTEAGMFAIRDD-----RTEVTMEDFLKAIEKVMGKEE  377 (389)
T ss_pred             HHHHHHHHHHHHHHHHcC-----CCCcCHHHHHHHHHHHhcccc
Confidence            344468999999998887     668999999999999876544

>PRK14087 dnaA chromosomal replication initiation protein; Provisional

Probab=99.80  E-value=3.6e-18  Score=175.87  Aligned_cols=247  Identities=17%  Similarity=0.230  Sum_probs=166.7

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhh-cCCceEEEEeccCCCCHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcC
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEI-KDAFKTIYINCNSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFDTK  296 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~-~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~  296 (490)
                      ..+.++|||++|+|||+|++++++++.. ..+..++|++      ..+++..+...+....     ..+ +.+.+.+   
T Consensus       140 ~~npl~i~G~~G~GKTHLl~Ai~~~l~~~~~~~~v~yv~------~~~f~~~~~~~l~~~~-----~~~-~~~~~~~---  204 (450)
T PRK14087        140 SYNPLFIYGESGMGKTHLLKAAKNYIESNFSDLKVSYMS------GDEFARKAVDILQKTH-----KEI-EQFKNEI---  204 (450)
T ss_pred             ccCceEEECCCCCcHHHHHHHHHHHHHHhCCCCeEEEEE------HHHHHHHHHHHHHHhh-----hHH-HHHHHHh---
Confidence            3467999999999999999999998753 3567888884      4556666666554210     111 2222222   


Q ss_pred             CCeEEEEEecCcccccc--CHHHHHHhHhCCCCCCCcEEEEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHH
Q psy200          297 HKSILLILDEIDALESR--KQTILYTIFEWPSIPGSKLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILE  374 (490)
Q Consensus       297 ~~~~vI~IDEid~l~~~--~~~~L~~l~~~~~~~~~~vilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~  374 (490)
                      ...-+|+|||+|.+...  .++.|+.+++.....+..+++. ..........+.+++.+||.++ ..+.+.+++.+++.+
T Consensus       205 ~~~dvLiIDDiq~l~~k~~~~e~lf~l~N~~~~~~k~iIlt-sd~~P~~l~~l~~rL~SR~~~G-l~~~L~~pd~e~r~~  282 (450)
T PRK14087        205 CQNDVLIIDDVQFLSYKEKTNEIFFTIFNNFIENDKQLFFS-SDKSPELLNGFDNRLITRFNMG-LSIAIQKLDNKTATA  282 (450)
T ss_pred             ccCCEEEEeccccccCCHHHHHHHHHHHHHHHHcCCcEEEE-CCCCHHHHhhccHHHHHHHhCC-ceeccCCcCHHHHHH
Confidence            33559999999999754  4678888887654444444443 2222234455678999999766 369999999999999


Q ss_pred             HHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHhccc-cC---------------CcccccCHH
Q psy200          375 IISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITNHLIDLTYDNVK-EN---------------GEVTGIGLK  438 (490)
Q Consensus       375 il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll~~a~~~a~~~~~-~~---------------~~~~~It~~  438 (490)
                      +|++++...+....+++++++.|+.   ...||+|.++.+|.++...+..... ..               .....|+++
T Consensus       283 iL~~~~~~~gl~~~l~~evl~~Ia~---~~~gd~R~L~gaL~~l~~~a~~~~~~~~it~~~v~~~l~~~~~~~~~~~t~~  359 (450)
T PRK14087        283 IIKKEIKNQNIKQEVTEEAINFISN---YYSDDVRKIKGSVSRLNFWSQQNPEEKIITIEIVSDLFRDIPTSKLGILNVK  359 (450)
T ss_pred             HHHHHHHhcCCCCCCCHHHHHHHHH---ccCCCHHHHHHHHHHHHHHHhcccCCCCCCHHHHHHHHhhccccccCCCCHH
Confidence            9999998764333699999999998   8889999999999988766654411 00               012237777


Q ss_pred             HHHHHHHHhccCccccccccccCCCChHhHHHH---HHHHHHhcCCCCCCcccC
Q psy200          439 EVLGVISSVYCTSQSLHCSKDEDSFPLQQKLAL---ASLLLLKSRPNVKDVTLG  489 (490)
Q Consensus       439 ~v~~a~~~~~~~~~~~~~~~~l~~L~~~qk~vL---~al~~~~~~~~~~~~~~g  489 (490)
                      .|.+++.+.++-..     +.+.+-...+..++   .||+++.+-.+.+...||
T Consensus       360 ~I~~~Va~~~~i~~-----~dl~s~~R~~~i~~~RqiamyL~r~~t~~sl~~IG  408 (450)
T PRK14087        360 KIKEVVSEKYGISV-----NAIDGKARSKSIVTARHIAMYLTKEILNHTLAQIG  408 (450)
T ss_pred             HHHHHHHHHcCCCH-----HHHhCCCCCccccHHHHHHHHHHHHHcCCCHHHHH
Confidence            77777777776444     33444444444343   467777666666665555

>PRK00440 rfc replication factor C small subunit; Reviewed

Probab=99.79  E-value=8.8e-18  Score=167.22  Aligned_cols=218  Identities=20%  Similarity=0.250  Sum_probs=155.3

Q ss_pred             ccCCCCcchHHHhhcCCCCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcC-CceEEEEe
Q psy200          177 LLFSEDKPKVEEKAKDSCELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKD-AFKTIYIN  255 (490)
Q Consensus       177 ~~~~~~~~~~~~~~l~~~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~-~~~~~~v~  255 (490)
                      ..+|.++|+|...    ++++|+++.++.|..++..    +..++++|+|++|+|||++++.+++++.... ...++.++
T Consensus         4 ~~~w~~kyrP~~~----~~~~g~~~~~~~l~~~i~~----~~~~~~ll~G~~G~GKt~~~~~l~~~l~~~~~~~~~i~~~   75 (319)
T PRK00440          4 EEIWVEKYRPRTL----DEIVGQEEIVERLKSYVKE----KNMPHLLFAGPPGTGKTTAALALARELYGEDWRENFLELN   75 (319)
T ss_pred             cCccchhhCCCcH----HHhcCcHHHHHHHHHHHhC----CCCCeEEEECCCCCCHHHHHHHHHHHHcCCccccceEEec
Confidence            3479999999888    8999999999999888863    4455789999999999999999999874222 22445555


Q ss_pred             ccCCCCHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHh----cCCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCc
Q psy200          256 CNSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFD----TKHKSILLILDEIDALESRKQTILYTIFEWPSIPGSK  331 (490)
Q Consensus       256 ~~~~~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~----~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~  331 (490)
                      +....... .                   +.+.+.....    ......+|+|||+|.+....+..|..+++... ... 
T Consensus        76 ~~~~~~~~-~-------------------~~~~i~~~~~~~~~~~~~~~vviiDe~~~l~~~~~~~L~~~le~~~-~~~-  133 (319)
T PRK00440         76 ASDERGID-V-------------------IRNKIKEFARTAPVGGAPFKIIFLDEADNLTSDAQQALRRTMEMYS-QNT-  133 (319)
T ss_pred             cccccchH-H-------------------HHHHHHHHHhcCCCCCCCceEEEEeCcccCCHHHHHHHHHHHhcCC-CCC-
Confidence            44322111 1                   1111111111    11235699999999998777777887776432 233 


Q ss_pred             EEEEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHH
Q psy200          332 LVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKA  411 (490)
Q Consensus       332 vilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~a  411 (490)
                       .+|.+++.   ...+.+.+++|+.    .+.|.+++.+++..++..++...  ...+++++++.+++   ...||+|.+
T Consensus       134 -~lIl~~~~---~~~l~~~l~sr~~----~~~~~~l~~~ei~~~l~~~~~~~--~~~i~~~al~~l~~---~~~gd~r~~  200 (319)
T PRK00440        134 -RFILSCNY---SSKIIDPIQSRCA----VFRFSPLKKEAVAERLRYIAENE--GIEITDDALEAIYY---VSEGDMRKA  200 (319)
T ss_pred             -eEEEEeCC---ccccchhHHHHhh----eeeeCCCCHHHHHHHHHHHHHHc--CCCCCHHHHHHHHH---HcCCCHHHH
Confidence             33434442   2445667888886    79999999999999999999876  35689999999987   678999999


Q ss_pred             HHHHHHHHHHHHhccccCCcccccCHHHHHHHHHHh
Q psy200          412 IDITNHLIDLTYDNVKENGEVTGIGLKEVLGVISSV  447 (490)
Q Consensus       412 i~ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~~~~  447 (490)
                      ++.++.+...    +      ..|+.++|.+++...
T Consensus       201 ~~~l~~~~~~----~------~~it~~~v~~~~~~~  226 (319)
T PRK00440        201 INALQAAAAT----G------KEVTEEAVYKITGTA  226 (319)
T ss_pred             HHHHHHHHHc----C------CCCCHHHHHHHhCCC
Confidence            9999876542    2      268888887776543

>KOG0733|consensus

Probab=99.79  E-value=4.6e-18  Score=171.22  Aligned_cols=202  Identities=16%  Similarity=0.257  Sum_probs=147.5

Q ss_pred             CCCCChHHHHHHHHHHHHhhhc--------cCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVN--------NETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASV  265 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~--------~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l  265 (490)
                      .++-|.++.+.+|.+.+.....        -.+++++||+||||||||+||++++.+++    ++|+.+++..+-+    
T Consensus       190 ~diGG~d~~~~el~~li~~i~~Pe~~~~lGv~PprGvLlHGPPGCGKT~lA~AiAgel~----vPf~~isApeivS----  261 (802)
T KOG0733|consen  190 SDIGGLDKTLAELCELIIHIKHPEVFSSLGVRPPRGVLLHGPPGCGKTSLANAIAGELG----VPFLSISAPEIVS----  261 (802)
T ss_pred             hhccChHHHHHHHHHHHHHhcCchhHhhcCCCCCCceeeeCCCCccHHHHHHHHhhhcC----CceEeecchhhhc----
Confidence            7899999999999998765211        23788999999999999999999999986    8889998776533    


Q ss_pred             HHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCH--------HHHHHh---HhCCC---CCCCc
Q psy200          266 YETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQ--------TILYTI---FEWPS---IPGSK  331 (490)
Q Consensus       266 ~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~--------~~L~~l---~~~~~---~~~~~  331 (490)
                                ...|++++.+++.|.++..  ..|||+||||||.+...++        ....+|   |+-..   ..+..
T Consensus       262 ----------GvSGESEkkiRelF~~A~~--~aPcivFiDeIDAI~pkRe~aqreMErRiVaQLlt~mD~l~~~~~~g~~  329 (802)
T KOG0733|consen  262 ----------GVSGESEKKIRELFDQAKS--NAPCIVFIDEIDAITPKREEAQREMERRIVAQLLTSMDELSNEKTKGDP  329 (802)
T ss_pred             ----------ccCcccHHHHHHHHHHHhc--cCCeEEEeecccccccchhhHHHHHHHHHHHHHHHhhhcccccccCCCC
Confidence                      5567899999999998876  5699999999999987752        122222   33222   13578


Q ss_pred             EEEEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHH
Q psy200          332 LVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKA  411 (490)
Q Consensus       332 vilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~a  411 (490)
                      |+|||+||+.|   .+++.|+ |.|.....|.+.-++..+..+||+..|........|+   ++.|++   .+.|-+..-
T Consensus       330 VlVIgATnRPD---slDpaLR-RaGRFdrEI~l~vP~e~aR~~IL~~~~~~lrl~g~~d---~~qlA~---lTPGfVGAD  399 (802)
T KOG0733|consen  330 VLVIGATNRPD---SLDPALR-RAGRFDREICLGVPSETAREEILRIICRGLRLSGDFD---FKQLAK---LTPGFVGAD  399 (802)
T ss_pred             eEEEecCCCCc---ccCHHHh-ccccccceeeecCCchHHHHHHHHHHHhhCCCCCCcC---HHHHHh---cCCCccchh
Confidence            99999999754   4455554 3343346899999999999999999998764333444   566776   344544333


Q ss_pred             H-HHHHHHHHHHHhc
Q psy200          412 I-DITNHLIDLTYDN  425 (490)
Q Consensus       412 i-~ll~~a~~~a~~~  425 (490)
                      + .+|..|...|..+
T Consensus       400 L~AL~~~Aa~vAikR  414 (802)
T KOG0733|consen  400 LMALCREAAFVAIKR  414 (802)
T ss_pred             HHHHHHHHHHHHHHH
Confidence            3 3666666666543

>PRK08451 DNA polymerase III subunits gamma and tau; Validated

Probab=99.79  E-value=4.5e-18  Score=176.05  Aligned_cols=231  Identities=16%  Similarity=0.198  Sum_probs=158.1

Q ss_pred             CCCCcchHHHhhcCCCCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccC
Q psy200          179 FSEDKPKVEEKAKDSCELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNS  258 (490)
Q Consensus       179 ~~~~~~~~~~~~l~~~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~  258 (490)
                      .|.++|+|...    ++++|++..++.|..++..   +.-++.++||||+|+|||++|+.+++.+.......  .-.|..
T Consensus         3 ~l~~KyRP~~f----deiiGqe~v~~~L~~~I~~---grl~hayLf~Gp~G~GKTt~Ar~LAk~L~c~~~~~--~~pC~~   73 (535)
T PRK08451          3 ALALKYRPKHF----DELIGQESVSKTLSLALDN---NRLAHAYLFSGLRGSGKTSSARIFARALVCEQGPS--STPCDT   73 (535)
T ss_pred             cHHHHHCCCCH----HHccCcHHHHHHHHHHHHc---CCCCeeEEEECCCCCcHHHHHHHHHHHhcCCCCCC--CCCCcc
Confidence            45678888888    9999999999999988864   33455668999999999999999999985322110  001221


Q ss_pred             CCCHHHHHHHHHH---HhcCCCCCCcHHHHHHHHHHHHh--cCCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEE
Q psy200          259 VRNAASVYETIVN---ELKLKPGGKSERHQLGAILKYFD--TKHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLV  333 (490)
Q Consensus       259 ~~~~~~l~~~i~~---~l~~~~~~~s~~~~~~~l~~~l~--~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vi  333 (490)
                      +.+...+.....-   .++. ......+.+++.+.....  ..++..|+||||+|.|....++.|+..++.+   ...++
T Consensus        74 C~~C~~~~~~~h~dv~elda-as~~gId~IRelie~~~~~P~~~~~KVvIIDEad~Lt~~A~NALLK~LEEp---p~~t~  149 (535)
T PRK08451         74 CIQCQSALENRHIDIIEMDA-ASNRGIDDIRELIEQTKYKPSMARFKIFIIDEVHMLTKEAFNALLKTLEEP---PSYVK  149 (535)
T ss_pred             cHHHHHHhhcCCCeEEEecc-ccccCHHHHHHHHHHHhhCcccCCeEEEEEECcccCCHHHHHHHHHHHhhc---CCceE
Confidence            1111111100000   0000 001234555555543211  1245679999999999988888898888754   23455


Q ss_pred             EEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHH
Q psy200          334 LVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAID  413 (490)
Q Consensus       334 lI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~  413 (490)
                      ||.+++.   ...+.+.+++||.    .+.|.+++.+++...+.+.+..++  ..+++++++.|++   ...|++|.+++
T Consensus       150 FIL~ttd---~~kL~~tI~SRc~----~~~F~~Ls~~ei~~~L~~Il~~EG--i~i~~~Al~~Ia~---~s~GdlR~aln  217 (535)
T PRK08451        150 FILATTD---PLKLPATILSRTQ----HFRFKQIPQNSIISHLKTILEKEG--VSYEPEALEILAR---SGNGSLRDTLT  217 (535)
T ss_pred             EEEEECC---hhhCchHHHhhce----eEEcCCCCHHHHHHHHHHHHHHcC--CCCCHHHHHHHHH---HcCCcHHHHHH
Confidence            5555542   3677788999985    899999999999999999998874  5689999999998   77899999999


Q ss_pred             HHHHHHHHHHhccccCCcccccCHHHHHHH
Q psy200          414 ITNHLIDLTYDNVKENGEVTGIGLKEVLGV  443 (490)
Q Consensus       414 ll~~a~~~a~~~~~~~~~~~~It~~~v~~a  443 (490)
                      +|++++..+  .+       .|+.++|...
T Consensus       218 lLdqai~~~--~~-------~It~~~V~~~  238 (535)
T PRK08451        218 LLDQAIIYC--KN-------AITESKVADM  238 (535)
T ss_pred             HHHHHHHhc--CC-------CCCHHHHHHH
Confidence            999988665  22       4555555544

>TIGR00602 rad24 checkpoint protein rad24

Probab=99.79  E-value=1.6e-18  Score=182.79  Aligned_cols=253  Identities=16%  Similarity=0.163  Sum_probs=159.1

Q ss_pred             ccCCCCcchHHHhhcCCCCCCChHHHHHHHHHHHHhhhccC-CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEe
Q psy200          177 LLFSEDKPKVEEKAKDSCELPGREVQLEGIRQFLLGHVNNE-TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYIN  255 (490)
Q Consensus       177 ~~~~~~~~~~~~~~l~~~~lvgre~~~~~l~~~L~~~~~~~-~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~  255 (490)
                      ..+|.++|+|...    ++|+|+++++++|..||....... ....++|+||+|+||||+++.++..+...-.-..-.++
T Consensus        71 ~~pW~eKyrP~~l----del~~~~~ki~~l~~~l~~~~~~~~~~~illL~GP~GsGKTTl~~~la~~l~~~~~Ew~npv~  146 (637)
T TIGR00602        71 NEPWVEKYKPETQ----HELAVHKKKIEEVETWLKAQVLENAPKRILLITGPSGCGKSTTIKILSKELGIQVQEWSNPTL  146 (637)
T ss_pred             cCchHHHhCCCCH----HHhcCcHHHHHHHHHHHHhcccccCCCcEEEEECCCCCCHHHHHHHHHHHhhhHHHHHhhhhh
Confidence            3489999999999    999999999999999998754333 34569999999999999999999987511000011122


Q ss_pred             ccCCCCHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHh--------cCCCeEEEEEecCccccccCHHHHHHhHhCCCC
Q psy200          256 CNSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFD--------TKHKSILLILDEIDALESRKQTILYTIFEWPSI  327 (490)
Q Consensus       256 ~~~~~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~--------~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~  327 (490)
                      |....+.......+...+...  ....+.+.+++..+-.        ..++..|||||||+++.......+..++.|...
T Consensus       147 ~~~~~~~~~~~~s~~~~~~~~--~s~~~~F~~fl~~a~~~~~~~g~~~~~~~~IILIDEiPn~~~r~~~~lq~lLr~~~~  224 (637)
T TIGR00602       147 PDFQKNDHKVTLSLESCFSNF--QSQIEVFSEFLLRATNKLQMLGDDLMTDKKIILVEDLPNQFYRDTRALHEILRWKYV  224 (637)
T ss_pred             hcccccccccchhhhhccccc--cchHHHHHHHHHHHHhhhcccccccCCceeEEEeecchhhchhhHHHHHHHHHHHhh
Confidence            222222222222222222211  1233444444443321        124678999999999987776777777764443


Q ss_pred             CCCcEEEEEecCCCC----------hh-Hh-hhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCC----CC-CCC
Q psy200          328 PGSKLVLVGVANALD----------LT-DR-MLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDK----FN-MFN  390 (490)
Q Consensus       328 ~~~~vilI~~tn~~~----------~~-~~-l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~----~~-~~~  390 (490)
                      ...++.+|++++...          +. .+ +.+.+.++...  ..|.|+|++..++.+.|...+..+..    .. ..+
T Consensus       225 e~~~~pLI~I~TE~~~~~~~~~~~~f~~~~lL~~eLls~~rv--~~I~FnPia~t~l~K~L~rIl~~E~~~~~~~~~~p~  302 (637)
T TIGR00602       225 SIGRCPLVFIITESLEGDNNQRRLLFPAETIMNKEILEEPRV--SNISFNPIAPTIMKKFLNRIVTIEAKKNGEKIKVPK  302 (637)
T ss_pred             cCCCceEEEEecCCccccccccccccchhcccCHhHhcccce--eEEEeCCCCHHHHHHHHHHHHHhhhhccccccccCC
Confidence            445565665554210          11 11 22566653332  47999999999999999988876521    11 225


Q ss_pred             HHHHHHHHHHHHHhhCCHHHHHHHHHHHHH----HHHhccccCCcccccCHHHHHHHHH
Q psy200          391 ASALQLLAGKVAAVSGDIRKAIDITNHLID----LTYDNVKENGEVTGIGLKEVLGVIS  445 (490)
Q Consensus       391 ~~~i~~i~~~i~~~~Gd~r~ai~ll~~a~~----~a~~~~~~~~~~~~It~~~v~~a~~  445 (490)
                      +++++.|+.   ...||+|.||+.|+.++.    ++...+     ...++..++..+..
T Consensus       303 ~~~l~~I~~---~s~GDiRsAIn~LQf~~~~~g~~a~~~~-----~~~vs~~hv~~a~~  353 (637)
T TIGR00602       303 KTSVELLCQ---GCSGDIRSAINSLQFSSSKSGSLPIKKR-----MSTKSDAHASKSKI  353 (637)
T ss_pred             HHHHHHHHH---hCCChHHHHHHHHHHHHhcCCccccccc-----cccccHHHhhhccc
Confidence            678888876   789999999999998743    222223     34566666555543

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

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

Probab=99.79  E-value=1.1e-17  Score=169.05  Aligned_cols=220  Identities=15%  Similarity=0.164  Sum_probs=153.6

Q ss_pred             CCCCChHHHHHHHHHHHHhhhcc---------CCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVNN---------ETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAAS  264 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~---------~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~  264 (490)
                      +++.|.+.++++|.+.+...+..         ..+++++|+||||||||++++++++++.    ..++.+.+..      
T Consensus       145 ~digGl~~~k~~l~~~v~~pl~~~~~~~~~Gl~~pkgvLL~GppGTGKT~LAkalA~~l~----~~fi~i~~s~------  214 (398)
T PTZ00454        145 SDIGGLDIQKQEIREAVELPLTCPELYEQIGIDPPRGVLLYGPPGTGKTMLAKAVAHHTT----ATFIRVVGSE------  214 (398)
T ss_pred             HHcCCHHHHHHHHHHHHHHHhcCHHHHHhcCCCCCceEEEECCCCCCHHHHHHHHHHhcC----CCEEEEehHH------
Confidence            67999999999999988644321         3578999999999999999999999864    4566665432      


Q ss_pred             HHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccC-----------HHHHHHhHhCCC--CCCCc
Q psy200          265 VYETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRK-----------QTILYTIFEWPS--IPGSK  331 (490)
Q Consensus       265 l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~-----------~~~L~~l~~~~~--~~~~~  331 (490)
                      +..        .+.+.+...+.+.|..+..  ..|+||||||+|.+....           +..+..++.+..  ....+
T Consensus       215 l~~--------k~~ge~~~~lr~lf~~A~~--~~P~ILfIDEID~i~~~r~~~~~~~d~~~~r~l~~LL~~ld~~~~~~~  284 (398)
T PTZ00454        215 FVQ--------KYLGEGPRMVRDVFRLARE--NAPSIIFIDEVDSIATKRFDAQTGADREVQRILLELLNQMDGFDQTTN  284 (398)
T ss_pred             HHH--------HhcchhHHHHHHHHHHHHh--cCCeEEEEECHhhhccccccccCCccHHHHHHHHHHHHHhhccCCCCC
Confidence            211        2233444455555554433  568999999999986431           234445543321  23457


Q ss_pred             EEEEEecCCCChhHhhhHHhhh--ccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhC-CH
Q psy200          332 LVLVGVANALDLTDRMLPRLQA--NVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSG-DI  408 (490)
Q Consensus       332 vilI~~tn~~~~~~~l~~~l~~--R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~G-d~  408 (490)
                      +++|++||+.   +.+++.+.+  ||.   ..|.|++++.++...|++..+...+..   .+..+..++.   ...| ..
T Consensus       285 v~VI~aTN~~---d~LDpAllR~GRfd---~~I~~~~P~~~~R~~Il~~~~~~~~l~---~dvd~~~la~---~t~g~sg  352 (398)
T PTZ00454        285 VKVIMATNRA---DTLDPALLRPGRLD---RKIEFPLPDRRQKRLIFQTITSKMNLS---EEVDLEDFVS---RPEKISA  352 (398)
T ss_pred             EEEEEecCCc---hhCCHHHcCCCccc---EEEEeCCcCHHHHHHHHHHHHhcCCCC---cccCHHHHHH---HcCCCCH
Confidence            8899999954   556666654  666   589999999999999999887665221   2233566665   2333 34


Q ss_pred             HHHHHHHHHHHHHHHhccccCCcccccCHHHHHHHHHHhccC
Q psy200          409 RKAIDITNHLIDLTYDNVKENGEVTGIGLKEVLGVISSVYCT  450 (490)
Q Consensus       409 r~ai~ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~~~~~~~  450 (490)
                      ..+.++|..|...|.+++     ...|+.+||.+|+..+...
T Consensus       353 aDI~~l~~eA~~~A~r~~-----~~~i~~~df~~A~~~v~~~  389 (398)
T PTZ00454        353 ADIAAICQEAGMQAVRKN-----RYVILPKDFEKGYKTVVRK  389 (398)
T ss_pred             HHHHHHHHHHHHHHHHcC-----CCccCHHHHHHHHHHHHhc
Confidence            555679999999999888     6789999999999997643

>CHL00195 ycf46 Ycf46; Provisional

Probab=99.79  E-value=1.1e-17  Score=172.54  Aligned_cols=223  Identities=16%  Similarity=0.156  Sum_probs=156.5

Q ss_pred             CCCCChHHHHHHHHHHHHhhh------ccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHV------NNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYE  267 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~------~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~  267 (490)
                      +++.|.+..++.+.+......      .-..++++||+||||||||++|++++++++    ..++.+++...        
T Consensus       228 ~dvgGl~~lK~~l~~~~~~~~~~~~~~gl~~pkGILL~GPpGTGKTllAkaiA~e~~----~~~~~l~~~~l--------  295 (489)
T CHL00195        228 SDIGGLDNLKDWLKKRSTSFSKQASNYGLPTPRGLLLVGIQGTGKSLTAKAIANDWQ----LPLLRLDVGKL--------  295 (489)
T ss_pred             HHhcCHHHHHHHHHHHHHHhhHHHHhcCCCCCceEEEECCCCCcHHHHHHHHHHHhC----CCEEEEEhHHh--------
Confidence            678898877776665432211      113568999999999999999999999975    67788876432        


Q ss_pred             HHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccC---------HHHHHHhHhCCCCCCCcEEEEEec
Q psy200          268 TIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRK---------QTILYTIFEWPSIPGSKLVLVGVA  338 (490)
Q Consensus       268 ~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~---------~~~L~~l~~~~~~~~~~vilI~~t  338 (490)
                            ...+.|.+...+.+.|..+..  ..|+||||||||.++...         ...+..++.|......+++||++|
T Consensus       296 ------~~~~vGese~~l~~~f~~A~~--~~P~IL~IDEID~~~~~~~~~~d~~~~~rvl~~lL~~l~~~~~~V~vIaTT  367 (489)
T CHL00195        296 ------FGGIVGESESRMRQMIRIAEA--LSPCILWIDEIDKAFSNSESKGDSGTTNRVLATFITWLSEKKSPVFVVATA  367 (489)
T ss_pred             ------cccccChHHHHHHHHHHHHHh--cCCcEEEehhhhhhhccccCCCCchHHHHHHHHHHHHHhcCCCceEEEEec
Confidence                  224556667777777665433  468999999999886531         123434444444456789999999


Q ss_pred             CCCChhHhhhHHhhh--ccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHHHHH
Q psy200          339 NALDLTDRMLPRLQA--NVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITN  416 (490)
Q Consensus       339 n~~~~~~~l~~~l~~--R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll~  416 (490)
                      |..   +.+++.+.+  ||.   ..+.++.++.++..+|++.++.+.. .....+..++.+++...+++|  ..+-++|.
T Consensus       368 N~~---~~Ld~allR~GRFD---~~i~v~lP~~~eR~~Il~~~l~~~~-~~~~~~~dl~~La~~T~GfSG--AdI~~lv~  438 (489)
T CHL00195        368 NNI---DLLPLEILRKGRFD---EIFFLDLPSLEEREKIFKIHLQKFR-PKSWKKYDIKKLSKLSNKFSG--AEIEQSII  438 (489)
T ss_pred             CCh---hhCCHHHhCCCcCC---eEEEeCCcCHHHHHHHHHHHHhhcC-CCcccccCHHHHHhhcCCCCH--HHHHHHHH
Confidence            954   455666654  776   5899999999999999999988752 122345557778774433333  33445778


Q ss_pred             HHHHHHHhccccCCcccccCHHHHHHHHHHhccCc
Q psy200          417 HLIDLTYDNVKENGEVTGIGLKEVLGVISSVYCTS  451 (490)
Q Consensus       417 ~a~~~a~~~~~~~~~~~~It~~~v~~a~~~~~~~~  451 (490)
                      .|...|..++      ..++.+|+..|+..+.+..
T Consensus       439 eA~~~A~~~~------~~lt~~dl~~a~~~~~Pls  467 (489)
T CHL00195        439 EAMYIAFYEK------REFTTDDILLALKQFIPLA  467 (489)
T ss_pred             HHHHHHHHcC------CCcCHHHHHHHHHhcCCCc
Confidence            8888777666      4699999999999988753

>PRK12402 replication factor C small subunit 2; Reviewed

Probab=99.78  E-value=8.7e-18  Score=168.59  Aligned_cols=236  Identities=15%  Similarity=0.200  Sum_probs=157.0

Q ss_pred             cCCCCcchHHHhhcCCCCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcC-CceEEEEec
Q psy200          178 LFSEDKPKVEEKAKDSCELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKD-AFKTIYINC  256 (490)
Q Consensus       178 ~~~~~~~~~~~~~l~~~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~-~~~~~~v~~  256 (490)
                      .+|.++|+|...    ++|+|++..++.|..++..    +..++++|+||+|+|||++|+++++++.... ...+++++|
T Consensus         3 ~~w~~ky~P~~~----~~~~g~~~~~~~L~~~~~~----~~~~~lll~Gp~GtGKT~la~~~~~~l~~~~~~~~~~~i~~   74 (337)
T PRK12402          3 PLWTEKYRPALL----EDILGQDEVVERLSRAVDS----PNLPHLLVQGPPGSGKTAAVRALARELYGDPWENNFTEFNV   74 (337)
T ss_pred             CchHHhhCCCcH----HHhcCCHHHHHHHHHHHhC----CCCceEEEECCCCCCHHHHHHHHHHHhcCcccccceEEech
Confidence            379999999988    8999999999998888863    4445799999999999999999999885332 235677777


Q ss_pred             cCCCCH-HHHHHH---HHHHhcCC-CCCC-cHHHHHHHHHHHHhc---CCCeEEEEEecCccccccCHHHHHHhHhCCCC
Q psy200          257 NSVRNA-ASVYET---IVNELKLK-PGGK-SERHQLGAILKYFDT---KHKSILLILDEIDALESRKQTILYTIFEWPSI  327 (490)
Q Consensus       257 ~~~~~~-~~l~~~---i~~~l~~~-~~~~-s~~~~~~~l~~~l~~---~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~  327 (490)
                      ...... ...+..   +...+... ..+. ....+.+.+......   .+...+|||||+|.+....+..|..+++... 
T Consensus        75 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vlilDe~~~l~~~~~~~L~~~le~~~-  153 (337)
T PRK12402         75 ADFFDQGKKYLVEDPRFAHFLGTDKRIRSSKIDNFKHVLKEYASYRPLSADYKTILLDNAEALREDAQQALRRIMEQYS-  153 (337)
T ss_pred             hhhhhcchhhhhcCcchhhhhhhhhhhccchHHHHHHHHHHHHhcCCCCCCCcEEEEeCcccCCHHHHHHHHHHHHhcc-
Confidence            553210 000000   00000000 0001 112222222222111   1334599999999998777777877776432 


Q ss_pred             CCCcEEEEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCC
Q psy200          328 PGSKLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGD  407 (490)
Q Consensus       328 ~~~~vilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd  407 (490)
                      ....++  .+++.   ...+.+.+++|+.    .+.|.|++.+++..++...+...+  ..+++++++.+++   ...||
T Consensus       154 ~~~~~I--l~~~~---~~~~~~~L~sr~~----~v~~~~~~~~~~~~~l~~~~~~~~--~~~~~~al~~l~~---~~~gd  219 (337)
T PRK12402        154 RTCRFI--IATRQ---PSKLIPPIRSRCL----PLFFRAPTDDELVDVLESIAEAEG--VDYDDDGLELIAY---YAGGD  219 (337)
T ss_pred             CCCeEE--EEeCC---hhhCchhhcCCce----EEEecCCCHHHHHHHHHHHHHHcC--CCCCHHHHHHHHH---HcCCC
Confidence            223333  33432   2345677888874    799999999999999999988763  4589999999998   66899


Q ss_pred             HHHHHHHHHHHHHHHHhccccCCcccccCHHHHHHHHHH
Q psy200          408 IRKAIDITNHLIDLTYDNVKENGEVTGIGLKEVLGVISS  446 (490)
Q Consensus       408 ~r~ai~ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~~~  446 (490)
                      +|.+++.++.+.    ...      ..|+.+++.+++..
T Consensus       220 lr~l~~~l~~~~----~~~------~~It~~~v~~~~~~  248 (337)
T PRK12402        220 LRKAILTLQTAA----LAA------GEITMEAAYEALGD  248 (337)
T ss_pred             HHHHHHHHHHHH----HcC------CCCCHHHHHHHhCC
Confidence            999999887654    112      36888888877654

>CHL00176 ftsH cell division protein; Validated

Probab=99.78  E-value=8e-18  Score=178.96  Aligned_cols=219  Identities=19%  Similarity=0.226  Sum_probs=156.5

Q ss_pred             CCCCChHHHHHHHHHHHHhhhc--------cCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVN--------NETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASV  265 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~--------~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l  265 (490)
                      ++++|.++..+++.+.+.....        ...+++++|+||||||||++|++++.+++    .++++++|..+.     
T Consensus       183 ~dv~G~~~~k~~l~eiv~~lk~~~~~~~~g~~~p~gVLL~GPpGTGKT~LAralA~e~~----~p~i~is~s~f~-----  253 (638)
T CHL00176        183 RDIAGIEEAKEEFEEVVSFLKKPERFTAVGAKIPKGVLLVGPPGTGKTLLAKAIAGEAE----VPFFSISGSEFV-----  253 (638)
T ss_pred             HhccChHHHHHHHHHHHHHHhCHHHHhhccCCCCceEEEECCCCCCHHHHHHHHHHHhC----CCeeeccHHHHH-----
Confidence            7899999888888776643211        12467899999999999999999999864    677888765531     


Q ss_pred             HHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCcccccc-----------CHHHHHHhHhCC--CCCCCcE
Q psy200          266 YETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESR-----------KQTILYTIFEWP--SIPGSKL  332 (490)
Q Consensus       266 ~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~-----------~~~~L~~l~~~~--~~~~~~v  332 (490)
                       .        .+.+.....+...|..+..  ..|+||||||+|.+...           .+..+..++...  ......+
T Consensus       254 -~--------~~~g~~~~~vr~lF~~A~~--~~P~ILfIDEID~l~~~r~~~~~~~~~e~~~~L~~LL~~~dg~~~~~~V  322 (638)
T CHL00176        254 -E--------MFVGVGAARVRDLFKKAKE--NSPCIVFIDEIDAVGRQRGAGIGGGNDEREQTLNQLLTEMDGFKGNKGV  322 (638)
T ss_pred             -H--------HhhhhhHHHHHHHHHHHhc--CCCcEEEEecchhhhhcccCCCCCCcHHHHHHHHHHHhhhccccCCCCe
Confidence             1        1112334455666665543  56899999999999532           123455554322  2245679


Q ss_pred             EEEEecCCCChhHhhhHHhhh--ccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhC-CHH
Q psy200          333 VLVGVANALDLTDRMLPRLQA--NVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSG-DIR  409 (490)
Q Consensus       333 ilI~~tn~~~~~~~l~~~l~~--R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~G-d~r  409 (490)
                      +||++||..   +.+++.+.+  ||+   ..+.|.+|+.++..+||+.++...   ....+..+..+++   .+.| +.+
T Consensus       323 iVIaaTN~~---~~LD~ALlRpGRFd---~~I~v~lPd~~~R~~IL~~~l~~~---~~~~d~~l~~lA~---~t~G~sga  390 (638)
T CHL00176        323 IVIAATNRV---DILDAALLRPGRFD---RQITVSLPDREGRLDILKVHARNK---KLSPDVSLELIAR---RTPGFSGA  390 (638)
T ss_pred             eEEEecCch---HhhhhhhhccccCc---eEEEECCCCHHHHHHHHHHHHhhc---ccchhHHHHHHHh---cCCCCCHH
Confidence            999999964   445556654  565   489999999999999999988764   2344566777776   5566 566


Q ss_pred             HHHHHHHHHHHHHHhccccCCcccccCHHHHHHHHHHhcc
Q psy200          410 KAIDITNHLIDLTYDNVKENGEVTGIGLKEVLGVISSVYC  449 (490)
Q Consensus       410 ~ai~ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~~~~~~  449 (490)
                      .+-+++..|+..+.+.+     ...|+.++|..|+..+..
T Consensus       391 DL~~lvneAal~a~r~~-----~~~It~~dl~~Ai~rv~~  425 (638)
T CHL00176        391 DLANLLNEAAILTARRK-----KATITMKEIDTAIDRVIA  425 (638)
T ss_pred             HHHHHHHHHHHHHHHhC-----CCCcCHHHHHHHHHHHHh
Confidence            77788999988887777     568999999999998753

>PRK05563 DNA polymerase III subunits gamma and tau; Validated

Probab=99.78  E-value=1.2e-17  Score=176.22  Aligned_cols=232  Identities=17%  Similarity=0.246  Sum_probs=158.5

Q ss_pred             CCCcchHHHhhcCCCCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCC
Q psy200          180 SEDKPKVEEKAKDSCELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSV  259 (490)
Q Consensus       180 ~~~~~~~~~~~l~~~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~  259 (490)
                      ++.+|+|...    ++++|++..++.|..++..   +..++.+|++||+|+|||++|+.+++.+.+.....  ...|..+
T Consensus         6 l~~k~rP~~f----~~viGq~~v~~~L~~~i~~---~~~~hayLf~Gp~GtGKTt~Ak~lAkal~c~~~~~--~~pC~~C   76 (559)
T PRK05563          6 LYRKWRPQTF----EDVVGQEHITKTLKNAIKQ---GKISHAYLFSGPRGTGKTSAAKIFAKAVNCLNPPD--GEPCNEC   76 (559)
T ss_pred             HHHHhCCCcH----HhccCcHHHHHHHHHHHHc---CCCCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCC--CCCCCcc
Confidence            4567777777    9999999999999888864   34456688999999999999999999875322110  0123332


Q ss_pred             CCHHHHHHHHHHHh-cC-CCCCCcHHHHHHHHHHHHh--cCCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEE
Q psy200          260 RNAASVYETIVNEL-KL-KPGGKSERHQLGAILKYFD--TKHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLV  335 (490)
Q Consensus       260 ~~~~~l~~~i~~~l-~~-~~~~~s~~~~~~~l~~~l~--~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI  335 (490)
                      .+...+.....-++ .. .....+.+++++.+.....  ..++..|+||||+|.|.....+.|...++.   ....++||
T Consensus        77 ~~C~~i~~g~~~dv~eidaas~~~vd~ir~i~~~v~~~p~~~~~kViIIDE~~~Lt~~a~naLLKtLEe---pp~~~ifI  153 (559)
T PRK05563         77 EICKAITNGSLMDVIEIDAASNNGVDEIRDIRDKVKYAPSEAKYKVYIIDEVHMLSTGAFNALLKTLEE---PPAHVIFI  153 (559)
T ss_pred             HHHHHHhcCCCCCeEEeeccccCCHHHHHHHHHHHhhCcccCCeEEEEEECcccCCHHHHHHHHHHhcC---CCCCeEEE
Confidence            22111111000000 00 0111334555554444321  135577999999999987777777776653   34567777


Q ss_pred             EecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHHHH
Q psy200          336 GVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDIT  415 (490)
Q Consensus       336 ~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll  415 (490)
                      .+|+.   .+.+.+.+++||.    .+.|.+++.+++..++...+...  ...+++++++.|++   ...|++|.++++|
T Consensus       154 latt~---~~ki~~tI~SRc~----~~~f~~~~~~ei~~~L~~i~~~e--gi~i~~~al~~ia~---~s~G~~R~al~~L  221 (559)
T PRK05563        154 LATTE---PHKIPATILSRCQ----RFDFKRISVEDIVERLKYILDKE--GIEYEDEALRLIAR---AAEGGMRDALSIL  221 (559)
T ss_pred             EEeCC---hhhCcHHHHhHhe----EEecCCCCHHHHHHHHHHHHHHc--CCCCCHHHHHHHHH---HcCCCHHHHHHHH
Confidence            66652   4677888999996    79999999999999999999876  35689999999998   6789999999999


Q ss_pred             HHHHHHHHhccccCCcccccCHHHHHHHH
Q psy200          416 NHLIDLTYDNVKENGEVTGIGLKEVLGVI  444 (490)
Q Consensus       416 ~~a~~~a~~~~~~~~~~~~It~~~v~~a~  444 (490)
                      ++++...  .+       .|+.++|..++
T Consensus       222 dq~~~~~--~~-------~It~~~V~~vl  241 (559)
T PRK05563        222 DQAISFG--DG-------KVTYEDALEVT  241 (559)
T ss_pred             HHHHHhc--cC-------CCCHHHHHHHh
Confidence            9887653  22       46666665543

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

Probab=99.78  E-value=1.1e-17  Score=170.20  Aligned_cols=220  Identities=13%  Similarity=0.154  Sum_probs=151.4

Q ss_pred             CCCCChHHHHHHHHHHHHhhhcc---------CCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVNN---------ETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAAS  264 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~---------~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~  264 (490)
                      .++.|.++++++|.+++...+..         ..+.+++|+||||||||++|+++++++.    ..++.+.+..+.    
T Consensus       183 ~DIgGl~~qi~~l~e~v~lpl~~p~~~~~~gi~~p~gVLL~GPPGTGKT~LAraIA~el~----~~fi~V~~seL~----  254 (438)
T PTZ00361        183 ADIGGLEQQIQEIKEAVELPLTHPELYDDIGIKPPKGVILYGPPGTGKTLLAKAVANETS----ATFLRVVGSELI----  254 (438)
T ss_pred             HHhcCHHHHHHHHHHHHHhhhhCHHHHHhcCCCCCcEEEEECCCCCCHHHHHHHHHHhhC----CCEEEEecchhh----
Confidence            67899999999999988644322         3567899999999999999999999875    455666544321    


Q ss_pred             HHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccC-----------HHHHHHhHhCC--CCCCCc
Q psy200          265 VYETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRK-----------QTILYTIFEWP--SIPGSK  331 (490)
Q Consensus       265 l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~-----------~~~L~~l~~~~--~~~~~~  331 (490)
                        .        .+.|.....+...|..+..  +.++||||||||.+....           +..+..++...  ......
T Consensus       255 --~--------k~~Ge~~~~vr~lF~~A~~--~~P~ILfIDEID~l~~kR~~~~sgg~~e~qr~ll~LL~~Ldg~~~~~~  322 (438)
T PTZ00361        255 --Q--------KYLGDGPKLVRELFRVAEE--NAPSIVFIDEIDAIGTKRYDATSGGEKEIQRTMLELLNQLDGFDSRGD  322 (438)
T ss_pred             --h--------hhcchHHHHHHHHHHHHHh--CCCcEEeHHHHHHHhccCCCCCCcccHHHHHHHHHHHHHHhhhcccCC
Confidence              1        2233444445555554433  568999999999986431           23344444321  123457


Q ss_pred             EEEEEecCCCChhHhhhHHhhh--ccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHH
Q psy200          332 LVLVGVANALDLTDRMLPRLQA--NVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIR  409 (490)
Q Consensus       332 vilI~~tn~~~~~~~l~~~l~~--R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r  409 (490)
                      +.||++||..   +.+++.+.+  ||.   ..|.|++|+.++..+||..++......   .+..++.++....+.+  ..
T Consensus       323 V~VI~ATNr~---d~LDpaLlRpGRfd---~~I~~~~Pd~~~R~~Il~~~~~k~~l~---~dvdl~~la~~t~g~s--gA  391 (438)
T PTZ00361        323 VKVIMATNRI---ESLDPALIRPGRID---RKIEFPNPDEKTKRRIFEIHTSKMTLA---EDVDLEEFIMAKDELS--GA  391 (438)
T ss_pred             eEEEEecCCh---HHhhHHhccCCeeE---EEEEeCCCCHHHHHHHHHHHHhcCCCC---cCcCHHHHHHhcCCCC--HH
Confidence            8899999954   455666653  666   589999999999999999887665221   2223455554222233  33


Q ss_pred             HHHHHHHHHHHHHHhccccCCcccccCHHHHHHHHHHhcc
Q psy200          410 KAIDITNHLIDLTYDNVKENGEVTGIGLKEVLGVISSVYC  449 (490)
Q Consensus       410 ~ai~ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~~~~~~  449 (490)
                      .+-.+|..|...|.+++     ...|+.+||..|+..+..
T Consensus       392 dI~~i~~eA~~~Alr~~-----r~~Vt~~D~~~A~~~v~~  426 (438)
T PTZ00361        392 DIKAICTEAGLLALRER-----RMKVTQADFRKAKEKVLY  426 (438)
T ss_pred             HHHHHHHHHHHHHHHhc-----CCccCHHHHHHHHHHHHh
Confidence            34468999999999988     678999999999999754

>PRK14963 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.78  E-value=1.4e-17  Score=173.05  Aligned_cols=228  Identities=19%  Similarity=0.241  Sum_probs=153.0

Q ss_pred             CcchHHHhhcCCCCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCC
Q psy200          182 DKPKVEEKAKDSCELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRN  261 (490)
Q Consensus       182 ~~~~~~~~~l~~~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~  261 (490)
                      ++|+|...    ++++|+++.++.|..++..   +..++.++|+||+|+||||+|+++++.+.......   ..|..+.+
T Consensus         6 ~KyRP~~~----~dvvGq~~v~~~L~~~i~~---~~l~ha~Lf~GppGtGKTTlA~~lA~~l~c~~~~~---~~cg~C~s   75 (504)
T PRK14963          6 QRARPITF----DEVVGQEHVKEVLLAALRQ---GRLGHAYLFSGPRGVGKTTTARLIAMAVNCSGEDP---KPCGECES   75 (504)
T ss_pred             HhhCCCCH----HHhcChHHHHHHHHHHHHc---CCCCeEEEEECCCCCCHHHHHHHHHHHHhccCCCC---CCCCcChh
Confidence            57777777    8999999999999888874   23445569999999999999999999986322111   12222221


Q ss_pred             HHHHHHHH---HHHhcCCCCCCcHHHHHHHHHHHHh--cCCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEEE
Q psy200          262 AASVYETI---VNELKLKPGGKSERHQLGAILKYFD--TKHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVG  336 (490)
Q Consensus       262 ~~~l~~~i---~~~l~~~~~~~s~~~~~~~l~~~l~--~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI~  336 (490)
                      ...+....   +..++.. ...+.+.+++.......  ..+++.||||||+|.+....++.|...++.   ....+++|.
T Consensus        76 c~~i~~~~h~dv~el~~~-~~~~vd~iR~l~~~~~~~p~~~~~kVVIIDEad~ls~~a~naLLk~LEe---p~~~t~~Il  151 (504)
T PRK14963         76 CLAVRRGAHPDVLEIDAA-SNNSVEDVRDLREKVLLAPLRGGRKVYILDEAHMMSKSAFNALLKTLEE---PPEHVIFIL  151 (504)
T ss_pred             hHHHhcCCCCceEEeccc-ccCCHHHHHHHHHHHhhccccCCCeEEEEECccccCHHHHHHHHHHHHh---CCCCEEEEE
Confidence            11111000   0001111 11234444443222111  124566999999999977667777666653   234566666


Q ss_pred             ecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHHHHH
Q psy200          337 VANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITN  416 (490)
Q Consensus       337 ~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll~  416 (490)
                      +++.   ...+.+.+.+||.    .+.|.+++.+++..+|.+.+..++  ..+++++++.|++   ...||+|.++++|+
T Consensus       152 ~t~~---~~kl~~~I~SRc~----~~~f~~ls~~el~~~L~~i~~~eg--i~i~~~Al~~ia~---~s~GdlR~aln~Le  219 (504)
T PRK14963        152 ATTE---PEKMPPTILSRTQ----HFRFRRLTEEEIAGKLRRLLEAEG--REAEPEALQLVAR---LADGAMRDAESLLE  219 (504)
T ss_pred             EcCC---hhhCChHHhcceE----EEEecCCCHHHHHHHHHHHHHHcC--CCCCHHHHHHHHH---HcCCCHHHHHHHHH
Confidence            6653   3566778889985    899999999999999999998873  5679999999998   77899999999999


Q ss_pred             HHHHHHHhccccCCcccccCHHHHHHHHH
Q psy200          417 HLIDLTYDNVKENGEVTGIGLKEVLGVIS  445 (490)
Q Consensus       417 ~a~~~a~~~~~~~~~~~~It~~~v~~a~~  445 (490)
                      .++..    +      ..|+.++|.+++.
T Consensus       220 kl~~~----~------~~It~~~V~~~l~  238 (504)
T PRK14963        220 RLLAL----G------TPVTRKQVEEALG  238 (504)
T ss_pred             HHHhc----C------CCCCHHHHHHHHC
Confidence            88542    2      2577777666543

>TIGR02881 spore_V_K stage V sporulation protein K

Probab=99.78  E-value=1.7e-17  Score=160.10  Aligned_cols=208  Identities=17%  Similarity=0.142  Sum_probs=138.9

Q ss_pred             CCCCChHHHHHHHHHHHHhhhc-----------cCCCCeEEEECCCCCcHHHHHHHHHHHhhhc---CCceEEEEeccCC
Q psy200          194 CELPGREVQLEGIRQFLLGHVN-----------NETSGSMYISGPPGTGKSASLNLLVSRAEIK---DAFKTIYINCNSV  259 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~-----------~~~~~~ill~GppGtGKTtla~~l~~~l~~~---~~~~~~~v~~~~~  259 (490)
                      ++++|.++.++.|.+++.....           .....+++|+||||||||++|+.+++.+...   ....+++++|...
T Consensus         6 ~~~~Gl~~vk~~i~~~~~~~~~~~~~~~~g~~~~~~~~~vll~GppGtGKTtlA~~ia~~l~~~~~~~~~~~v~~~~~~l   85 (261)
T TIGR02881         6 SRMVGLDEVKALIKEIYAWIQINEKRKEEGLKTSKQVLHMIFKGNPGTGKTTVARILGKLFKEMNVLSKGHLIEVERADL   85 (261)
T ss_pred             HHhcChHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCcceEEEEcCCCCCHHHHHHHHHHHHHhcCcccCCceEEecHHHh
Confidence            5699999998888766543211           1244689999999999999999999886421   1224556655432


Q ss_pred             CCHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccC-----HHHHHHhHhCCCCCCCcEEE
Q psy200          260 RNAASVYETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRK-----QTILYTIFEWPSIPGSKLVL  334 (490)
Q Consensus       260 ~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~-----~~~L~~l~~~~~~~~~~vil  334 (490)
                            .        ..+.+.......+.|..+.     ..||||||+|.|....     .+.+..++.........+++
T Consensus        86 ------~--------~~~~g~~~~~~~~~~~~a~-----~~VL~IDE~~~L~~~~~~~~~~~~i~~Ll~~~e~~~~~~~v  146 (261)
T TIGR02881        86 ------V--------GEYIGHTAQKTREVIKKAL-----GGVLFIDEAYSLARGGEKDFGKEAIDTLVKGMEDNRNEFVL  146 (261)
T ss_pred             ------h--------hhhccchHHHHHHHHHhcc-----CCEEEEechhhhccCCccchHHHHHHHHHHHHhccCCCEEE
Confidence                  1        1223334444444444332     2499999999987421     23334443332223455666


Q ss_pred             EEecCCC--ChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHH-------hh
Q psy200          335 VGVANAL--DLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAA-------VS  405 (490)
Q Consensus       335 I~~tn~~--~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~-------~~  405 (490)
                      |+++...  +....+.+.+++||.   ..+.|++|+.+++.+|+++.+...  ...+++++++.+++.+..       ..
T Consensus       147 ila~~~~~~~~~~~~~p~L~sRf~---~~i~f~~~~~~el~~Il~~~~~~~--~~~l~~~a~~~l~~~~~~~~~~~~~~~  221 (261)
T TIGR02881       147 ILAGYSDEMDYFLSLNPGLRSRFP---ISIDFPDYTVEELMEIAERMVKER--EYKLTEEAKWKLREHLYKVDQLSSREF  221 (261)
T ss_pred             EecCCcchhHHHHhcChHHHhccc---eEEEECCCCHHHHHHHHHHHHHHc--CCccCHHHHHHHHHHHHHHHhccCCCC
Confidence            6655432  233445689999996   379999999999999999998765  456899999998765433       35


Q ss_pred             CCHHHHHHHHHHHHHHHHhc
Q psy200          406 GDIRKAIDITNHLIDLTYDN  425 (490)
Q Consensus       406 Gd~r~ai~ll~~a~~~a~~~  425 (490)
                      ||.|.+.++++.|+.....+
T Consensus       222 gn~R~~~n~~e~a~~~~~~r  241 (261)
T TIGR02881       222 SNARYVRNIIEKAIRRQAVR  241 (261)
T ss_pred             chHHHHHHHHHHHHHHHHHH
Confidence            89999999999988665443

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.

>PRK06893 DNA replication initiation factor; Validated

Probab=99.78  E-value=1.8e-17  Score=156.53  Aligned_cols=190  Identities=16%  Similarity=0.216  Sum_probs=131.6

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcC
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFDTK  296 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~  296 (490)
                      ...+.++|+||+|+|||+|++++++++... +..+.|+++...   ..+                ...   .+.. +   
T Consensus        37 ~~~~~l~l~G~~G~GKThL~~ai~~~~~~~-~~~~~y~~~~~~---~~~----------------~~~---~~~~-~---   89 (229)
T PRK06893         37 LQQPFFYIWGGKSSGKSHLLKAVSNHYLLN-QRTAIYIPLSKS---QYF----------------SPA---VLEN-L---   89 (229)
T ss_pred             cCCCeEEEECCCCCCHHHHHHHHHHHHHHc-CCCeEEeeHHHh---hhh----------------hHH---HHhh-c---
Confidence            344678999999999999999999987532 335566654211   000                001   1111 1   


Q ss_pred             CCeEEEEEecCcccccc--CHHHHHHhHhCCCCCCCcEEEEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHH
Q psy200          297 HKSILLILDEIDALESR--KQTILYTIFEWPSIPGSKLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILE  374 (490)
Q Consensus       297 ~~~~vI~IDEid~l~~~--~~~~L~~l~~~~~~~~~~vilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~  374 (490)
                      .+..+|+|||+|.+...  .+..|+.+++.....+..+++++...........++.+++|+..+ ..+.+.+++.+++++
T Consensus        90 ~~~dlLilDDi~~~~~~~~~~~~l~~l~n~~~~~~~~illits~~~p~~l~~~~~~L~sRl~~g-~~~~l~~pd~e~~~~  168 (229)
T PRK06893         90 EQQDLVCLDDLQAVIGNEEWELAIFDLFNRIKEQGKTLLLISADCSPHALSIKLPDLASRLTWG-EIYQLNDLTDEQKII  168 (229)
T ss_pred             ccCCEEEEeChhhhcCChHHHHHHHHHHHHHHHcCCcEEEEeCCCChHHccccchhHHHHHhcC-CeeeCCCCCHHHHHH
Confidence            23459999999998644  345677777654434445555555443333333457889988654 368999999999999


Q ss_pred             HHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHhccccCCcccccCHHHHHHHHH
Q psy200          375 IISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITNHLIDLTYDNVKENGEVTGIGLKEVLGVIS  445 (490)
Q Consensus       375 il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~~  445 (490)
                      ++++.+...  ...+++++++.|++   ...||+|.+++++.+....+..++      ..||.+.+.+++.
T Consensus       169 iL~~~a~~~--~l~l~~~v~~~L~~---~~~~d~r~l~~~l~~l~~~~~~~~------~~it~~~v~~~L~  228 (229)
T PRK06893        169 VLQRNAYQR--GIELSDEVANFLLK---RLDRDMHTLFDALDLLDKASLQAQ------RKLTIPFVKEILG  228 (229)
T ss_pred             HHHHHHHHc--CCCCCHHHHHHHHH---hccCCHHHHHHHHHHHHHHHHhcC------CCCCHHHHHHHhc
Confidence            999988765  46789999999998   788999999999988654334333      4799999988763

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

Probab=99.78  E-value=1.6e-16  Score=154.27  Aligned_cols=217  Identities=19%  Similarity=0.292  Sum_probs=149.7

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHH---h
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYF---D  294 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l---~  294 (490)
                      ..+.++|+|++|+||||+++.+++.+.. ..+.+.++ +....+..+++..|+..++....+.........+...+   .
T Consensus        42 ~~~~~~l~G~~G~GKTtl~~~l~~~l~~-~~~~~~~~-~~~~~~~~~~l~~i~~~lG~~~~~~~~~~~~~~l~~~l~~~~  119 (269)
T TIGR03015        42 REGFILITGEVGAGKTTLIRNLLKRLDQ-ERVVAAKL-VNTRVDAEDLLRMVAADFGLETEGRDKAALLRELEDFLIEQF  119 (269)
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHHhcCC-CCeEEeee-eCCCCCHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHHHHHHH
Confidence            4567899999999999999999988752 12222232 12223677888999998887655444444444433322   1


Q ss_pred             cCCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEEEecCCCChhHhh----hHHhhhccCCCCeeEEeCCCCHH
Q psy200          295 TKHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVANALDLTDRM----LPRLQANVTLQPTLMNFAPYSRE  370 (490)
Q Consensus       295 ~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI~~tn~~~~~~~l----~~~l~~R~~~~~~~i~~~pls~~  370 (490)
                      ..+++.+|+|||+|.+.....+.|..+.+........+.++.+.. .++.+.+    ...+.+|+.   ..+.+++++.+
T Consensus       120 ~~~~~~vliiDe~~~l~~~~~~~l~~l~~~~~~~~~~~~vvl~g~-~~~~~~l~~~~~~~l~~r~~---~~~~l~~l~~~  195 (269)
T TIGR03015       120 AAGKRALLVVDEAQNLTPELLEELRMLSNFQTDNAKLLQIFLVGQ-PEFRETLQSPQLQQLRQRII---ASCHLGPLDRE  195 (269)
T ss_pred             hCCCCeEEEEECcccCCHHHHHHHHHHhCcccCCCCeEEEEEcCC-HHHHHHHcCchhHHHHhhee---eeeeCCCCCHH
Confidence            236678999999999976656666655443322222232232222 1233332    235667765   47999999999


Q ss_pred             HHHHHHHHHHhccCC--CCCCCHHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHhccccCCcccccCHHHHHHHHHHhc
Q psy200          371 QILEIISQKLKQTDK--FNMFNASALQLLAGKVAAVSGDIRKAIDITNHLIDLTYDNVKENGEVTGIGLKEVLGVISSVY  448 (490)
Q Consensus       371 e~~~il~~~l~~~~~--~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~~~~~  448 (490)
                      |+.+++.+++...+.  ...+++++++.|++   .+.|+++.+..++..++..|..++     ...|+.++|..++.++.
T Consensus       196 e~~~~l~~~l~~~g~~~~~~~~~~~~~~i~~---~s~G~p~~i~~l~~~~~~~a~~~~-----~~~i~~~~v~~~~~~~~  267 (269)
T TIGR03015       196 ETREYIEHRLERAGNRDAPVFSEGAFDAIHR---FSRGIPRLINILCDRLLLSAFLEE-----KREIGGEEVREVIAEID  267 (269)
T ss_pred             HHHHHHHHHHHHcCCCCCCCcCHHHHHHHHH---HcCCcccHHHHHHHHHHHHHHHcC-----CCCCCHHHHHHHHHHhh
Confidence            999999999876532  24589999999997   667788887779999999988888     67899999999998764

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.

>PRK14969 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.77  E-value=5.1e-18  Score=177.96  Aligned_cols=232  Identities=16%  Similarity=0.233  Sum_probs=157.6

Q ss_pred             CCcchHHHhhcCCCCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCC
Q psy200          181 EDKPKVEEKAKDSCELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVR  260 (490)
Q Consensus       181 ~~~~~~~~~~l~~~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~  260 (490)
                      ..+|+|...    ++++|++..++.|..++..   +..++.++|+||+|+||||+|+.+++.+......  ..-.|..+.
T Consensus         7 ~~k~rP~~f----~divGq~~v~~~L~~~i~~---~~~~ha~Lf~Gp~G~GKTt~A~~lAk~l~c~~~~--~~~pcg~C~   77 (527)
T PRK14969          7 ARKWRPKSF----SELVGQEHVVRALTNALEQ---QRLHHAYLFTGTRGVGKTTLARILAKSLNCETGV--TATPCGVCS   77 (527)
T ss_pred             HHHhCCCcH----HHhcCcHHHHHHHHHHHHc---CCCCEEEEEECCCCCCHHHHHHHHHHHhcCCCCC--CCCCCCCCH
Confidence            346666666    8999999999988888863   2344567899999999999999999998632211  011233221


Q ss_pred             CHHHHHHHHHHHh-cCC-CCCCcHHHHHHHHHHHHhc--CCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEEE
Q psy200          261 NAASVYETIVNEL-KLK-PGGKSERHQLGAILKYFDT--KHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVG  336 (490)
Q Consensus       261 ~~~~l~~~i~~~l-~~~-~~~~s~~~~~~~l~~~l~~--~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI~  336 (490)
                      ....+-..-+-++ ... ......+.+++.+..+...  .++..|+||||+|.|....++.|...++.   ....++||+
T Consensus        78 ~C~~i~~~~~~d~~ei~~~~~~~vd~ir~l~~~~~~~p~~~~~kVvIIDEad~ls~~a~naLLK~LEe---pp~~~~fIL  154 (527)
T PRK14969         78 ACLEIDSGRFVDLIEVDAASNTQVDAMRELLDNAQYAPTRGRFKVYIIDEVHMLSKSAFNAMLKTLEE---PPEHVKFIL  154 (527)
T ss_pred             HHHHHhcCCCCceeEeeccccCCHHHHHHHHHHHhhCcccCCceEEEEcCcccCCHHHHHHHHHHHhC---CCCCEEEEE
Confidence            1111110000000 000 1123455555555443221  25567999999999988778888877764   334566666


Q ss_pred             ecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHHHHH
Q psy200          337 VANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITN  416 (490)
Q Consensus       337 ~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll~  416 (490)
                      +|+.   ...+...+++||.    .+.|.+++.+++.+.+.+.+..++  ..+++++++.|++   ...|++|.++++++
T Consensus       155 ~t~d---~~kil~tI~SRc~----~~~f~~l~~~~i~~~L~~il~~eg--i~~~~~al~~la~---~s~Gslr~al~lld  222 (527)
T PRK14969        155 ATTD---PQKIPVTVLSRCL----QFNLKQMPPPLIVSHLQHILEQEN--IPFDATALQLLAR---AAAGSMRDALSLLD  222 (527)
T ss_pred             EeCC---hhhCchhHHHHHH----HHhcCCCCHHHHHHHHHHHHHHcC--CCCCHHHHHHHHH---HcCCCHHHHHHHHH
Confidence            6653   3456667899995    799999999999999999998763  5689999999997   67899999999999


Q ss_pred             HHHHHHHhccccCCcccccCHHHHHHHHH
Q psy200          417 HLIDLTYDNVKENGEVTGIGLKEVLGVIS  445 (490)
Q Consensus       417 ~a~~~a~~~~~~~~~~~~It~~~v~~a~~  445 (490)
                      +++..  ..       ..|+.++|...+.
T Consensus       223 qai~~--~~-------~~I~~~~v~~~~~  242 (527)
T PRK14969        223 QAIAY--GG-------GTVNESEVRAMLG  242 (527)
T ss_pred             HHHHh--cC-------CCcCHHHHHHHHC
Confidence            98754  22       3577777776654

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

Probab=99.77  E-value=2e-17  Score=180.99  Aligned_cols=235  Identities=19%  Similarity=0.190  Sum_probs=165.5

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhc------CCceEEEEeccCCCCHHHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIK------DAFKTIYINCNSVRNAASVYE  267 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~------~~~~~~~v~~~~~~~~~~l~~  267 (490)
                      ++++||+++++.+.+.|..    ....+++|+||||||||++++.+++.+...      .+..++.+++.....      
T Consensus       182 ~~~igr~~ei~~~~~~L~~----~~~~n~lL~G~pG~GKT~l~~~la~~~~~~~~p~~l~~~~~~~~~~~~l~a------  251 (731)
T TIGR02639       182 DPLIGREDELERTIQVLCR----RKKNNPLLVGEPGVGKTAIAEGLALRIAEGKVPENLKNAKIYSLDMGSLLA------  251 (731)
T ss_pred             CcccCcHHHHHHHHHHHhc----CCCCceEEECCCCCCHHHHHHHHHHHHHhCCCchhhcCCeEEEecHHHHhh------
Confidence            7999999999998888854    456789999999999999999999988421      134566665433211      


Q ss_pred             HHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccC-----HHHHHHhHhCCCCCCCcEEEEEecCCCC
Q psy200          268 TIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRK-----QTILYTIFEWPSIPGSKLVLVGVANALD  342 (490)
Q Consensus       268 ~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~-----~~~L~~l~~~~~~~~~~vilI~~tn~~~  342 (490)
                            +..+.|.....+.+.+.++..  ..++||||||+|.+...+     .....+++. .......+.+||+||..+
T Consensus       252 ------~~~~~g~~e~~l~~i~~~~~~--~~~~ILfiDEih~l~~~g~~~~~~~~~~~~L~-~~l~~g~i~~IgaTt~~e  322 (731)
T TIGR02639       252 ------GTKYRGDFEERLKAVVSEIEK--EPNAILFIDEIHTIVGAGATSGGSMDASNLLK-PALSSGKLRCIGSTTYEE  322 (731)
T ss_pred             ------hccccchHHHHHHHHHHHHhc--cCCeEEEEecHHHHhccCCCCCccHHHHHHHH-HHHhCCCeEEEEecCHHH
Confidence                  112333444555555554433  347899999999997532     111122221 223456899999999655


Q ss_pred             hhH--hhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhcc--CCCCCCCHHHHHHHHHHHHHhhCC---HHHHHHHH
Q psy200          343 LTD--RMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQT--DKFNMFNASALQLLAGKVAAVSGD---IRKAIDIT  415 (490)
Q Consensus       343 ~~~--~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~--~~~~~~~~~~i~~i~~~i~~~~Gd---~r~ai~ll  415 (490)
                      +..  ..++.+.+||.    .+.+.+++.+++.+||+.....+  .....+++++++.+++....+-++   +..+|+++
T Consensus       323 ~~~~~~~d~al~rRf~----~i~v~~p~~~~~~~il~~~~~~~e~~~~v~i~~~al~~~~~ls~ryi~~r~~P~kai~ll  398 (731)
T TIGR02639       323 YKNHFEKDRALSRRFQ----KIDVGEPSIEETVKILKGLKEKYEEFHHVKYSDEALEAAVELSARYINDRFLPDKAIDVI  398 (731)
T ss_pred             HHHHhhhhHHHHHhCc----eEEeCCCCHHHHHHHHHHHHHHHHhccCcccCHHHHHHHHHhhhcccccccCCHHHHHHH
Confidence            433  24688999996    79999999999999999766543  134678999999999877777666   88899999


Q ss_pred             HHHHHHHHhccccCCcccccCHHHHHHHHHHhccCcc
Q psy200          416 NHLIDLTYDNVKENGEVTGIGLKEVLGVISSVYCTSQ  452 (490)
Q Consensus       416 ~~a~~~a~~~~~~~~~~~~It~~~v~~a~~~~~~~~~  452 (490)
                      +.|.......... .....|+.++|..++..+.+-+.
T Consensus       399 d~a~a~~~~~~~~-~~~~~v~~~~i~~~i~~~tgiP~  434 (731)
T TIGR02639       399 DEAGASFRLRPKA-KKKANVSVKDIENVVAKMAHIPV  434 (731)
T ss_pred             HHhhhhhhcCccc-ccccccCHHHHHHHHHHHhCCCh
Confidence            9988655433210 01346999999999999876654

>PRK05896 DNA polymerase III subunits gamma and tau; Validated

Probab=99.77  E-value=2.3e-17  Score=171.75  Aligned_cols=233  Identities=16%  Similarity=0.214  Sum_probs=158.8

Q ss_pred             CCCCcchHHHhhcCCCCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccC
Q psy200          179 FSEDKPKVEEKAKDSCELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNS  258 (490)
Q Consensus       179 ~~~~~~~~~~~~l~~~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~  258 (490)
                      .|.++|+|...    ++++|++..++.|..++..   +..++.++|+||+|+|||++|+.+++.+.+......  -.|..
T Consensus         5 ~~~~KyRP~~F----~dIIGQe~iv~~L~~aI~~---~rl~hA~Lf~GP~GvGKTTlA~~lAk~L~C~~~~~~--~~Cg~   75 (605)
T PRK05896          5 TFYRKYRPHNF----KQIIGQELIKKILVNAILN---NKLTHAYIFSGPRGIGKTSIAKIFAKAINCLNPKDG--DCCNS   75 (605)
T ss_pred             hHHHHhCCCCH----HHhcCcHHHHHHHHHHHHc---CCCCceEEEECCCCCCHHHHHHHHHHHhcCCCCCCC--CCCcc
Confidence            57788888888    9999999999998888853   345577999999999999999999999853221110  12322


Q ss_pred             CCCHHHHHHHHHHHh-cCC-CCCCcHHHHHHHHHHHHhc--CCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEE
Q psy200          259 VRNAASVYETIVNEL-KLK-PGGKSERHQLGAILKYFDT--KHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVL  334 (490)
Q Consensus       259 ~~~~~~l~~~i~~~l-~~~-~~~~s~~~~~~~l~~~l~~--~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vil  334 (490)
                      +.....+.....-++ ... ....+.+++++.+......  .++..|+||||+|.|....++.|...++.   ....+++
T Consensus        76 C~sCr~i~~~~h~DiieIdaas~igVd~IReIi~~~~~~P~~~~~KVIIIDEad~Lt~~A~NaLLKtLEE---Pp~~tvf  152 (605)
T PRK05896         76 CSVCESINTNQSVDIVELDAASNNGVDEIRNIIDNINYLPTTFKYKVYIIDEAHMLSTSAWNALLKTLEE---PPKHVVF  152 (605)
T ss_pred             cHHHHHHHcCCCCceEEeccccccCHHHHHHHHHHHHhchhhCCcEEEEEechHhCCHHHHHHHHHHHHh---CCCcEEE
Confidence            221111111000000 000 0112344555444332211  13455899999999987778888888774   3345666


Q ss_pred             EEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHHH
Q psy200          335 VGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDI  414 (490)
Q Consensus       335 I~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~l  414 (490)
                      |.+|+.   ...+.+.+++||.    .+.|.+++.+++..+|...+...  ...+++++++.+++   ...|++|.++++
T Consensus       153 IL~Tt~---~~KLl~TI~SRcq----~ieF~~Ls~~eL~~~L~~il~ke--gi~Is~eal~~La~---lS~GdlR~Alnl  220 (605)
T PRK05896        153 IFATTE---FQKIPLTIISRCQ----RYNFKKLNNSELQELLKSIAKKE--KIKIEDNAIDKIAD---LADGSLRDGLSI  220 (605)
T ss_pred             EEECCC---hHhhhHHHHhhhh----hcccCCCCHHHHHHHHHHHHHHc--CCCCCHHHHHHHHH---HcCCcHHHHHHH
Confidence            666652   5677889999996    79999999999999999999876  35689999999987   677999999999


Q ss_pred             HHHHHHHHHhccccCCcccccCHHHHHHHH
Q psy200          415 TNHLIDLTYDNVKENGEVTGIGLKEVLGVI  444 (490)
Q Consensus       415 l~~a~~~a~~~~~~~~~~~~It~~~v~~a~  444 (490)
                      ++.+.....  .       .|+.+++...+
T Consensus       221 LekL~~y~~--~-------~It~e~V~ell  241 (605)
T PRK05896        221 LDQLSTFKN--S-------EIDIEDINKTF  241 (605)
T ss_pred             HHHHHhhcC--C-------CCCHHHHHHHh
Confidence            998654321  2       37776666643

>PRK07133 DNA polymerase III subunits gamma and tau; Validated

Probab=99.77  E-value=2.9e-17  Score=174.26  Aligned_cols=230  Identities=18%  Similarity=0.287  Sum_probs=157.3

Q ss_pred             CCCCcchHHHhhcCCCCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccC
Q psy200          179 FSEDKPKVEEKAKDSCELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNS  258 (490)
Q Consensus       179 ~~~~~~~~~~~~l~~~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~  258 (490)
                      .|..+|+|...    ++++|++..++.|..++..   +.-.+.+|++||+|+|||++|+.+++.+.+... ....-.|..
T Consensus         7 ~l~~KyRP~~f----~dIiGQe~~v~~L~~aI~~---~rl~HAYLF~GP~GtGKTt~AriLAk~LnC~~~-~~~~~pC~~   78 (725)
T PRK07133          7 ALYRKYRPKTF----DDIVGQDHIVQTLKNIIKS---NKISHAYLFSGPRGTGKTSVAKIFANALNCSHK-TDLLEPCQE   78 (725)
T ss_pred             hHHHHhCCCCH----HHhcCcHHHHHHHHHHHHc---CCCCeEEEEECCCCCcHHHHHHHHHHHhccccc-CCCCCchhH
Confidence            57778888877    8999999999998888863   344566789999999999999999998753211 000011211


Q ss_pred             CCCHHHHHHHHHHHhcCC-CCCCcHHHHHHHHHHHHh--cCCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEE
Q psy200          259 VRNAASVYETIVNELKLK-PGGKSERHQLGAILKYFD--TKHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLV  335 (490)
Q Consensus       259 ~~~~~~l~~~i~~~l~~~-~~~~s~~~~~~~l~~~l~--~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI  335 (490)
                      +..   ....-..-+... ....+.+++++.+..+..  ..++..|+||||+|.|....++.|...++.   +...+++|
T Consensus        79 C~~---~~~~~~Dvieidaasn~~vd~IReLie~~~~~P~~g~~KV~IIDEa~~LT~~A~NALLKtLEE---PP~~tifI  152 (725)
T PRK07133         79 CIE---NVNNSLDIIEMDAASNNGVDEIRELIENVKNLPTQSKYKIYIIDEVHMLSKSAFNALLKTLEE---PPKHVIFI  152 (725)
T ss_pred             HHH---hhcCCCcEEEEeccccCCHHHHHHHHHHHHhchhcCCCEEEEEEChhhCCHHHHHHHHHHhhc---CCCceEEE
Confidence            110   000000000000 011234555554433321  125567999999999988778888877774   34466777


Q ss_pred             EecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHHHH
Q psy200          336 GVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDIT  415 (490)
Q Consensus       336 ~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll  415 (490)
                      ++|+.   .+.+.+.+++||.    .+.|.+++.+++..+|...+...+  ..+++++++.+++   ...|++|.+++++
T Consensus       153 LaTte---~~KLl~TI~SRcq----~ieF~~L~~eeI~~~L~~il~keg--I~id~eAl~~LA~---lS~GslR~AlslL  220 (725)
T PRK07133        153 LATTE---VHKIPLTILSRVQ----RFNFRRISEDEIVSRLEFILEKEN--ISYEKNALKLIAK---LSSGSLRDALSIA  220 (725)
T ss_pred             EEcCC---hhhhhHHHHhhce----eEEccCCCHHHHHHHHHHHHHHcC--CCCCHHHHHHHHH---HcCCCHHHHHHHH
Confidence            66652   4677888999995    899999999999999999888763  5688999999987   6779999999999


Q ss_pred             HHHHHHHHhccccCCcccccCHHHHHHH
Q psy200          416 NHLIDLTYDNVKENGEVTGIGLKEVLGV  443 (490)
Q Consensus       416 ~~a~~~a~~~~~~~~~~~~It~~~v~~a  443 (490)
                      +.+....  .+       .|+.+++..+
T Consensus       221 ekl~~y~--~~-------~It~e~V~el  239 (725)
T PRK07133        221 EQVSIFG--NN-------KITLKNVEEL  239 (725)
T ss_pred             HHHHHhc--cC-------CCCHHHHHHH
Confidence            9876442  22       3666666554

>PRK09111 DNA polymerase III subunits gamma and tau; Validated

Probab=99.76  E-value=2.6e-17  Score=173.81  Aligned_cols=236  Identities=12%  Similarity=0.155  Sum_probs=161.2

Q ss_pred             CCCCcchHHHhhcCCCCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCce---EEEEe
Q psy200          179 FSEDKPKVEEKAKDSCELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFK---TIYIN  255 (490)
Q Consensus       179 ~~~~~~~~~~~~l~~~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~---~~~v~  255 (490)
                      .+..+|+|...    ++++|++..++.|..++..   +..++.++|+||+|+|||++|+.+++.+.+.....   ...-.
T Consensus        13 ~la~KyRP~~f----~dliGq~~~v~~L~~~~~~---gri~ha~L~~Gp~GvGKTt~Ar~lAk~L~c~~~~~~~~~~~~~   85 (598)
T PRK09111         13 VLARKYRPQTF----DDLIGQEAMVRTLTNAFET---GRIAQAFMLTGVRGVGKTTTARILARALNYEGPDGDGGPTIDL   85 (598)
T ss_pred             hHHhhhCCCCH----HHhcCcHHHHHHHHHHHHc---CCCCceEEEECCCCCCHHHHHHHHHHhhCcCCccccCCCcccc
Confidence            45567777766    9999999999999998864   44567899999999999999999999986321100   00012


Q ss_pred             ccCCCCHHHHHHHHHHHhc-CC-CCCCcHHHHHHHHHHHHh--cCCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCc
Q psy200          256 CNSVRNAASVYETIVNELK-LK-PGGKSERHQLGAILKYFD--TKHKSILLILDEIDALESRKQTILYTIFEWPSIPGSK  331 (490)
Q Consensus       256 ~~~~~~~~~l~~~i~~~l~-~~-~~~~s~~~~~~~l~~~l~--~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~  331 (490)
                      |..+.+...+...-.-++. .. ....+.+++++.+.....  ..++..||||||+|.|....++.|...++.+   ...
T Consensus        86 cg~c~~C~~i~~g~h~Dv~e~~a~s~~gvd~IReIie~~~~~P~~a~~KVvIIDEad~Ls~~a~naLLKtLEeP---p~~  162 (598)
T PRK09111         86 CGVGEHCQAIMEGRHVDVLEMDAASHTGVDDIREIIESVRYRPVSARYKVYIIDEVHMLSTAAFNALLKTLEEP---PPH  162 (598)
T ss_pred             CcccHHHHHHhcCCCCceEEecccccCCHHHHHHHHHHHHhchhcCCcEEEEEEChHhCCHHHHHHHHHHHHhC---CCC
Confidence            2222222111110000000 00 111345555555443321  1245669999999999887788888777643   334


Q ss_pred             EEEEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHH
Q psy200          332 LVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKA  411 (490)
Q Consensus       332 vilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~a  411 (490)
                      ++||.+++.   .+.+...+++||.    .+.|.+++.+++..+|...+..+  ...+++++++.|++   ...|++|.+
T Consensus       163 ~~fIl~tte---~~kll~tI~SRcq----~~~f~~l~~~el~~~L~~i~~ke--gi~i~~eAl~lIa~---~a~Gdlr~a  230 (598)
T PRK09111        163 VKFIFATTE---IRKVPVTVLSRCQ----RFDLRRIEADVLAAHLSRIAAKE--GVEVEDEALALIAR---AAEGSVRDG  230 (598)
T ss_pred             eEEEEEeCC---hhhhhHHHHhhee----EEEecCCCHHHHHHHHHHHHHHc--CCCCCHHHHHHHHH---HcCCCHHHH
Confidence            555555653   3456778999995    89999999999999999999877  45689999999987   778999999


Q ss_pred             HHHHHHHHHHHHhccccCCcccccCHHHHHHHHH
Q psy200          412 IDITNHLIDLTYDNVKENGEVTGIGLKEVLGVIS  445 (490)
Q Consensus       412 i~ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~~  445 (490)
                      +++++.++...  .+       .|+.++|.+.+.
T Consensus       231 l~~Ldkli~~g--~g-------~It~e~V~~llg  255 (598)
T PRK09111        231 LSLLDQAIAHG--AG-------EVTAEAVRDMLG  255 (598)
T ss_pred             HHHHHHHHhhc--CC-------CcCHHHHHHHhC
Confidence            99998876442  22       588888887665

>PRK14965 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.76  E-value=1.2e-17  Score=177.08  Aligned_cols=230  Identities=13%  Similarity=0.197  Sum_probs=156.0

Q ss_pred             CCCcchHHHhhcCCCCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCC
Q psy200          180 SEDKPKVEEKAKDSCELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSV  259 (490)
Q Consensus       180 ~~~~~~~~~~~l~~~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~  259 (490)
                      +.++|+|...    ++++|+++.++.|..++..   +.-++.+||+||+|+|||++++.+++.+.+.....  .-.|..+
T Consensus         6 l~~k~RP~~f----~~iiGq~~v~~~L~~~i~~---~~~~hayLf~Gp~G~GKtt~A~~lak~l~c~~~~~--~~~c~~c   76 (576)
T PRK14965          6 LARKYRPQTF----SDLTGQEHVSRTLQNAIDT---GRVAHAFLFTGARGVGKTSTARILAKALNCEQGLT--AEPCNVC   76 (576)
T ss_pred             HHHHhCCCCH----HHccCcHHHHHHHHHHHHc---CCCCeEEEEECCCCCCHHHHHHHHHHhhcCCCCCC--CCCCCcc
Confidence            3456777666    8999999999999888864   33456678999999999999999999986322110  0012222


Q ss_pred             CCHHHHHHHHHH---HhcCCCCCCcHHHHHHHHHHHHh--cCCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEE
Q psy200          260 RNAASVYETIVN---ELKLKPGGKSERHQLGAILKYFD--TKHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVL  334 (490)
Q Consensus       260 ~~~~~l~~~i~~---~l~~~~~~~s~~~~~~~l~~~l~--~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vil  334 (490)
                      .....+..--..   .+.. ......+++.+.+.....  ..++..|+||||+|.|....++.|...++.+   ...++|
T Consensus        77 ~~c~~i~~g~~~d~~eid~-~s~~~v~~ir~l~~~~~~~p~~~~~KVvIIdev~~Lt~~a~naLLk~LEep---p~~~~f  152 (576)
T PRK14965         77 PPCVEITEGRSVDVFEIDG-ASNTGVDDIRELRENVKYLPSRSRYKIFIIDEVHMLSTNAFNALLKTLEEP---PPHVKF  152 (576)
T ss_pred             HHHHHHhcCCCCCeeeeec-cCccCHHHHHHHHHHHHhccccCCceEEEEEChhhCCHHHHHHHHHHHHcC---CCCeEE
Confidence            111111000000   0000 011234455444333221  1245669999999999988888888888743   346666


Q ss_pred             EEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHHH
Q psy200          335 VGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDI  414 (490)
Q Consensus       335 I~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~l  414 (490)
                      |.+|+.   ...+.+.+++||.    .+.|.+++.+++...+...+..+  ...++++++..|++   ...||+|.++++
T Consensus       153 Il~t~~---~~kl~~tI~SRc~----~~~f~~l~~~~i~~~L~~i~~~e--gi~i~~~al~~la~---~a~G~lr~al~~  220 (576)
T PRK14965        153 IFATTE---PHKVPITILSRCQ----RFDFRRIPLQKIVDRLRYIADQE--GISISDAALALVAR---KGDGSMRDSLST  220 (576)
T ss_pred             EEEeCC---hhhhhHHHHHhhh----hhhcCCCCHHHHHHHHHHHHHHh--CCCCCHHHHHHHHH---HcCCCHHHHHHH
Confidence            666653   4677888999996    79999999999999999999887  35689999999998   778999999999


Q ss_pred             HHHHHHHHHhccccCCcccccCHHHHHHH
Q psy200          415 TNHLIDLTYDNVKENGEVTGIGLKEVLGV  443 (490)
Q Consensus       415 l~~a~~~a~~~~~~~~~~~~It~~~v~~a  443 (490)
                      |++++....  +       .|+.+++...
T Consensus       221 Ldqliay~g--~-------~It~edV~~l  240 (576)
T PRK14965        221 LDQVLAFCG--D-------AVGDDDVAEL  240 (576)
T ss_pred             HHHHHHhcc--C-------CCCHHHHHHH
Confidence            998875532  2       3666665544

>PRK14088 dnaA chromosomal replication initiation protein; Provisional

Probab=99.76  E-value=6e-17  Score=166.74  Aligned_cols=243  Identities=16%  Similarity=0.203  Sum_probs=166.2

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHhhhc-CCceEEEEeccCCCCHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCC
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRAEIK-DAFKTIYINCNSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFDTKH  297 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l~~~-~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~  297 (490)
                      .++++|||++|+|||+|++++++++... ++..++|+++      .+++..+...+..    .....+.+.    +.  .
T Consensus       130 ~n~l~lyG~~G~GKTHLl~ai~~~l~~~~~~~~v~yi~~------~~f~~~~~~~~~~----~~~~~f~~~----~~--~  193 (440)
T PRK14088        130 YNPLFIYGGVGLGKTHLLQSIGNYVVQNEPDLRVMYITS------EKFLNDLVDSMKE----GKLNEFREK----YR--K  193 (440)
T ss_pred             CCeEEEEcCCCCcHHHHHHHHHHHHHHhCCCCeEEEEEH------HHHHHHHHHHHhc----ccHHHHHHH----HH--h
Confidence            4679999999999999999999987532 3567888864      4566666555532    122222222    21  1


Q ss_pred             CeEEEEEecCccccccC--HHHHHHhHhCCCCCCCcEEEEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHH
Q psy200          298 KSILLILDEIDALESRK--QTILYTIFEWPSIPGSKLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEI  375 (490)
Q Consensus       298 ~~~vI~IDEid~l~~~~--~~~L~~l~~~~~~~~~~vilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~i  375 (490)
                      .+-+|+|||++.+....  +..++.+++.....+. .+++++.........+.+++.+||.++ ..+.+.+++.+.+.+|
T Consensus       194 ~~dvLlIDDi~~l~~~~~~q~elf~~~n~l~~~~k-~iIitsd~~p~~l~~l~~rL~SR~~~g-l~v~i~~pd~e~r~~I  271 (440)
T PRK14088        194 KVDVLLIDDVQFLIGKTGVQTELFHTFNELHDSGK-QIVICSDREPQKLSEFQDRLVSRFQMG-LVAKLEPPDEETRKKI  271 (440)
T ss_pred             cCCEEEEechhhhcCcHHHHHHHHHHHHHHHHcCC-eEEEECCCCHHHHHHHHHHHhhHHhcC-ceEeeCCCCHHHHHHH
Confidence            34599999999986543  5566666654333333 344443333334455678999999765 3689999999999999


Q ss_pred             HHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHhccccC----------------CcccccCHHH
Q psy200          376 ISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITNHLIDLTYDNVKEN----------------GEVTGIGLKE  439 (490)
Q Consensus       376 l~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll~~a~~~a~~~~~~~----------------~~~~~It~~~  439 (490)
                      +++++...  ...+++++++.|++   ...||+|.+..++.+....+...+..-                .....|+++.
T Consensus       272 L~~~~~~~--~~~l~~ev~~~Ia~---~~~~~~R~L~g~l~~l~~~~~~~~~~it~~~a~~~L~~~~~~~~~~~~i~~~~  346 (440)
T PRK14088        272 ARKMLEIE--HGELPEEVLNFVAE---NVDDNLRRLRGAIIKLLVYKETTGEEVDLKEAILLLKDFIKPNRVKAMDPIDE  346 (440)
T ss_pred             HHHHHHhc--CCCCCHHHHHHHHh---ccccCHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhccccccCCCCHHH
Confidence            99998765  46689999999998   778999998887777654443322100                0012478888


Q ss_pred             HHHHHHHhccCccccccccccCCCChHhHHHHH---HHHHHhcCCCCCCcccC
Q psy200          440 VLGVISSVYCTSQSLHCSKDEDSFPLQQKLALA---SLLLLKSRPNVKDVTLG  489 (490)
Q Consensus       440 v~~a~~~~~~~~~~~~~~~~l~~L~~~qk~vL~---al~~~~~~~~~~~~~~g  489 (490)
                      +.+++.+.++-..     +.+.+...++..++.   ||+++.+..+.+...||
T Consensus       347 I~~~V~~~~~i~~-----~~l~s~~R~~~i~~aR~iamyl~r~~~~~s~~~Ig  394 (440)
T PRK14088        347 LIEIVAKVTGVSR-----EEILSNSRNVKALLARRIGMYVAKNYLGSSLRTIA  394 (440)
T ss_pred             HHHHHHHHcCCcH-----HHHhCCCCCccccHHHHHHHHHHHHHhCCCHHHHH
Confidence            8888888875444     566777777777776   78877777666666655

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX

Probab=99.76  E-value=4.5e-17  Score=158.36  Aligned_cols=203  Identities=19%  Similarity=0.172  Sum_probs=139.0

Q ss_pred             CCCCChHHHHHHHHHHHHhhh----------c-cCCCCeEEEECCCCCcHHHHHHHHHHHhhhcC---CceEEEEeccCC
Q psy200          194 CELPGREVQLEGIRQFLLGHV----------N-NETSGSMYISGPPGTGKSASLNLLVSRAEIKD---AFKTIYINCNSV  259 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~----------~-~~~~~~ill~GppGtGKTtla~~l~~~l~~~~---~~~~~~v~~~~~  259 (490)
                      .+++|.++.+++|.++.....          . ..+..+++|+||||||||++|+++++.+....   .-.++++++.. 
T Consensus        22 ~~l~Gl~~vk~~i~e~~~~~~~~~~r~~~g~~~~~~~~~vll~G~pGTGKT~lA~~ia~~l~~~g~~~~~~~v~v~~~~-  100 (284)
T TIGR02880        22 RELIGLKPVKTRIREIAALLLVERLRQRLGLASAAPTLHMSFTGNPGTGKTTVALRMAQILHRLGYVRKGHLVSVTRDD-  100 (284)
T ss_pred             HhccCHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCCCceEEEEcCCCCCHHHHHHHHHHHHHHcCCcccceEEEecHHH-
Confidence            479999998888877544311          0 11345899999999999999999988875322   12567776432 


Q ss_pred             CCHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCcccccc---------CHHHHHHhHhCCCCCCC
Q psy200          260 RNAASVYETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESR---------KQTILYTIFEWPSIPGS  330 (490)
Q Consensus       260 ~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~---------~~~~L~~l~~~~~~~~~  330 (490)
                           ++.    .    ..|.+.....+.+.++.     ..+|||||++.|...         .++.|+.+++   ....
T Consensus       101 -----l~~----~----~~g~~~~~~~~~~~~a~-----~gvL~iDEi~~L~~~~~~~~~~~~~~~~Ll~~le---~~~~  159 (284)
T TIGR02880       101 -----LVG----Q----YIGHTAPKTKEILKRAM-----GGVLFIDEAYYLYRPDNERDYGQEAIEILLQVME---NQRD  159 (284)
T ss_pred             -----HhH----h----hcccchHHHHHHHHHcc-----CcEEEEechhhhccCCCccchHHHHHHHHHHHHh---cCCC
Confidence                 221    1    12233344444444332     249999999988422         2345555554   2345


Q ss_pred             cEEEEEecCC--CChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHH-----H
Q psy200          331 KLVLVGVANA--LDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVA-----A  403 (490)
Q Consensus       331 ~vilI~~tn~--~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~-----~  403 (490)
                      .+++|++++.  ++....+.+.+.+||.   ..|.|++|+.+|+..|+.+.+...  ...+++++++.+.+.+.     .
T Consensus       160 ~~~vI~a~~~~~~~~~~~~np~L~sR~~---~~i~fp~l~~edl~~I~~~~l~~~--~~~l~~~a~~~L~~~l~~~~~~~  234 (284)
T TIGR02880       160 DLVVILAGYKDRMDSFFESNPGFSSRVA---HHVDFPDYSEAELLVIAGLMLKEQ--QYRFSAEAEEAFADYIALRRTQP  234 (284)
T ss_pred             CEEEEEeCCcHHHHHHHhhCHHHHhhCC---cEEEeCCcCHHHHHHHHHHHHHHh--ccccCHHHHHHHHHHHHHhCCCC
Confidence            6777777653  3334445789999998   479999999999999999999876  35688999888877443     6


Q ss_pred             hhCCHHHHHHHHHHHHHHHH
Q psy200          404 VSGDIRKAIDITNHLIDLTY  423 (490)
Q Consensus       404 ~~Gd~r~ai~ll~~a~~~a~  423 (490)
                      |.||.|.+.+++++++....
T Consensus       235 ~~GN~R~lrn~ve~~~~~~~  254 (284)
T TIGR02880       235 HFANARSIRNAIDRARLRQA  254 (284)
T ss_pred             CCChHHHHHHHHHHHHHHHH
Confidence            78999999999999876544

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.

>TIGR01241 FtsH_fam ATP-dependent metalloprotease FtsH

Probab=99.76  E-value=5.1e-17  Score=170.67  Aligned_cols=220  Identities=16%  Similarity=0.157  Sum_probs=151.6

Q ss_pred             CCCCChHHHHHHHHHHHHhhh--------ccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHV--------NNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASV  265 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~--------~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l  265 (490)
                      ++++|.++.++++.+++....        ....+++++|+||||||||+++++++.++.    ..++++++..+      
T Consensus        55 ~di~g~~~~k~~l~~~~~~l~~~~~~~~~g~~~~~giLL~GppGtGKT~la~alA~~~~----~~~~~i~~~~~------  124 (495)
T TIGR01241        55 KDVAGIDEAKEELMEIVDFLKNPSKFTKLGAKIPKGVLLVGPPGTGKTLLAKAVAGEAG----VPFFSISGSDF------  124 (495)
T ss_pred             HHhCCHHHHHHHHHHHHHHHHCHHHHHhcCCCCCCcEEEECCCCCCHHHHHHHHHHHcC----CCeeeccHHHH------
Confidence            778999888888877665321        123567899999999999999999999864    56677755432      


Q ss_pred             HHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCH-----------HHHHHhHhCC--CCCCCcE
Q psy200          266 YETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQ-----------TILYTIFEWP--SIPGSKL  332 (490)
Q Consensus       266 ~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~-----------~~L~~l~~~~--~~~~~~v  332 (490)
                      ..        .+.+.+...+.+.|..+..  ..|+||||||+|.+....+           ..+..++...  ......+
T Consensus       125 ~~--------~~~g~~~~~l~~~f~~a~~--~~p~Il~iDEid~l~~~r~~~~~~~~~~~~~~~~~lL~~~d~~~~~~~v  194 (495)
T TIGR01241       125 VE--------MFVGVGASRVRDLFEQAKK--NAPCIIFIDEIDAVGRQRGAGLGGGNDEREQTLNQLLVEMDGFGTNTGV  194 (495)
T ss_pred             HH--------HHhcccHHHHHHHHHHHHh--cCCCEEEEechhhhhhccccCcCCccHHHHHHHHHHHhhhccccCCCCe
Confidence            11        1223445566666666544  4578999999999864321           2233333221  1234569


Q ss_pred             EEEEecCCCChhHhhhHHhhh--ccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhC-CHH
Q psy200          333 VLVGVANALDLTDRMLPRLQA--NVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSG-DIR  409 (490)
Q Consensus       333 ilI~~tn~~~~~~~l~~~l~~--R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~G-d~r  409 (490)
                      +||++||.   ++.+++.+.+  ||.   ..+.+..++.++..+|++.++.....   -.+..+..+++   .+.| ...
T Consensus       195 ~vI~aTn~---~~~ld~al~r~gRfd---~~i~i~~Pd~~~R~~il~~~l~~~~~---~~~~~l~~la~---~t~G~sga  262 (495)
T TIGR01241       195 IVIAATNR---PDVLDPALLRPGRFD---RQVVVDLPDIKGREEILKVHAKNKKL---APDVDLKAVAR---RTPGFSGA  262 (495)
T ss_pred             EEEEecCC---hhhcCHHHhcCCcce---EEEEcCCCCHHHHHHHHHHHHhcCCC---CcchhHHHHHH---hCCCCCHH
Confidence            99999985   4566677765  666   58999999999999999998876421   13445667776   3344 334


Q ss_pred             HHHHHHHHHHHHHHhccccCCcccccCHHHHHHHHHHhccC
Q psy200          410 KAIDITNHLIDLTYDNVKENGEVTGIGLKEVLGVISSVYCT  450 (490)
Q Consensus       410 ~ai~ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~~~~~~~  450 (490)
                      .+.++|+.|...+.+++     ...|+.+++..|+..+...
T Consensus       263 dl~~l~~eA~~~a~~~~-----~~~i~~~~l~~a~~~~~~~  298 (495)
T TIGR01241       263 DLANLLNEAALLAARKN-----KTEITMNDIEEAIDRVIAG  298 (495)
T ss_pred             HHHHHHHHHHHHHHHcC-----CCCCCHHHHHHHHHHHhcc
Confidence            55568888887777766     5689999999999987643

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.

>PRK08084 DNA replication initiation factor; Provisional

Probab=99.76  E-value=8.3e-17  Score=152.51  Aligned_cols=208  Identities=14%  Similarity=0.203  Sum_probs=138.1

Q ss_pred             CCCCC-hHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHH
Q psy200          194 CELPG-REVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNE  272 (490)
Q Consensus       194 ~~lvg-re~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~  272 (490)
                      +.++| ....+..+..+..    ......++|+||+|+|||+|++++++++.. .+..+.|+++.....           
T Consensus        23 ~f~~~~n~~a~~~l~~~~~----~~~~~~l~l~Gp~G~GKThLl~a~~~~~~~-~~~~v~y~~~~~~~~-----------   86 (235)
T PRK08084         23 SFYPGDNDSLLAALQNALR----QEHSGYIYLWSREGAGRSHLLHAACAELSQ-RGRAVGYVPLDKRAW-----------   86 (235)
T ss_pred             ccccCccHHHHHHHHHHHh----CCCCCeEEEECCCCCCHHHHHHHHHHHHHh-CCCeEEEEEHHHHhh-----------
Confidence            34445 3344444444443    345578999999999999999999998753 245666765432100           


Q ss_pred             hcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCcccccc--CHHHHHHhHhCCCCCCCcEEEEEec-CCCChhHhhhH
Q psy200          273 LKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESR--KQTILYTIFEWPSIPGSKLVLVGVA-NALDLTDRMLP  349 (490)
Q Consensus       273 l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~--~~~~L~~l~~~~~~~~~~vilI~~t-n~~~~~~~l~~  349 (490)
                              ...++.+.    +..   ..+|+|||+|.+...  .+..|+.+++.....+ +..+|+++ +.......+.+
T Consensus        87 --------~~~~~~~~----~~~---~dlliiDdi~~~~~~~~~~~~lf~l~n~~~e~g-~~~li~ts~~~p~~l~~~~~  150 (235)
T PRK08084         87 --------FVPEVLEG----MEQ---LSLVCIDNIECIAGDELWEMAIFDLYNRILESG-RTRLLITGDRPPRQLNLGLP  150 (235)
T ss_pred             --------hhHHHHHH----hhh---CCEEEEeChhhhcCCHHHHHHHHHHHHHHHHcC-CCeEEEeCCCChHHcCcccH
Confidence                    01112222    211   238999999999754  3566777765432222 22233333 33222233578


Q ss_pred             HhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHhccccC
Q psy200          350 RLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITNHLIDLTYDNVKEN  429 (490)
Q Consensus       350 ~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll~~a~~~a~~~~~~~  429 (490)
                      .+++|+.++. .+.+.+++.+++.+++++++...  ...+++++++.|++   ...||+|.+++++++....+...+   
T Consensus       151 ~L~SRl~~g~-~~~l~~~~~~~~~~~l~~~a~~~--~~~l~~~v~~~L~~---~~~~d~r~l~~~l~~l~~~~l~~~---  221 (235)
T PRK08084        151 DLASRLDWGQ-IYKLQPLSDEEKLQALQLRARLR--GFELPEDVGRFLLK---RLDREMRTLFMTLDQLDRASITAQ---  221 (235)
T ss_pred             HHHHHHhCCc-eeeecCCCHHHHHHHHHHHHHHc--CCCCCHHHHHHHHH---hhcCCHHHHHHHHHHHHHHHHhcC---
Confidence            9999996553 69999999999999998877665  46799999999998   889999999999998643443333   


Q ss_pred             CcccccCHHHHHHHHH
Q psy200          430 GEVTGIGLKEVLGVIS  445 (490)
Q Consensus       430 ~~~~~It~~~v~~a~~  445 (490)
                         ..||.+.+.+++.
T Consensus       222 ---~~it~~~~k~~l~  234 (235)
T PRK08084        222 ---RKLTIPFVKEILK  234 (235)
T ss_pred             ---CCCCHHHHHHHHc
Confidence               4699999988763

>TIGR02397 dnaX_nterm DNA polymerase III, subunit gamma and tau

Probab=99.75  E-value=9.6e-17  Score=162.25  Aligned_cols=234  Identities=17%  Similarity=0.252  Sum_probs=155.3

Q ss_pred             CCCCcchHHHhhcCCCCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccC
Q psy200          179 FSEDKPKVEEKAKDSCELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNS  258 (490)
Q Consensus       179 ~~~~~~~~~~~~l~~~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~  258 (490)
                      +|.++|.+...    ++++|+++.++.|..++..   +..++.++|+||+|+|||++++.+++.+.....-.  +..|..
T Consensus         3 ~~~~~~rp~~~----~~iig~~~~~~~l~~~~~~---~~~~~~~Ll~G~~G~GKt~~a~~la~~l~~~~~~~--~~~c~~   73 (355)
T TIGR02397         3 VLARKYRPQTF----EDVIGQEHIVQTLKNAIKN---GRIAHAYLFSGPRGTGKTSIARIFAKALNCQNGPD--GEPCNE   73 (355)
T ss_pred             cHHHHhCCCcH----hhccCcHHHHHHHHHHHHc---CCCCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCC--CCCCCC
Confidence            57778888777    8999999999999998863   34456789999999999999999999875321100  011222


Q ss_pred             CCCHHHHHHHHHHHhc-CC-CCCCcHHHHHHHHHHHHhc--CCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEE
Q psy200          259 VRNAASVYETIVNELK-LK-PGGKSERHQLGAILKYFDT--KHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVL  334 (490)
Q Consensus       259 ~~~~~~l~~~i~~~l~-~~-~~~~s~~~~~~~l~~~l~~--~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vil  334 (490)
                      +.+...+.....-.+. .. ....+...+.+.+..+...  .+...||||||+|.+....++.|...++.   ....+++
T Consensus        74 c~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~p~~~~~~vviidea~~l~~~~~~~Ll~~le~---~~~~~~l  150 (355)
T TIGR02397        74 CESCKEINSGSSLDVIEIDAASNNGVDDIREILDNVKYAPSSGKYKVYIIDEVHMLSKSAFNALLKTLEE---PPEHVVF  150 (355)
T ss_pred             CHHHHHHhcCCCCCEEEeeccccCCHHHHHHHHHHHhcCcccCCceEEEEeChhhcCHHHHHHHHHHHhC---CccceeE
Confidence            1111111100000000 00 0012233344443332211  24456999999999987667777776653   2345666


Q ss_pred             EEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHHH
Q psy200          335 VGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDI  414 (490)
Q Consensus       335 I~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~l  414 (490)
                      |.+++.   .+.+.+.+++||.    .+.|.+++.+++..++..++...  ...+++++++.+++   ...||++.+++.
T Consensus       151 Il~~~~---~~~l~~~l~sr~~----~~~~~~~~~~~l~~~l~~~~~~~--g~~i~~~a~~~l~~---~~~g~~~~a~~~  218 (355)
T TIGR02397       151 ILATTE---PHKIPATILSRCQ----RFDFKRIPLEDIVERLKKILDKE--GIKIEDEALELIAR---AADGSLRDALSL  218 (355)
T ss_pred             EEEeCC---HHHHHHHHHhhee----EEEcCCCCHHHHHHHHHHHHHHc--CCCCCHHHHHHHHH---HcCCChHHHHHH
Confidence            666653   4566788999985    79999999999999999999876  35689999999987   677999999999


Q ss_pred             HHHHHHHHHhccccCCcccccCHHHHHHHHH
Q psy200          415 TNHLIDLTYDNVKENGEVTGIGLKEVLGVIS  445 (490)
Q Consensus       415 l~~a~~~a~~~~~~~~~~~~It~~~v~~a~~  445 (490)
                      ++.+....  .+       .|+.++|.+++.
T Consensus       219 lekl~~~~--~~-------~it~~~v~~~~~  240 (355)
T TIGR02397       219 LDQLISFG--NG-------NITYEDVNELLG  240 (355)
T ss_pred             HHHHHhhc--CC-------CCCHHHHHHHhC
Confidence            98887642  12       477777766554

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.

>TIGR02902 spore_lonB ATP-dependent protease LonB

Probab=99.75  E-value=7.3e-18  Score=177.29  Aligned_cols=243  Identities=18%  Similarity=0.231  Sum_probs=166.6

Q ss_pred             ccCCCCcchHHHhhcCCCCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhc------CCce
Q psy200          177 LLFSEDKPKVEEKAKDSCELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIK------DAFK  250 (490)
Q Consensus       177 ~~~~~~~~~~~~~~l~~~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~------~~~~  250 (490)
                      ..+|.++|++...    ++++|++..++.+...+.    .....+++|+||+|||||++|+++++.....      .+..
T Consensus        52 ~~~~~~~~rp~~f----~~iiGqs~~i~~l~~al~----~~~~~~vLi~Ge~GtGKt~lAr~i~~~~~~~~~s~~~~~~~  123 (531)
T TIGR02902        52 TEPLSEKTRPKSF----DEIIGQEEGIKALKAALC----GPNPQHVIIYGPPGVGKTAAARLVLEEAKKNPASPFKEGAA  123 (531)
T ss_pred             cchHHHhhCcCCH----HHeeCcHHHHHHHHHHHh----CCCCceEEEECCCCCCHHHHHHHHHHHhhhccCCCcCCCCC
Confidence            3467778887766    889999999988886653    4567899999999999999999998765321      1346


Q ss_pred             EEEEeccCCC-CHHHHHHHHHHHhcCC-CCCCc---HHHHHHHHHHHHhcCCCeEEEEEecCccccccCHHHHHHhHhCC
Q psy200          251 TIYINCNSVR-NAASVYETIVNELKLK-PGGKS---ERHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWP  325 (490)
Q Consensus       251 ~~~v~~~~~~-~~~~l~~~i~~~l~~~-~~~~s---~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~  325 (490)
                      ++.++|.... +...+...++.....+ +.+..   .......-...+.. ...-+|||||++.|....|+.|..+++..
T Consensus       124 fi~id~~~~~~~~~~~~~~li~~~~~p~~~~~~~~g~~g~~~~~~G~l~~-a~gG~L~IdEI~~L~~~~q~~LL~~Le~~  202 (531)
T TIGR02902       124 FVEIDATTARFDERGIADPLIGSVHDPIYQGAGPLGIAGIPQPKPGAVTR-AHGGVLFIDEIGELHPVQMNKLLKVLEDR  202 (531)
T ss_pred             EEEEccccccCCccccchhhcCCcccchhccccccccCCcccccCchhhc-cCCcEEEEechhhCCHHHHHHHHHHHHhC
Confidence            7889886431 2222211221111000 00000   00000000001111 11349999999999999999888876532


Q ss_pred             C-------------------------CCCCcEEEEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHH
Q psy200          326 S-------------------------IPGSKLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKL  380 (490)
Q Consensus       326 ~-------------------------~~~~~vilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l  380 (490)
                      .                         .....+.+|++|+..  ++.+.+.+++||.    .+.|.+|+.+++..++++.+
T Consensus       203 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~rlI~ATt~~--p~~L~paLrsR~~----~I~f~pL~~eei~~Il~~~a  276 (531)
T TIGR02902       203 KVFLDSAYYNSENPNIPSHIHDIFQNGLPADFRLIGATTRN--PEEIPPALRSRCV----EIFFRPLLDEEIKEIAKNAA  276 (531)
T ss_pred             eeeeccccccccCcccccchhhhcccCcccceEEEEEecCC--cccCChHHhhhhh----eeeCCCCCHHHHHHHHHHHH
Confidence            1                         012356777776532  3456788999985    79999999999999999999


Q ss_pred             hccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHhccccCCcccccCHHHHHHHHH
Q psy200          381 KQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITNHLIDLTYDNVKENGEVTGIGLKEVLGVIS  445 (490)
Q Consensus       381 ~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~~  445 (490)
                      ...  ...+++++++.|..    ++.|.|.++++++.|..+|..++     ...|+.+||..++.
T Consensus       277 ~k~--~i~is~~al~~I~~----y~~n~Rel~nll~~Aa~~A~~~~-----~~~It~~dI~~vl~  330 (531)
T TIGR02902       277 EKI--GINLEKHALELIVK----YASNGREAVNIVQLAAGIALGEG-----RKRILAEDIEWVAE  330 (531)
T ss_pred             HHc--CCCcCHHHHHHHHH----hhhhHHHHHHHHHHHHHHHhhCC-----CcEEcHHHHHHHhC
Confidence            876  36789999998876    44589999999999998887776     56899999999986

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.

>PRK14955 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.75  E-value=3.5e-17  Score=166.96  Aligned_cols=237  Identities=14%  Similarity=0.181  Sum_probs=158.1

Q ss_pred             CcchHHHhhcCCCCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCce------EEEEe
Q psy200          182 DKPKVEEKAKDSCELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFK------TIYIN  255 (490)
Q Consensus       182 ~~~~~~~~~l~~~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~------~~~v~  255 (490)
                      ++|+|...    ++++|++..++.|..++..   +.-++.++|+||+|+||||+|+.+++.+.......      ...-.
T Consensus         8 ~k~RP~~~----~eiiGq~~~~~~L~~~~~~---~~~~ha~lf~Gp~G~GKtt~A~~~a~~l~c~~~~~~~~~~~~~~~~   80 (397)
T PRK14955          8 RKYRPKKF----ADITAQEHITRTIQNSLRM---GRVGHGYIFSGLRGVGKTTAARVFAKAVNCQRMIDDADYLQEVTEP   80 (397)
T ss_pred             HhcCCCcH----hhccChHHHHHHHHHHHHh---CCcceeEEEECCCCCCHHHHHHHHHHHhcCCCCcCcccccccCCCC
Confidence            46777666    9999999999988888863   33455699999999999999999999986421100      00113


Q ss_pred             ccCCCCHHHHHHHHHHHhc-CCC-CCCcHHHHHHHHHHHHh--cCCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCc
Q psy200          256 CNSVRNAASVYETIVNELK-LKP-GGKSERHQLGAILKYFD--TKHKSILLILDEIDALESRKQTILYTIFEWPSIPGSK  331 (490)
Q Consensus       256 ~~~~~~~~~l~~~i~~~l~-~~~-~~~s~~~~~~~l~~~l~--~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~  331 (490)
                      |..+.+...+..-..-.+. ... .....+++.+.......  ..+...||||||+|.|....++.|...++.   ....
T Consensus        81 c~~c~~c~~~~~~~~~n~~~~~~~~~~~id~Ir~l~~~~~~~p~~~~~kvvIIdea~~l~~~~~~~LLk~LEe---p~~~  157 (397)
T PRK14955         81 CGECESCRDFDAGTSLNISEFDAASNNSVDDIRLLRENVRYGPQKGRYRVYIIDEVHMLSIAAFNAFLKTLEE---PPPH  157 (397)
T ss_pred             CCCCHHHHHHhcCCCCCeEeecccccCCHHHHHHHHHHHhhchhcCCeEEEEEeChhhCCHHHHHHHHHHHhc---CCCC
Confidence            3333222222110000000 000 11224555554433321  124566999999999987777777777663   2334


Q ss_pred             EEEEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHH
Q psy200          332 LVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKA  411 (490)
Q Consensus       332 vilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~a  411 (490)
                      .++|.+++.   ...+.+.+++|+.    .+.|.+++.+++.+++...+...  ...+++++++.+++   ...|+++.+
T Consensus       158 t~~Il~t~~---~~kl~~tl~sR~~----~v~f~~l~~~ei~~~l~~~~~~~--g~~i~~~al~~l~~---~s~g~lr~a  225 (397)
T PRK14955        158 AIFIFATTE---LHKIPATIASRCQ----RFNFKRIPLEEIQQQLQGICEAE--GISVDADALQLIGR---KAQGSMRDA  225 (397)
T ss_pred             eEEEEEeCC---hHHhHHHHHHHHH----HhhcCCCCHHHHHHHHHHHHHHc--CCCCCHHHHHHHHH---HcCCCHHHH
Confidence            455545542   3677788999985    79999999999999999998876  45689999999987   778999999


Q ss_pred             HHHHHHHHHHHHhccccCCcccccCHHHHHHHH
Q psy200          412 IDITNHLIDLTYDNVKENGEVTGIGLKEVLGVI  444 (490)
Q Consensus       412 i~ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~  444 (490)
                      ++.|+.+...+...+.    ...|+.++|.+++
T Consensus       226 ~~~L~kl~~~~~~~~~----~~~It~~~v~~~v  254 (397)
T PRK14955        226 QSILDQVIAFSVESEG----EGSIRYDKVAELL  254 (397)
T ss_pred             HHHHHHHHHhccccCC----CCccCHHHHHHHH
Confidence            9999988776642111    2478888887665

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=99.75  E-value=9.2e-17  Score=166.84  Aligned_cols=211  Identities=17%  Similarity=0.250  Sum_probs=142.0

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhc-CCceEEEEeccCCCCHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcC
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIK-DAFKTIYINCNSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFDTK  296 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~-~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~  296 (490)
                      ..+.++|||++|+|||+|++++++++... .+..++|+++..      +...+...+..    .....+    .+.+.  
T Consensus       147 ~~~~l~l~G~~G~GKThL~~ai~~~~~~~~~~~~v~yi~~~~------~~~~~~~~~~~----~~~~~~----~~~~~--  210 (450)
T PRK00149        147 AYNPLFIYGGVGLGKTHLLHAIGNYILEKNPNAKVVYVTSEK------FTNDFVNALRN----NTMEEF----KEKYR--  210 (450)
T ss_pred             cCCeEEEECCCCCCHHHHHHHHHHHHHHhCCCCeEEEEEHHH------HHHHHHHHHHc----CcHHHH----HHHHh--
Confidence            34679999999999999999999998633 256788886543      34444444421    112222    22232  


Q ss_pred             CCeEEEEEecCccccccC--HHHHHHhHhCCCCCCCcEEEEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHH
Q psy200          297 HKSILLILDEIDALESRK--QTILYTIFEWPSIPGSKLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILE  374 (490)
Q Consensus       297 ~~~~vI~IDEid~l~~~~--~~~L~~l~~~~~~~~~~vilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~  374 (490)
                       ...+|+|||+|.+....  ++.++.+++.....+.. ++|++.........+.+++.+||..+ ..+.|.+++.+++.+
T Consensus       211 -~~dlLiiDDi~~l~~~~~~~~~l~~~~n~l~~~~~~-iiits~~~p~~l~~l~~~l~SRl~~g-l~v~i~~pd~~~r~~  287 (450)
T PRK00149        211 -SVDVLLIDDIQFLAGKERTQEEFFHTFNALHEAGKQ-IVLTSDRPPKELPGLEERLRSRFEWG-LTVDIEPPDLETRIA  287 (450)
T ss_pred             -cCCEEEEehhhhhcCCHHHHHHHHHHHHHHHHCCCc-EEEECCCCHHHHHHHHHHHHhHhcCC-eeEEecCCCHHHHHH
Confidence             24599999999997653  56677766544333333 44443333333344678899999644 369999999999999


Q ss_pred             HHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHhcccc--------------CCcccccCHHHH
Q psy200          375 IISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITNHLIDLTYDNVKE--------------NGEVTGIGLKEV  440 (490)
Q Consensus       375 il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll~~a~~~a~~~~~~--------------~~~~~~It~~~v  440 (490)
                      +|+.++...  ...+++++++.|++   ...||+|.+..+|......+...+..              ......|+.+.|
T Consensus       288 il~~~~~~~--~~~l~~e~l~~ia~---~~~~~~R~l~~~l~~l~~~~~~~~~~it~~~~~~~l~~~~~~~~~~~~~~~i  362 (450)
T PRK00149        288 ILKKKAEEE--GIDLPDEVLEFIAK---NITSNVRELEGALNRLIAYASLTGKPITLELAKEALKDLLAAQKKKITIENI  362 (450)
T ss_pred             HHHHHHHHc--CCCCCHHHHHHHHc---CcCCCHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCCCCCHHHH
Confidence            999998865  46789999999998   78999999988887776665443310              011234667777


Q ss_pred             HHHHHHhccCcc
Q psy200          441 LGVISSVYCTSQ  452 (490)
Q Consensus       441 ~~a~~~~~~~~~  452 (490)
                      .+++.+.++-..
T Consensus       363 ~~~v~~~~~i~~  374 (450)
T PRK00149        363 QKVVAEYYNIKV  374 (450)
T ss_pred             HHHHHHHcCCCH
Confidence            777766665433

>PRK14086 dnaA chromosomal replication initiation protein; Provisional

Probab=99.75  E-value=1.5e-16  Score=165.85  Aligned_cols=264  Identities=14%  Similarity=0.188  Sum_probs=169.8

Q ss_pred             CCCCChHHHH--HHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhh-cCCceEEEEeccCCCCHHHHHHHHH
Q psy200          194 CELPGREVQL--EGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEI-KDAFKTIYINCNSVRNAASVYETIV  270 (490)
Q Consensus       194 ~~lvgre~~~--~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~-~~~~~~~~v~~~~~~~~~~l~~~i~  270 (490)
                      +.++|-...+  ..+..++..  .....+.++|||++|+|||+|++++++++.. ..++.++|+++      .+|+..+.
T Consensus       289 nFvvG~sN~~A~aaa~avae~--~~~~~NpL~LyG~sGsGKTHLL~AIa~~a~~~~~g~~V~Yita------eef~~el~  360 (617)
T PRK14086        289 TFVIGASNRFAHAAAVAVAEA--PAKAYNPLFIYGESGLGKTHLLHAIGHYARRLYPGTRVRYVSS------EEFTNEFI  360 (617)
T ss_pred             hhcCCCccHHHHHHHHHHHhC--ccccCCcEEEECCCCCCHHHHHHHHHHHHHHhCCCCeEEEeeH------HHHHHHHH
Confidence            4555665442  233333332  1223456999999999999999999999853 24578888854      44444444


Q ss_pred             HHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccC--HHHHHHhHhCCCCCCCcEEEEEecC-CCChhHhh
Q psy200          271 NELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRK--QTILYTIFEWPSIPGSKLVLVGVAN-ALDLTDRM  347 (490)
Q Consensus       271 ~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~--~~~L~~l~~~~~~~~~~vilI~~tn-~~~~~~~l  347 (490)
                      ..+..    .....    |.+.+.   ..-+|+||||+.+....  ++.|+++++.....+..++|.  ++ .......+
T Consensus       361 ~al~~----~~~~~----f~~~y~---~~DLLlIDDIq~l~gke~tqeeLF~l~N~l~e~gk~IIIT--Sd~~P~eL~~l  427 (617)
T PRK14086        361 NSIRD----GKGDS----FRRRYR---EMDILLVDDIQFLEDKESTQEEFFHTFNTLHNANKQIVLS--SDRPPKQLVTL  427 (617)
T ss_pred             HHHHh----ccHHH----HHHHhh---cCCEEEEehhccccCCHHHHHHHHHHHHHHHhcCCCEEEe--cCCChHhhhhc
Confidence            44322    11222    223332   24599999999997653  677888887655445555543  33 22223456


Q ss_pred             hHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHhccc
Q psy200          348 LPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITNHLIDLTYDNVK  427 (490)
Q Consensus       348 ~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll~~a~~~a~~~~~  427 (490)
                      .++|++||.++. .+.+.+++.+...+||++++...  ...++++++++|++   ...+|+|.+..+|.+....+...+.
T Consensus       428 ~~rL~SRf~~GL-vv~I~~PD~EtR~aIL~kka~~r--~l~l~~eVi~yLa~---r~~rnvR~LegaL~rL~a~a~~~~~  501 (617)
T PRK14086        428 EDRLRNRFEWGL-ITDVQPPELETRIAILRKKAVQE--QLNAPPEVLEFIAS---RISRNIRELEGALIRVTAFASLNRQ  501 (617)
T ss_pred             cHHHHhhhhcCc-eEEcCCCCHHHHHHHHHHHHHhc--CCCCCHHHHHHHHH---hccCCHHHHHHHHHHHHHHHHhhCC
Confidence            788999997663 69999999999999999998876  56789999999998   7788999988877776555543321


Q ss_pred             cC---------------CcccccCHHHHHHHHHHhccCccccccccccCCCChHhHHHH---HHHHHHhcCCCCCCcccC
Q psy200          428 EN---------------GEVTGIGLKEVLGVISSVYCTSQSLHCSKDEDSFPLQQKLAL---ASLLLLKSRPNVKDVTLG  489 (490)
Q Consensus       428 ~~---------------~~~~~It~~~v~~a~~~~~~~~~~~~~~~~l~~L~~~qk~vL---~al~~~~~~~~~~~~~~g  489 (490)
                      .-               .....|+.+.|.+++.+.++-..     +.|.+-.....+++   .||+++.+..+.+...||
T Consensus       502 ~itl~la~~vL~~~~~~~~~~~it~d~I~~~Va~~f~v~~-----~dl~s~~R~~~i~~aRqiAMYL~r~lt~~Sl~~IG  576 (617)
T PRK14086        502 PVDLGLTEIVLRDLIPEDSAPEITAAAIMAATADYFGLTV-----EDLCGTSRSRVLVTARQIAMYLCRELTDLSLPKIG  576 (617)
T ss_pred             CCCHHHHHHHHHHhhccccCCcCCHHHHHHHHHHHhCCCH-----HHHhCCCCCcccchHHHHHHHHHHHHcCCCHHHHH
Confidence            10               11235788888888888876544     23333333333332   366666666666665555

>KOG0733|consensus

Probab=99.75  E-value=3.5e-17  Score=164.98  Aligned_cols=229  Identities=17%  Similarity=0.225  Sum_probs=157.8

Q ss_pred             CCCCChHHHHHHHHHHHHhhhcc---------CCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVNN---------ETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAAS  264 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~---------~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~  264 (490)
                      +++-+.++...+|..++.+-++.         ..+.++||+||||||||.||++++++.+    ..|+.|-++.+     
T Consensus       511 ~dIGaL~~vR~eL~~aI~~PiK~pd~~k~lGi~~PsGvLL~GPPGCGKTLlAKAVANEag----~NFisVKGPEL-----  581 (802)
T KOG0733|consen  511 DDIGALEEVRLELNMAILAPIKRPDLFKALGIDAPSGVLLCGPPGCGKTLLAKAVANEAG----ANFISVKGPEL-----  581 (802)
T ss_pred             hhcccHHHHHHHHHHHHhhhccCHHHHHHhCCCCCCceEEeCCCCccHHHHHHHHhhhcc----CceEeecCHHH-----
Confidence            67788888888888777655432         2578999999999999999999999954    66677755543     


Q ss_pred             HHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccC--------HHHHHHhH-hCC-CCCCCcEEE
Q psy200          265 VYETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRK--------QTILYTIF-EWP-SIPGSKLVL  334 (490)
Q Consensus       265 l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~--------~~~L~~l~-~~~-~~~~~~vil  334 (490)
                       ++        .|.|+++..++..|.++..  ..|||||+||+|.|...+        ...+.+|+ ++. ......|.|
T Consensus       582 -lN--------kYVGESErAVR~vFqRAR~--saPCVIFFDEiDaL~p~R~~~~s~~s~RvvNqLLtElDGl~~R~gV~v  650 (802)
T KOG0733|consen  582 -LN--------KYVGESERAVRQVFQRARA--SAPCVIFFDEIDALVPRRSDEGSSVSSRVVNQLLTELDGLEERRGVYV  650 (802)
T ss_pred             -HH--------HHhhhHHHHHHHHHHHhhc--CCCeEEEecchhhcCcccCCCCchhHHHHHHHHHHHhcccccccceEE
Confidence             22        5678899999999998776  569999999999998663        22344443 333 235678999


Q ss_pred             EEecCCCChhHhhhHHhh--hccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHH--HhhC-CHH
Q psy200          335 VGVANALDLTDRMLPRLQ--ANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVA--AVSG-DIR  409 (490)
Q Consensus       335 I~~tn~~~~~~~l~~~l~--~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~--~~~G-d~r  409 (490)
                      |++||+.|+.+   +++.  .||+   ..+++..++.+|..+||+...+.. ....-++-.++.|++...  +++| |+-
T Consensus       651 iaATNRPDiID---pAiLRPGRlD---k~LyV~lPn~~eR~~ILK~~tkn~-k~pl~~dVdl~eia~~~~c~gftGADLa  723 (802)
T KOG0733|consen  651 IAATNRPDIID---PAILRPGRLD---KLLYVGLPNAEERVAILKTITKNT-KPPLSSDVDLDEIARNTKCEGFTGADLA  723 (802)
T ss_pred             EeecCCCcccc---hhhcCCCccC---ceeeecCCCHHHHHHHHHHHhccC-CCCCCcccCHHHHhhcccccCCchhhHH
Confidence            99999876654   3333  2444   689999999999999999988753 222334455777876322  2222 222


Q ss_pred             HHHHHHHHHHHHHHhccccC-------Cc----ccccCHHHHHHHHHHhccCcc
Q psy200          410 KAIDITNHLIDLTYDNVKEN-------GE----VTGIGLKEVLGVISSVYCTSQ  452 (490)
Q Consensus       410 ~ai~ll~~a~~~a~~~~~~~-------~~----~~~It~~~v~~a~~~~~~~~~  452 (490)
                         .+++.|...|.++...+       ..    ...++..||.+|+..+.++..
T Consensus       724 ---aLvreAsi~AL~~~~~~~~~~~~~~~~~~~~~~~t~~hF~eA~~~i~pSv~  774 (802)
T KOG0733|consen  724 ---ALVREASILALRESLFEIDSSEDDVTVRSSTIIVTYKHFEEAFQRIRPSVS  774 (802)
T ss_pred             ---HHHHHHHHHHHHHHHhhccccCcccceeeeeeeecHHHHHHHHHhcCCCcc
Confidence               35666655554432211       11    224778899999998886544

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=99.75  E-value=1.8e-16  Score=162.71  Aligned_cols=243  Identities=16%  Similarity=0.236  Sum_probs=158.5

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhc-CCceEEEEeccCCCCHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcC
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIK-DAFKTIYINCNSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFDTK  296 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~-~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~  296 (490)
                      ..+.++|||++|+|||+|++++++++... .+..++|+++.      ++...+...+...    ....+.+    .+.. 
T Consensus       135 ~~n~l~l~G~~G~GKThL~~ai~~~l~~~~~~~~v~yi~~~------~~~~~~~~~~~~~----~~~~~~~----~~~~-  199 (405)
T TIGR00362       135 AYNPLFIYGGVGLGKTHLLHAIGNEILENNPNAKVVYVSSE------KFTNDFVNALRNN----KMEEFKE----KYRS-  199 (405)
T ss_pred             cCCeEEEECCCCCcHHHHHHHHHHHHHHhCCCCcEEEEEHH------HHHHHHHHHHHcC----CHHHHHH----HHHh-
Confidence            34679999999999999999999998633 25678888643      3444444444321    2223322    2322 


Q ss_pred             CCeEEEEEecCcccccc--CHHHHHHhHhCCCCCCCcEEEEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHH
Q psy200          297 HKSILLILDEIDALESR--KQTILYTIFEWPSIPGSKLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILE  374 (490)
Q Consensus       297 ~~~~vI~IDEid~l~~~--~~~~L~~l~~~~~~~~~~vilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~  374 (490)
                        .-+|+|||+|.+...  .++.++.+++.....+..+ +|++.........+.+++.+||..+ ..+.|.+++.+++..
T Consensus       200 --~dlLiiDDi~~l~~~~~~~~~l~~~~n~~~~~~~~i-iits~~~p~~l~~l~~~l~SRl~~g-~~v~i~~pd~~~r~~  275 (405)
T TIGR00362       200 --VDLLLIDDIQFLAGKERTQEEFFHTFNALHENGKQI-VLTSDRPPKELPGLEERLRSRFEWG-LVVDIEPPDLETRLA  275 (405)
T ss_pred             --CCEEEEehhhhhcCCHHHHHHHHHHHHHHHHCCCCE-EEecCCCHHHHhhhhhhhhhhccCC-eEEEeCCCCHHHHHH
Confidence              349999999998765  3566777665433333343 3333333333444678899999643 369999999999999


Q ss_pred             HHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHhccccC--------------CcccccCHHHH
Q psy200          375 IISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITNHLIDLTYDNVKEN--------------GEVTGIGLKEV  440 (490)
Q Consensus       375 il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll~~a~~~a~~~~~~~--------------~~~~~It~~~v  440 (490)
                      |++.++...  ...+++++++.|++   ...||+|.+..++.+....+...+..-              .....|+.++|
T Consensus       276 il~~~~~~~--~~~l~~e~l~~ia~---~~~~~~r~l~~~l~~l~~~a~~~~~~it~~~~~~~L~~~~~~~~~~it~~~I  350 (405)
T TIGR00362       276 ILQKKAEEE--GLELPDEVLEFIAK---NIRSNVRELEGALNRLLAYASLTGKPITLELAKEALKDLLRAKKKEITIENI  350 (405)
T ss_pred             HHHHHHHHc--CCCCCHHHHHHHHH---hcCCCHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccCCCCCHHHH
Confidence            999999876  46789999999998   788999988777776655554322100              11345888888


Q ss_pred             HHHHHHhccCccccccccccCCCChHhHHHH---HHHHHHhcCCCCCCcccC
Q psy200          441 LGVISSVYCTSQSLHCSKDEDSFPLQQKLAL---ASLLLLKSRPNVKDVTLG  489 (490)
Q Consensus       441 ~~a~~~~~~~~~~~~~~~~l~~L~~~qk~vL---~al~~~~~~~~~~~~~~g  489 (490)
                      .+++.+.++-..     +.+.+-......+.   .||+++.+..+.+...||
T Consensus       351 ~~~Va~~~~v~~-----~~l~~~~r~~~~~~~R~~amyl~~~~~~~s~~~ig  397 (405)
T TIGR00362       351 QEVVAKYYNIKV-----SDLKSKKRTRNIVRPRQIAMYLAKELTDLSLPEIG  397 (405)
T ss_pred             HHHHHHHcCCCH-----HHHhCCCCCcccchHHHHHHHHHHHHcCCCHHHHH
Confidence            888888776444     33333333333322   366666666666655555

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).

>PRK14953 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.74  E-value=1.7e-16  Score=164.59  Aligned_cols=233  Identities=18%  Similarity=0.216  Sum_probs=153.7

Q ss_pred             CCCCcchHHHhhcCCCCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccC
Q psy200          179 FSEDKPKVEEKAKDSCELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNS  258 (490)
Q Consensus       179 ~~~~~~~~~~~~l~~~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~  258 (490)
                      +|..+|+|...    ++++|++..+..|..++..   +.-.+.++|+||+|+|||++|+.+++.+.+.....  .-.|..
T Consensus         5 ~~~~kyRP~~f----~diiGq~~i~~~L~~~i~~---~~i~hayLf~Gp~G~GKTtlAr~lAk~L~c~~~~~--~~pc~~   75 (486)
T PRK14953          5 PFARKYRPKFF----KEVIGQEIVVRILKNAVKL---QRVSHAYIFAGPRGTGKTTIARILAKVLNCLNPQE--GEPCGK   75 (486)
T ss_pred             HHHHhhCCCcH----HHccChHHHHHHHHHHHHc---CCCCeEEEEECCCCCCHHHHHHHHHHHhcCcCCCC--CCCCCc
Confidence            56778888777    8999999999998888864   23445577999999999999999999875311100  001111


Q ss_pred             CCCHHHHHHHHHHH---hcCCCCCCcHHHHHHHHHHHH--hcCCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEE
Q psy200          259 VRNAASVYETIVNE---LKLKPGGKSERHQLGAILKYF--DTKHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLV  333 (490)
Q Consensus       259 ~~~~~~l~~~i~~~---l~~~~~~~s~~~~~~~l~~~l--~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vi  333 (490)
                      +.+...+...-..+   +.. ......+.++.......  -..++..|+||||+|.|....++.|...++.+   ...++
T Consensus        76 c~nc~~i~~g~~~d~~eida-as~~gvd~ir~I~~~~~~~P~~~~~KVvIIDEad~Lt~~a~naLLk~LEep---p~~~v  151 (486)
T PRK14953         76 CENCVEIDKGSFPDLIEIDA-ASNRGIDDIRALRDAVSYTPIKGKYKVYIIDEAHMLTKEAFNALLKTLEEP---PPRTI  151 (486)
T ss_pred             cHHHHHHhcCCCCcEEEEeC-ccCCCHHHHHHHHHHHHhCcccCCeeEEEEEChhhcCHHHHHHHHHHHhcC---CCCeE
Confidence            11111100000000   000 01122333333222211  11255679999999999877777777777643   33445


Q ss_pred             EEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHH
Q psy200          334 LVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAID  413 (490)
Q Consensus       334 lI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~  413 (490)
                      +|.+++.   .+.+.+.+.+||.    .+.|.+++.+++..++..++...+  ..+++++++.|++   ...|++|.+++
T Consensus       152 ~Il~tt~---~~kl~~tI~SRc~----~i~f~~ls~~el~~~L~~i~k~eg--i~id~~al~~La~---~s~G~lr~al~  219 (486)
T PRK14953        152 FILCTTE---YDKIPPTILSRCQ----RFIFSKPTKEQIKEYLKRICNEEK--IEYEEKALDLLAQ---ASEGGMRDAAS  219 (486)
T ss_pred             EEEEECC---HHHHHHHHHHhce----EEEcCCCCHHHHHHHHHHHHHHcC--CCCCHHHHHHHHH---HcCCCHHHHHH
Confidence            5545542   4556778889985    799999999999999999998873  5689999999997   67799999999


Q ss_pred             HHHHHHHHHHhccccCCcccccCHHHHHHHHH
Q psy200          414 ITNHLIDLTYDNVKENGEVTGIGLKEVLGVIS  445 (490)
Q Consensus       414 ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~~  445 (490)
                      +|+.++..+  .       ..|+.++|..++.
T Consensus       220 ~Ldkl~~~~--~-------~~It~~~V~~~lg  242 (486)
T PRK14953        220 LLDQASTYG--E-------GKVTIKVVEEFLG  242 (486)
T ss_pred             HHHHHHHhc--C-------CCcCHHHHHHHhC
Confidence            999987442  2       2577777777543

>TIGR01242 26Sp45 26S proteasome subunit P45 family

Probab=99.74  E-value=7.1e-17  Score=163.26  Aligned_cols=218  Identities=17%  Similarity=0.202  Sum_probs=145.0

Q ss_pred             CCCCChHHHHHHHHHHHHhhhcc---------CCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVNN---------ETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAAS  264 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~---------~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~  264 (490)
                      +++.|+++++++|.+++...+..         ..+.+++|+||||||||++|+++++++.    ..++.+.+.      .
T Consensus       122 ~di~Gl~~~~~~l~~~i~~~~~~~~~~~~~g~~~p~gvLL~GppGtGKT~lakaia~~l~----~~~~~v~~~------~  191 (364)
T TIGR01242       122 EDIGGLEEQIREIREAVELPLKHPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAHETN----ATFIRVVGS------E  191 (364)
T ss_pred             HHhCChHHHHHHHHHHHHHHhcCHHHHHhcCCCCCceEEEECCCCCCHHHHHHHHHHhCC----CCEEecchH------H
Confidence            68999999999999988654332         2467899999999999999999999875    344444322      2


Q ss_pred             HHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccC-----------HHHHHHhHhCC--CCCCCc
Q psy200          265 VYETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRK-----------QTILYTIFEWP--SIPGSK  331 (490)
Q Consensus       265 l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~-----------~~~L~~l~~~~--~~~~~~  331 (490)
                      +...        +.+.....+...+..+.  ...++||||||+|.+....           +..+..++...  .....+
T Consensus       192 l~~~--------~~g~~~~~i~~~f~~a~--~~~p~il~iDEiD~l~~~~~~~~~~~~~~~~~~l~~ll~~ld~~~~~~~  261 (364)
T TIGR01242       192 LVRK--------YIGEGARLVREIFELAK--EKAPSIIFIDEIDAIAAKRTDSGTSGDREVQRTLMQLLAELDGFDPRGN  261 (364)
T ss_pred             HHHH--------hhhHHHHHHHHHHHHHH--hcCCcEEEhhhhhhhccccccCCCCccHHHHHHHHHHHHHhhCCCCCCC
Confidence            2211        12222333333333322  2457899999999985331           23444444321  123457


Q ss_pred             EEEEEecCCCChhHhhhHHhhh--ccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHH
Q psy200          332 LVLVGVANALDLTDRMLPRLQA--NVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIR  409 (490)
Q Consensus       332 vilI~~tn~~~~~~~l~~~l~~--R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r  409 (490)
                      +.||++||..   +.+++.+.+  ||.   ..+.|++|+.++..+|+..++......   .+..++.+++...+..  .+
T Consensus       262 v~vI~ttn~~---~~ld~al~r~grfd---~~i~v~~P~~~~r~~Il~~~~~~~~l~---~~~~~~~la~~t~g~s--g~  330 (364)
T TIGR01242       262 VKVIAATNRP---DILDPALLRPGRFD---RIIEVPLPDFEGRLEILKIHTRKMKLA---EDVDLEAIAKMTEGAS--GA  330 (364)
T ss_pred             EEEEEecCCh---hhCChhhcCcccCc---eEEEeCCcCHHHHHHHHHHHHhcCCCC---ccCCHHHHHHHcCCCC--HH
Confidence            8999999854   445566653  565   479999999999999999887654211   1123566665332222  33


Q ss_pred             HHHHHHHHHHHHHHhccccCCcccccCHHHHHHHHHHh
Q psy200          410 KAIDITNHLIDLTYDNVKENGEVTGIGLKEVLGVISSV  447 (490)
Q Consensus       410 ~ai~ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~~~~  447 (490)
                      .+..+|..|...|..++     ...|+.+||.+|+..+
T Consensus       331 dl~~l~~~A~~~a~~~~-----~~~i~~~d~~~a~~~~  363 (364)
T TIGR01242       331 DLKAICTEAGMFAIREE-----RDYVTMDDFIKAVEKV  363 (364)
T ss_pred             HHHHHHHHHHHHHHHhC-----CCccCHHHHHHHHHHh
Confidence            44468999999998888     6789999999999875

Many proteins may score above the trusted cutoff because an internal

>KOG1970|consensus

Probab=99.74  E-value=7.2e-17  Score=161.42  Aligned_cols=229  Identities=15%  Similarity=0.225  Sum_probs=141.8

Q ss_pred             CccccCCCCcchHHHhhcCCCCCCChHHHHHHHHHHHHhhh---ccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCce
Q psy200          174 PRKLLFSEDKPKVEEKAKDSCELPGREVQLEGIRQFLLGHV---NNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFK  250 (490)
Q Consensus       174 p~~~~~~~~~~~~~~~~l~~~~lvgre~~~~~l~~~L~~~~---~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~  250 (490)
                      ......|.++|.|...    ++|..|.+.+.+|.+||....   ..-..+.+||+||+||||||+++.++++++    +.
T Consensus        66 ~d~~elW~eKy~P~t~----eeLAVHkkKI~eVk~WL~~~~~~~~~l~~~iLLltGPsGcGKSTtvkvLskelg----~~  137 (634)
T KOG1970|consen   66 EDEFELWVEKYKPRTL----EELAVHKKKISEVKQWLKQVAEFTPKLGSRILLLTGPSGCGKSTTVKVLSKELG----YQ  137 (634)
T ss_pred             ccccchhHHhcCcccH----HHHhhhHHhHHHHHHHHHHHHHhccCCCceEEEEeCCCCCCchhHHHHHHHhhC----ce
Confidence            4567789999999999    999999999999999998322   223567899999999999999999999987    55


Q ss_pred             EEEEe-ccCCCCHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHh----------cCCCeEEEEEecCcccccc-CHHHH
Q psy200          251 TIYIN-CNSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFD----------TKHKSILLILDEIDALESR-KQTIL  318 (490)
Q Consensus       251 ~~~v~-~~~~~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~----------~~~~~~vI~IDEid~l~~~-~~~~L  318 (490)
                      ++.+. ...+.....+ +.--..+. .........+..++..+.+          ..+.+.+|+|||+.+.+.. ..+.+
T Consensus       138 ~~Ew~Npi~~~~~~~~-h~~t~~~~-~~~~s~L~~fesFler~~kyg~l~~~g~~~~~~~~liLveDLPn~~~~d~~~~f  215 (634)
T KOG1970|consen  138 LIEWSNPINLKEPENL-HNETSFLM-FPYQSQLAVFESFLLRATKYGSLQMSGDDLRTDKKLILVEDLPNQFYRDDSETF  215 (634)
T ss_pred             eeeecCCccccccccc-cccchhcc-cchhhHHHHHHHHHHHHHhhchhhhcccccccCceEEEeeccchhhhhhhHHHH
Confidence            55544 2222111100 00000000 0000112223333333322          1134679999999999876 44444


Q ss_pred             HHhHhCC-CCCCCcEEEEEecCC----CChhHhhh-HHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCC----
Q psy200          319 YTIFEWP-SIPGSKLVLVGVANA----LDLTDRML-PRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNM----  388 (490)
Q Consensus       319 ~~l~~~~-~~~~~~vilI~~tn~----~~~~~~l~-~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~----  388 (490)
                      ...+... ......+|+ ++|+.    .+..+++. ..+..+.++  ..|.|+|+...-+++.|...|..+.....    
T Consensus       216 ~evL~~y~s~g~~PlIf-~iTd~~~~g~nnq~rlf~~d~q~~~ri--~~IsFNPIa~T~MKK~L~ric~~e~~~~s~~k~  292 (634)
T KOG1970|consen  216 REVLRLYVSIGRCPLIF-IITDSLSNGNNNQDRLFPKDIQEEPRI--SNISFNPIAPTIMKKFLKRICRIEANKKSGIKV  292 (634)
T ss_pred             HHHHHHHHhcCCCcEEE-EEeccccCCCcchhhhchhhhhhccCc--ceEeecCCcHHHHHHHHHHHHHHhcccccCCcC
Confidence            4443322 233444444 44431    12233332 234433333  58999999999999999999988732211    


Q ss_pred             CCHHHHHHHHHHHHHhhCCHHHHHHHHHHH
Q psy200          389 FNASALQLLAGKVAAVSGDIRKAIDITNHL  418 (490)
Q Consensus       389 ~~~~~i~~i~~~i~~~~Gd~r~ai~ll~~a  418 (490)
                      -+...++.|+.   +..||+|.||+.|+..
T Consensus       293 ~~~~~v~~i~~---~s~GDIRsAInsLQls  319 (634)
T KOG1970|consen  293 PDTAEVELICQ---GSGGDIRSAINSLQLS  319 (634)
T ss_pred             chhHHHHHHHH---hcCccHHHHHhHhhhh
Confidence            12444566655   7999999999998876

>PRK14954 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.74  E-value=7.7e-17  Score=170.47  Aligned_cols=237  Identities=14%  Similarity=0.191  Sum_probs=159.6

Q ss_pred             cchHHHhhcCCCCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCce------EEEEec
Q psy200          183 KPKVEEKAKDSCELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFK------TIYINC  256 (490)
Q Consensus       183 ~~~~~~~~l~~~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~------~~~v~~  256 (490)
                      +|+|...    ++++|++..+..|..++..   +.-++.++|+||+|+||||+|+.+++.+.......      -..-.|
T Consensus         9 kyRP~~f----~eivGQe~i~~~L~~~i~~---~ri~ha~Lf~Gp~GvGKttlA~~lAk~L~c~~~~~~~~~~~~~~~~C   81 (620)
T PRK14954          9 KYRPSKF----ADITAQEHITHTIQNSLRM---DRVGHGYIFSGLRGVGKTTAARVFAKAVNCQRMIDDPVYLQEVTEPC   81 (620)
T ss_pred             HHCCCCH----HHhcCcHHHHHHHHHHHHc---CCCCeeEEEECCCCCCHHHHHHHHHHHhCCCCcCCccccccccCCCC
Confidence            5666656    8999999999988888763   34456699999999999999999999986422110      001134


Q ss_pred             cCCCCHHHHHHHHHHHhc-CC-CCCCcHHHHHHHHHHHHh--cCCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcE
Q psy200          257 NSVRNAASVYETIVNELK-LK-PGGKSERHQLGAILKYFD--TKHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKL  332 (490)
Q Consensus       257 ~~~~~~~~l~~~i~~~l~-~~-~~~~s~~~~~~~l~~~l~--~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~v  332 (490)
                      ..+.+...+..--.-.+. .. ....+.+++++.+.....  ..+...|+||||+|.|....++.|...++.+   ....
T Consensus        82 g~C~sC~~~~~g~~~n~~~~d~~s~~~vd~Ir~l~e~~~~~P~~~~~KVvIIdEad~Lt~~a~naLLK~LEeP---p~~t  158 (620)
T PRK14954         82 GECESCRDFDAGTSLNISEFDAASNNSVDDIRQLRENVRYGPQKGRYRVYIIDEVHMLSTAAFNAFLKTLEEP---PPHA  158 (620)
T ss_pred             ccCHHHHHHhccCCCCeEEecccccCCHHHHHHHHHHHHhhhhcCCCEEEEEeChhhcCHHHHHHHHHHHhCC---CCCe
Confidence            444332222110000000 00 011235566655444321  1244569999999999887788888877643   3345


Q ss_pred             EEEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHH
Q psy200          333 VLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAI  412 (490)
Q Consensus       333 ilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai  412 (490)
                      ++|.+++.   ...+.+.+++||.    .+.|.+++.+++..++...+..+  ...+++++++.|++   ...||++.++
T Consensus       159 v~IL~t~~---~~kLl~TI~SRc~----~vef~~l~~~ei~~~L~~i~~~e--gi~I~~eal~~La~---~s~Gdlr~al  226 (620)
T PRK14954        159 IFIFATTE---LHKIPATIASRCQ----RFNFKRIPLDEIQSQLQMICRAE--GIQIDADALQLIAR---KAQGSMRDAQ  226 (620)
T ss_pred             EEEEEeCC---hhhhhHHHHhhce----EEecCCCCHHHHHHHHHHHHHHc--CCCCCHHHHHHHHH---HhCCCHHHHH
Confidence            55555542   4677888999985    89999999999999999988876  35689999999987   7789999999


Q ss_pred             HHHHHHHHHHHhccccCCcccccCHHHHHHHHH
Q psy200          413 DITNHLIDLTYDNVKENGEVTGIGLKEVLGVIS  445 (490)
Q Consensus       413 ~ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~~  445 (490)
                      +.++....++...+.    ...|+.++|.+.+.
T Consensus       227 ~eLeKL~~y~~~~~~----~~~It~~~V~~lv~  255 (620)
T PRK14954        227 SILDQVIAFSVGSEA----EKVIAYQGVAELLN  255 (620)
T ss_pred             HHHHHHHHhcccccc----CCccCHHHHHHHHc
Confidence            999988776632211    24688877776653

>KOG0728|consensus

Probab=99.74  E-value=5.7e-17  Score=147.11  Aligned_cols=225  Identities=16%  Similarity=0.227  Sum_probs=158.5

Q ss_pred             CCCCChHHHHHHHHHHHHhhhc---------cCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVN---------NETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAAS  264 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~---------~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~  264 (490)
                      +.+-|.+++++++.+.++-.++         -..+++++||||||+|||.|+++++++    ..+.|+.++++      +
T Consensus       147 eMiGgLd~QIkeIkEVIeLPvKHPELF~aLGIaQPKGvlLygppgtGktLlaraVahh----t~c~firvsgs------e  216 (404)
T KOG0728|consen  147 EMIGGLDKQIKEIKEVIELPVKHPELFEALGIAQPKGVLLYGPPGTGKTLLARAVAHH----TDCTFIRVSGS------E  216 (404)
T ss_pred             HHhccHHHHHHHHHHHHhccccCHHHHHhcCCCCCcceEEecCCCCchhHHHHHHHhh----cceEEEEechH------H
Confidence            5567779999999987764432         236789999999999999999999987    44778888543      3


Q ss_pred             HHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccC-----------HHHHHHhHhC--CCCCCCc
Q psy200          265 VYETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRK-----------QTILYTIFEW--PSIPGSK  331 (490)
Q Consensus       265 l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~-----------~~~L~~l~~~--~~~~~~~  331 (490)
                      +..        .+.|.....+++.|.-+..  ..|.+||+||||.+...+           |..++.+++-  ......+
T Consensus       217 lvq--------k~igegsrmvrelfvmare--hapsiifmdeidsigs~r~e~~~ggdsevqrtmlellnqldgfeatkn  286 (404)
T KOG0728|consen  217 LVQ--------KYIGEGSRMVRELFVMARE--HAPSIIFMDEIDSIGSSRVESGSGGDSEVQRTMLELLNQLDGFEATKN  286 (404)
T ss_pred             HHH--------HHhhhhHHHHHHHHHHHHh--cCCceEeeecccccccccccCCCCccHHHHHHHHHHHHhccccccccc
Confidence            333        2334556667777765555  568999999999996442           3333343321  1345678


Q ss_pred             EEEEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHH
Q psy200          332 LVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKA  411 (490)
Q Consensus       332 vilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~a  411 (490)
                      +-+|.+||+.|+.+..   +. |-+.-...|.|+|++.+...+||+-+-++.+...   .-.++.|++++.+.+|.  ..
T Consensus       287 ikvimatnridild~a---ll-rpgridrkiefp~p~e~ar~~ilkihsrkmnl~r---gi~l~kiaekm~gasga--ev  357 (404)
T KOG0728|consen  287 IKVIMATNRIDILDPA---LL-RPGRIDRKIEFPPPNEEARLDILKIHSRKMNLTR---GINLRKIAEKMPGASGA--EV  357 (404)
T ss_pred             eEEEEeccccccccHh---hc-CCCcccccccCCCCCHHHHHHHHHHhhhhhchhc---ccCHHHHHHhCCCCccc--hh
Confidence            8999999988775543   22 2222224799999999999999886655542112   22367888866666664  23


Q ss_pred             HHHHHHHHHHHHhccccCCcccccCHHHHHHHHHHhccCcc
Q psy200          412 IDITNHLIDLTYDNVKENGEVTGIGLKEVLGVISSVYCTSQ  452 (490)
Q Consensus       412 i~ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~~~~~~~~~  452 (490)
                      -.+|..|.+.|.++.     .-.||.+||+.|+.++.....
T Consensus       358 k~vcteagm~alrer-----rvhvtqedfemav~kvm~k~~  393 (404)
T KOG0728|consen  358 KGVCTEAGMYALRER-----RVHVTQEDFEMAVAKVMQKDS  393 (404)
T ss_pred             hhhhhhhhHHHHHHh-----hccccHHHHHHHHHHHHhccc
Confidence            458999999998888     678999999999999875443

>PRK06305 DNA polymerase III subunits gamma and tau; Validated

Probab=99.74  E-value=1.4e-16  Score=164.22  Aligned_cols=232  Identities=16%  Similarity=0.187  Sum_probs=151.4

Q ss_pred             CCcchHHHhhcCCCCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCC
Q psy200          181 EDKPKVEEKAKDSCELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVR  260 (490)
Q Consensus       181 ~~~~~~~~~~l~~~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~  260 (490)
                      .++|+|...    ++++|++..++.|..++..   +.-++.++|+||+|+|||++|+.+++.+.......- .-.|..+.
T Consensus         8 ~~kyRP~~~----~diiGq~~~v~~L~~~i~~---~~i~ha~Lf~Gp~G~GKtt~A~~lAk~l~c~~~~~~-~~~c~~c~   79 (451)
T PRK06305          8 SRKYRPQTF----SEILGQDAVVAVLKNALRF---NRAAHAYLFSGIRGTGKTTLARIFAKALNCQNPTED-QEPCNQCA   79 (451)
T ss_pred             HHHhCCCCH----HHhcCcHHHHHHHHHHHHc---CCCceEEEEEcCCCCCHHHHHHHHHHHhcCCCcccC-CCCCcccH
Confidence            345666666    8999999999988888863   334567899999999999999999998853211000 00011110


Q ss_pred             CHHHHHHH---HHHHhcCCCCCCcHHHHHHHHHHHH--hcCCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEE
Q psy200          261 NAASVYET---IVNELKLKPGGKSERHQLGAILKYF--DTKHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLV  335 (490)
Q Consensus       261 ~~~~l~~~---i~~~l~~~~~~~s~~~~~~~l~~~l--~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI  335 (490)
                      +...+-..   -+..+.+. ...+.+++.+......  ...+...||||||+|.|....++.|...++..   ...+++|
T Consensus        80 ~C~~i~~~~~~d~~~i~g~-~~~gid~ir~i~~~l~~~~~~~~~kvvIIdead~lt~~~~n~LLk~lEep---~~~~~~I  155 (451)
T PRK06305         80 SCKEISSGTSLDVLEIDGA-SHRGIEDIRQINETVLFTPSKSRYKIYIIDEVHMLTKEAFNSLLKTLEEP---PQHVKFF  155 (451)
T ss_pred             HHHHHhcCCCCceEEeecc-ccCCHHHHHHHHHHHHhhhhcCCCEEEEEecHHhhCHHHHHHHHHHhhcC---CCCceEE
Confidence            10000000   00000000 0112334433222111  11245679999999999877778887777643   3456666


Q ss_pred             EecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHHHH
Q psy200          336 GVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDIT  415 (490)
Q Consensus       336 ~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll  415 (490)
                      ++++.   ...+.+.+++||.    .+.|.+++.+++..++...+...  ...+++++++.|++   ...||+|.+++.+
T Consensus       156 l~t~~---~~kl~~tI~sRc~----~v~f~~l~~~el~~~L~~~~~~e--g~~i~~~al~~L~~---~s~gdlr~a~~~L  223 (451)
T PRK06305        156 LATTE---IHKIPGTILSRCQ----KMHLKRIPEETIIDKLALIAKQE--GIETSREALLPIAR---AAQGSLRDAESLY  223 (451)
T ss_pred             EEeCC---hHhcchHHHHhce----EEeCCCCCHHHHHHHHHHHHHHc--CCCCCHHHHHHHHH---HcCCCHHHHHHHH
Confidence            66653   3677889999996    89999999999999999988876  35689999999997   6789999999999


Q ss_pred             HHHHHHHHhccccCCcccccCHHHHHHHHH
Q psy200          416 NHLIDLTYDNVKENGEVTGIGLKEVLGVIS  445 (490)
Q Consensus       416 ~~a~~~a~~~~~~~~~~~~It~~~v~~a~~  445 (490)
                      +.+....  .+       .|+.++|..++.
T Consensus       224 ekl~~~~--~~-------~It~~~V~~l~~  244 (451)
T PRK06305        224 DYVVGLF--PK-------SLDPDSVAKALG  244 (451)
T ss_pred             HHHHHhc--cC-------CcCHHHHHHHHC
Confidence            8875431  12       477777665543

>PRK06647 DNA polymerase III subunits gamma and tau; Validated

Probab=99.74  E-value=1.7e-16  Score=166.99  Aligned_cols=230  Identities=16%  Similarity=0.269  Sum_probs=157.0

Q ss_pred             CcchHHHhhcCCCCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCC
Q psy200          182 DKPKVEEKAKDSCELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRN  261 (490)
Q Consensus       182 ~~~~~~~~~l~~~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~  261 (490)
                      .+|+|...    ++++|++..++.|..++..   +.-++.++|+||+|+|||++|+.+++.+.......  ...|..+.+
T Consensus         8 ~kyRP~~f----~diiGqe~iv~~L~~~i~~---~~i~hayLf~Gp~G~GKTt~Ar~lAk~L~c~~~~~--~~pC~~C~~   78 (563)
T PRK06647          8 TKRRPRDF----NSLEGQDFVVETLKHSIES---NKIANAYIFSGPRGVGKTSSARAFARCLNCVNGPT--PMPCGECSS   78 (563)
T ss_pred             HHhCCCCH----HHccCcHHHHHHHHHHHHc---CCCCeEEEEECCCCCCHHHHHHHHHHhhccccCCC--CCCCccchH
Confidence            46666666    8999999999999998874   34556789999999999999999999986321110  012332222


Q ss_pred             HHHHHHHHHHHh-cCC-CCCCcHHHHHHHHHHHHh--cCCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEEEe
Q psy200          262 AASVYETIVNEL-KLK-PGGKSERHQLGAILKYFD--TKHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGV  337 (490)
Q Consensus       262 ~~~l~~~i~~~l-~~~-~~~~s~~~~~~~l~~~l~--~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI~~  337 (490)
                      ...+...-.-.+ ... ......+++++.......  ..++..|+||||+|.|....++.|...++.   ....++||++
T Consensus        79 C~~i~~~~~~dv~~idgas~~~vddIr~l~e~~~~~p~~~~~KVvIIDEa~~Ls~~a~naLLK~LEe---pp~~~vfI~~  155 (563)
T PRK06647         79 CKSIDNDNSLDVIEIDGASNTSVQDVRQIKEEIMFPPASSRYRVYIIDEVHMLSNSAFNALLKTIEE---PPPYIVFIFA  155 (563)
T ss_pred             HHHHHcCCCCCeEEecCcccCCHHHHHHHHHHHHhchhcCCCEEEEEEChhhcCHHHHHHHHHhhcc---CCCCEEEEEe
Confidence            222111000000 000 001234555554433221  124567999999999987777777776653   4456777777


Q ss_pred             cCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHHHHHH
Q psy200          338 ANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITNH  417 (490)
Q Consensus       338 tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll~~  417 (490)
                      ++.   ...+.+.+++||.    .+.|.+++.+++..++...+...  ...+++++++.|++   ...|++|.++++|++
T Consensus       156 tte---~~kL~~tI~SRc~----~~~f~~l~~~el~~~L~~i~~~e--gi~id~eAl~lLa~---~s~GdlR~alslLdk  223 (563)
T PRK06647        156 TTE---VHKLPATIKSRCQ----HFNFRLLSLEKIYNMLKKVCLED--QIKYEDEALKWIAY---KSTGSVRDAYTLFDQ  223 (563)
T ss_pred             cCC---hHHhHHHHHHhce----EEEecCCCHHHHHHHHHHHHHHc--CCCCCHHHHHHHHH---HcCCCHHHHHHHHHH
Confidence            753   3667789999996    79999999999999999988776  45689999999998   778999999999998


Q ss_pred             HHHHHHhccccCCcccccCHHHHHHHH
Q psy200          418 LIDLTYDNVKENGEVTGIGLKEVLGVI  444 (490)
Q Consensus       418 a~~~a~~~~~~~~~~~~It~~~v~~a~  444 (490)
                      ++..+  .+       .|+.+++..++
T Consensus       224 lis~~--~~-------~It~e~V~~ll  241 (563)
T PRK06647        224 VVSFS--DS-------DITLEQIRSKM  241 (563)
T ss_pred             HHhhc--CC-------CCCHHHHHHHh
Confidence            76542  22       46776666644

>CHL00181 cbbX CbbX; Provisional

Probab=99.74  E-value=1.1e-16  Score=155.48  Aligned_cols=203  Identities=17%  Similarity=0.153  Sum_probs=133.7

Q ss_pred             CCCCChHHHHHHHHHHHHhhhc-----------cCCCCeEEEECCCCCcHHHHHHHHHHHhhhc---CCceEEEEeccCC
Q psy200          194 CELPGREVQLEGIRQFLLGHVN-----------NETSGSMYISGPPGTGKSASLNLLVSRAEIK---DAFKTIYINCNSV  259 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~-----------~~~~~~ill~GppGtGKTtla~~l~~~l~~~---~~~~~~~v~~~~~  259 (490)
                      ++++|.++.+++|.+++.....           ...+.+++|+||||||||++|+++++.+...   ..-.++++++.  
T Consensus        23 ~~l~Gl~~vK~~i~e~~~~~~~~~~~~~~g~~~~~~~~~ill~G~pGtGKT~lAr~la~~~~~~g~~~~~~~~~v~~~--  100 (287)
T CHL00181         23 EELVGLAPVKTRIREIAALLLIDRLRKNLGLTSSNPGLHMSFTGSPGTGKTTVALKMADILYKLGYIKKGHLLTVTRD--  100 (287)
T ss_pred             HhcCCcHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCCceEEEECCCCCCHHHHHHHHHHHHHHcCCCCCCceEEecHH--
Confidence            5799998888887776532110           1134569999999999999999999886421   11245666532  


Q ss_pred             CCHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCcccccc---------CHHHHHHhHhCCCCCCC
Q psy200          260 RNAASVYETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESR---------KQTILYTIFEWPSIPGS  330 (490)
Q Consensus       260 ~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~---------~~~~L~~l~~~~~~~~~  330 (490)
                          ++...        +.|.+.......+.++.     ..||||||++.+...         .++.|..+++   ....
T Consensus       101 ----~l~~~--------~~g~~~~~~~~~l~~a~-----ggVLfIDE~~~l~~~~~~~~~~~e~~~~L~~~me---~~~~  160 (287)
T CHL00181        101 ----DLVGQ--------YIGHTAPKTKEVLKKAM-----GGVLFIDEAYYLYKPDNERDYGSEAIEILLQVME---NQRD  160 (287)
T ss_pred             ----HHHHH--------HhccchHHHHHHHHHcc-----CCEEEEEccchhccCCCccchHHHHHHHHHHHHh---cCCC
Confidence                22221        12223333344444321     239999999998422         2344444444   2335


Q ss_pred             cEEEEEecCCCCh--hHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHH-----
Q psy200          331 KLVLVGVANALDL--TDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAA-----  403 (490)
Q Consensus       331 ~vilI~~tn~~~~--~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~-----  403 (490)
                      .+++|++++...+  ...+.+.+.+||.   ..+.|++|+.+|+..|+...+...  ...++++++..+...+..     
T Consensus       161 ~~~vI~ag~~~~~~~~~~~np~L~sR~~---~~i~F~~~t~~el~~I~~~~l~~~--~~~l~~~~~~~L~~~i~~~~~~~  235 (287)
T CHL00181        161 DLVVIFAGYKDRMDKFYESNPGLSSRIA---NHVDFPDYTPEELLQIAKIMLEEQ--QYQLTPEAEKALLDYIKKRMEQP  235 (287)
T ss_pred             CEEEEEeCCcHHHHHHHhcCHHHHHhCC---ceEEcCCcCHHHHHHHHHHHHHHh--cCCCChhHHHHHHHHHHHhCCCC
Confidence            6777777753322  1223488999998   489999999999999999999876  455788888777765543     


Q ss_pred             hhCCHHHHHHHHHHHHHHHH
Q psy200          404 VSGDIRKAIDITNHLIDLTY  423 (490)
Q Consensus       404 ~~Gd~r~ai~ll~~a~~~a~  423 (490)
                      +.||.|.+.+++++++....
T Consensus       236 ~~GNaR~vrn~ve~~~~~~~  255 (287)
T CHL00181        236 LFANARSVRNALDRARMRQA  255 (287)
T ss_pred             CCccHHHHHHHHHHHHHHHH
Confidence            44889999999988876543

>KOG0739|consensus

Probab=99.74  E-value=1.7e-17  Score=154.08  Aligned_cols=185  Identities=17%  Similarity=0.241  Sum_probs=140.6

Q ss_pred             CCCCChHHHHHHHHHHHHhhhc--------cCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVN--------NETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASV  265 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~--------~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l  265 (490)
                      +++.|.+...+.|.+.+---++        ..+.+.+||||||||||+.||++|+.+..    -.|+.++.      .++
T Consensus       133 sDVAGLE~AKeALKEAVILPIKFPqlFtGkR~PwrgiLLyGPPGTGKSYLAKAVATEAn----STFFSvSS------SDL  202 (439)
T KOG0739|consen  133 SDVAGLEGAKEALKEAVILPIKFPQLFTGKRKPWRGILLYGPPGTGKSYLAKAVATEAN----STFFSVSS------SDL  202 (439)
T ss_pred             hhhccchhHHHHHHhheeecccchhhhcCCCCcceeEEEeCCCCCcHHHHHHHHHhhcC----CceEEeeh------HHH
Confidence            7899999999999886532221        22568999999999999999999999854    45566643      333


Q ss_pred             HHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCH------------HHHHHhHhCCCCCCCcEE
Q psy200          266 YETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQ------------TILYTIFEWPSIPGSKLV  333 (490)
Q Consensus       266 ~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~------------~~L~~l~~~~~~~~~~vi  333 (490)
                      ++        .|.|.++.-+...|+-+..  .+|.||||||||.++..+.            +.|.++-. .......++
T Consensus       203 vS--------KWmGESEkLVknLFemARe--~kPSIIFiDEiDslcg~r~enEseasRRIKTEfLVQMqG-VG~d~~gvL  271 (439)
T KOG0739|consen  203 VS--------KWMGESEKLVKNLFEMARE--NKPSIIFIDEIDSLCGSRSENESEASRRIKTEFLVQMQG-VGNDNDGVL  271 (439)
T ss_pred             HH--------HHhccHHHHHHHHHHHHHh--cCCcEEEeehhhhhccCCCCCchHHHHHHHHHHHHhhhc-cccCCCceE
Confidence            33        5667788888888775554  6799999999999986631            22322222 234567899


Q ss_pred             EEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCC
Q psy200          334 LVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGD  407 (490)
Q Consensus       334 lI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd  407 (490)
                      |+|+||   +++.++..+++||.   .+|+++-+.......+++-++...  .+.+++..++.++++..+++|.
T Consensus       272 VLgATN---iPw~LDsAIRRRFe---kRIYIPLPe~~AR~~MF~lhlG~t--p~~LT~~d~~eL~~kTeGySGs  337 (439)
T KOG0739|consen  272 VLGATN---IPWVLDSAIRRRFE---KRIYIPLPEAHARARMFKLHLGDT--PHVLTEQDFKELARKTEGYSGS  337 (439)
T ss_pred             EEecCC---CchhHHHHHHHHhh---cceeccCCcHHHhhhhheeccCCC--ccccchhhHHHHHhhcCCCCcC
Confidence            999998   78888999999998   578888888888888888777765  6788999999999988888874

>PRK14948 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.73  E-value=8.9e-17  Score=170.93  Aligned_cols=215  Identities=20%  Similarity=0.261  Sum_probs=152.9

Q ss_pred             CCCCcchHHHhhcCCCCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccC
Q psy200          179 FSEDKPKVEEKAKDSCELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNS  258 (490)
Q Consensus       179 ~~~~~~~~~~~~l~~~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~  258 (490)
                      +|..+|++...    ++++|++..++.|..++..   +...+.+||+||+|+|||++|+.+++.+.+........-.|..
T Consensus         5 pl~~kyRP~~f----~~liGq~~i~~~L~~~l~~---~rl~~a~Lf~Gp~G~GKttlA~~lAk~L~c~~~~~~~~~~Cg~   77 (620)
T PRK14948          5 PLHHKYRPQRF----DELVGQEAIATTLKNALIS---NRIAPAYLFTGPRGTGKTSSARILAKSLNCLNSDKPTPEPCGK   77 (620)
T ss_pred             hHHHHhCCCcH----hhccChHHHHHHHHHHHHc---CCCCceEEEECCCCCChHHHHHHHHHHhcCCCcCCCCCCCCcc
Confidence            45667877767    8999999999999988874   3345789999999999999999999998632211111112332


Q ss_pred             CCCHHHHHHHHHHHhcC------CCCCCcHHHHHHHHHHHHhc--CCCeEEEEEecCccccccCHHHHHHhHhCCCCCCC
Q psy200          259 VRNAASVYETIVNELKL------KPGGKSERHQLGAILKYFDT--KHKSILLILDEIDALESRKQTILYTIFEWPSIPGS  330 (490)
Q Consensus       259 ~~~~~~l~~~i~~~l~~------~~~~~s~~~~~~~l~~~l~~--~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~  330 (490)
                      +    ..+..+......      .......+.+++.+..+...  .++..||||||+|.|....++.|+..++.   ...
T Consensus        78 C----~~C~~i~~g~h~D~~ei~~~~~~~vd~IReii~~a~~~p~~~~~KViIIDEad~Lt~~a~naLLK~LEe---Pp~  150 (620)
T PRK14948         78 C----ELCRAIAAGNALDVIEIDAASNTGVDNIRELIERAQFAPVQARWKVYVIDECHMLSTAAFNALLKTLEE---PPP  150 (620)
T ss_pred             c----HHHHHHhcCCCccEEEEeccccCCHHHHHHHHHHHhhChhcCCceEEEEECccccCHHHHHHHHHHHhc---CCc
Confidence            2    122222111110      11224455666665443321  24567999999999988778888887773   345


Q ss_pred             cEEEEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHH
Q psy200          331 KLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRK  410 (490)
Q Consensus       331 ~vilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~  410 (490)
                      .++||++++.   ..++.+.+++||.    .+.|.+++.+++...+...+..+  ...++++++..|++   ...|++|.
T Consensus       151 ~tvfIL~t~~---~~~llpTIrSRc~----~~~f~~l~~~ei~~~L~~ia~ke--gi~is~~al~~La~---~s~G~lr~  218 (620)
T PRK14948        151 RVVFVLATTD---PQRVLPTIISRCQ----RFDFRRIPLEAMVQHLSEIAEKE--SIEIEPEALTLVAQ---RSQGGLRD  218 (620)
T ss_pred             CeEEEEEeCC---hhhhhHHHHhhee----EEEecCCCHHHHHHHHHHHHHHh--CCCCCHHHHHHHHH---HcCCCHHH
Confidence            6777777763   4568889999996    89999999999999999888776  35588999999987   67899999


Q ss_pred             HHHHHHHHH
Q psy200          411 AIDITNHLI  419 (490)
Q Consensus       411 ai~ll~~a~  419 (490)
                      ++++++...
T Consensus       219 A~~lLekls  227 (620)
T PRK14948        219 AESLLDQLS  227 (620)
T ss_pred             HHHHHHHHH
Confidence            999988754

>PRK14950 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.73  E-value=1.1e-16  Score=170.63  Aligned_cols=229  Identities=16%  Similarity=0.205  Sum_probs=154.1

Q ss_pred             CCCcchHHHhhcCCCCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCC
Q psy200          180 SEDKPKVEEKAKDSCELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSV  259 (490)
Q Consensus       180 ~~~~~~~~~~~l~~~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~  259 (490)
                      |.++|++...    ++++|+++.++.|..++..   +..++.++|+||+|+|||++++.+++.+....... ..-.|..+
T Consensus         6 l~~kyRP~~~----~eiiGq~~~~~~L~~~i~~---~~i~~a~Lf~Gp~G~GKTtlA~~lA~~l~c~~~~~-~~~~c~~c   77 (585)
T PRK14950          6 LYRKWRSQTF----AELVGQEHVVQTLRNAIAE---GRVAHAYLFTGPRGVGKTSTARILAKAVNCTTNDP-KGRPCGTC   77 (585)
T ss_pred             HHHHhCCCCH----HHhcCCHHHHHHHHHHHHh---CCCceEEEEECCCCCCHHHHHHHHHHHhcCCCCCC-CCCCCccC
Confidence            4467877777    9999999999998888864   33456679999999999999999999885221100 00122222


Q ss_pred             CCHHHHHHHHHHHhcC-----CC-CCCcHHHHHHHHHHHHh--cCCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCc
Q psy200          260 RNAASVYETIVNELKL-----KP-GGKSERHQLGAILKYFD--TKHKSILLILDEIDALESRKQTILYTIFEWPSIPGSK  331 (490)
Q Consensus       260 ~~~~~l~~~i~~~l~~-----~~-~~~s~~~~~~~l~~~l~--~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~  331 (490)
                          .....+......     .. ...+.+++++.+.....  ..+...||||||+|.|....++.|...++..   ...
T Consensus        78 ----~~c~~i~~~~~~d~~~i~~~~~~~vd~ir~ii~~~~~~p~~~~~kVvIIDEa~~L~~~a~naLLk~LEep---p~~  150 (585)
T PRK14950         78 ----EMCRAIAEGSAVDVIEMDAASHTSVDDAREIIERVQFRPALARYKVYIIDEVHMLSTAAFNALLKTLEEP---PPH  150 (585)
T ss_pred             ----HHHHHHhcCCCCeEEEEeccccCCHHHHHHHHHHHhhCcccCCeEEEEEeChHhCCHHHHHHHHHHHhcC---CCC
Confidence                122222221111     00 12334455444332221  1245679999999999887777787777643   234


Q ss_pred             EEEEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHH
Q psy200          332 LVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKA  411 (490)
Q Consensus       332 vilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~a  411 (490)
                      ++||.+++.   .+.+.+.+++||.    .+.|.+++..++..++...+...  ...+++++++.|++   ...||++.+
T Consensus       151 tv~Il~t~~---~~kll~tI~SR~~----~i~f~~l~~~el~~~L~~~a~~e--gl~i~~eal~~La~---~s~Gdlr~a  218 (585)
T PRK14950        151 AIFILATTE---VHKVPATILSRCQ----RFDFHRHSVADMAAHLRKIAAAE--GINLEPGALEAIAR---AATGSMRDA  218 (585)
T ss_pred             eEEEEEeCC---hhhhhHHHHhccc----eeeCCCCCHHHHHHHHHHHHHHc--CCCCCHHHHHHHHH---HcCCCHHHH
Confidence            555555542   4557788899985    79999999999999999988876  35689999999987   677999999


Q ss_pred             HHHHHHHHHHHHhccccCCcccccCHHHHHHHH
Q psy200          412 IDITNHLIDLTYDNVKENGEVTGIGLKEVLGVI  444 (490)
Q Consensus       412 i~ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~  444 (490)
                      ++.|+.....  . +      ..|+.+++...+
T Consensus       219 l~~LekL~~y--~-~------~~It~e~V~~ll  242 (585)
T PRK14950        219 ENLLQQLATT--Y-G------GEISLSQVQSLL  242 (585)
T ss_pred             HHHHHHHHHh--c-C------CCCCHHHHHHHh
Confidence            9999876542  1 2      357777776543

>PRK08727 hypothetical protein; Validated

Probab=99.73  E-value=4.7e-16  Score=147.19  Aligned_cols=208  Identities=14%  Similarity=0.218  Sum_probs=140.8

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHh
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNEL  273 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l  273 (490)
                      +.++|-...+..+.....    +.....++|+|++|+|||+|++++++++.. .+..++|++....      .       
T Consensus        20 ~f~~~~~n~~~~~~~~~~----~~~~~~l~l~G~~G~GKThL~~a~~~~~~~-~~~~~~y~~~~~~------~-------   81 (233)
T PRK08727         20 SYIAAPDGLLAQLQALAA----GQSSDWLYLSGPAGTGKTHLALALCAAAEQ-AGRSSAYLPLQAA------A-------   81 (233)
T ss_pred             hccCCcHHHHHHHHHHHh----ccCCCeEEEECCCCCCHHHHHHHHHHHHHH-cCCcEEEEeHHHh------h-------
Confidence            345555555544443332    234467999999999999999999988753 3456777753221      1       


Q ss_pred             cCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCcccccc--CHHHHHHhHhCCCCCCCcEEEEEecC-CCChhHhhhHH
Q psy200          274 KLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESR--KQTILYTIFEWPSIPGSKLVLVGVAN-ALDLTDRMLPR  350 (490)
Q Consensus       274 ~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~--~~~~L~~l~~~~~~~~~~vilI~~tn-~~~~~~~l~~~  350 (490)
                               ..+.+.+.. +   .+.-+|+|||++.+...  .+..++++++.....+..+++  +++ ....+..+++.
T Consensus        82 ---------~~~~~~~~~-l---~~~dlLiIDDi~~l~~~~~~~~~lf~l~n~~~~~~~~vI~--ts~~~p~~l~~~~~d  146 (233)
T PRK08727         82 ---------GRLRDALEA-L---EGRSLVALDGLESIAGQREDEVALFDFHNRARAAGITLLY--TARQMPDGLALVLPD  146 (233)
T ss_pred             ---------hhHHHHHHH-H---hcCCEEEEeCcccccCChHHHHHHHHHHHHHHHcCCeEEE--ECCCChhhhhhhhHH
Confidence                     111112222 2   23449999999998754  345677776544333333333  343 33334445789


Q ss_pred             hhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHhccccCC
Q psy200          351 LQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITNHLIDLTYDNVKENG  430 (490)
Q Consensus       351 l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll~~a~~~a~~~~~~~~  430 (490)
                      +++|+..+ ..+.|++++.+++..++++++...  ...+++++++.|++   ...||+|.++++++.....+...+    
T Consensus       147 L~SRl~~~-~~~~l~~~~~e~~~~iL~~~a~~~--~l~l~~e~~~~La~---~~~rd~r~~l~~L~~l~~~~~~~~----  216 (233)
T PRK08727        147 LRSRLAQC-IRIGLPVLDDVARAAVLRERAQRR--GLALDEAAIDWLLT---HGERELAGLVALLDRLDRESLAAK----  216 (233)
T ss_pred             HHHHHhcC-ceEEecCCCHHHHHHHHHHHHHHc--CCCCCHHHHHHHHH---hCCCCHHHHHHHHHHHHHHHHHhC----
Confidence            99997543 379999999999999999988765  46789999999998   677999999999998775555444    


Q ss_pred             cccccCHHHHHHHHHH
Q psy200          431 EVTGIGLKEVLGVISS  446 (490)
Q Consensus       431 ~~~~It~~~v~~a~~~  446 (490)
                        ..||.+.+.+++..
T Consensus       217 --~~it~~~~~~~l~~  230 (233)
T PRK08727        217 --RRVTVPFLRRVLEE  230 (233)
T ss_pred             --CCCCHHHHHHHHhh
Confidence              37999999988753

>PRK14970 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.72  E-value=3.4e-16  Score=158.75  Aligned_cols=216  Identities=17%  Similarity=0.259  Sum_probs=151.4

Q ss_pred             CCCCcchHHHhhcCCCCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhc------C--Cce
Q psy200          179 FSEDKPKVEEKAKDSCELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIK------D--AFK  250 (490)
Q Consensus       179 ~~~~~~~~~~~~l~~~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~------~--~~~  250 (490)
                      .|.++|+|...    ++++|++..++.+..++..   +..+++++||||+|+|||++++.+++.+...      .  .+.
T Consensus         6 ~~~~k~rP~~~----~~iig~~~~~~~l~~~i~~---~~~~~~~L~~G~~G~GKt~~a~~la~~l~~~~~~~~~~~~~~~   78 (367)
T PRK14970          6 VSARKYRPQTF----DDVVGQSHITNTLLNAIEN---NHLAQALLFCGPRGVGKTTCARILARKINQPGYDDPNEDFSFN   78 (367)
T ss_pred             HHHHHHCCCcH----HhcCCcHHHHHHHHHHHHc---CCCCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCCcc
Confidence            35567777777    9999999999998888864   3456689999999999999999999987531      1  123


Q ss_pred             EEEEeccCCCCHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHh--cCCCeEEEEEecCccccccCHHHHHHhHhCCCCC
Q psy200          251 TIYINCNSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFD--TKHKSILLILDEIDALESRKQTILYTIFEWPSIP  328 (490)
Q Consensus       251 ~~~v~~~~~~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~--~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~  328 (490)
                      ++.++....                    ...+.+.+.+.++..  ..+++.||||||+|.+....++.|...++.   .
T Consensus        79 ~~~l~~~~~--------------------~~~~~i~~l~~~~~~~p~~~~~kiviIDE~~~l~~~~~~~ll~~le~---~  135 (367)
T PRK14970         79 IFELDAASN--------------------NSVDDIRNLIDQVRIPPQTGKYKIYIIDEVHMLSSAAFNAFLKTLEE---P  135 (367)
T ss_pred             eEEeccccC--------------------CCHHHHHHHHHHHhhccccCCcEEEEEeChhhcCHHHHHHHHHHHhC---C
Confidence            333332211                    123344443333211  123456999999999987666666665543   2


Q ss_pred             CCcEEEEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCH
Q psy200          329 GSKLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDI  408 (490)
Q Consensus       329 ~~~vilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~  408 (490)
                      ....++|.+++.   ...+.+.+.+||.    .+.|.+++.+++..++...+...  ...+++++++.++.   ...||+
T Consensus       136 ~~~~~~Il~~~~---~~kl~~~l~sr~~----~v~~~~~~~~~l~~~l~~~~~~~--g~~i~~~al~~l~~---~~~gdl  203 (367)
T PRK14970        136 PAHAIFILATTE---KHKIIPTILSRCQ----IFDFKRITIKDIKEHLAGIAVKE--GIKFEDDALHIIAQ---KADGAL  203 (367)
T ss_pred             CCceEEEEEeCC---cccCCHHHHhcce----eEecCCccHHHHHHHHHHHHHHc--CCCCCHHHHHHHHH---hCCCCH
Confidence            334455555542   3566788889986    79999999999999999998876  35689999999997   677899


Q ss_pred             HHHHHHHHHHHHHHHhccccCCcccccCHHHHHHHHH
Q psy200          409 RKAIDITNHLIDLTYDNVKENGEVTGIGLKEVLGVIS  445 (490)
Q Consensus       409 r~ai~ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~~  445 (490)
                      |.+++.|+.....+.  .       .|+.+++..++.
T Consensus       204 r~~~~~lekl~~y~~--~-------~it~~~v~~~~~  231 (367)
T PRK14970        204 RDALSIFDRVVTFCG--K-------NITRQAVTENLN  231 (367)
T ss_pred             HHHHHHHHHHHHhcC--C-------CCCHHHHHHHhC
Confidence            999999988765432  1       266666665543

>COG2812 DnaX DNA polymerase III, gamma/tau subunits [DNA replication, recombination, and repair]

Probab=99.72  E-value=2.9e-17  Score=167.96  Aligned_cols=218  Identities=17%  Similarity=0.255  Sum_probs=159.6

Q ss_pred             CcchHHHhhcCCCCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCC
Q psy200          182 DKPKVEEKAKDSCELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRN  261 (490)
Q Consensus       182 ~~~~~~~~~l~~~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~  261 (490)
                      .+|+|...    ++++|++.....|...+..   +.-.+..+++||.||||||+|+.+++.+.+...  ...-.|..+..
T Consensus         8 rKyRP~~F----~evvGQe~v~~~L~nal~~---~ri~hAYlfsG~RGvGKTt~Ari~AkalNC~~~--~~~ePC~~C~~   78 (515)
T COG2812           8 RKYRPKTF----DDVVGQEHVVKTLSNALEN---GRIAHAYLFSGPRGVGKTTIARILAKALNCENG--PTAEPCGKCIS   78 (515)
T ss_pred             HHhCcccH----HHhcccHHHHHHHHHHHHh---CcchhhhhhcCCCCcCchhHHHHHHHHhcCCCC--CCCCcchhhhh
Confidence            36777777    8999999999999998874   456678889999999999999999999874432  11112332222


Q ss_pred             HHHHHHH-HHHHhcC-CCCCCcHHHHHHHHHHHHhc--CCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEEEe
Q psy200          262 AASVYET-IVNELKL-KPGGKSERHQLGAILKYFDT--KHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGV  337 (490)
Q Consensus       262 ~~~l~~~-i~~~l~~-~~~~~s~~~~~~~l~~~l~~--~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI~~  337 (490)
                      ...+-.. ..+-+.. .....+.+++++...+..-.  .++.-|.+|||+|.|.....++|+..++   .+...|+||.+
T Consensus        79 Ck~I~~g~~~DviEiDaASn~gVddiR~i~e~v~y~P~~~ryKVyiIDEvHMLS~~afNALLKTLE---EPP~hV~FIlA  155 (515)
T COG2812          79 CKEINEGSLIDVIEIDAASNTGVDDIREIIEKVNYAPSEGRYKVYIIDEVHMLSKQAFNALLKTLE---EPPSHVKFILA  155 (515)
T ss_pred             hHhhhcCCcccchhhhhhhccChHHHHHHHHHhccCCccccceEEEEecHHhhhHHHHHHHhcccc---cCccCeEEEEe
Confidence            2111110 0000000 01123566666666654422  3667799999999999877777766655   46678988888


Q ss_pred             cCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHHHHHH
Q psy200          338 ANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITNH  417 (490)
Q Consensus       338 tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll~~  417 (490)
                      |+.   ..++...+.+||.    ++.|..++.+++...|...+..+  ...++++++..|++   ...|.+|.++.+|.+
T Consensus       156 TTe---~~Kip~TIlSRcq----~f~fkri~~~~I~~~L~~i~~~E--~I~~e~~aL~~ia~---~a~Gs~RDalslLDq  223 (515)
T COG2812         156 TTE---PQKIPNTILSRCQ----RFDFKRLDLEEIAKHLAAILDKE--GINIEEDALSLIAR---AAEGSLRDALSLLDQ  223 (515)
T ss_pred             cCC---cCcCchhhhhccc----cccccCCCHHHHHHHHHHHHHhc--CCccCHHHHHHHHH---HcCCChhhHHHHHHH
Confidence            873   4566678889996    89999999999999999999987  57789999999998   889999999999999


Q ss_pred             HHHHHH
Q psy200          418 LIDLTY  423 (490)
Q Consensus       418 a~~~a~  423 (490)
                      ++....
T Consensus       224 ~i~~~~  229 (515)
T COG2812         224 AIAFGE  229 (515)
T ss_pred             HHHccC
Confidence            987654

>KOG1969|consensus

Probab=99.72  E-value=1.8e-16  Score=162.93  Aligned_cols=214  Identities=20%  Similarity=0.298  Sum_probs=161.3

Q ss_pred             CCCCcchHHHhhcCCCCCCChHHHHHHHHHHHHhhhc------------------------------cCCCCeEEEECCC
Q psy200          179 FSEDKPKVEEKAKDSCELPGREVQLEGIRQFLLGHVN------------------------------NETSGSMYISGPP  228 (490)
Q Consensus       179 ~~~~~~~~~~~~l~~~~lvgre~~~~~l~~~L~~~~~------------------------------~~~~~~ill~Gpp  228 (490)
                      .|+++|.+...    .+|+|-+..=..+..||..|-.                              ....+.+||+|||
T Consensus       260 LWVdky~Pk~F----tdLLsDe~tNR~~L~WLK~WD~~VFg~~vsrl~~s~~~~~ke~~~~~~~~s~RP~kKilLL~Gpp  335 (877)
T KOG1969|consen  260 LWVDKYRPKKF----TDLLSDEKTNRRMLGWLKQWDPCVFGQKVSRLLASKGPTEKEVLDMELDPSKRPPKKILLLCGPP  335 (877)
T ss_pred             eeecccChhHH----HHHhcchhHHHHHHHHHHhhcHHhhcchHhhhccccccchhhhhhcccCccCCCccceEEeecCC
Confidence            89999999988    8999999999999999988710                              1234689999999


Q ss_pred             CCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCc
Q psy200          229 GTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEID  308 (490)
Q Consensus       229 GtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid  308 (490)
                      |.||||||+.+|++.+    |.++.+|++..++...+-..|...+...              ..+....+|.+|||||||
T Consensus       336 GlGKTTLAHViAkqaG----YsVvEINASDeRt~~~v~~kI~~avq~~--------------s~l~adsrP~CLViDEID  397 (877)
T KOG1969|consen  336 GLGKTTLAHVIAKQAG----YSVVEINASDERTAPMVKEKIENAVQNH--------------SVLDADSRPVCLVIDEID  397 (877)
T ss_pred             CCChhHHHHHHHHhcC----ceEEEecccccccHHHHHHHHHHHHhhc--------------cccccCCCcceEEEeccc
Confidence            9999999999999965    9999999999877665554443333221              113345789999999999


Q ss_pred             cccccCHHHHHHhHhCC-----CCCC-------------CcEEEEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHH
Q psy200          309 ALESRKQTILYTIFEWP-----SIPG-------------SKLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSRE  370 (490)
Q Consensus       309 ~l~~~~~~~L~~l~~~~-----~~~~-------------~~vilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~  370 (490)
                      --.....+.++.++...     ...+             ..=-+||+||.  +....++.|+.-+    ..+.|.|++..
T Consensus       398 Ga~~~~Vdvilslv~a~~k~~~Gkq~~~~~~rkkkr~~~L~RPIICICNd--LYaPaLR~Lr~~A----~ii~f~~p~~s  471 (877)
T KOG1969|consen  398 GAPRAAVDVILSLVKATNKQATGKQAKKDKKRKKKRSKLLTRPIICICND--LYAPALRPLRPFA----EIIAFVPPSQS  471 (877)
T ss_pred             CCcHHHHHHHHHHHHhhcchhhcCcccchhhhhhhccccccCCEEEEecC--ccchhhhhcccce----EEEEecCCChh
Confidence            98766667777765421     0011             11147788884  4455566666544    48999999999


Q ss_pred             HHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHhc
Q psy200          371 QILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITNHLIDLTYDN  425 (490)
Q Consensus       371 e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll~~a~~~a~~~  425 (490)
                      -+.+-|+..|.+++  ...+..++..+++   .+.+|+|..||.|+-....+...
T Consensus       472 ~Lv~RL~~IC~rE~--mr~d~~aL~~L~e---l~~~DIRsCINtLQfLa~~~~r~  521 (877)
T KOG1969|consen  472 RLVERLNEICHREN--MRADSKALNALCE---LTQNDIRSCINTLQFLASNVDRR  521 (877)
T ss_pred             HHHHHHHHHHhhhc--CCCCHHHHHHHHH---HhcchHHHHHHHHHHHHHhcccc
Confidence            99999999999884  5578888998887   77899999999998877665554

>PHA02544 44 clamp loader, small subunit; Provisional

Probab=99.72  E-value=2.8e-16  Score=156.19  Aligned_cols=201  Identities=16%  Similarity=0.188  Sum_probs=140.2

Q ss_pred             ccCCCCcchHHHhhcCCCCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEec
Q psy200          177 LLFSEDKPKVEEKAKDSCELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINC  256 (490)
Q Consensus       177 ~~~~~~~~~~~~~~l~~~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~  256 (490)
                      ...|.++|+|...    ++++|++...+.+..++..   +..++.++|+||+|+|||++++++++++.    ..++++++
T Consensus         8 ~~~w~~kyrP~~~----~~~~~~~~~~~~l~~~~~~---~~~~~~lll~G~~G~GKT~la~~l~~~~~----~~~~~i~~   76 (316)
T PHA02544          8 EFMWEQKYRPSTI----DECILPAADKETFKSIVKK---GRIPNMLLHSPSPGTGKTTVAKALCNEVG----AEVLFVNG   76 (316)
T ss_pred             CCcceeccCCCcH----HHhcCcHHHHHHHHHHHhc---CCCCeEEEeeCcCCCCHHHHHHHHHHHhC----ccceEecc
Confidence            4489999999888    9999999999999999863   33456666799999999999999999864    45677877


Q ss_pred             cCCCCHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccc-cccCHHHHHHhHhCCCCCCCcEEEE
Q psy200          257 NSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDAL-ESRKQTILYTIFEWPSIPGSKLVLV  335 (490)
Q Consensus       257 ~~~~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l-~~~~~~~L~~l~~~~~~~~~~vilI  335 (490)
                      ... . ...+...               +.++ .......+...+|||||+|.+ ....+..|..+++..   ...+.+|
T Consensus        77 ~~~-~-~~~i~~~---------------l~~~-~~~~~~~~~~~vliiDe~d~l~~~~~~~~L~~~le~~---~~~~~~I  135 (316)
T PHA02544         77 SDC-R-IDFVRNR---------------LTRF-ASTVSLTGGGKVIIIDEFDRLGLADAQRHLRSFMEAY---SKNCSFI  135 (316)
T ss_pred             Ccc-c-HHHHHHH---------------HHHH-HHhhcccCCCeEEEEECcccccCHHHHHHHHHHHHhc---CCCceEE
Confidence            652 2 1111110               1111 111111134569999999999 444567777766643   2345566


Q ss_pred             EecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhcc-----CCCCCCCHHHHHHHHHHHHHhhCCHHH
Q psy200          336 GVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQT-----DKFNMFNASALQLLAGKVAAVSGDIRK  410 (490)
Q Consensus       336 ~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~-----~~~~~~~~~~i~~i~~~i~~~~Gd~r~  410 (490)
                      +++|.   ...+.+.+++||.    .+.|..++.++...++...+...     .....++++++..+++   ...||+|.
T Consensus       136 lt~n~---~~~l~~~l~sR~~----~i~~~~p~~~~~~~il~~~~~~~~~~~~~~~~~i~~~al~~l~~---~~~~d~r~  205 (316)
T PHA02544        136 ITANN---KNGIIEPLRSRCR----VIDFGVPTKEEQIEMMKQMIVRCKGILEAEGVEVDMKVLAALVK---KNFPDFRR  205 (316)
T ss_pred             EEcCC---hhhchHHHHhhce----EEEeCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHH---hcCCCHHH
Confidence            66763   3567889999996    79999999988876655432221     1245678999999987   67789999


Q ss_pred             HHHHHHHHH
Q psy200          411 AIDITNHLI  419 (490)
Q Consensus       411 ai~ll~~a~  419 (490)
                      +++.++...
T Consensus       206 ~l~~l~~~~  214 (316)
T PHA02544        206 TINELQRYA  214 (316)
T ss_pred             HHHHHHHHH
Confidence            998887553

>KOG0731|consensus

Probab=99.72  E-value=3e-16  Score=165.06  Aligned_cols=224  Identities=17%  Similarity=0.177  Sum_probs=160.0

Q ss_pred             CCCCChHHHHHHHHHHHHhh--------hccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGH--------VNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASV  265 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~--------~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l  265 (490)
                      .+++|.++..++|.+++.-.        +....++++||+||||||||.||+++|.+.    +++|+.++++++      
T Consensus       311 kDVAG~deAK~El~E~V~fLKNP~~Y~~lGAKiPkGvLL~GPPGTGKTLLAKAiAGEA----gVPF~svSGSEF------  380 (774)
T KOG0731|consen  311 KDVAGVDEAKEELMEFVKFLKNPEQYQELGAKIPKGVLLVGPPGTGKTLLAKAIAGEA----GVPFFSVSGSEF------  380 (774)
T ss_pred             ccccCcHHHHHHHHHHHHHhcCHHHHHHcCCcCcCceEEECCCCCcHHHHHHHHhccc----CCceeeechHHH------
Confidence            78999999988888876532        123477899999999999999999999984    488988866543      


Q ss_pred             HHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccC------------HHHHHHhH-hCC-CCCCCc
Q psy200          266 YETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRK------------QTILYTIF-EWP-SIPGSK  331 (490)
Q Consensus       266 ~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~------------~~~L~~l~-~~~-~~~~~~  331 (490)
                      ++        ...+.....+++.|..+..  ..|++|||||||.+...+            ...|.+++ ++. ......
T Consensus       381 vE--------~~~g~~asrvr~lf~~ar~--~aP~iifideida~~~~r~G~~~~~~~~e~e~tlnQll~emDgf~~~~~  450 (774)
T KOG0731|consen  381 VE--------MFVGVGASRVRDLFPLARK--NAPSIIFIDEIDAVGRKRGGKGTGGGQDEREQTLNQLLVEMDGFETSKG  450 (774)
T ss_pred             HH--------HhcccchHHHHHHHHHhhc--cCCeEEEecccccccccccccccCCCChHHHHHHHHHHHHhcCCcCCCc
Confidence            22        1223345667777775554  679999999999986543            12344443 332 334577


Q ss_pred             EEEEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHH-
Q psy200          332 LVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRK-  410 (490)
Q Consensus       332 vilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~-  410 (490)
                      +|++++||+.|..+.   .+. |.+.....|.++.++..+..+|+..++....  ...++..+..++.   .+.|.... 
T Consensus       451 vi~~a~tnr~d~ld~---all-rpGRfdr~i~i~~p~~~~r~~i~~~h~~~~~--~~~e~~dl~~~a~---~t~gf~gad  521 (774)
T KOG0731|consen  451 VIVLAATNRPDILDP---ALL-RPGRFDRQIQIDLPDVKGRASILKVHLRKKK--LDDEDVDLSKLAS---LTPGFSGAD  521 (774)
T ss_pred             EEEEeccCCccccCH---Hhc-CCCccccceeccCCchhhhHHHHHHHhhccC--CCcchhhHHHHHh---cCCCCcHHH
Confidence            999999997765443   333 3333336899999999999999999887652  2124444444555   55565443 


Q ss_pred             HHHHHHHHHHHHHhccccCCcccccCHHHHHHHHHHhccCc
Q psy200          411 AIDITNHLIDLTYDNVKENGEVTGIGLKEVLGVISSVYCTS  451 (490)
Q Consensus       411 ai~ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~~~~~~~~  451 (490)
                      +.|+|..|..+|.+++     ...|+..|+..|+..+....
T Consensus       522 l~n~~neaa~~a~r~~-----~~~i~~~~~~~a~~Rvi~G~  557 (774)
T KOG0731|consen  522 LANLCNEAALLAARKG-----LREIGTKDLEYAIERVIAGM  557 (774)
T ss_pred             HHhhhhHHHHHHHHhc-----cCccchhhHHHHHHHHhccc
Confidence            3479999999999988     77999999999999766543

>PRK12422 chromosomal replication initiation protein; Provisional

Probab=99.72  E-value=4.5e-16  Score=159.86  Aligned_cols=241  Identities=15%  Similarity=0.263  Sum_probs=156.4

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCC
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFDTKHK  298 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~  298 (490)
                      .+.++|||++|+|||+|++++++++.. .+..++|+++      ..+...+...+...    ..    +.+...+   ..
T Consensus       141 ~npl~L~G~~G~GKTHLl~Ai~~~l~~-~~~~v~yi~~------~~f~~~~~~~l~~~----~~----~~f~~~~---~~  202 (445)
T PRK12422        141 FNPIYLFGPEGSGKTHLMQAAVHALRE-SGGKILYVRS------ELFTEHLVSAIRSG----EM----QRFRQFY---RN  202 (445)
T ss_pred             CceEEEEcCCCCCHHHHHHHHHHHHHH-cCCCEEEeeH------HHHHHHHHHHHhcc----hH----HHHHHHc---cc
Confidence            468999999999999999999998853 3467788853      34444554444321    11    1222222   23


Q ss_pred             eEEEEEecCcccccc--CHHHHHHhHhCCCCCCCcEEEEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHH
Q psy200          299 SILLILDEIDALESR--KQTILYTIFEWPSIPGSKLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEII  376 (490)
Q Consensus       299 ~~vI~IDEid~l~~~--~~~~L~~l~~~~~~~~~~vilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il  376 (490)
                      .-+|+|||+|.+...  .++.++.+++.....+.. +++++.........+.+++.+||.++ ..+.+.+++.+++..||
T Consensus       203 ~dvLiIDDiq~l~~k~~~qeelf~l~N~l~~~~k~-IIlts~~~p~~l~~l~~rL~SR~~~G-l~~~l~~pd~e~r~~iL  280 (445)
T PRK12422        203 VDALFIEDIEVFSGKGATQEEFFHTFNSLHTEGKL-IVISSTCAPQDLKAMEERLISRFEWG-IAIPLHPLTKEGLRSFL  280 (445)
T ss_pred             CCEEEEcchhhhcCChhhHHHHHHHHHHHHHCCCc-EEEecCCCHHHHhhhHHHHHhhhcCC-eEEecCCCCHHHHHHHH
Confidence            459999999999754  467777776533323333 34333332333345678999999654 47999999999999999


Q ss_pred             HHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHHHHHHHHH---HHHhcccc--------------C-CcccccCHH
Q psy200          377 SQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITNHLID---LTYDNVKE--------------N-GEVTGIGLK  438 (490)
Q Consensus       377 ~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll~~a~~---~a~~~~~~--------------~-~~~~~It~~  438 (490)
                      ++++...  ...+++++++.|+.   ...+|+|.+++.+...+.   .+...+..              . .....|+++
T Consensus       281 ~~k~~~~--~~~l~~evl~~la~---~~~~dir~L~g~l~~l~~~~a~~~~~~~~i~~~~~~~~l~~~~~~~~~~~~t~~  355 (445)
T PRK12422        281 ERKAEAL--SIRIEETALDFLIE---ALSSNVKSLLHALTLLAKRVAYKKLSHQLLYVDDIKALLHDVLEAAESVRLTPS  355 (445)
T ss_pred             HHHHHHc--CCCCCHHHHHHHHH---hcCCCHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhhcccCCCCCHH
Confidence            9999876  46789999999997   788999999987777642   22111100              0 001247777


Q ss_pred             HHHHHHHHhccCccccccccccCCCChHhHHHH---HHHHHHhcCCCCCCcccC
Q psy200          439 EVLGVISSVYCTSQSLHCSKDEDSFPLQQKLAL---ASLLLLKSRPNVKDVTLG  489 (490)
Q Consensus       439 ~v~~a~~~~~~~~~~~~~~~~l~~L~~~qk~vL---~al~~~~~~~~~~~~~~g  489 (490)
                      .|.+++.+.++-..     +.+.+-...+..++   .||+++.+..+.+...||
T Consensus       356 ~I~~~Va~~~~v~~-----~dl~s~~R~~~i~~~Rqiamyl~r~~t~~s~~~IG  404 (445)
T PRK12422        356 KIIRAVAQYYGVSP-----ESILGRSQSREYVLPRQVAMYLCRQKLSLSYVKIG  404 (445)
T ss_pred             HHHHHHHHHhCCCH-----HHHhcCCCCcccccHHHHHHHHHHHhcCCCHHHHH
Confidence            77777777766444     33333334433333   467777666666666665

>KOG0736|consensus

Probab=99.72  E-value=2.2e-16  Score=163.07  Aligned_cols=227  Identities=14%  Similarity=0.220  Sum_probs=150.6

Q ss_pred             CCCCChHHHHHHHHHHHHhhhcc-----C---CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVNN-----E---TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASV  265 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~-----~---~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l  265 (490)
                      +++-|.++.+.+|.+-+.--++.     .   +-.+|+||||||||||.+|++||.++.    ..|+.|.+++.-+    
T Consensus       672 dDVGGLeevK~eIldTIqlPL~hpeLfssglrkRSGILLYGPPGTGKTLlAKAVATEcs----L~FlSVKGPELLN----  743 (953)
T KOG0736|consen  672 DDVGGLEEVKTEILDTIQLPLKHPELFSSGLRKRSGILLYGPPGTGKTLLAKAVATECS----LNFLSVKGPELLN----  743 (953)
T ss_pred             hcccCHHHHHHHHHHHhcCcccChhhhhccccccceeEEECCCCCchHHHHHHHHhhce----eeEEeecCHHHHH----
Confidence            88999999999998877653221     1   345899999999999999999999975    5666665544321    


Q ss_pred             HHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccC--------------HHHHHHhHhCCCCCCCc
Q psy200          266 YETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRK--------------QTILYTIFEWPSIPGSK  331 (490)
Q Consensus       266 ~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~--------------~~~L~~l~~~~~~~~~~  331 (490)
                                .+.|++++++++.|+++..  ..|||||+||+|.+...+              ...|..+-.+.......
T Consensus       744 ----------MYVGqSE~NVR~VFerAR~--A~PCVIFFDELDSlAP~RG~sGDSGGVMDRVVSQLLAELDgls~~~s~~  811 (953)
T KOG0736|consen  744 ----------MYVGQSEENVREVFERARS--AAPCVIFFDELDSLAPNRGRSGDSGGVMDRVVSQLLAELDGLSDSSSQD  811 (953)
T ss_pred             ----------HHhcchHHHHHHHHHHhhc--cCCeEEEeccccccCccCCCCCCccccHHHHHHHHHHHhhcccCCCCCc
Confidence                      5678899999999998876  569999999999998663              12333333333335678


Q ss_pred             EEEEEecCCCChhHhhhHHhh--hccCCCCeeEEeCCCCHHHHHH-HHHHHHhccCCCCCCC-HHHHHHHHHHHHH-hhC
Q psy200          332 LVLVGVANALDLTDRMLPRLQ--ANVTLQPTLMNFAPYSREQILE-IISQKLKQTDKFNMFN-ASALQLLAGKVAA-VSG  406 (490)
Q Consensus       332 vilI~~tn~~~~~~~l~~~l~--~R~~~~~~~i~~~pls~~e~~~-il~~~l~~~~~~~~~~-~~~i~~i~~~i~~-~~G  406 (490)
                      |.|||+||+.|+.+.   .+.  .||+   +.+++.+-..++.+. +|+..-++.    .++ +-.+..|+++... .+|
T Consensus       812 VFViGATNRPDLLDp---ALLRPGRFD---KLvyvG~~~d~esk~~vL~AlTrkF----kLdedVdL~eiAk~cp~~~TG  881 (953)
T KOG0736|consen  812 VFVIGATNRPDLLDP---ALLRPGRFD---KLVYVGPNEDAESKLRVLEALTRKF----KLDEDVDLVEIAKKCPPNMTG  881 (953)
T ss_pred             eEEEecCCCccccCh---hhcCCCccc---eeEEecCCccHHHHHHHHHHHHHHc----cCCCCcCHHHHHhhCCcCCch
Confidence            999999998776554   333  2555   678888777665544 333333322    122 2336666663211 112


Q ss_pred             CHHHHHHHHHHHHHHHHhccc------------cCCcccccCHHHHHHHHHHhccCcc
Q psy200          407 DIRKAIDITNHLIDLTYDNVK------------ENGEVTGIGLKEVLGVISSVYCTSQ  452 (490)
Q Consensus       407 d~r~ai~ll~~a~~~a~~~~~------------~~~~~~~It~~~v~~a~~~~~~~~~  452 (490)
                        ..+-.+|..|+..|..+.-            .+.+.-.|+++||.++++++.++..
T Consensus       882 --ADlYsLCSdA~l~AikR~i~~ie~g~~~~~e~~~~~v~V~~eDflks~~~l~PSvS  937 (953)
T KOG0736|consen  882 --ADLYSLCSDAMLAAIKRTIHDIESGTISEEEQESSSVRVTMEDFLKSAKRLQPSVS  937 (953)
T ss_pred             --hHHHHHHHHHHHHHHHHHHHHhhhccccccccCCceEEEEHHHHHHHHHhcCCccc
Confidence              1223467777666644311            1123457999999999999987765

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=99.71  E-value=5.9e-16  Score=170.00  Aligned_cols=228  Identities=17%  Similarity=0.191  Sum_probs=156.1

Q ss_pred             CCCCChHHHHHHHHHHHHhhhc---------cCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVN---------NETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAAS  264 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~---------~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~  264 (490)
                      +++.|.+..++.|.+.+...+.         ...+++++||||||||||++|++++++++    +.++.+.++.+     
T Consensus       453 ~di~g~~~~k~~l~~~v~~~~~~~~~~~~~g~~~~~giLL~GppGtGKT~lakalA~e~~----~~fi~v~~~~l-----  523 (733)
T TIGR01243       453 SDIGGLEEVKQELREAVEWPLKHPEIFEKMGIRPPKGVLLFGPPGTGKTLLAKAVATESG----ANFIAVRGPEI-----  523 (733)
T ss_pred             hhcccHHHHHHHHHHHHHhhhhCHHHHHhcCCCCCceEEEECCCCCCHHHHHHHHHHhcC----CCEEEEehHHH-----
Confidence            7789999999999887764332         13567899999999999999999999875    56777765533     


Q ss_pred             HHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccC---------HHHHHHhHhCC--CCCCCcEE
Q psy200          265 VYETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRK---------QTILYTIFEWP--SIPGSKLV  333 (490)
Q Consensus       265 l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~---------~~~L~~l~~~~--~~~~~~vi  333 (490)
                               ...+.|.+...+...|..+..  ..++||||||+|.+....         ...+..++...  .....+++
T Consensus       524 ---------~~~~vGese~~i~~~f~~A~~--~~p~iifiDEid~l~~~r~~~~~~~~~~~~~~~lL~~ldg~~~~~~v~  592 (733)
T TIGR01243       524 ---------LSKWVGESEKAIREIFRKARQ--AAPAIIFFDEIDAIAPARGARFDTSVTDRIVNQLLTEMDGIQELSNVV  592 (733)
T ss_pred             ---------hhcccCcHHHHHHHHHHHHHh--cCCEEEEEEChhhhhccCCCCCCccHHHHHHHHHHHHhhcccCCCCEE
Confidence                     124566777777777776655  458999999999986432         12333333221  12456899


Q ss_pred             EEEecCCCChhHhhhHHhhh--ccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHH
Q psy200          334 LVGVANALDLTDRMLPRLQA--NVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKA  411 (490)
Q Consensus       334 lI~~tn~~~~~~~l~~~l~~--R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~a  411 (490)
                      ||++||+.   +.+++.+.+  ||.   ..+.|++++.++..+|++..+....   .-++..++.+++...+++|  ..+
T Consensus       593 vI~aTn~~---~~ld~allRpgRfd---~~i~v~~Pd~~~R~~i~~~~~~~~~---~~~~~~l~~la~~t~g~sg--adi  661 (733)
T TIGR01243       593 VIAATNRP---DILDPALLRPGRFD---RLILVPPPDEEARKEIFKIHTRSMP---LAEDVDLEELAEMTEGYTG--ADI  661 (733)
T ss_pred             EEEeCCCh---hhCCHhhcCCCccc---eEEEeCCcCHHHHHHHHHHHhcCCC---CCccCCHHHHHHHcCCCCH--HHH
Confidence            99999954   556666664  787   5899999999999999987765541   1133347777773333332  223


Q ss_pred             HHHHHHHHHHHHhccccC-------------CcccccCHHHHHHHHHHhccCcc
Q psy200          412 IDITNHLIDLTYDNVKEN-------------GEVTGIGLKEVLGVISSVYCTSQ  452 (490)
Q Consensus       412 i~ll~~a~~~a~~~~~~~-------------~~~~~It~~~v~~a~~~~~~~~~  452 (490)
                      -++|+.|...|..+....             .....|+.+||..|+..+.++..
T Consensus       662 ~~~~~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~f~~al~~~~ps~~  715 (733)
T TIGR01243       662 EAVCREAAMAALRESIGSPAKEKLEVGEEEFLKDLKVEMRHFLEALKKVKPSVS  715 (733)
T ss_pred             HHHHHHHHHHHHHHHhhhccchhhhcccccccccCcccHHHHHHHHHHcCCCCC
Confidence            346777776665532100             11347999999999998876544

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.

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=99.71  E-value=1e-15  Score=144.75  Aligned_cols=205  Identities=16%  Similarity=0.244  Sum_probs=140.8

Q ss_pred             CCCC-Ch-HHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHH
Q psy200          194 CELP-GR-EVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVN  271 (490)
Q Consensus       194 ~~lv-gr-e~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~  271 (490)
                      ++|+ |. +..+..+..+...   .....+++|+|++|+|||++++++++++. ..+..+++++|.....          
T Consensus        18 d~f~~~~~~~~~~~l~~~~~~---~~~~~~~~l~G~~G~GKT~La~ai~~~~~-~~~~~~~~i~~~~~~~----------   83 (227)
T PRK08903         18 DNFVAGENAELVARLRELAAG---PVADRFFYLWGEAGSGRSHLLQALVADAS-YGGRNARYLDAASPLL----------   83 (227)
T ss_pred             cccccCCcHHHHHHHHHHHhc---cCCCCeEEEECCCCCCHHHHHHHHHHHHH-hCCCcEEEEehHHhHH----------
Confidence            4444 43 4444555555431   24567899999999999999999999864 2345777887654310          


Q ss_pred             HhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEEEecCCCChhHhhhHHh
Q psy200          272 ELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVANALDLTDRMLPRL  351 (490)
Q Consensus       272 ~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI~~tn~~~~~~~l~~~l  351 (490)
                                      .+ ...   ....+|||||+|.+....+..|+.+++.....+..++++ +++.......+.+.+
T Consensus        84 ----------------~~-~~~---~~~~~liiDdi~~l~~~~~~~L~~~~~~~~~~~~~~vl~-~~~~~~~~~~l~~~L  142 (227)
T PRK08903         84 ----------------AF-DFD---PEAELYAVDDVERLDDAQQIALFNLFNRVRAHGQGALLV-AGPAAPLALPLREDL  142 (227)
T ss_pred             ----------------HH-hhc---ccCCEEEEeChhhcCchHHHHHHHHHHHHHHcCCcEEEE-eCCCCHHhCCCCHHH
Confidence                            00 011   123489999999998777888888876433222223333 333222222345677


Q ss_pred             hhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHhccccCCc
Q psy200          352 QANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITNHLIDLTYDNVKENGE  431 (490)
Q Consensus       352 ~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll~~a~~~a~~~~~~~~~  431 (490)
                      .+|+... ..+.++|++.++...++.+.+...  ...+++++++.|++   .+.||++.+.++++.....+...+     
T Consensus       143 ~sr~~~~-~~i~l~pl~~~~~~~~l~~~~~~~--~v~l~~~al~~L~~---~~~gn~~~l~~~l~~l~~~~~~~~-----  211 (227)
T PRK08903        143 RTRLGWG-LVYELKPLSDADKIAALKAAAAER--GLQLADEVPDYLLT---HFRRDMPSLMALLDALDRYSLEQK-----  211 (227)
T ss_pred             HHHHhcC-eEEEecCCCHHHHHHHHHHHHHHc--CCCCCHHHHHHHHH---hccCCHHHHHHHHHHHHHHHHHhC-----
Confidence            7787322 379999999999888988877665  46789999999998   799999999999998665554444     


Q ss_pred             ccccCHHHHHHHHH
Q psy200          432 VTGIGLKEVLGVIS  445 (490)
Q Consensus       432 ~~~It~~~v~~a~~  445 (490)
                       ..||...+.+++.
T Consensus       212 -~~i~~~~~~~~l~  224 (227)
T PRK08903        212 -RPVTLPLLREMLA  224 (227)
T ss_pred             -CCCCHHHHHHHHh
Confidence             4899999999875

>TIGR03689 pup_AAA proteasome ATPase

Probab=99.71  E-value=1.5e-15  Score=156.65  Aligned_cols=172  Identities=17%  Similarity=0.277  Sum_probs=115.7

Q ss_pred             CCCCChHHHHHHHHHHHHhhhc---------cCCCCeEEEECCCCCcHHHHHHHHHHHhhhc----CCceEEEEeccCCC
Q psy200          194 CELPGREVQLEGIRQFLLGHVN---------NETSGSMYISGPPGTGKSASLNLLVSRAEIK----DAFKTIYINCNSVR  260 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~---------~~~~~~ill~GppGtGKTtla~~l~~~l~~~----~~~~~~~v~~~~~~  260 (490)
                      +++.|.+.+++++.+.+...+.         -..+++++||||||||||++++++++++...    ......++++... 
T Consensus       182 ~dIgGl~~~i~~i~~~v~lp~~~~~l~~~~gl~~p~GILLyGPPGTGKT~LAKAlA~eL~~~i~~~~~~~~~fl~v~~~-  260 (512)
T TIGR03689       182 ADIGGLDSQIEQIRDAVELPFLHPELYREYDLKPPKGVLLYGPPGCGKTLIAKAVANSLAQRIGAETGDKSYFLNIKGP-  260 (512)
T ss_pred             HHcCChHHHHHHHHHHHHHHhhCHHHHHhccCCCCcceEEECCCCCcHHHHHHHHHHhhccccccccCCceeEEeccch-
Confidence            6789999999999998754221         1356789999999999999999999998522    0122333333221 


Q ss_pred             CHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHh--cCCCeEEEEEecCccccccCH---------HHHHHhHhCC-C-C
Q psy200          261 NAASVYETIVNELKLKPGGKSERHQLGAILKYFD--TKHKSILLILDEIDALESRKQ---------TILYTIFEWP-S-I  327 (490)
Q Consensus       261 ~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~--~~~~~~vI~IDEid~l~~~~~---------~~L~~l~~~~-~-~  327 (490)
                         .+        ...+.+.....+...|..+..  ..++++||||||+|.++..+.         ..+..++... . .
T Consensus       261 ---eL--------l~kyvGete~~ir~iF~~Ar~~a~~g~p~IIfIDEiD~L~~~R~~~~s~d~e~~il~~LL~~LDgl~  329 (512)
T TIGR03689       261 ---EL--------LNKYVGETERQIRLIFQRAREKASDGRPVIVFFDEMDSIFRTRGSGVSSDVETTVVPQLLSELDGVE  329 (512)
T ss_pred             ---hh--------cccccchHHHHHHHHHHHHHHHhhcCCCceEEEehhhhhhcccCCCccchHHHHHHHHHHHHhcccc
Confidence               11        113344455555555554432  235799999999999975421         1233333221 1 1


Q ss_pred             CCCcEEEEEecCCCChhHhhhHHhhh--ccCCCCeeEEeCCCCHHHHHHHHHHHHhcc
Q psy200          328 PGSKLVLVGVANALDLTDRMLPRLQA--NVTLQPTLMNFAPYSREQILEIISQKLKQT  383 (490)
Q Consensus       328 ~~~~vilI~~tn~~~~~~~l~~~l~~--R~~~~~~~i~~~pls~~e~~~il~~~l~~~  383 (490)
                      ...++++|++||+   .+.+++.+.+  ||.   ..|.|++++.++..+||..++...
T Consensus       330 ~~~~ViVI~ATN~---~d~LDpALlRpGRfD---~~I~~~~Pd~e~r~~Il~~~l~~~  381 (512)
T TIGR03689       330 SLDNVIVIGASNR---EDMIDPAILRPGRLD---VKIRIERPDAEAAADIFSKYLTDS  381 (512)
T ss_pred             cCCceEEEeccCC---hhhCCHhhcCccccc---eEEEeCCCCHHHHHHHHHHHhhcc
Confidence            2357999999995   4567788876  887   479999999999999999988653

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.

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=99.70  E-value=6.3e-16  Score=170.41  Aligned_cols=224  Identities=13%  Similarity=0.150  Sum_probs=152.7

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhc------CCceEEEEeccCCCCHHHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIK------DAFKTIYINCNSVRNAASVYE  267 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~------~~~~~~~v~~~~~~~~~~l~~  267 (490)
                      ++++||++++.++.+.|..    +...+++|+||||||||++++.+++.+...      .+..++.++...+..      
T Consensus       187 d~~iGr~~ei~~~i~~l~r----~~~~n~lLvG~pGvGKTal~~~La~~i~~~~v~~~l~~~~i~~l~l~~l~a------  256 (852)
T TIGR03345       187 DPVLGRDDEIRQMIDILLR----RRQNNPILTGEAGVGKTAVVEGLALRIAAGDVPPALRNVRLLSLDLGLLQA------  256 (852)
T ss_pred             CcccCCHHHHHHHHHHHhc----CCcCceeEECCCCCCHHHHHHHHHHHHhhCCCCccccCCeEEEeehhhhhc------
Confidence            8999999999999888854    556788999999999999999999987522      122344444332210      


Q ss_pred             HHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCcccccc-----CHHHHHHhHhCCCCCCCcEEEEEecCCCC
Q psy200          268 TIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESR-----KQTILYTIFEWPSIPGSKLVLVGVANALD  342 (490)
Q Consensus       268 ~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~-----~~~~L~~l~~~~~~~~~~vilI~~tn~~~  342 (490)
                            +..+.|.....+...+.+... .+.++||||||+|.+...     .++. .+++ .+....+.+.+||+|+..+
T Consensus       257 ------g~~~~ge~e~~lk~ii~e~~~-~~~~~ILfIDEih~l~~~g~~~~~~d~-~n~L-kp~l~~G~l~~IgaTT~~e  327 (852)
T TIGR03345       257 ------GASVKGEFENRLKSVIDEVKA-SPQPIILFIDEAHTLIGAGGQAGQGDA-ANLL-KPALARGELRTIAATTWAE  327 (852)
T ss_pred             ------ccccchHHHHHHHHHHHHHHh-cCCCeEEEEeChHHhccCCCccccccH-HHHh-hHHhhCCCeEEEEecCHHH
Confidence                  112333344555556655433 256889999999999752     2332 1222 2334567899999998654


Q ss_pred             hhH--hhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhcc--CCCCCCCHHHHHHHHHHHHHhhCC---HHHHHHHH
Q psy200          343 LTD--RMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQT--DKFNMFNASALQLLAGKVAAVSGD---IRKAIDIT  415 (490)
Q Consensus       343 ~~~--~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~--~~~~~~~~~~i~~i~~~i~~~~Gd---~r~ai~ll  415 (490)
                      +..  ..++.|.+||.    .|.+.+++.++...||+......  .....++++++..+++....+-++   +.+||+++
T Consensus       328 ~~~~~~~d~AL~rRf~----~i~v~eps~~~~~~iL~~~~~~~e~~~~v~i~d~al~~~~~ls~ryi~~r~LPDKAIdll  403 (852)
T TIGR03345       328 YKKYFEKDPALTRRFQ----VVKVEEPDEETAIRMLRGLAPVLEKHHGVLILDEAVVAAVELSHRYIPGRQLPDKAVSLL  403 (852)
T ss_pred             HhhhhhccHHHHHhCe----EEEeCCCCHHHHHHHHHHHHHhhhhcCCCeeCHHHHHHHHHHcccccccccCccHHHHHH
Confidence            432  34789999996    79999999999999975544332  134678999999999855555554   66899999


Q ss_pred             HHHHHHHHhccccCCcccccCHHHHHHHH
Q psy200          416 NHLIDLTYDNVKENGEVTGIGLKEVLGVI  444 (490)
Q Consensus       416 ~~a~~~a~~~~~~~~~~~~It~~~v~~a~  444 (490)
                      ..|+........    ..++..+++.+.+
T Consensus       404 dea~a~~~~~~~----~~p~~~~~~~~~~  428 (852)
T TIGR03345       404 DTACARVALSQN----ATPAALEDLRRRI  428 (852)
T ss_pred             HHHHHHHHHhcc----CCchhHHHHHHHH
Confidence            999876554321    2355555555444

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.

>COG0464 SpoVK ATPases of the AAA+ class [Posttranslational modification, protein turnover, chaperones]

Probab=99.70  E-value=8.6e-16  Score=161.86  Aligned_cols=223  Identities=17%  Similarity=0.207  Sum_probs=163.2

Q ss_pred             CCCCChHHHHHHHHHHHHhhhc---------cCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVN---------NETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAAS  264 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~---------~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~  264 (490)
                      .++.|.+...+.+.+.+...+.         -....++||+||||||||++|+++++++.    ..|+.+..+.+     
T Consensus       242 ~diggl~~~k~~l~e~v~~~~~~~e~~~~~~~~~~~giLl~GpPGtGKT~lAkava~~~~----~~fi~v~~~~l-----  312 (494)
T COG0464         242 DDIGGLEEAKEELKEAIETPLKRPELFRKLGLRPPKGVLLYGPPGTGKTLLAKAVALESR----SRFISVKGSEL-----  312 (494)
T ss_pred             ehhhcHHHHHHHHHHHHHhHhhChHHHHhcCCCCCCeeEEECCCCCCHHHHHHHHHhhCC----CeEEEeeCHHH-----
Confidence            5677777777777776654432         13566999999999999999999999754    67788866543     


Q ss_pred             HHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCH--------HHHHHhHhCC--CCCCCcEEE
Q psy200          265 VYETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQ--------TILYTIFEWP--SIPGSKLVL  334 (490)
Q Consensus       265 l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~--------~~L~~l~~~~--~~~~~~vil  334 (490)
                               ...+.|.+.+.+.+.|..+..  ..++||||||+|.+.....        ..+.+++.+.  ......|++
T Consensus       313 ---------~sk~vGesek~ir~~F~~A~~--~~p~iiFiDEiDs~~~~r~~~~~~~~~r~~~~lL~~~d~~e~~~~v~v  381 (494)
T COG0464         313 ---------LSKWVGESEKNIRELFEKARK--LAPSIIFIDEIDSLASGRGPSEDGSGRRVVGQLLTELDGIEKAEGVLV  381 (494)
T ss_pred             ---------hccccchHHHHHHHHHHHHHc--CCCcEEEEEchhhhhccCCCCCchHHHHHHHHHHHHhcCCCccCceEE
Confidence                     226788899999999998875  5689999999999976532        3444443322  345667899


Q ss_pred             EEecCCCChhHhhhHHhhh--ccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhC-CHHHH
Q psy200          335 VGVANALDLTDRMLPRLQA--NVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSG-DIRKA  411 (490)
Q Consensus       335 I~~tn~~~~~~~l~~~l~~--R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~G-d~r~a  411 (490)
                      |++||+.   +.+++.+.+  ||.   ..+.+++++.++..++++.++.... .....+-.++.+++   ...| .-..+
T Consensus       382 i~aTN~p---~~ld~a~lR~gRfd---~~i~v~~pd~~~r~~i~~~~~~~~~-~~~~~~~~~~~l~~---~t~~~sgadi  451 (494)
T COG0464         382 IAATNRP---DDLDPALLRPGRFD---RLIYVPLPDLEERLEIFKIHLRDKK-PPLAEDVDLEELAE---ITEGYSGADI  451 (494)
T ss_pred             EecCCCc---cccCHhhcccCccc---eEeecCCCCHHHHHHHHHHHhcccC-CcchhhhhHHHHHH---HhcCCCHHHH
Confidence            9999954   555666666  777   5899999999999999999988642 12234566777776   3333 23344


Q ss_pred             HHHHHHHHHHHHhccccCCcccccCHHHHHHHHHHhccC
Q psy200          412 IDITNHLIDLTYDNVKENGEVTGIGLKEVLGVISSVYCT  450 (490)
Q Consensus       412 i~ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~~~~~~~  450 (490)
                      ..+|+.|...+..+..    ...|+++|+..|+..+.+.
T Consensus       452 ~~i~~ea~~~~~~~~~----~~~~~~~~~~~a~~~~~p~  486 (494)
T COG0464         452 AALVREAALEALREAR----RREVTLDDFLDALKKIKPS  486 (494)
T ss_pred             HHHHHHHHHHHHHHhc----cCCccHHHHHHHHHhcCCC
Confidence            5689999988887762    3479999999999985543

>PRK14971 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.70  E-value=9.5e-16  Score=163.15  Aligned_cols=219  Identities=17%  Similarity=0.252  Sum_probs=149.8

Q ss_pred             CCCcchHHHhhcCCCCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCC
Q psy200          180 SEDKPKVEEKAKDSCELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSV  259 (490)
Q Consensus       180 ~~~~~~~~~~~l~~~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~  259 (490)
                      |.++|+|...    ++++|++..++.|..++..   +.-++.+||+||+|+|||++++.+++.+.+.... .-.-.|..+
T Consensus         7 ~~~kyRP~~f----~~viGq~~~~~~L~~~i~~---~~l~hayLf~Gp~G~GKtt~A~~lAk~l~c~~~~-~~~~~Cg~C   78 (614)
T PRK14971          7 SARKYRPSTF----ESVVGQEALTTTLKNAIAT---NKLAHAYLFCGPRGVGKTTCARIFAKTINCQNLT-ADGEACNEC   78 (614)
T ss_pred             HHHHHCCCCH----HHhcCcHHHHHHHHHHHHc---CCCCeeEEEECCCCCCHHHHHHHHHHHhCCCCCC-CCCCCCCcc
Confidence            4457777766    9999999999999998864   3445668999999999999999999987522100 000112222


Q ss_pred             CCHHHHHHHH---HHHhcCCCCCCcHHHHHHHHHHHHh--cCCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEE
Q psy200          260 RNAASVYETI---VNELKLKPGGKSERHQLGAILKYFD--TKHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVL  334 (490)
Q Consensus       260 ~~~~~l~~~i---~~~l~~~~~~~s~~~~~~~l~~~l~--~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vil  334 (490)
                      .+...+-..-   +..+.. ....+.+++.+.+.++..  ..+...|+||||+|.|....++.|..+++.+   ....+|
T Consensus        79 ~sC~~~~~~~~~n~~~ld~-~~~~~vd~Ir~li~~~~~~P~~~~~KVvIIdea~~Ls~~a~naLLK~LEep---p~~tif  154 (614)
T PRK14971         79 ESCVAFNEQRSYNIHELDA-ASNNSVDDIRNLIEQVRIPPQIGKYKIYIIDEVHMLSQAAFNAFLKTLEEP---PSYAIF  154 (614)
T ss_pred             hHHHHHhcCCCCceEEecc-cccCCHHHHHHHHHHHhhCcccCCcEEEEEECcccCCHHHHHHHHHHHhCC---CCCeEE
Confidence            2222111000   000000 011234555555543321  1244669999999999888888888888743   334556


Q ss_pred             EEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHHH
Q psy200          335 VGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDI  414 (490)
Q Consensus       335 I~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~l  414 (490)
                      |.+++.   ...+.+.+++||.    .+.|.+++.+++..++...+..+  ...+++++++.|+.   ...||+|.++++
T Consensus       155 IL~tt~---~~kIl~tI~SRc~----iv~f~~ls~~ei~~~L~~ia~~e--gi~i~~~al~~La~---~s~gdlr~al~~  222 (614)
T PRK14971        155 ILATTE---KHKILPTILSRCQ----IFDFNRIQVADIVNHLQYVASKE--GITAEPEALNVIAQ---KADGGMRDALSI  222 (614)
T ss_pred             EEEeCC---chhchHHHHhhhh----eeecCCCCHHHHHHHHHHHHHHc--CCCCCHHHHHHHHH---HcCCCHHHHHHH
Confidence            666652   3677889999996    79999999999999999998887  35689999999987   678999999999


Q ss_pred             HHHHHHHH
Q psy200          415 TNHLIDLT  422 (490)
Q Consensus       415 l~~a~~~a  422 (490)
                      ++.....+
T Consensus       223 Lekl~~y~  230 (614)
T PRK14971        223 FDQVVSFT  230 (614)
T ss_pred             HHHHHHhc
Confidence            98876543

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

Probab=99.70  E-value=1.4e-15  Score=151.50  Aligned_cols=263  Identities=16%  Similarity=0.215  Sum_probs=173.7

Q ss_pred             CCCCChHHHHHH--HHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhh-hcCCceEEEEeccCCCCHHHHHHHHH
Q psy200          194 CELPGREVQLEG--IRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAE-IKDAFKTIYINCNSVRNAASVYETIV  270 (490)
Q Consensus       194 ~~lvgre~~~~~--l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~-~~~~~~~~~v~~~~~~~~~~l~~~i~  270 (490)
                      +.++|-...+..  ...+-..  .+...+.++|||+.|.|||+|+++++++.. ...+..++|+      +...++..++
T Consensus        88 nFv~g~~N~~A~aa~~~va~~--~g~~~nplfi~G~~GlGKTHLl~Aign~~~~~~~~a~v~y~------~se~f~~~~v  159 (408)
T COG0593          88 NFVVGPSNRLAYAAAKAVAEN--PGGAYNPLFIYGGVGLGKTHLLQAIGNEALANGPNARVVYL------TSEDFTNDFV  159 (408)
T ss_pred             heeeCCchHHHHHHHHHHHhc--cCCcCCcEEEECCCCCCHHHHHHHHHHHHHhhCCCceEEec------cHHHHHHHHH
Confidence            556776544432  1222221  223578999999999999999999999875 2344577887      5566666665


Q ss_pred             HHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccC--HHHHHHhHhCCCCCCCcEEEEEecCCCChhHhhh
Q psy200          271 NELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRK--QTILYTIFEWPSIPGSKLVLVGVANALDLTDRML  348 (490)
Q Consensus       271 ~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~--~~~L~~l~~~~~~~~~~vilI~~tn~~~~~~~l~  348 (490)
                      ..+..    ...+++.+.    .    .--+++|||+|.+....  |+.++++++.....+..+++.+...+.+ ...+.
T Consensus       160 ~a~~~----~~~~~Fk~~----y----~~dlllIDDiq~l~gk~~~qeefFh~FN~l~~~~kqIvltsdr~P~~-l~~~~  226 (408)
T COG0593         160 KALRD----NEMEKFKEK----Y----SLDLLLIDDIQFLAGKERTQEEFFHTFNALLENGKQIVLTSDRPPKE-LNGLE  226 (408)
T ss_pred             HHHHh----hhHHHHHHh----h----ccCeeeechHhHhcCChhHHHHHHHHHHHHHhcCCEEEEEcCCCchh-hcccc
Confidence            55433    112222222    2    23399999999998764  8888888876655555555543322222 33456


Q ss_pred             HHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHhcccc
Q psy200          349 PRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITNHLIDLTYDNVKE  428 (490)
Q Consensus       349 ~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll~~a~~~a~~~~~~  428 (490)
                      +++++||.++ ..+.+.|++.+....+|.+++...  ...++++++..+++   ....|+|.+...+.+....+...+..
T Consensus       227 ~rL~SR~~~G-l~~~I~~Pd~e~r~aiL~kka~~~--~~~i~~ev~~~la~---~~~~nvReLegaL~~l~~~a~~~~~~  300 (408)
T COG0593         227 DRLRSRLEWG-LVVEIEPPDDETRLAILRKKAEDR--GIEIPDEVLEFLAK---RLDRNVRELEGALNRLDAFALFTKRA  300 (408)
T ss_pred             HHHHHHHhce-eEEeeCCCCHHHHHHHHHHHHHhc--CCCCCHHHHHHHHH---HhhccHHHHHHHHHHHHHHHHhcCcc
Confidence            8999999887 579999999999999999988776  57799999999998   77889999888887776666544421


Q ss_pred             C--------------CcccccCHHHHHHHHHHhccCccccccccccCCCChHhHHHH---HHHHHHhcCCCCCCcccC
Q psy200          429 N--------------GEVTGIGLKEVLGVISSVYCTSQSLHCSKDEDSFPLQQKLAL---ASLLLLKSRPNVKDVTLG  489 (490)
Q Consensus       429 ~--------------~~~~~It~~~v~~a~~~~~~~~~~~~~~~~l~~L~~~qk~vL---~al~~~~~~~~~~~~~~g  489 (490)
                      -              .... |++++|.+++.+.++-..     +.+.+-....-.++   .||+++......+...||
T Consensus       301 iTi~~v~e~L~~~~~~~~~-itie~I~~~Va~~y~v~~-----~dl~s~~R~~~i~~~RqiamyL~r~lt~~Slp~IG  372 (408)
T COG0593         301 ITIDLVKEILKDLLRAGEK-ITIEDIQKIVAEYYNVKV-----SDLLSKSRTRNIVRPRQIAMYLARELTNLSLPEIG  372 (408)
T ss_pred             CcHHHHHHHHHHhhccccc-CCHHHHHHHHHHHhCCCH-----HHhhccccccccchHHHHHHHHHHHHccCcHHHHH
Confidence            0              1124 888888888888776544     22222222222222   366666666666666655

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=99.70  E-value=1.9e-15  Score=142.77  Aligned_cols=201  Identities=18%  Similarity=0.276  Sum_probs=138.2

Q ss_pred             hHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCCCC
Q psy200          199 REVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKPG  278 (490)
Q Consensus       199 re~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~  278 (490)
                      .+..++.+..++.    .....+++|+|++|||||++++++++.+.. .+..+++++|.......               
T Consensus        22 ~~~~~~~l~~~~~----~~~~~~lll~G~~G~GKT~la~~~~~~~~~-~~~~~~~i~~~~~~~~~---------------   81 (226)
T TIGR03420        22 NAELLAALRQLAA----GKGDRFLYLWGESGSGKSHLLQAACAAAEE-RGKSAIYLPLAELAQAD---------------   81 (226)
T ss_pred             cHHHHHHHHHHHh----cCCCCeEEEECCCCCCHHHHHHHHHHHHHh-cCCcEEEEeHHHHHHhH---------------
Confidence            4556666666653    356789999999999999999999988752 34577888877652100               


Q ss_pred             CCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccC--HHHHHHhHhCCCCCCCcEEEEEecC-CCChhHhhhHHhhhcc
Q psy200          279 GKSERHQLGAILKYFDTKHKSILLILDEIDALESRK--QTILYTIFEWPSIPGSKLVLVGVAN-ALDLTDRMLPRLQANV  355 (490)
Q Consensus       279 ~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~--~~~L~~l~~~~~~~~~~vilI~~tn-~~~~~~~l~~~l~~R~  355 (490)
                          ..+   + ..+.   +..+|||||+|.+....  ++.|+.+++.....+..+++  +++ .........+.+.+|+
T Consensus        82 ----~~~---~-~~~~---~~~lLvIDdi~~l~~~~~~~~~L~~~l~~~~~~~~~iIi--ts~~~~~~~~~~~~~L~~r~  148 (226)
T TIGR03420        82 ----PEV---L-EGLE---QADLVCLDDVEAIAGQPEWQEALFHLYNRVREAGGRLLI--AGRAAPAQLPLRLPDLRTRL  148 (226)
T ss_pred             ----HHH---H-hhcc---cCCEEEEeChhhhcCChHHHHHHHHHHHHHHHcCCeEEE--ECCCChHHCCcccHHHHHHH
Confidence                111   1 1122   23499999999998754  77777776532222233333  333 2111111125667776


Q ss_pred             CCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHhccccCCccccc
Q psy200          356 TLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITNHLIDLTYDNVKENGEVTGI  435 (490)
Q Consensus       356 ~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll~~a~~~a~~~~~~~~~~~~I  435 (490)
                      ... ..+.++|++.++...++...+...  ...+++++++.|++   .+.||++.+.++++.+...+...+      ..|
T Consensus       149 ~~~-~~i~l~~l~~~e~~~~l~~~~~~~--~~~~~~~~l~~L~~---~~~gn~r~L~~~l~~~~~~~~~~~------~~i  216 (226)
T TIGR03420       149 AWG-LVFQLPPLSDEEKIAALQSRAARR--GLQLPDEVADYLLR---HGSRDMGSLMALLDALDRASLAAK------RKI  216 (226)
T ss_pred             hcC-eeEecCCCCHHHHHHHHHHHHHHc--CCCCCHHHHHHHHH---hccCCHHHHHHHHHHHHHHHHHhC------CCC
Confidence            321 379999999999999999877654  45689999999998   699999999999999876665555      479


Q ss_pred             CHHHHHHHH
Q psy200          436 GLKEVLGVI  444 (490)
Q Consensus       436 t~~~v~~a~  444 (490)
                      +.+.+.+++
T Consensus       217 ~~~~~~~~~  225 (226)
T TIGR03420       217 TIPFVKEVL  225 (226)
T ss_pred             CHHHHHHHh
Confidence            999888765

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.

>KOG0652|consensus

Probab=99.70  E-value=5.5e-16  Score=141.50  Aligned_cols=224  Identities=13%  Similarity=0.203  Sum_probs=152.7

Q ss_pred             CCCCChHHHHHHHHHHHHhhhc---------cCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVN---------NETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAAS  264 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~---------~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~  264 (490)
                      .++-|.++++++|.+.+.-.+.         -.+++++++|||||||||.+|++++.+-.    ..|+.+.++       
T Consensus       171 sDiGGldkQIqELvEAiVLpmth~ekF~~lgi~pPKGvLmYGPPGTGKTlmARAcAaqT~----aTFLKLAgP-------  239 (424)
T KOG0652|consen  171 SDIGGLDKQIQELVEAIVLPMTHKEKFENLGIRPPKGVLMYGPPGTGKTLMARACAAQTN----ATFLKLAGP-------  239 (424)
T ss_pred             cccccHHHHHHHHHHHhccccccHHHHHhcCCCCCCceEeeCCCCCcHHHHHHHHHHhcc----chHHHhcch-------
Confidence            6899999999999887653321         23788999999999999999999987632    222322222       


Q ss_pred             HHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccC-----------HHHHHHhHhC--CCCCCCc
Q psy200          265 VYETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRK-----------QTILYTIFEW--PSIPGSK  331 (490)
Q Consensus       265 l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~-----------~~~L~~l~~~--~~~~~~~  331 (490)
                             +|-..+.|...+-+++.|.-+  +...|.||||||+|.+..++           |..++.+++-  ......+
T Consensus       240 -------QLVQMfIGdGAkLVRDAFaLA--KEkaP~IIFIDElDAIGtKRfDSek~GDREVQRTMLELLNQLDGFss~~~  310 (424)
T KOG0652|consen  240 -------QLVQMFIGDGAKLVRDAFALA--KEKAPTIIFIDELDAIGTKRFDSEKAGDREVQRTMLELLNQLDGFSSDDR  310 (424)
T ss_pred             -------HHHhhhhcchHHHHHHHHHHh--hccCCeEEEEechhhhccccccccccccHHHHHHHHHHHHhhcCCCCccc
Confidence                   112234455666677777643  34679999999999997553           3333333321  2345678


Q ss_pred             EEEEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHH
Q psy200          332 LVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKA  411 (490)
Q Consensus       332 vilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~a  411 (490)
                      +-+|++||+.|+.+.   .+.+ -+.-...|.|+-++.+....|++-+-++.+   .-++-..+.+++-.....|-  ++
T Consensus       311 vKviAATNRvDiLDP---ALlR-SGRLDRKIEfP~Pne~aRarIlQIHsRKMn---v~~DvNfeELaRsTddFNGA--Qc  381 (424)
T KOG0652|consen  311 VKVIAATNRVDILDP---ALLR-SGRLDRKIEFPHPNEEARARILQIHSRKMN---VSDDVNFEELARSTDDFNGA--QC  381 (424)
T ss_pred             eEEEeecccccccCH---HHhh-cccccccccCCCCChHHHHHHHHHhhhhcC---CCCCCCHHHHhhcccccCch--hh
Confidence            999999998876554   3322 122224799999999999999887766542   22344467787733333343  33


Q ss_pred             HHHHHHHHHHHHhccccCCcccccCHHHHHHHHHHhccCc
Q psy200          412 IDITNHLIDLTYDNVKENGEVTGIGLKEVLGVISSVYCTS  451 (490)
Q Consensus       412 i~ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~~~~~~~~  451 (490)
                      -.+|-.|.++|.+++     ...|+-++|..++.++....
T Consensus       382 KAVcVEAGMiALRr~-----atev~heDfmegI~eVqakK  416 (424)
T KOG0652|consen  382 KAVCVEAGMIALRRG-----ATEVTHEDFMEGILEVQAKK  416 (424)
T ss_pred             eeeehhhhHHHHhcc-----cccccHHHHHHHHHHHHHhh
Confidence            347889999999999     78999999999998876543

>PF03215 Rad17: Rad17 cell cycle checkpoint protein

Probab=99.70  E-value=2.8e-16  Score=163.21  Aligned_cols=229  Identities=15%  Similarity=0.196  Sum_probs=145.1

Q ss_pred             ccCCCCcchHHHhhcCCCCCCChHHHHHHHHHHHHhhhccC-CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEe
Q psy200          177 LLFSEDKPKVEEKAKDSCELPGREVQLEGIRQFLLGHVNNE-TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYIN  255 (490)
Q Consensus       177 ~~~~~~~~~~~~~~l~~~~lvgre~~~~~l~~~L~~~~~~~-~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~  255 (490)
                      ..+|.++|.|...    ++|+.+++.+++|..||...+... ..+.++|+||+||||||+++.++++++    +.+.++.
T Consensus         6 ~~~W~~ky~P~~~----~eLavhkkKv~eV~~wl~~~~~~~~~~~iLlLtGP~G~GKtttv~~La~elg----~~v~Ew~   77 (519)
T PF03215_consen    6 SEPWVEKYAPKTL----DELAVHKKKVEEVRSWLEEMFSGSSPKRILLLTGPSGCGKTTTVKVLAKELG----FEVQEWI   77 (519)
T ss_pred             cCccchhcCCCCH----HHhhccHHHHHHHHHHHHHHhccCCCcceEEEECCCCCCHHHHHHHHHHHhC----CeeEEec
Confidence            4489999999999    999999999999999999876544 357888999999999999999999986    6666654


Q ss_pred             ccCCCCHHHH----HHHHHHHhcCCCCCCcHHHHHHHHHHHHh----------cCCCeEEEEEecCccccccCHHHHHHh
Q psy200          256 CNSVRNAASV----YETIVNELKLKPGGKSERHQLGAILKYFD----------TKHKSILLILDEIDALESRKQTILYTI  321 (490)
Q Consensus       256 ~~~~~~~~~l----~~~i~~~l~~~~~~~s~~~~~~~l~~~l~----------~~~~~~vI~IDEid~l~~~~~~~L~~l  321 (490)
                      .+........    +........ .+ ......+.+++...-+          ...++.||+|||+.+++......+..+
T Consensus        78 np~~~~~~~~~~~d~~s~~~~~~-~f-~sq~~~F~~f~l~~s~y~~l~~~g~~~~~~~kvILVEDlPN~~~~~~~~f~~~  155 (519)
T PF03215_consen   78 NPVSFRESDNQEDDFESDFNKFD-EF-LSQSDKFSEFLLRASKYSSLSMSGSNSSSNKKVILVEDLPNVFHRDTSRFREA  155 (519)
T ss_pred             CCCCccccccccccccccccccc-cc-cchhhhhccccccccccccccccCCCcCCCceEEEeeccccccchhHHHHHHH
Confidence            3332110000    000000000 00 0011112222111100          013577999999999988776555554


Q ss_pred             Hh-CCCCCCC-cEEEEEecC--CC---Ch------hHhhh-HHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhcc----
Q psy200          322 FE-WPSIPGS-KLVLVGVAN--AL---DL------TDRML-PRLQANVTLQPTLMNFAPYSREQILEIISQKLKQT----  383 (490)
Q Consensus       322 ~~-~~~~~~~-~vilI~~tn--~~---~~------~~~l~-~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~----  383 (490)
                      +. +...... ++|||.+-.  ..   ..      .++++ +.+....+.  ..|.|+|....-+.+.|...+..+    
T Consensus       156 L~~~l~~~~~~PlV~iiSe~~~~~~~~~~~~~~~t~~~L~~~~il~~~~i--~~I~FNpIa~T~mkKaL~rI~~~E~~~~  233 (519)
T PF03215_consen  156 LRQYLRSSRCLPLVFIISETESLSGDNSYRSNSFTAERLFPKEILNHPGI--TRIKFNPIAPTFMKKALKRILKKEARSS  233 (519)
T ss_pred             HHHHHHcCCCCCEEEEEecccccCCCCcccccchhhhhccCHHHHhCCCc--eEEEecCCCHHHHHHHHHHHHHHHhhhh
Confidence            43 3333444 777776621  00   00      11232 345554443  689999999999999999988876    


Q ss_pred             -CC-CCCCCHHHHHHHHHHHHHhhCCHHHHHHHHHHHHH
Q psy200          384 -DK-FNMFNASALQLLAGKVAAVSGDIRKAIDITNHLID  420 (490)
Q Consensus       384 -~~-~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll~~a~~  420 (490)
                       +. ...-..+.|+.|+.   ...||+|.||+.|+-...
T Consensus       234 ~~~~~~p~~~~~l~~I~~---~s~GDIRsAIn~LQf~~~  269 (519)
T PF03215_consen  234 SGKNKVPDKQSVLDSIAE---SSNGDIRSAINNLQFWCL  269 (519)
T ss_pred             cCCccCCChHHHHHHHHH---hcCchHHHHHHHHHHHhc
Confidence             11 11122345888876   567999999999987765

>PRK05642 DNA replication initiation factor; Validated

Probab=99.69  E-value=2.4e-15  Score=142.31  Aligned_cols=187  Identities=15%  Similarity=0.244  Sum_probs=132.3

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCC
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFDTKHK  298 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~  298 (490)
                      ...++|+|++|+|||+|++++++++.. .+..++|+++..      +...             ..    .+.+.+..   
T Consensus        45 ~~~l~l~G~~G~GKTHLl~a~~~~~~~-~~~~v~y~~~~~------~~~~-------------~~----~~~~~~~~---   97 (234)
T PRK05642         45 ESLIYLWGKDGVGRSHLLQAACLRFEQ-RGEPAVYLPLAE------LLDR-------------GP----ELLDNLEQ---   97 (234)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHHh-CCCcEEEeeHHH------HHhh-------------hH----HHHHhhhh---
Confidence            468999999999999999999988752 245677886432      2110             01    12222222   


Q ss_pred             eEEEEEecCcccccc--CHHHHHHhHhCCCCCCCcEEEEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHH
Q psy200          299 SILLILDEIDALESR--KQTILYTIFEWPSIPGSKLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEII  376 (490)
Q Consensus       299 ~~vI~IDEid~l~~~--~~~~L~~l~~~~~~~~~~vilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il  376 (490)
                      .-+|+|||++.+...  .++.|+.+++.....+ +.++++++........+.+.+++|+.++ ..+.+.+++.++...++
T Consensus        98 ~d~LiiDDi~~~~~~~~~~~~Lf~l~n~~~~~g-~~ilits~~~p~~l~~~~~~L~SRl~~g-l~~~l~~~~~e~~~~il  175 (234)
T PRK05642         98 YELVCLDDLDVIAGKADWEEALFHLFNRLRDSG-RRLLLAASKSPRELPIKLPDLKSRLTLA-LVFQMRGLSDEDKLRAL  175 (234)
T ss_pred             CCEEEEechhhhcCChHHHHHHHHHHHHHHhcC-CEEEEeCCCCHHHcCccCccHHHHHhcC-eeeecCCCCHHHHHHHH
Confidence            238999999988654  3567888887543333 4455555543333333468899999654 36889999999999999


Q ss_pred             HHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHhccccCCcccccCHHHHHHHHH
Q psy200          377 SQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITNHLIDLTYDNVKENGEVTGIGLKEVLGVIS  445 (490)
Q Consensus       377 ~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~~  445 (490)
                      +.++...  ...+++++++.|++   ...||+|.++++++.....+...+      ..||+..+.+++.
T Consensus       176 ~~ka~~~--~~~l~~ev~~~L~~---~~~~d~r~l~~~l~~l~~~~l~~~------~~it~~~~~~~L~  233 (234)
T PRK05642        176 QLRASRR--GLHLTDEVGHFILT---RGTRSMSALFDLLERLDQASLQAQ------RKLTIPFLKETLG  233 (234)
T ss_pred             HHHHHHc--CCCCCHHHHHHHHH---hcCCCHHHHHHHHHHHHHHHHHcC------CcCCHHHHHHHhc
Confidence            9777654  36789999999998   889999999999888865444433      4799999888764

>CHL00095 clpC Clp protease ATP binding subunit

Probab=99.68  E-value=3.3e-15  Score=165.48  Aligned_cols=206  Identities=20%  Similarity=0.210  Sum_probs=143.8

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhc------CCceEEEEeccCCCCHHHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIK------DAFKTIYINCNSVRNAASVYE  267 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~------~~~~~~~v~~~~~~~~~~l~~  267 (490)
                      +.++||+++++++.++|..    ...++++|+||||||||++++.++..+...      .+..++.++...+..      
T Consensus       179 ~~~igr~~ei~~~~~~L~r----~~~~n~lL~G~pGvGKTal~~~la~~i~~~~vp~~l~~~~i~~l~~~~l~a------  248 (821)
T CHL00095        179 DPVIGREKEIERVIQILGR----RTKNNPILIGEPGVGKTAIAEGLAQRIVNRDVPDILEDKLVITLDIGLLLA------  248 (821)
T ss_pred             CCCCCcHHHHHHHHHHHcc----cccCCeEEECCCCCCHHHHHHHHHHHHHhCCCChhhcCCeEEEeeHHHHhc------
Confidence            7899999999999999964    456688999999999999999999987521      134566665432210      


Q ss_pred             HHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCH----HHHHHhHhCCCCCCCcEEEEEecCCCCh
Q psy200          268 TIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQ----TILYTIFEWPSIPGSKLVLVGVANALDL  343 (490)
Q Consensus       268 ~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~----~~L~~l~~~~~~~~~~vilI~~tn~~~~  343 (490)
                            +..+.|...+.+...+.++..  .+++||||||+|.+...+.    ..+.+++. +......+.+||+|+..++
T Consensus       249 ------g~~~~ge~e~rl~~i~~~~~~--~~~~ILfiDEih~l~~~g~~~g~~~~a~lLk-p~l~rg~l~~IgaTt~~ey  319 (821)
T CHL00095        249 ------GTKYRGEFEERLKRIFDEIQE--NNNIILVIDEVHTLIGAGAAEGAIDAANILK-PALARGELQCIGATTLDEY  319 (821)
T ss_pred             ------cCCCccHHHHHHHHHHHHHHh--cCCeEEEEecHHHHhcCCCCCCcccHHHHhH-HHHhCCCcEEEEeCCHHHH
Confidence                  223444445555555555433  3578999999999976431    01122222 2334567999999986554


Q ss_pred             hHh--hhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhcc--CCCCCCCHHHHHHHHHHHHHhhCC---HHHHHHHHH
Q psy200          344 TDR--MLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQT--DKFNMFNASALQLLAGKVAAVSGD---IRKAIDITN  416 (490)
Q Consensus       344 ~~~--l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~--~~~~~~~~~~i~~i~~~i~~~~Gd---~r~ai~ll~  416 (490)
                      ...  .++.+.+||.    .+.+..++.++...+++......  .....++++++..++....++-++   +..+|++++
T Consensus       320 ~~~ie~D~aL~rRf~----~I~v~ep~~~e~~aILr~l~~~~e~~~~v~i~deal~~i~~ls~~yi~~r~lPdkaidlld  395 (821)
T CHL00095        320 RKHIEKDPALERRFQ----PVYVGEPSVEETIEILFGLRSRYEKHHNLSISDKALEAAAKLSDQYIADRFLPDKAIDLLD  395 (821)
T ss_pred             HHHHhcCHHHHhcce----EEecCCCCHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhhccCccccCchHHHHHHH
Confidence            332  3678899996    78999999999988887644322  123458999999998866666666   788999998


Q ss_pred             HHHHHH
Q psy200          417 HLIDLT  422 (490)
Q Consensus       417 ~a~~~a  422 (490)
                      .|....
T Consensus       396 ~a~a~~  401 (821)
T CHL00095        396 EAGSRV  401 (821)
T ss_pred             HHHHHH
Confidence            887544

>PLN00020 ribulose bisphosphate carboxylase/oxygenase activase -RuBisCO activase (RCA); Provisional

Probab=99.68  E-value=2.7e-15  Score=145.74  Aligned_cols=176  Identities=15%  Similarity=0.184  Sum_probs=124.0

Q ss_pred             CCCCChHHHHHHHHHHHHhhh----ccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHV----NNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETI  269 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~----~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i  269 (490)
                      ..+.....-++++...+....    .-..+.+++||||||||||.++++++++++    ..++.+++.++.         
T Consensus       119 g~~~~~p~f~dk~~~hi~kn~l~~~~ik~PlgllL~GPPGcGKTllAraiA~elg----~~~i~vsa~eL~---------  185 (413)
T PLN00020        119 GGYYIAPAFMDKVAVHIAKNFLALPNIKVPLILGIWGGKGQGKSFQCELVFKKMG----IEPIVMSAGELE---------  185 (413)
T ss_pred             CccccCHHHHHHHHHHHHhhhhhccCCCCCeEEEeeCCCCCCHHHHHHHHHHHcC----CCeEEEEHHHhh---------
Confidence            334444444444443333222    235778999999999999999999999986    667888766543         


Q ss_pred             HHHhcCCCCCCcHHHHHHHHHHHHh---cCCCeEEEEEecCccccccC---------H---HHHHHhHh----------C
Q psy200          270 VNELKLKPGGKSERHQLGAILKYFD---TKHKSILLILDEIDALESRK---------Q---TILYTIFE----------W  324 (490)
Q Consensus       270 ~~~l~~~~~~~s~~~~~~~l~~~l~---~~~~~~vI~IDEid~l~~~~---------~---~~L~~l~~----------~  324 (490)
                           ..+.|++++.+++.|..+..   ..++|+||||||||.+....         +   ..|..+++          |
T Consensus       186 -----sk~vGEsEk~IR~~F~~A~~~a~~~~aPcVLFIDEIDA~~g~r~~~~~tv~~qiV~~tLLnl~D~p~~v~l~G~w  260 (413)
T PLN00020        186 -----SENAGEPGKLIRQRYREAADIIKKKGKMSCLFINDLDAGAGRFGTTQYTVNNQMVNGTLMNIADNPTNVSLGGDW  260 (413)
T ss_pred             -----cCcCCcHHHHHHHHHHHHHHHhhccCCCeEEEEehhhhcCCCCCCCCcchHHHHHHHHHHHHhcCCccccccccc
Confidence                 37888999999999988764   35789999999999997652         1   12233332          1


Q ss_pred             -CCCCCCcEEEEEecCCCChhHhhhHHhhh--ccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHH
Q psy200          325 -PSIPGSKLVLVGVANALDLTDRMLPRLQA--NVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAG  399 (490)
Q Consensus       325 -~~~~~~~vilI~~tn~~~~~~~l~~~l~~--R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~  399 (490)
                       ......++.||++||+   ++.+++.|.+  ||.   ..  |..++.++..+|++.++...    .++...+..|++
T Consensus       261 ~~~~~~~~V~VIaTTNr---pd~LDpALlRpGRfD---k~--i~lPd~e~R~eIL~~~~r~~----~l~~~dv~~Lv~  326 (413)
T PLN00020        261 REKEEIPRVPIIVTGND---FSTLYAPLIRDGRME---KF--YWAPTREDRIGVVHGIFRDD----GVSREDVVKLVD  326 (413)
T ss_pred             cccccCCCceEEEeCCC---cccCCHhHcCCCCCC---ce--eCCCCHHHHHHHHHHHhccC----CCCHHHHHHHHH
Confidence             1234567999999995   4556777776  776   22  45789999999999888764    356777888877

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

Probab=99.67  E-value=4e-15  Score=161.07  Aligned_cols=240  Identities=17%  Similarity=0.171  Sum_probs=157.1

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCC-CHHHHHHHHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVR-NAASVYETIVNE  272 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~-~~~~l~~~i~~~  272 (490)
                      +.++||+++++++.+.|..    ....+++|+||||||||++++.++..+.. .+.+....+|.-+. +...++    . 
T Consensus       186 ~~liGR~~ei~~~i~iL~r----~~~~n~LLvGppGvGKT~lae~la~~i~~-~~vP~~l~~~~~~~l~~~~ll----a-  255 (758)
T PRK11034        186 DPLIGREKELERAIQVLCR----RRKNNPLLVGESGVGKTAIAEGLAWRIVQ-GDVPEVMADCTIYSLDIGSLL----A-  255 (758)
T ss_pred             CcCcCCCHHHHHHHHHHhc----cCCCCeEEECCCCCCHHHHHHHHHHHHHh-cCCCchhcCCeEEeccHHHHh----c-
Confidence            7899999999999998875    45678899999999999999999987642 22222222222111 111111    0 


Q ss_pred             hcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccC-----HHHHHHhHhCCCCCCCcEEEEEecCCCChh--H
Q psy200          273 LKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRK-----QTILYTIFEWPSIPGSKLVLVGVANALDLT--D  345 (490)
Q Consensus       273 l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~-----~~~L~~l~~~~~~~~~~vilI~~tn~~~~~--~  345 (490)
                       +..+.|.....+...+..+..  ..+.||||||||.+...+     +.-+.+++. +......+.+||+||..++.  .
T Consensus       256 -G~~~~Ge~e~rl~~l~~~l~~--~~~~ILfIDEIh~L~g~g~~~~g~~d~~nlLk-p~L~~g~i~vIgATt~~E~~~~~  331 (758)
T PRK11034        256 -GTKYRGDFEKRFKALLKQLEQ--DTNSILFIDEIHTIIGAGAASGGQVDAANLIK-PLLSSGKIRVIGSTTYQEFSNIF  331 (758)
T ss_pred             -ccchhhhHHHHHHHHHHHHHh--cCCCEEEeccHHHHhccCCCCCcHHHHHHHHH-HHHhCCCeEEEecCChHHHHHHh
Confidence             122333334444444443332  346799999999995432     222323322 12245689999999965542  2


Q ss_pred             hhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhcc--CCCCCCCHHHHHHHHHHHHHhhC---CHHHHHHHHHHHHH
Q psy200          346 RMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQT--DKFNMFNASALQLLAGKVAAVSG---DIRKAIDITNHLID  420 (490)
Q Consensus       346 ~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~--~~~~~~~~~~i~~i~~~i~~~~G---d~r~ai~ll~~a~~  420 (490)
                      ..++.+.+||.    .+.+++++.++...||+......  .....+++++++.+++....+-.   -+.+++++|+.|..
T Consensus       332 ~~D~AL~rRFq----~I~v~ePs~~~~~~IL~~~~~~ye~~h~v~i~~~al~~a~~ls~ryi~~r~lPdKaidlldea~a  407 (758)
T PRK11034        332 EKDRALARRFQ----KIDITEPSIEETVQIINGLKPKYEAHHDVRYTAKAVRAAVELAVKYINDRHLPDKAIDVIDEAGA  407 (758)
T ss_pred             hccHHHHhhCc----EEEeCCCCHHHHHHHHHHHHHHhhhccCCCcCHHHHHHHHHHhhccccCccChHHHHHHHHHHHH
Confidence            34788999996    79999999999999998765443  24577899999988764433332   25689999999986


Q ss_pred             HHHhccccCCcccccCHHHHHHHHHHhccCcc
Q psy200          421 LTYDNVKENGEVTGIGLKEVLGVISSVYCTSQ  452 (490)
Q Consensus       421 ~a~~~~~~~~~~~~It~~~v~~a~~~~~~~~~  452 (490)
                      ........ .....|+.++|.++++...+-+.
T Consensus       408 ~~~~~~~~-~~~~~v~~~~i~~v~~~~tgip~  438 (758)
T PRK11034        408 RARLMPVS-KRKKTVNVADIESVVARIARIPE  438 (758)
T ss_pred             hhccCccc-ccccccChhhHHHHHHHHhCCCh
Confidence            54321100 01346899999999998877655

>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=99.67  E-value=3.9e-15  Score=139.32  Aligned_cols=182  Identities=20%  Similarity=0.334  Sum_probs=126.0

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhh-cCCceEEEEeccCCCCHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcC
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEI-KDAFKTIYINCNSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFDTK  296 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~-~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~  296 (490)
                      ....++|||++|+|||+|++++++++.. .++..++|++      ..+|...+...+..    ....++    .+.+.. 
T Consensus        33 ~~~~l~l~G~~G~GKTHLL~Ai~~~~~~~~~~~~v~y~~------~~~f~~~~~~~~~~----~~~~~~----~~~~~~-   97 (219)
T PF00308_consen   33 RYNPLFLYGPSGLGKTHLLQAIANEAQKQHPGKRVVYLS------AEEFIREFADALRD----GEIEEF----KDRLRS-   97 (219)
T ss_dssp             SSSEEEEEESTTSSHHHHHHHHHHHHHHHCTTS-EEEEE------HHHHHHHHHHHHHT----TSHHHH----HHHHCT-
T ss_pred             CCCceEEECCCCCCHHHHHHHHHHHHHhccccccceeec------HHHHHHHHHHHHHc----ccchhh----hhhhhc-
Confidence            3467999999999999999999998863 3567889994      45566665555533    112222    222332 


Q ss_pred             CCeEEEEEecCccccccC--HHHHHHhHhCCCCCCCcEEEEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHH
Q psy200          297 HKSILLILDEIDALESRK--QTILYTIFEWPSIPGSKLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILE  374 (490)
Q Consensus       297 ~~~~vI~IDEid~l~~~~--~~~L~~l~~~~~~~~~~vilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~  374 (490)
                        .-+|+|||+|.+....  |+.|+.+++.....+.++++.+.....++ ..+.+++.+|+..+. .+.+.+++.++...
T Consensus        98 --~DlL~iDDi~~l~~~~~~q~~lf~l~n~~~~~~k~li~ts~~~P~~l-~~~~~~L~SRl~~Gl-~~~l~~pd~~~r~~  173 (219)
T PF00308_consen   98 --ADLLIIDDIQFLAGKQRTQEELFHLFNRLIESGKQLILTSDRPPSEL-SGLLPDLRSRLSWGL-VVELQPPDDEDRRR  173 (219)
T ss_dssp             --SSEEEEETGGGGTTHHHHHHHHHHHHHHHHHTTSEEEEEESS-TTTT-TTS-HHHHHHHHCSE-EEEE----HHHHHH
T ss_pred             --CCEEEEecchhhcCchHHHHHHHHHHHHHHhhCCeEEEEeCCCCccc-cccChhhhhhHhhcc-hhhcCCCCHHHHHH
Confidence              3499999999998764  78888887765445556555443333333 346788999997663 69999999999999


Q ss_pred             HHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHH
Q psy200          375 IISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITNHLIDLTY  423 (490)
Q Consensus       375 il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll~~a~~~a~  423 (490)
                      ++++++...  ...+++++++.|++   ...+|+|.+..++.+....+.
T Consensus       174 il~~~a~~~--~~~l~~~v~~~l~~---~~~~~~r~L~~~l~~l~~~~~  217 (219)
T PF00308_consen  174 ILQKKAKER--GIELPEEVIEYLAR---RFRRDVRELEGALNRLDAYAQ  217 (219)
T ss_dssp             HHHHHHHHT--T--S-HHHHHHHHH---HTTSSHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHh--CCCCcHHHHHHHHH---hhcCCHHHHHHHHHHHHHHhh
Confidence            999999886  45699999999998   778899999988888766553

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.

>KOG0727|consensus

Probab=99.67  E-value=1.2e-15  Score=138.67  Aligned_cols=222  Identities=18%  Similarity=0.166  Sum_probs=147.0

Q ss_pred             CCCCChHHHHHHHHHHHHhh---------hccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHH
Q psy200          194 CELPGREVQLEGIRQFLLGH---------VNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAAS  264 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~---------~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~  264 (490)
                      .++-|.+-+.+++++.++-.         +.-.+++++++|||||||||+|+++++++-.    ..|+.+.++.      
T Consensus       155 ~diggld~qkqeireavelplt~~~ly~qigidpprgvllygppg~gktml~kava~~t~----a~firvvgse------  224 (408)
T KOG0727|consen  155 ADIGGLDVQKQEIREAVELPLTHADLYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTT----AAFIRVVGSE------  224 (408)
T ss_pred             cccccchhhHHHHHHHHhccchHHHHHHHhCCCCCcceEEeCCCCCcHHHHHHHHhhccc----hheeeeccHH------
Confidence            46677777777777665432         2234789999999999999999999998743    5667775543      


Q ss_pred             HHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccC-----------HHHHHHhHhCC--CCCCCc
Q psy200          265 VYETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRK-----------QTILYTIFEWP--SIPGSK  331 (490)
Q Consensus       265 l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~-----------~~~L~~l~~~~--~~~~~~  331 (490)
                      |..        .+.|+....+++.|.-+..  +.|.||||||+|.+..++           |..|..+++-.  .....+
T Consensus       225 fvq--------kylgegprmvrdvfrlake--napsiifideidaiatkrfdaqtgadrevqril~ellnqmdgfdq~~n  294 (408)
T KOG0727|consen  225 FVQ--------KYLGEGPRMVRDVFRLAKE--NAPSIIFIDEIDAIATKRFDAQTGADREVQRILIELLNQMDGFDQTTN  294 (408)
T ss_pred             HHH--------HHhccCcHHHHHHHHHHhc--cCCcEEEeehhhhHhhhhccccccccHHHHHHHHHHHHhccCcCcccc
Confidence            222        3455677778888875444  668999999999997553           44555554322  345678


Q ss_pred             EEEEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHH-HHHHHHhhCCHHH
Q psy200          332 LVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLL-AGKVAAVSGDIRK  410 (490)
Q Consensus       332 vilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i-~~~i~~~~Gd~r~  410 (490)
                      +-+|++||+.|-   ++|.+.+ -+.-...|.|+-++..+-+-++.....+.+..   ++-.++.+ ++ -...+  ...
T Consensus       295 vkvimatnradt---ldpallr-pgrldrkiefplpdrrqkrlvf~titskm~ls---~~vdle~~v~r-pdkis--~ad  364 (408)
T KOG0727|consen  295 VKVIMATNRADT---LDPALLR-PGRLDRKIEFPLPDRRQKRLVFSTITSKMNLS---DEVDLEDLVAR-PDKIS--GAD  364 (408)
T ss_pred             eEEEEecCcccc---cCHhhcC-CccccccccCCCCchhhhhhhHHhhhhcccCC---cccCHHHHhcC-ccccc--hhh
Confidence            999999997653   3444432 22222479999888888777777666554211   22223333 32 11111  122


Q ss_pred             HHHHHHHHHHHHHhccccCCcccccCHHHHHHHHHHhccC
Q psy200          411 AIDITNHLIDLTYDNVKENGEVTGIGLKEVLGVISSVYCT  450 (490)
Q Consensus       411 ai~ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~~~~~~~  450 (490)
                      +-.+|+.|.+.|.+..     .-.|...+|+++.......
T Consensus       365 i~aicqeagm~avr~n-----ryvvl~kd~e~ay~~~vk~  399 (408)
T KOG0727|consen  365 INAICQEAGMLAVREN-----RYVVLQKDFEKAYKTVVKK  399 (408)
T ss_pred             HHHHHHHHhHHHHHhc-----ceeeeHHHHHHHHHhhcCC
Confidence            3348999999999888     6689999999999876643

>KOG2228|consensus

Probab=99.66  E-value=1.4e-14  Score=137.22  Aligned_cols=267  Identities=16%  Similarity=0.257  Sum_probs=188.3

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhh-hcCCceEEEEeccCCCCHHHHHHHHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAE-IKDAFKTIYINCNSVRNAASVYETIVNE  272 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~-~~~~~~~~~v~~~~~~~~~~l~~~i~~~  272 (490)
                      -.|+|..++...+.+++++.+..+..+.++|.||.|+|||+++........ ...++-.+.+|+.-.. .+-.+..|..+
T Consensus        24 ~~l~g~~~~~~~l~~~lkqt~~~gEsnsviiigprgsgkT~li~~~Ls~~q~~~E~~l~v~Lng~~~~-dk~al~~I~rq  102 (408)
T KOG2228|consen   24 INLFGVQDEQKHLSELLKQTILHGESNSVIIIGPRGSGKTILIDTRLSDIQENGENFLLVRLNGELQT-DKIALKGITRQ  102 (408)
T ss_pred             cceeehHHHHHHHHHHHHHHHHhcCCCceEEEccCCCCceEeeHHHHhhHHhcCCeEEEEEECccchh-hHHHHHHHHHH
Confidence            679999999999999999999899999999999999999999988877632 2356677777766554 44456666666


Q ss_pred             hcCC-----CCCCcHHHHHHHHHHHHhcC----CCeEEEEEecCcccccc-CHHHHHHhHhCCCCCCCcEEEEEecCCCC
Q psy200          273 LKLK-----PGGKSERHQLGAILKYFDTK----HKSILLILDEIDALESR-KQTILYTIFEWPSIPGSKLVLVGVANALD  342 (490)
Q Consensus       273 l~~~-----~~~~s~~~~~~~l~~~l~~~----~~~~vI~IDEid~l~~~-~~~~L~~l~~~~~~~~~~vilI~~tn~~~  342 (490)
                      +...     ....+..+...++..+++.+    +.+++.|+||||.+... +|-.|+++|+..+....++++||.|++.|
T Consensus       103 l~~e~~~~~k~~gsfte~l~~lL~~L~~~~~~t~~~ViFIldEfDlf~~h~rQtllYnlfDisqs~r~Piciig~Ttrld  182 (408)
T KOG2228|consen  103 LALELNRIVKSFGSFTENLSKLLEALKKGDETTSGKVIFILDEFDLFAPHSRQTLLYNLFDISQSARAPICIIGVTTRLD  182 (408)
T ss_pred             HHHHHhhhheeecccchhHHHHHHHHhcCCCCCCceEEEEeehhhccccchhhHHHHHHHHHHhhcCCCeEEEEeecccc
Confidence            5321     11123444555555556543    45788888999998655 78899999999888889999999999999


Q ss_pred             hhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHH---H----HHH
Q psy200          343 LTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKA---I----DIT  415 (490)
Q Consensus       343 ~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~a---i----~ll  415 (490)
                      ..+.+..++++||... .++-+++++-++..+++++.+.--   ..+.+ .++.+.+.+...-.|.|.+   +    .++
T Consensus       183 ~lE~LEKRVKSRFshr-~I~m~~~~~l~~yv~l~r~ll~v~---~e~~~-~~~~wn~~~~~~L~d~~sl~k~l~~~~~~l  257 (408)
T KOG2228|consen  183 ILELLEKRVKSRFSHR-VIFMLPSLPLGDYVDLYRKLLSVP---AEFSD-FAEKWNRSVQEVLSDHRSLSKNLRSLHDLL  257 (408)
T ss_pred             HHHHHHHHHHhhcccc-eeeccCCCChHHHHHHHHHHhcCC---ccCcc-HHHHHHhhhhHhhcchhhHHHHHHHhhHHH
Confidence            9999999999999842 234455667889999999877432   22233 3444433222222333332   2    223


Q ss_pred             HHHHHHHHhccccCCcccccCHHHHHHHHHHhccCccccccccccCCCChHhHHHHHHHHH
Q psy200          416 NHLIDLTYDNVKENGEVTGIGLKEVLGVISSVYCTSQSLHCSKDEDSFPLQQKLALASLLL  476 (490)
Q Consensus       416 ~~a~~~a~~~~~~~~~~~~It~~~v~~a~~~~~~~~~~~~~~~~l~~L~~~qk~vL~al~~  476 (490)
                      ..++..-...      .+-+|.++++.+-..+..+..    .+.+.+|+.-...++.++..
T Consensus       258 ~~~l~~~vas------~p~~ta~~~~~v~~~ys~d~K----ie~l~gLSvLEL~LII~~~r  308 (408)
T KOG2228|consen  258 KNALNRLVAS------HPLMTAEDLAEVSRQYSVDPK----IELLSGLSVLELYLIICMKR  308 (408)
T ss_pred             Hhhhhhhhcc------CcchhHHHHHHHHHHhccChH----HHHhcCchHHHHHHHHHHHH
Confidence            3232221111      256889999998888887776    68889999888888877775

>PRK06620 hypothetical protein; Validated

Probab=99.66  E-value=5.8e-15  Score=137.48  Aligned_cols=194  Identities=14%  Similarity=0.169  Sum_probs=127.8

Q ss_pred             CCCCChHH--HHHHHHHHHHhhhccCC-CCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHH
Q psy200          194 CELPGREV--QLEGIRQFLLGHVNNET-SGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIV  270 (490)
Q Consensus       194 ~~lvgre~--~~~~l~~~L~~~~~~~~-~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~  270 (490)
                      +.++|...  .+..+..+...+ ..++ .+.++||||+|+|||+|++++++...    .  .++.....           
T Consensus        17 ~Fvvg~~N~~a~~~~~~~~~~~-~~~~~~~~l~l~Gp~G~GKThLl~a~~~~~~----~--~~~~~~~~-----------   78 (214)
T PRK06620         17 EFIVSSSNDQAYNIIKNWQCGF-GVNPYKFTLLIKGPSSSGKTYLTKIWQNLSN----A--YIIKDIFF-----------   78 (214)
T ss_pred             hhEecccHHHHHHHHHHHHHcc-ccCCCcceEEEECCCCCCHHHHHHHHHhccC----C--EEcchhhh-----------
Confidence            45666523  444444444321 1112 26799999999999999999877642    1  12210000           


Q ss_pred             HHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEEEecCCCChhHhhhHH
Q psy200          271 NELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVANALDLTDRMLPR  350 (490)
Q Consensus       271 ~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI~~tn~~~~~~~l~~~  350 (490)
                                 ..       +.+.   ...+|+|||||.+   .+..|+.+++.....+. .++++++....... + ++
T Consensus        79 -----------~~-------~~~~---~~d~lliDdi~~~---~~~~lf~l~N~~~e~g~-~ilits~~~p~~l~-l-~~  131 (214)
T PRK06620         79 -----------NE-------EILE---KYNAFIIEDIENW---QEPALLHIFNIINEKQK-YLLLTSSDKSRNFT-L-PD  131 (214)
T ss_pred             -----------ch-------hHHh---cCCEEEEeccccc---hHHHHHHHHHHHHhcCC-EEEEEcCCCccccc-h-HH
Confidence                       00       1111   1248999999965   23567777665443443 55555554332222 4 88


Q ss_pred             hhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHhccccCC
Q psy200          351 LQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITNHLIDLTYDNVKENG  430 (490)
Q Consensus       351 l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll~~a~~~a~~~~~~~~  430 (490)
                      +++|+..+ ..+.+.+++.+++..++++.+...  ...+++++++.|++   ...||+|.++++++.....+...+    
T Consensus       132 L~SRl~~g-l~~~l~~pd~~~~~~~l~k~~~~~--~l~l~~ev~~~L~~---~~~~d~r~l~~~l~~l~~~~~~~~----  201 (214)
T PRK06620        132 LSSRIKSV-LSILLNSPDDELIKILIFKHFSIS--SVTISRQIIDFLLV---NLPREYSKIIEILENINYFALISK----  201 (214)
T ss_pred             HHHHHhCC-ceEeeCCCCHHHHHHHHHHHHHHc--CCCCCHHHHHHHHH---HccCCHHHHHHHHHHHHHHHHHcC----
Confidence            99998754 369999999999999999888754  46689999999998   789999999999988654444433    


Q ss_pred             cccccCHHHHHHHH
Q psy200          431 EVTGIGLKEVLGVI  444 (490)
Q Consensus       431 ~~~~It~~~v~~a~  444 (490)
                        ..||.+.+.+++
T Consensus       202 --~~it~~~~~~~l  213 (214)
T PRK06620        202 --RKITISLVKEVL  213 (214)
T ss_pred             --CCCCHHHHHHHh
Confidence              469999988875

>KOG0740|consensus

Probab=99.66  E-value=3.2e-15  Score=148.79  Aligned_cols=228  Identities=18%  Similarity=0.208  Sum_probs=159.9

Q ss_pred             CCCCChHHHHHHHHHHHHhhhc--------cCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVN--------NETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASV  265 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~--------~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l  265 (490)
                      +++.|.+.....+.+.+-..+.        ....+.+|+.||||+|||+|+++||.+..    ..|+.+..+++      
T Consensus       153 ~di~gl~~~k~~l~e~vi~p~lr~d~F~glr~p~rglLLfGPpgtGKtmL~~aiAsE~~----atff~iSassL------  222 (428)
T KOG0740|consen  153 DDIAGLEDAKQSLKEAVILPLLRPDLFLGLREPVRGLLLFGPPGTGKTMLAKAIATESG----ATFFNISASSL------  222 (428)
T ss_pred             cCCcchhhHHHHhhhhhhhcccchHhhhccccccchhheecCCCCchHHHHHHHHhhhc----ceEeeccHHHh------
Confidence            7889988887777775543322        23668999999999999999999999864    55666654443      


Q ss_pred             HHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccC------------HHHHHHhHhCCCCCCCcEE
Q psy200          266 YETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRK------------QTILYTIFEWPSIPGSKLV  333 (490)
Q Consensus       266 ~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~------------~~~L~~l~~~~~~~~~~vi  333 (490)
                              ...+.|.++..++..|.  +++..+|.||||||+|.++...            .+.|.++.........+|+
T Consensus       223 --------tsK~~Ge~eK~vralf~--vAr~~qPsvifidEidslls~Rs~~e~e~srr~ktefLiq~~~~~s~~~drvl  292 (428)
T KOG0740|consen  223 --------TSKYVGESEKLVRALFK--VARSLQPSVIFIDEIDSLLSKRSDNEHESSRRLKTEFLLQFDGKNSAPDDRVL  292 (428)
T ss_pred             --------hhhccChHHHHHHHHHH--HHHhcCCeEEEechhHHHHhhcCCcccccchhhhhHHHhhhccccCCCCCeEE
Confidence                    23677777555555554  3344679999999999997553            1233333333344567999


Q ss_pred             EEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhC-CHHHHH
Q psy200          334 LVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSG-DIRKAI  412 (490)
Q Consensus       334 lI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~G-d~r~ai  412 (490)
                      |||+||   .++.++..+++||.   .++.++.++.+....++.+.+...  ...+.+..++.|++...++.| |+..  
T Consensus       293 vigaTN---~P~e~Dea~~Rrf~---kr~yiplPd~etr~~~~~~ll~~~--~~~l~~~d~~~l~~~Tegysgsdi~~--  362 (428)
T KOG0740|consen  293 VIGATN---RPWELDEAARRRFV---KRLYIPLPDYETRSLLWKQLLKEQ--PNGLSDLDISLLAKVTEGYSGSDITA--  362 (428)
T ss_pred             EEecCC---CchHHHHHHHHHhh---ceeeecCCCHHHHHHHHHHHHHhC--CCCccHHHHHHHHHHhcCcccccHHH--
Confidence            999999   56778888888887   578899999999999999988876  456788889999986666554 4443  


Q ss_pred             HHHHHHHHHHH--hccc------cCCcccccCHHHHHHHHHHhccCcc
Q psy200          413 DITNHLIDLTY--DNVK------ENGEVTGIGLKEVLGVISSVYCTSQ  452 (490)
Q Consensus       413 ~ll~~a~~~a~--~~~~------~~~~~~~It~~~v~~a~~~~~~~~~  452 (490)
                       +|+.|...-.  ..+.      .......|+..++..++..+.....
T Consensus       363 -l~kea~~~p~r~~~~~~~~~~~~~~~~r~i~~~df~~a~~~i~~~~s  409 (428)
T KOG0740|consen  363 -LCKEAAMGPLRELGGTTDLEFIDADKIRPITYPDFKNAFKNIKPSVS  409 (428)
T ss_pred             -HHHHhhcCchhhcccchhhhhcchhccCCCCcchHHHHHHhhccccC
Confidence             4444432111  1110      0012567999999999998877655

>CHL00206 ycf2 Ycf2; Provisional

Probab=99.65  E-value=1.1e-14  Score=164.00  Aligned_cols=214  Identities=11%  Similarity=0.088  Sum_probs=135.9

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHH--HHH-HH--------------HHHHhcCC---
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAA--SVY-ET--------------IVNELKLK---  276 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~--~l~-~~--------------i~~~l~~~---  276 (490)
                      ..+++|||+||||||||.||+++|.+..    ++++.+++.......  ... ..              +..++...   
T Consensus      1628 ~pPKGILLiGPPGTGKTlLAKALA~es~----VPFIsISgs~fl~~~~~~~~~d~i~iges~~~~~~~~~~~~~~~e~~e 1703 (2281)
T CHL00206       1628 SPSRGILVIGSIGTGRSYLVKYLATNSY----VPFITVFLNKFLDNKPKGFLIDDIDIDDSDDIDDSDDIDRDLDTELLT 1703 (2281)
T ss_pred             CCCCceEEECCCCCCHHHHHHHHHHhcC----CceEEEEHHHHhhcccccccccccccccccccccccccccccchhhhh
Confidence            4678999999999999999999999854    788888765543110  000 00              00000000   


Q ss_pred             -------CCCCcHHH--HHHHHHHHHhcCCCeEEEEEecCccccccCH-----HHHHHhHhCCC--CCCCcEEEEEecCC
Q psy200          277 -------PGGKSERH--QLGAILKYFDTKHKSILLILDEIDALESRKQ-----TILYTIFEWPS--IPGSKLVLVGVANA  340 (490)
Q Consensus       277 -------~~~~s~~~--~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~-----~~L~~l~~~~~--~~~~~vilI~~tn~  340 (490)
                             ..+.++..  +...|..+.+  ..||||+|||||.+.....     ..|...++-..  .....|+|||+||+
T Consensus      1704 ~~n~~~~~m~~~e~~~rIr~lFelARk--~SPCIIFIDEIDaL~~~ds~~ltL~qLLneLDg~~~~~s~~~VIVIAATNR 1781 (2281)
T CHL00206       1704 MMNALTMDMMPKIDRFYITLQFELAKA--MSPCIIWIPNIHDLNVNESNYLSLGLLVNSLSRDCERCSTRNILVIASTHI 1781 (2281)
T ss_pred             hcchhhhhhhhhhhHHHHHHHHHHHHH--CCCeEEEEEchhhcCCCccceehHHHHHHHhccccccCCCCCEEEEEeCCC
Confidence                   01112222  4455555444  5699999999999986632     23333333211  23457999999995


Q ss_pred             CChhHhhhHHhhh--ccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCC-HHHHHHHHHH
Q psy200          341 LDLTDRMLPRLQA--NVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGD-IRKAIDITNH  417 (490)
Q Consensus       341 ~~~~~~l~~~l~~--R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd-~r~ai~ll~~  417 (490)
                         ++.+++++.+  ||+   ..|.+..++..+..+++...+...+....-+...++.+|+   .+.|- .+.+-++|..
T Consensus      1782 ---PD~LDPALLRPGRFD---R~I~Ir~Pd~p~R~kiL~ILl~tkg~~L~~~~vdl~~LA~---~T~GfSGADLanLvNE 1852 (2281)
T CHL00206       1782 ---PQKVDPALIAPNKLN---TCIKIRRLLIPQQRKHFFTLSYTRGFHLEKKMFHTNGFGS---ITMGSNARDLVALTNE 1852 (2281)
T ss_pred             ---cccCCHhHcCCCCCC---eEEEeCCCCchhHHHHHHHHHhhcCCCCCcccccHHHHHH---hCCCCCHHHHHHHHHH
Confidence               4566777775  776   5899998887777776654322211111111123667776   44553 4556679999


Q ss_pred             HHHHHHhccccCCcccccCHHHHHHHHHHhccC
Q psy200          418 LIDLTYDNVKENGEVTGIGLKEVLGVISSVYCT  450 (490)
Q Consensus       418 a~~~a~~~~~~~~~~~~It~~~v~~a~~~~~~~  450 (490)
                      |+.+|..++     ...|+.+++..|+......
T Consensus      1853 AaliAirq~-----ks~Id~~~I~~Al~Rq~~g 1880 (2281)
T CHL00206       1853 ALSISITQK-----KSIIDTNTIRSALHRQTWD 1880 (2281)
T ss_pred             HHHHHHHcC-----CCccCHHHHHHHHHHHHhh
Confidence            999999998     6789999999999987654

>PRK09087 hypothetical protein; Validated

Probab=99.64  E-value=1.8e-14  Score=135.39  Aligned_cols=189  Identities=15%  Similarity=0.161  Sum_probs=132.9

Q ss_pred             HHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCCCCCCcHHHHHHH
Q psy200          209 FLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKPGGKSERHQLGA  288 (490)
Q Consensus       209 ~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~~~s~~~~~~~  288 (490)
                      ++..+. ....+.++|+|++|+|||||++++++..      ...|++....                          ...
T Consensus        35 ~l~~~~-~~~~~~l~l~G~~GsGKThLl~~~~~~~------~~~~i~~~~~--------------------------~~~   81 (226)
T PRK09087         35 LVDHWP-NWPSPVVVLAGPVGSGKTHLASIWREKS------DALLIHPNEI--------------------------GSD   81 (226)
T ss_pred             HHHhcc-cCCCCeEEEECCCCCCHHHHHHHHHHhc------CCEEecHHHc--------------------------chH
Confidence            454432 2335569999999999999999988764      2235532211                          111


Q ss_pred             HHHHHhcCCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCC
Q psy200          289 ILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYS  368 (490)
Q Consensus       289 l~~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls  368 (490)
                      +...+..    -+|+|||+|.+. ..++.|+++++.....+ ..++++++..........+.+++|+..+ ..+.+.+++
T Consensus        82 ~~~~~~~----~~l~iDDi~~~~-~~~~~lf~l~n~~~~~g-~~ilits~~~p~~~~~~~~dL~SRl~~g-l~~~l~~pd  154 (226)
T PRK09087         82 AANAAAE----GPVLIEDIDAGG-FDETGLFHLINSVRQAG-TSLLMTSRLWPSSWNVKLPDLKSRLKAA-TVVEIGEPD  154 (226)
T ss_pred             HHHhhhc----CeEEEECCCCCC-CCHHHHHHHHHHHHhCC-CeEEEECCCChHHhccccccHHHHHhCC-ceeecCCCC
Confidence            1111211    288899999874 45777888887554444 3455544433323333468899998654 379999999


Q ss_pred             HHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHhccccCCcccccCHHHHHHHHHHhc
Q psy200          369 REQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITNHLIDLTYDNVKENGEVTGIGLKEVLGVISSVY  448 (490)
Q Consensus       369 ~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~~~~~  448 (490)
                      .+++..++++++...  ...+++++++.|++   ...|+++.++.++.+....+...+      ..||...+.+++..+.
T Consensus       155 ~e~~~~iL~~~~~~~--~~~l~~ev~~~La~---~~~r~~~~l~~~l~~L~~~~~~~~------~~it~~~~~~~l~~~~  223 (226)
T PRK09087        155 DALLSQVIFKLFADR--QLYVDPHVVYYLVS---RMERSLFAAQTIVDRLDRLALERK------SRITRALAAEVLNEMG  223 (226)
T ss_pred             HHHHHHHHHHHHHHc--CCCCCHHHHHHHHH---HhhhhHHHHHHHHHHHHHHHHHhC------CCCCHHHHHHHHHhhc
Confidence            999999999999875  46799999999998   778999999998888766666555      4799999999998753

>PRK10733 hflB ATP-dependent metalloprotease; Reviewed

Probab=99.64  E-value=1.4e-14  Score=155.94  Aligned_cols=220  Identities=12%  Similarity=0.151  Sum_probs=150.9

Q ss_pred             CCCCChHHHHHHHHHHHHhhh--------ccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHV--------NNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASV  265 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~--------~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l  265 (490)
                      .++.|.+..++++.+.+....        ....+++++|+||+|+|||+++++++.++.    ..++.+++..+..    
T Consensus       152 ~di~g~~~~~~~l~~i~~~~~~~~~~~~~~~~~~~gill~G~~G~GKt~~~~~~a~~~~----~~f~~is~~~~~~----  223 (644)
T PRK10733        152 ADVAGCDEAKEEVAELVEYLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGEAK----VPFFTISGSDFVE----  223 (644)
T ss_pred             HHHcCHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCcEEEECCCCCCHHHHHHHHHHHcC----CCEEEEehHHhHH----
Confidence            567888877777776654321        112356799999999999999999999865    5677776654311    


Q ss_pred             HHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccC-----------HHHHHHhHh-CC-CCCCCcE
Q psy200          266 YETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRK-----------QTILYTIFE-WP-SIPGSKL  332 (490)
Q Consensus       266 ~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~-----------~~~L~~l~~-~~-~~~~~~v  332 (490)
                                .+.+.....+.+.|..+..  ..|+||||||+|.+....           ...+..++. +. ......+
T Consensus       224 ----------~~~g~~~~~~~~~f~~a~~--~~P~IifIDEiD~l~~~r~~~~~g~~~~~~~~ln~lL~~mdg~~~~~~v  291 (644)
T PRK10733        224 ----------MFVGVGASRVRDMFEQAKK--AAPCIIFIDEIDAVGRQRGAGLGGGHDEREQTLNQMLVEMDGFEGNEGI  291 (644)
T ss_pred             ----------hhhcccHHHHHHHHHHHHh--cCCcEEEehhHhhhhhccCCCCCCCchHHHHHHHHHHHhhhcccCCCCe
Confidence                      1223445566666665543  468999999999995431           123333332 21 2345679


Q ss_pred             EEEEecCCCChhHhhhHHhhh--ccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhC-CHH
Q psy200          333 VLVGVANALDLTDRMLPRLQA--NVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSG-DIR  409 (490)
Q Consensus       333 ilI~~tn~~~~~~~l~~~l~~--R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~G-d~r  409 (490)
                      ++|++||+   ++.+++++.+  ||.   ..+.|..++.++..+|+..++......   .+..+..+++   .+.| ...
T Consensus       292 ivIaaTN~---p~~lD~Al~RpgRfd---r~i~v~~Pd~~~R~~Il~~~~~~~~l~---~~~d~~~la~---~t~G~sga  359 (644)
T PRK10733        292 IVIAATNR---PDVLDPALLRPGRFD---RQVVVGLPDVRGREQILKVHMRRVPLA---PDIDAAIIAR---GTPGFSGA  359 (644)
T ss_pred             eEEEecCC---hhhcCHHHhCCcccc---eEEEcCCCCHHHHHHHHHHHhhcCCCC---CcCCHHHHHh---hCCCCCHH
Confidence            99999995   4566666664  676   589999999999999999988765211   1223455665   4455 345


Q ss_pred             HHHHHHHHHHHHHHhccccCCcccccCHHHHHHHHHHhccC
Q psy200          410 KAIDITNHLIDLTYDNVKENGEVTGIGLKEVLGVISSVYCT  450 (490)
Q Consensus       410 ~ai~ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~~~~~~~  450 (490)
                      .+-++|..|...|.+.+     ...|+.+++..|+..+...
T Consensus       360 dl~~l~~eAa~~a~r~~-----~~~i~~~d~~~a~~~v~~g  395 (644)
T PRK10733        360 DLANLVNEAALFAARGN-----KRVVSMVEFEKAKDKIMMG  395 (644)
T ss_pred             HHHHHHHHHHHHHHHcC-----CCcccHHHHHHHHHHHhcc
Confidence            55578889998888877     6789999999999987643

>KOG0737|consensus

Probab=99.64  E-value=1.1e-14  Score=140.11  Aligned_cols=200  Identities=15%  Similarity=0.211  Sum_probs=132.4

Q ss_pred             CCCCChHHHHHHHHHHHHhhhc----------cCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVN----------NETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAA  263 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~----------~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~  263 (490)
                      +++-|.+..++.+.+.+.--+.          -.++.+|||+||||||||++|++++++.+    ..++-+..+.+.+  
T Consensus        92 ~DIggLe~v~~~L~e~VilPlr~pelF~~g~Ll~p~kGiLL~GPpG~GKTmlAKA~Akeag----a~fInv~~s~lt~--  165 (386)
T KOG0737|consen   92 DDIGGLEEVKDALQELVILPLRRPELFAKGKLLRPPKGILLYGPPGTGKTMLAKAIAKEAG----ANFINVSVSNLTS--  165 (386)
T ss_pred             hhccchHHHHHHHHHHHhhcccchhhhcccccccCCccceecCCCCchHHHHHHHHHHHcC----CCcceeeccccch--
Confidence            7899999999998886542221          12678999999999999999999999965    5566676666544  


Q ss_pred             HHHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccC----HHHHH----Hh-HhCC---CCCCCc
Q psy200          264 SVYETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRK----QTILY----TI-FEWP---SIPGSK  331 (490)
Q Consensus       264 ~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~----~~~L~----~l-~~~~---~~~~~~  331 (490)
                                  .|.|.+.+-+...|.-+  ..-.|++|||||+|.+...+    .++..    ++ +.|.   ...+.+
T Consensus       166 ------------KWfgE~eKlv~AvFslA--sKl~P~iIFIDEvds~L~~R~s~dHEa~a~mK~eFM~~WDGl~s~~~~r  231 (386)
T KOG0737|consen  166 ------------KWFGEAQKLVKAVFSLA--SKLQPSIIFIDEVDSFLGQRRSTDHEATAMMKNEFMALWDGLSSKDSER  231 (386)
T ss_pred             ------------hhHHHHHHHHHHHHhhh--hhcCcceeehhhHHHHHhhcccchHHHHHHHHHHHHHHhccccCCCCce
Confidence                        23334444444433322  23569999999999997443    12111    12 2343   345668


Q ss_pred             EEEEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHH
Q psy200          332 LVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKA  411 (490)
Q Consensus       332 vilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~a  411 (490)
                      |+|+|+||+.   ..++.++.+|+.   .++++.-++..+..+||+-.+..+...   ++-.+..++....+++|.  .+
T Consensus       232 VlVlgATNRP---~DlDeAiiRR~p---~rf~V~lP~~~qR~kILkviLk~e~~e---~~vD~~~iA~~t~GySGS--DL  300 (386)
T KOG0737|consen  232 VLVLGATNRP---FDLDEAIIRRLP---RRFHVGLPDAEQRRKILKVILKKEKLE---DDVDLDEIAQMTEGYSGS--DL  300 (386)
T ss_pred             EEEEeCCCCC---ccHHHHHHHhCc---ceeeeCCCchhhHHHHHHHHhcccccC---cccCHHHHHHhcCCCcHH--HH
Confidence            9999999964   334455556665   478888888999999999999887433   333466777744455553  44


Q ss_pred             HHHHHHHHHHHHh
Q psy200          412 IDITNHLIDLTYD  424 (490)
Q Consensus       412 i~ll~~a~~~a~~  424 (490)
                      .++|..|.....+
T Consensus       301 kelC~~Aa~~~ir  313 (386)
T KOG0737|consen  301 KELCRLAALRPIR  313 (386)
T ss_pred             HHHHHHHhHhHHH
Confidence            5577776655443

>COG1224 TIP49 DNA helicase TIP49, TBP-interacting protein [Transcription]

Probab=99.63  E-value=3.4e-14  Score=135.47  Aligned_cols=133  Identities=18%  Similarity=0.224  Sum_probs=100.0

Q ss_pred             eEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEEEecCC---------CChhHhhhHHhhhccCCCCeeEEeCCCCH
Q psy200          299 SILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVANA---------LDLTDRMLPRLQANVTLQPTLMNFAPYSR  369 (490)
Q Consensus       299 ~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI~~tn~---------~~~~~~l~~~l~~R~~~~~~~i~~~pls~  369 (490)
                      |-||||||+|.|.-.....|.+.++..   -++ ++|.+||+         ..-+.-+-..+.+|+-    +|...||+.
T Consensus       292 pGVLFIDEvHmLDIE~FsFlnrAlEse---~aP-Iii~AtNRG~~kiRGTd~~sPhGIP~DlLDRll----II~t~py~~  363 (450)
T COG1224         292 PGVLFIDEVHMLDIECFSFLNRALESE---LAP-IIILATNRGMTKIRGTDIESPHGIPLDLLDRLL----IISTRPYSR  363 (450)
T ss_pred             cceEEEechhhhhHHHHHHHHHHhhcc---cCc-EEEEEcCCceeeecccCCcCCCCCCHhhhhhee----EEecCCCCH
Confidence            569999999999766555666555522   223 44555662         1112222334555653    899999999


Q ss_pred             HHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHhccccCCcccccCHHHHHHHHHHhc
Q psy200          370 EQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITNHLIDLTYDNVKENGEVTGIGLKEVLGVISSVY  448 (490)
Q Consensus       370 ~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~~~~~  448 (490)
                      +|+++||+.++..+  ...+++++++.++.  .+..-.+|+++++|.-|..+|..++     ...|..+||.+|..-+.
T Consensus       364 ~EireIi~iRa~ee--~i~l~~~Ale~L~~--ig~etSLRYa~qLL~pa~iiA~~rg-----~~~V~~~dVe~a~~lF~  433 (450)
T COG1224         364 EEIREIIRIRAKEE--DIELSDDALEYLTD--IGEETSLRYAVQLLTPASIIAKRRG-----SKRVEVEDVERAKELFL  433 (450)
T ss_pred             HHHHHHHHHhhhhh--ccccCHHHHHHHHh--hchhhhHHHHHHhccHHHHHHHHhC-----CCeeehhHHHHHHHHHh
Confidence            99999999999887  67899999999987  4455689999999999999999998     67899999999876543

>COG0465 HflB ATP-dependent Zn proteases [Posttranslational modification, protein turnover, chaperones]

Probab=99.63  E-value=8e-15  Score=151.87  Aligned_cols=224  Identities=16%  Similarity=0.186  Sum_probs=159.9

Q ss_pred             CCCCChHHHHHHHHHHHHhhhc--------cCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVN--------NETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASV  265 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~--------~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l  265 (490)
                      .++.|.++.+++|.+.+.-...        ..-+++++++||||||||.||++++.+.    ++++++++.+.+      
T Consensus       150 ~DVAG~dEakeel~EiVdfLk~p~ky~~lGakiPkGvlLvGpPGTGKTLLAkAvAgEA----~VPFf~iSGS~F------  219 (596)
T COG0465         150 ADVAGVDEAKEELSELVDFLKNPKKYQALGAKIPKGVLLVGPPGTGKTLLAKAVAGEA----GVPFFSISGSDF------  219 (596)
T ss_pred             hhhcCcHHHHHHHHHHHHHHhCchhhHhcccccccceeEecCCCCCcHHHHHHHhccc----CCCceeccchhh------
Confidence            7899998888888776654321        2357899999999999999999999885    478888865543      


Q ss_pred             HHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccC-----------HHHHHHhH-hCC-CCCCCcE
Q psy200          266 YETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRK-----------QTILYTIF-EWP-SIPGSKL  332 (490)
Q Consensus       266 ~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~-----------~~~L~~l~-~~~-~~~~~~v  332 (490)
                      .+        -+.|.....+++.|.++.+  ..||||||||+|.+...+           ...|.+++ +.. ...+..|
T Consensus       220 Ve--------mfVGvGAsRVRdLF~qAkk--~aP~IIFIDEiDAvGr~Rg~g~GggnderEQTLNQlLvEmDGF~~~~gv  289 (596)
T COG0465         220 VE--------MFVGVGASRVRDLFEQAKK--NAPCIIFIDEIDAVGRQRGAGLGGGNDEREQTLNQLLVEMDGFGGNEGV  289 (596)
T ss_pred             hh--------hhcCCCcHHHHHHHHHhhc--cCCCeEEEehhhhcccccCCCCCCCchHHHHHHHHHHhhhccCCCCCce
Confidence            11        3456677888899988876  458999999999997553           12344443 222 2345789


Q ss_pred             EEEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCH-HHH
Q psy200          333 VLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDI-RKA  411 (490)
Q Consensus       333 ilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~-r~a  411 (490)
                      +++++||+.|..+..+-+- .||.   ..+.++.++-....+|++-++........++   +..|++   .+.|-. ..+
T Consensus       290 iviaaTNRpdVlD~ALlRp-gRFD---RqI~V~~PDi~gRe~IlkvH~~~~~l~~~Vd---l~~iAr---~tpGfsGAdL  359 (596)
T COG0465         290 IVIAATNRPDVLDPALLRP-GRFD---RQILVELPDIKGREQILKVHAKNKPLAEDVD---LKKIAR---GTPGFSGADL  359 (596)
T ss_pred             EEEecCCCcccchHhhcCC-CCcc---eeeecCCcchhhHHHHHHHHhhcCCCCCcCC---HHHHhh---hCCCcccchH
Confidence            9999999887665433221 1444   5899999999999999997776652222222   444776   444432 234


Q ss_pred             HHHHHHHHHHHHhccccCCcccccCHHHHHHHHHHhccCcc
Q psy200          412 IDITNHLIDLTYDNVKENGEVTGIGLKEVLGVISSVYCTSQ  452 (490)
Q Consensus       412 i~ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~~~~~~~~~  452 (490)
                      .|++..|..+|.+.+     ...|++.+|.+|+..+.....
T Consensus       360 ~nl~NEAal~aar~n-----~~~i~~~~i~ea~drv~~G~e  395 (596)
T COG0465         360 ANLLNEAALLAARRN-----KKEITMRDIEEAIDRVIAGPE  395 (596)
T ss_pred             hhhHHHHHHHHHHhc-----CeeEeccchHHHHHHHhcCcC
Confidence            578889998998888     678999999999999875544

>PF05621 TniB: Bacterial TniB protein; InterPro: IPR008868 This family consists of several bacterial TniB NTP-binding proteins

Probab=99.63  E-value=3.4e-14  Score=135.39  Aligned_cols=234  Identities=13%  Similarity=0.133  Sum_probs=156.9

Q ss_pred             CCCCChHHH---HHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhh-----cCCceEEEEeccCCCCHHHH
Q psy200          194 CELPGREVQ---LEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEI-----KDAFKTIYINCNSVRNAASV  265 (490)
Q Consensus       194 ~~lvgre~~---~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~-----~~~~~~~~v~~~~~~~~~~l  265 (490)
                      +..+|....   ++.|.+.+.. -......+++|+|++|.|||++++.+.+....     ...++++++.++...+...|
T Consensus        34 ~rWIgY~~A~~~L~~L~~Ll~~-P~~~Rmp~lLivG~snnGKT~Ii~rF~~~hp~~~d~~~~~~PVv~vq~P~~p~~~~~  112 (302)
T PF05621_consen   34 DRWIGYPRAKEALDRLEELLEY-PKRHRMPNLLIVGDSNNGKTMIIERFRRLHPPQSDEDAERIPVVYVQMPPEPDERRF  112 (302)
T ss_pred             CCeecCHHHHHHHHHHHHHHhC-CcccCCCceEEecCCCCcHHHHHHHHHHHCCCCCCCCCccccEEEEecCCCCChHHH
Confidence            566666444   4444444442 13346789999999999999999999886641     12358999999999999999


Q ss_pred             HHHHHHHhcCCCC-CCcHHHHHHHHHHHHhcCCCeEEEEEecCcccccc---CHHHHHHhHh-CCCCCCCcEEEEEecCC
Q psy200          266 YETIVNELKLKPG-GKSERHQLGAILKYFDTKHKSILLILDEIDALESR---KQTILYTIFE-WPSIPGSKLVLVGVANA  340 (490)
Q Consensus       266 ~~~i~~~l~~~~~-~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~---~~~~L~~l~~-~~~~~~~~vilI~~tn~  340 (490)
                      |..|+..|+.+.. ..+...........++. -+.-+|||||+|++...   .|..+.+++. +...-...++.+|+...
T Consensus       113 Y~~IL~~lgaP~~~~~~~~~~~~~~~~llr~-~~vrmLIIDE~H~lLaGs~~~qr~~Ln~LK~L~NeL~ipiV~vGt~~A  191 (302)
T PF05621_consen  113 YSAILEALGAPYRPRDRVAKLEQQVLRLLRR-LGVRMLIIDEFHNLLAGSYRKQREFLNALKFLGNELQIPIVGVGTREA  191 (302)
T ss_pred             HHHHHHHhCcccCCCCCHHHHHHHHHHHHHH-cCCcEEEeechHHHhcccHHHHHHHHHHHHHHhhccCCCeEEeccHHH
Confidence            9999999998763 34455555555555554 33569999999998544   2444444332 33444556666665532


Q ss_pred             CChhHhhhHHhhhccCCCCeeEEeCCCCHH-HHHHHHHHHHhcc---CCCCCCCHHHHHHHHHHHHHhhCCHHHHHHHHH
Q psy200          341 LDLTDRMLPRLQANVTLQPTLMNFAPYSRE-QILEIISQKLKQT---DKFNMFNASALQLLAGKVAAVSGDIRKAIDITN  416 (490)
Q Consensus       341 ~~~~~~l~~~l~~R~~~~~~~i~~~pls~~-e~~~il~~~l~~~---~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll~  416 (490)
                      .... +-++++.+||.    .+.++++..+ +...++...-...   ......+++....|..   .+.|.+-.+..++.
T Consensus       192 ~~al-~~D~QLa~RF~----~~~Lp~W~~d~ef~~LL~s~e~~LPLr~~S~l~~~~la~~i~~---~s~G~iG~l~~ll~  263 (302)
T PF05621_consen  192 YRAL-RTDPQLASRFE----PFELPRWELDEEFRRLLASFERALPLRKPSNLASPELARRIHE---RSEGLIGELSRLLN  263 (302)
T ss_pred             HHHh-ccCHHHHhccC----CccCCCCCCCcHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHH---HcCCchHHHHHHHH
Confidence            2211 12689999997    6888998855 4555554332222   1122234454556654   56688888889999


Q ss_pred             HHHHHHHhccccCCcccccCHHHHHH
Q psy200          417 HLIDLTYDNVKENGEVTGIGLKEVLG  442 (490)
Q Consensus       417 ~a~~~a~~~~~~~~~~~~It~~~v~~  442 (490)
                      .|...|...|     ...||.+.+..
T Consensus       264 ~aA~~AI~sG-----~E~It~~~l~~  284 (302)
T PF05621_consen  264 AAAIAAIRSG-----EERITREILDK  284 (302)
T ss_pred             HHHHHHHhcC-----CceecHHHHhh
Confidence            9999999999     67899888876

TniB is a probable ATP-binding protein [] which is involved in Tn5053 mercury resistance transposition [].

>TIGR02903 spore_lon_C ATP-dependent protease, Lon family

Probab=99.62  E-value=5e-14  Score=150.62  Aligned_cols=233  Identities=18%  Similarity=0.267  Sum_probs=153.3

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhc------CCceEEEEeccCCC-CHHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIK------DAFKTIYINCNSVR-NAASVY  266 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~------~~~~~~~v~~~~~~-~~~~l~  266 (490)
                      ++++|++..+..+...+.    .....+++|+||+||||||+|+.+++.....      .+..++.++|.... +...+.
T Consensus       154 ~~iiGqs~~~~~l~~~ia----~~~~~~vlL~Gp~GtGKTTLAr~i~~~~~~~~~~~~~~~~~fv~i~~~~l~~d~~~i~  229 (615)
T TIGR02903       154 SEIVGQERAIKALLAKVA----SPFPQHIILYGPPGVGKTTAARLALEEAKKLKHTPFAEDAPFVEVDGTTLRWDPREVT  229 (615)
T ss_pred             HhceeCcHHHHHHHHHHh----cCCCCeEEEECCCCCCHHHHHHHHHHhhhhccCCcccCCCCeEEEechhccCCHHHHh
Confidence            789999999988766653    3456789999999999999999998766321      23468889987653 222222


Q ss_pred             HHHHHHhcCCCCCCcHHHHHHHHHH---------HHhcCCCeEEEEEecCccccccCHHHHHHhHhCCC-----------
Q psy200          267 ETIVNELKLKPGGKSERHQLGAILK---------YFDTKHKSILLILDEIDALESRKQTILYTIFEWPS-----------  326 (490)
Q Consensus       267 ~~i~~~l~~~~~~~s~~~~~~~l~~---------~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~-----------  326 (490)
                      ..++..+    ...........+..         .+... ..-+|||||++.|....|..|..+++...           
T Consensus       230 ~~llg~~----~~~~~~~a~~~l~~~gl~~~~~g~v~~a-sgGvL~LDEi~~Ld~~~Q~~Ll~~Le~~~v~~~~~~~~~~  304 (615)
T TIGR02903       230 NPLLGSV----HDPIYQGARRDLAETGVPEPKTGLVTDA-HGGVLFIDEIGELDPLLQNKLLKVLEDKRVEFSSSYYDPD  304 (615)
T ss_pred             HHhcCCc----cHHHHHHHHHHHHHcCCCchhcCchhhc-CCCeEEEeccccCCHHHHHHHHHHHhhCeEEeecceeccC
Confidence            2221110    00000001111110         01110 12299999999999888888887775321           


Q ss_pred             --------------CCCCcEEEEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHH
Q psy200          327 --------------IPGSKLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNAS  392 (490)
Q Consensus       327 --------------~~~~~vilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~  392 (490)
                                    .....+++|++|+..  ...+.+.+++||.    .+.|.|++.++++.|+.+.+...  ...++++
T Consensus       305 ~~~~~~~ik~~~~~~~~~~~VLI~aTt~~--~~~l~~aLrSR~~----~i~~~pls~edi~~Il~~~a~~~--~v~ls~e  376 (615)
T TIGR02903       305 DPNVPKYIKKLFEEGAPADFVLIGATTRD--PEEINPALRSRCA----EVFFEPLTPEDIALIVLNAAEKI--NVHLAAG  376 (615)
T ss_pred             CcccchhhhhhcccCccceEEEEEecccc--ccccCHHHHhcee----EEEeCCCCHHHHHHHHHHHHHHc--CCCCCHH
Confidence                          123457888777542  2356778899986    78999999999999999998865  3457899


Q ss_pred             HHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHhccc---cCCcccccCHHHHHHHHHHh
Q psy200          393 ALQLLAGKVAAVSGDIRKAIDITNHLIDLTYDNVK---ENGEVTGIGLKEVLGVISSV  447 (490)
Q Consensus       393 ~i~~i~~~i~~~~Gd~r~ai~ll~~a~~~a~~~~~---~~~~~~~It~~~v~~a~~~~  447 (490)
                      +++.|++    ++++.|.++++|..+...+.....   +......|+.+++.+++..-
T Consensus       377 al~~L~~----ys~~gRraln~L~~~~~~~~~~~~~~~~~~~~~~I~~edv~~~l~~~  430 (615)
T TIGR02903       377 VEELIAR----YTIEGRKAVNILADVYGYALYRAAEAGKENDKVTITQDDVYEVIQIS  430 (615)
T ss_pred             HHHHHHH----CCCcHHHHHHHHHHHHHHHHHHHHHhccCCCCeeECHHHHHHHhCCC
Confidence            9999986    566789999988888655422210   00113479999999998753

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.

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=99.61  E-value=4e-14  Score=155.65  Aligned_cols=225  Identities=18%  Similarity=0.245  Sum_probs=147.9

Q ss_pred             CCCCChHHHHHHHHHHHHhhhcc---------CCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVNN---------ETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAAS  264 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~---------~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~  264 (490)
                      +++.|.+++++.|.+++...+..         ..+.+++|+||||||||++++++++++.    ..++.+++..+.+   
T Consensus       178 ~di~G~~~~~~~l~~~i~~~~~~~~~~~~~gi~~~~giLL~GppGtGKT~laraia~~~~----~~~i~i~~~~i~~---  250 (733)
T TIGR01243       178 EDIGGLKEAKEKIREMVELPMKHPELFEHLGIEPPKGVLLYGPPGTGKTLLAKAVANEAG----AYFISINGPEIMS---  250 (733)
T ss_pred             HHhcCHHHHHHHHHHHHHHHhhCHHHHHhcCCCCCceEEEECCCCCChHHHHHHHHHHhC----CeEEEEecHHHhc---
Confidence            67999999999999988643221         3567899999999999999999999875    5677787654321   


Q ss_pred             HHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccC-----------HHHHHHhHhCCCCCCCcEE
Q psy200          265 VYETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRK-----------QTILYTIFEWPSIPGSKLV  333 (490)
Q Consensus       265 l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~-----------~~~L~~l~~~~~~~~~~vi  333 (490)
                                 .+.+.+...+...|..+..  ..+.||||||+|.+....           +..|..+++-. .....++
T Consensus       251 -----------~~~g~~~~~l~~lf~~a~~--~~p~il~iDEid~l~~~r~~~~~~~~~~~~~~Ll~~ld~l-~~~~~vi  316 (733)
T TIGR01243       251 -----------KYYGESEERLREIFKEAEE--NAPSIIFIDEIDAIAPKREEVTGEVEKRVVAQLLTLMDGL-KGRGRVI  316 (733)
T ss_pred             -----------ccccHHHHHHHHHHHHHHh--cCCcEEEeehhhhhcccccCCcchHHHHHHHHHHHHhhcc-ccCCCEE
Confidence                       2334455566666665544  457899999999986542           12344444322 2356789


Q ss_pred             EEEecCCCChhHhhhHHhhh--ccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHH
Q psy200          334 LVGVANALDLTDRMLPRLQA--NVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKA  411 (490)
Q Consensus       334 lI~~tn~~~~~~~l~~~l~~--R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~a  411 (490)
                      +|+++|..   +.+++.+.+  ||.   ..+.|..++.++..+|++..+...   ....+..++.+++   ...|-...-
T Consensus       317 vI~atn~~---~~ld~al~r~gRfd---~~i~i~~P~~~~R~~Il~~~~~~~---~l~~d~~l~~la~---~t~G~~gad  384 (733)
T TIGR01243       317 VIGATNRP---DALDPALRRPGRFD---REIVIRVPDKRARKEILKVHTRNM---PLAEDVDLDKLAE---VTHGFVGAD  384 (733)
T ss_pred             EEeecCCh---hhcCHHHhCchhcc---EEEEeCCcCHHHHHHHHHHHhcCC---CCccccCHHHHHH---hCCCCCHHH
Confidence            99999854   445566654  665   479999999999999999766543   1123444677776   333433222


Q ss_pred             H-HHHHHHHHHHHhcccc----C----------CcccccCHHHHHHHHHHhccCc
Q psy200          412 I-DITNHLIDLTYDNVKE----N----------GEVTGIGLKEVLGVISSVYCTS  451 (490)
Q Consensus       412 i-~ll~~a~~~a~~~~~~----~----------~~~~~It~~~v~~a~~~~~~~~  451 (490)
                      + .+++.|...+..+...    .          .....|+.+++..|+..+.+..
T Consensus       385 l~~l~~~a~~~al~r~~~~~~~~~~~~~i~~~~~~~~~v~~~df~~Al~~v~ps~  439 (733)
T TIGR01243       385 LAALAKEAAMAALRRFIREGKINFEAEEIPAEVLKELKVTMKDFMEALKMVEPSA  439 (733)
T ss_pred             HHHHHHHHHHHHHHHHhhccccccccccccchhcccccccHHHHHHHHhhccccc
Confidence            2 3555555444332100    0          1134688999999999877654

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.

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=99.61  E-value=2.5e-14  Score=158.92  Aligned_cols=208  Identities=16%  Similarity=0.155  Sum_probs=145.3

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhc------CCceEEEEeccCCCCHHHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIK------DAFKTIYINCNSVRNAASVYE  267 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~------~~~~~~~v~~~~~~~~~~l~~  267 (490)
                      +.++||++++.++.+.|..    ...++++|+||||+|||++++.++..+...      .+..++.++......      
T Consensus       173 ~~~igr~~ei~~~~~~l~r----~~~~n~lL~G~pGvGKT~l~~~la~~i~~~~~p~~l~~~~~~~l~~~~l~a------  242 (852)
T TIGR03346       173 DPVIGRDEEIRRTIQVLSR----RTKNNPVLIGEPGVGKTAIVEGLAQRIVNGDVPESLKNKRLLALDMGALIA------  242 (852)
T ss_pred             CcCCCcHHHHHHHHHHHhc----CCCCceEEEcCCCCCHHHHHHHHHHHHhccCCchhhcCCeEEEeeHHHHhh------
Confidence            7899999999999998864    556788899999999999999999987421      134555554322100      


Q ss_pred             HHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccC----HHHHHHhHhCCCCCCCcEEEEEecCCCCh
Q psy200          268 TIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRK----QTILYTIFEWPSIPGSKLVLVGVANALDL  343 (490)
Q Consensus       268 ~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~----~~~L~~l~~~~~~~~~~vilI~~tn~~~~  343 (490)
                            +..+.|.....+...+.++.. .++++||||||+|.|...+    ..-..+++ .+......+.+||+|+..++
T Consensus       243 ------~~~~~g~~e~~l~~~l~~~~~-~~~~~ILfIDEih~l~~~g~~~~~~d~~~~L-k~~l~~g~i~~IgaTt~~e~  314 (852)
T TIGR03346       243 ------GAKYRGEFEERLKAVLNEVTK-SEGQIILFIDELHTLVGAGKAEGAMDAGNML-KPALARGELHCIGATTLDEY  314 (852)
T ss_pred             ------cchhhhhHHHHHHHHHHHHHh-cCCCeEEEeccHHHhhcCCCCcchhHHHHHh-chhhhcCceEEEEeCcHHHH
Confidence                  112333334445555554333 2468999999999997421    11122333 23345678999999986554


Q ss_pred             hH--hhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhcc--CCCCCCCHHHHHHHHHHHHHhhCC---HHHHHHHHH
Q psy200          344 TD--RMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQT--DKFNMFNASALQLLAGKVAAVSGD---IRKAIDITN  416 (490)
Q Consensus       344 ~~--~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~--~~~~~~~~~~i~~i~~~i~~~~Gd---~r~ai~ll~  416 (490)
                      ..  ..++.+.+||.    .+.+..++.++...||.......  .....+.++++..++.....+-.|   +.+||++++
T Consensus       315 r~~~~~d~al~rRf~----~i~v~~p~~~~~~~iL~~~~~~~e~~~~v~~~d~~i~~~~~ls~~yi~~r~lPdkAidlld  390 (852)
T TIGR03346       315 RKYIEKDAALERRFQ----PVFVDEPTVEDTISILRGLKERYEVHHGVRITDPAIVAAATLSHRYITDRFLPDKAIDLID  390 (852)
T ss_pred             HHHhhcCHHHHhcCC----EEEeCCCCHHHHHHHHHHHHHHhccccCCCCCHHHHHHHHHhccccccccCCchHHHHHHH
Confidence            22  34789999996    68999999999999988765553  234567899999888766666666   889999999


Q ss_pred             HHHHHHH
Q psy200          417 HLIDLTY  423 (490)
Q Consensus       417 ~a~~~a~  423 (490)
                      .|+..+.
T Consensus       391 ~a~a~~~  397 (852)
T TIGR03346       391 EAAARIR  397 (852)
T ss_pred             HHHHHHH
Confidence            9886554

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.

>KOG0990|consensus

Probab=99.61  E-value=1.6e-14  Score=136.15  Aligned_cols=238  Identities=19%  Similarity=0.177  Sum_probs=163.5

Q ss_pred             CCccccCCCCcchHHHhhcCCCCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCc--e
Q psy200          173 SPRKLLFSEDKPKVEEKAKDSCELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAF--K  250 (490)
Q Consensus       173 ~p~~~~~~~~~~~~~~~~l~~~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~--~  250 (490)
                      ++..+.+|.++|.+...    .+++++++.+..+.++..    .....++|+|||||+|||+.+.+.+..+....++  .
T Consensus        24 ~~~~~~pwvekyrP~~l----~dv~~~~ei~st~~~~~~----~~~lPh~L~YgPPGtGktsti~a~a~~ly~~~~~~~m   95 (360)
T KOG0990|consen   24 SPQYPQPWVEKYRPPFL----GIVIKQEPIWSTENRYSG----MPGLPHLLFYGPPGTGKTSTILANARDFYSPHPTTSM   95 (360)
T ss_pred             CcccCCCCccCCCCchh----hhHhcCCchhhHHHHhcc----CCCCCcccccCCCCCCCCCchhhhhhhhcCCCCchhH
Confidence            34556699999999999    999999999988888853    3556699999999999999999999987532211  1


Q ss_pred             EEEEeccCCCCHHHHHHHHHHHhcCCCCCCcHHHH-HHHHHH-----HHhcCCCeEEEEEecCccccccCHHHHHHhHhC
Q psy200          251 TIYINCNSVRNAASVYETIVNELKLKPGGKSERHQ-LGAILK-----YFDTKHKSILLILDEIDALESRKQTILYTIFEW  324 (490)
Q Consensus       251 ~~~v~~~~~~~~~~l~~~i~~~l~~~~~~~s~~~~-~~~l~~-----~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~  324 (490)
                      +..+|.+...                  |...... ...+..     .+.......+||+||+|.+....|.+|++.++.
T Consensus        96 ~lelnaSd~r------------------gid~vr~qi~~fast~~~~~fst~~~fKlvILDEADaMT~~AQnALRRviek  157 (360)
T KOG0990|consen   96 LLELNASDDR------------------GIDPVRQQIHLFASTQQPTTYSTHAAFKLVILDEADAMTRDAQNALRRVIEK  157 (360)
T ss_pred             HHHhhccCcc------------------CCcchHHHHHHHHhhccceeccccCceeEEEecchhHhhHHHHHHHHHHHHH
Confidence            2223322221                  1111111 111111     111122467999999999999999999997664


Q ss_pred             CCCCCCcEEEEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHh
Q psy200          325 PSIPGSKLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAV  404 (490)
Q Consensus       325 ~~~~~~~vilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~  404 (490)
                      . ..+.+|++|  +|   .+..+.+.+++||.    .+.|.|++..+....+.+.+..+  ....+++....+++   ..
T Consensus       158 ~-t~n~rF~ii--~n---~~~ki~pa~qsRct----rfrf~pl~~~~~~~r~shi~e~e--~~~~~~~~~~a~~r---~s  222 (360)
T KOG0990|consen  158 Y-TANTRFATI--SN---PPQKIHPAQQSRCT----RFRFAPLTMAQQTERQSHIRESE--QKETNPEGYSALGR---LS  222 (360)
T ss_pred             h-ccceEEEEe--cc---ChhhcCchhhcccc----cCCCCCCChhhhhhHHHHHHhcc--hhhcCHHHHHHHHH---Hh
Confidence            3 345555554  54   46777899999996    89999999999999999999887  56678877777666   78


Q ss_pred             hCCHHHHHHHHHHHHHHHHhccccCC--------cccccCHHHHHHHHHHhccCcc
Q psy200          405 SGDIRKAIDITNHLIDLTYDNVKENG--------EVTGIGLKEVLGVISSVYCTSQ  452 (490)
Q Consensus       405 ~Gd~r~ai~ll~~a~~~a~~~~~~~~--------~~~~It~~~v~~a~~~~~~~~~  452 (490)
                      .||+|.+++.|+....... ...+..        -.......++...+..+....+
T Consensus       223 ~gDmr~a~n~Lqs~~~~~~-~~~e~~~~~~~vy~c~g~p~~~dI~~I~~~il~~~~  277 (360)
T KOG0990|consen  223 VGDMRVALNYLQSILKKVM-ERKELNNPNDLVYQCKGAPQPSDIRQIIEKRMNGED  277 (360)
T ss_pred             HHHHHHHHHHHHHHHHHhC-CCCCCCCchhhHHHhcCCCChhHHHHHHHHHhcCch
Confidence            8999999999887654332 221110        0112334477777776665544

>PRK09112 DNA polymerase III subunit delta'; Validated

Probab=99.60  E-value=5.3e-14  Score=140.19  Aligned_cols=200  Identities=14%  Similarity=0.195  Sum_probs=135.0

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCC--c-eE-EEEeccCCCCHHHHHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDA--F-KT-IYINCNSVRNAASVYETI  269 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~--~-~~-~~v~~~~~~~~~~l~~~i  269 (490)
                      ..++|+++..+.|...+..   +..++.++|+||+|+|||++++.+++.+.....  . .. ....|...    ..+..+
T Consensus        23 ~~l~Gh~~a~~~L~~a~~~---grl~ha~L~~G~~G~GKttlA~~lA~~Llc~~~~~~~~~~~~~~~~~c----~~c~~i   95 (351)
T PRK09112         23 TRLFGHEEAEAFLAQAYRE---GKLHHALLFEGPEGIGKATLAFHLANHILSHPDPAEAPETLADPDPAS----PVWRQI   95 (351)
T ss_pred             hhccCcHHHHHHHHHHHHc---CCCCeeEeeECCCCCCHHHHHHHHHHHHcCCCccccCccccCCCCCCC----HHHHHH
Confidence            7899999999999988864   345567999999999999999999999864221  1 11 11122121    122222


Q ss_pred             HHH-------hcCC--------CCCCcHHHHHHHHHHHHh---cCCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCc
Q psy200          270 VNE-------LKLK--------PGGKSERHQLGAILKYFD---TKHKSILLILDEIDALESRKQTILYTIFEWPSIPGSK  331 (490)
Q Consensus       270 ~~~-------l~~~--------~~~~s~~~~~~~l~~~l~---~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~  331 (490)
                      ...       +..+        ....+.+++++. .+.+.   ..++..||||||+|.|....++.|+..++.+.   .+
T Consensus        96 ~~~~hPdl~~l~~~~~~~~~~~~~~I~vd~iR~l-~~~l~~~~~~g~~rVviIDeAd~l~~~aanaLLk~LEEpp---~~  171 (351)
T PRK09112         96 AQGAHPNLLHITRPFDEKTGKFKTAITVDEIRRV-GHFLSQTSGDGNWRIVIIDPADDMNRNAANAILKTLEEPP---AR  171 (351)
T ss_pred             HcCCCCCEEEeecccccccccccccCCHHHHHHH-HHHhhhccccCCceEEEEEchhhcCHHHHHHHHHHHhcCC---CC
Confidence            111       1100        012335555533 33332   13567799999999999888888888887532   23


Q ss_pred             EEEEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHH
Q psy200          332 LVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKA  411 (490)
Q Consensus       332 vilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~a  411 (490)
                      .++|.+++.   ..++++.+++||.    .+.|.|++.+++.++|.+.....    .++++++..+++   ...|+++.+
T Consensus       172 ~~fiLit~~---~~~llptIrSRc~----~i~l~pl~~~~~~~~L~~~~~~~----~~~~~~~~~i~~---~s~G~pr~A  237 (351)
T PRK09112        172 ALFILISHS---SGRLLPTIRSRCQ----PISLKPLDDDELKKALSHLGSSQ----GSDGEITEALLQ---RSKGSVRKA  237 (351)
T ss_pred             ceEEEEECC---hhhccHHHHhhcc----EEEecCCCHHHHHHHHHHhhccc----CCCHHHHHHHHH---HcCCCHHHH
Confidence            444444442   4577899999995    89999999999999999843222    277888888876   778999999


Q ss_pred             HHHHHHH
Q psy200          412 IDITNHL  418 (490)
Q Consensus       412 i~ll~~a  418 (490)
                      +++++..
T Consensus       238 l~ll~~~  244 (351)
T PRK09112        238 LLLLNYG  244 (351)
T ss_pred             HHHHhcC
Confidence            9987543

>KOG0726|consensus

Probab=99.60  E-value=1.1e-14  Score=134.95  Aligned_cols=222  Identities=15%  Similarity=0.175  Sum_probs=146.7

Q ss_pred             CCCCChHHHHHHHHHHHHhhhc---------cCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVN---------NETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAAS  264 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~---------~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~  264 (490)
                      .++-|.+.+++++.+.++-.+.         -.++++++|||+||||||.||+++++.-                  ...
T Consensus       185 ~diGGle~QiQEiKEsvELPLthPE~YeemGikpPKGVIlyG~PGTGKTLLAKAVANqT------------------SAT  246 (440)
T KOG0726|consen  185 ADIGGLESQIQEIKESVELPLTHPEYYEEMGIKPPKGVILYGEPGTGKTLLAKAVANQT------------------SAT  246 (440)
T ss_pred             cccccHHHHHHHHHHhhcCCCCCHHHHHHcCCCCCCeeEEeCCCCCchhHHHHHHhccc------------------chh
Confidence            6889999999999997764432         2377899999999999999999999863                  233


Q ss_pred             HHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccC-----------HHHHHHhHhC--CCCCCCc
Q psy200          265 VYETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRK-----------QTILYTIFEW--PSIPGSK  331 (490)
Q Consensus       265 l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~-----------~~~L~~l~~~--~~~~~~~  331 (490)
                      |++-+..+|-..+.|....-+++.|.-+-.  ..|.|+||||||.+...+           |..++.+++-  .......
T Consensus       247 FlRvvGseLiQkylGdGpklvRqlF~vA~e--~apSIvFiDEIdAiGtKRyds~SggerEiQrtmLELLNQldGFdsrgD  324 (440)
T KOG0726|consen  247 FLRVVGSELIQKYLGDGPKLVRELFRVAEE--HAPSIVFIDEIDAIGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGD  324 (440)
T ss_pred             hhhhhhHHHHHHHhccchHHHHHHHHHHHh--cCCceEEeehhhhhccccccCCCccHHHHHHHHHHHHHhccCccccCC
Confidence            344444444446666777777777765443  568999999999997553           3333344332  1335678


Q ss_pred             EEEEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHH
Q psy200          332 LVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKA  411 (490)
Q Consensus       332 vilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~a  411 (490)
                      +-+|.+||..+   .++|.+.+ -+.-...|.|+-++...-++||.-+-.+....   .+-.++.+...-...+|-  .+
T Consensus       325 vKvimATnrie---~LDPaLiR-PGrIDrKIef~~pDe~TkkkIf~IHTs~Mtl~---~dVnle~li~~kddlSGA--dI  395 (440)
T KOG0726|consen  325 VKVIMATNRIE---TLDPALIR-PGRIDRKIEFPLPDEKTKKKIFQIHTSRMTLA---EDVNLEELIMTKDDLSGA--DI  395 (440)
T ss_pred             eEEEEeccccc---ccCHhhcC-CCccccccccCCCchhhhceeEEEeecccchh---ccccHHHHhhcccccccc--cH
Confidence            89999999764   34444432 23222579999999888887776543332111   112233332211122221  22


Q ss_pred             HHHHHHHHHHHHhccccCCcccccCHHHHHHHHHHhcc
Q psy200          412 IDITNHLIDLTYDNVKENGEVTGIGLKEVLGVISSVYC  449 (490)
Q Consensus       412 i~ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~~~~~~  449 (490)
                      -.+|-.|..+|.++.     .-.|+++||.+|...++-
T Consensus       396 kAictEaGllAlRer-----Rm~vt~~DF~ka~e~V~~  428 (440)
T KOG0726|consen  396 KAICTEAGLLALRER-----RMKVTMEDFKKAKEKVLY  428 (440)
T ss_pred             HHHHHHHhHHHHHHH-----HhhccHHHHHHHHHHHHH
Confidence            347999999998887     668999999999998763

>PRK10865 protein disaggregation chaperone; Provisional

Probab=99.60  E-value=4.2e-14  Score=156.57  Aligned_cols=184  Identities=17%  Similarity=0.190  Sum_probs=125.5

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhc------CCceEEEEeccCCCCHHHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIK------DAFKTIYINCNSVRNAASVYE  267 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~------~~~~~~~v~~~~~~~~~~l~~  267 (490)
                      +.++||+++++++.+.|..    ...++++|+||||||||++++.++..+...      .++.+++++......      
T Consensus       178 ~~vigr~~ei~~~i~iL~r----~~~~n~lL~G~pGvGKT~l~~~la~~i~~~~vp~~l~~~~~~~l~l~~l~a------  247 (857)
T PRK10865        178 DPVIGRDEEIRRTIQVLQR----RTKNNPVLIGEPGVGKTAIVEGLAQRIINGEVPEGLKGRRVLALDMGALVA------  247 (857)
T ss_pred             CcCCCCHHHHHHHHHHHhc----CCcCceEEECCCCCCHHHHHHHHHHHhhcCCCchhhCCCEEEEEehhhhhh------
Confidence            8899999999999998864    556788999999999999999999987421      145666665443211      


Q ss_pred             HHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccC----HHHHHHhHhCCCCCCCcEEEEEecCCCCh
Q psy200          268 TIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRK----QTILYTIFEWPSIPGSKLVLVGVANALDL  343 (490)
Q Consensus       268 ~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~----~~~L~~l~~~~~~~~~~vilI~~tn~~~~  343 (490)
                            +..+.|.....+...|.+... .++++||||||+|.+.+.+    ..-..+++ .+....+.+.+||+|+..++
T Consensus       248 ------g~~~~g~~e~~lk~~~~~~~~-~~~~~ILfIDEih~l~~~~~~~~~~d~~~~l-kp~l~~g~l~~IgaTt~~e~  319 (857)
T PRK10865        248 ------GAKYRGEFEERLKGVLNDLAK-QEGNVILFIDELHTMVGAGKADGAMDAGNML-KPALARGELHCVGATTLDEY  319 (857)
T ss_pred             ------ccchhhhhHHHHHHHHHHHHH-cCCCeEEEEecHHHhccCCCCccchhHHHHh-cchhhcCCCeEEEcCCCHHH
Confidence                  112333444455555554433 2568899999999997552    00112222 34456778999999997665


Q ss_pred             h--HhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhcc--CCCCCCCHHHHHHHHH
Q psy200          344 T--DRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQT--DKFNMFNASALQLLAG  399 (490)
Q Consensus       344 ~--~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~--~~~~~~~~~~i~~i~~  399 (490)
                      .  -.+++.+.+||.    .|.+..++.++...+|+......  .....++++++..++.
T Consensus       320 r~~~~~d~al~rRf~----~i~v~eP~~~~~~~iL~~l~~~~e~~~~v~~~d~a~~~a~~  375 (857)
T PRK10865        320 RQYIEKDAALERRFQ----KVFVAEPSVEDTIAILRGLKERYELHHHVQITDPAIVAAAT  375 (857)
T ss_pred             HHHhhhcHHHHhhCC----EEEeCCCCHHHHHHHHHHHhhhhccCCCCCcCHHHHHHHHH
Confidence            2  234788999996    68888889999999987665443  1234566666665543

>KOG0729|consensus

Probab=99.58  E-value=2.1e-14  Score=131.67  Aligned_cols=223  Identities=17%  Similarity=0.172  Sum_probs=147.9

Q ss_pred             CCCCChHHHHHHHHHHHHhhhc---------cCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVN---------NETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAAS  264 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~---------~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~  264 (490)
                      .++-|.+++++.|++.++--+.         -.+++++++|||||+|||.+|+++++.    .+.+|+.+-++      +
T Consensus       177 ~dvggckeqieklrevve~pll~perfv~lgidppkgvllygppgtgktl~aravanr----tdacfirvigs------e  246 (435)
T KOG0729|consen  177 SDVGGCKEQIEKLREVVELPLLHPERFVNLGIDPPKGVLLYGPPGTGKTLCARAVANR----TDACFIRVIGS------E  246 (435)
T ss_pred             ccccchHHHHHHHHHHHhccccCHHHHhhcCCCCCCceEEeCCCCCchhHHHHHHhcc----cCceEEeehhH------H
Confidence            7889999999999998765432         237889999999999999999999987    44677777332      2


Q ss_pred             HHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccC-----------HHHHHHhHh-C-CCCCCCc
Q psy200          265 VYETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRK-----------QTILYTIFE-W-PSIPGSK  331 (490)
Q Consensus       265 l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~-----------~~~L~~l~~-~-~~~~~~~  331 (490)
                      ++        ..+.|+....+++.|+-+.  ..+.|+||+||||.+.+.+           |..++.++. + ......+
T Consensus       247 lv--------qkyvgegarmvrelf~mar--tkkaciiffdeidaiggarfddg~ggdnevqrtmleli~qldgfdprgn  316 (435)
T KOG0729|consen  247 LV--------QKYVGEGARMVRELFEMAR--TKKACIIFFDEIDAIGGARFDDGAGGDNEVQRTMLELINQLDGFDPRGN  316 (435)
T ss_pred             HH--------HHHhhhhHHHHHHHHHHhc--ccceEEEEeeccccccCccccCCCCCcHHHHHHHHHHHHhccCCCCCCC
Confidence            22        2445566666777776443  3678999999999986542           333334332 2 2456788


Q ss_pred             EEEEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHH
Q psy200          332 LVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKA  411 (490)
Q Consensus       332 vilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~a  411 (490)
                      +-++.+||+.+.   +++.+.+ -+.-...+.|.-++.+-...||+-+......+   .+--.++|+++.-...|  ..+
T Consensus       317 ikvlmatnrpdt---ldpallr-pgrldrkvef~lpdlegrt~i~kihaksmsve---rdir~ellarlcpnstg--aei  387 (435)
T KOG0729|consen  317 IKVLMATNRPDT---LDPALLR-PGRLDRKVEFGLPDLEGRTHIFKIHAKSMSVE---RDIRFELLARLCPNSTG--AEI  387 (435)
T ss_pred             eEEEeecCCCCC---cCHhhcC-CcccccceeccCCcccccceeEEEeccccccc---cchhHHHHHhhCCCCcc--hHH
Confidence            999999997643   3444432 22222468888888887777776544332111   12234556552223333  122


Q ss_pred             HHHHHHHHHHHHhccccCCcccccCHHHHHHHHHHhccC
Q psy200          412 IDITNHLIDLTYDNVKENGEVTGIGLKEVLGVISSVYCT  450 (490)
Q Consensus       412 i~ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~~~~~~~  450 (490)
                      -.+|-.|.+.|.+..     ....|..+|..|++++...
T Consensus       388 rsvcteagmfairar-----rk~atekdfl~av~kvvkg  421 (435)
T KOG0729|consen  388 RSVCTEAGMFAIRAR-----RKVATEKDFLDAVNKVVKG  421 (435)
T ss_pred             HHHHHHhhHHHHHHH-----hhhhhHHHHHHHHHHHHHH
Confidence            358889998888776     5688999999999987643

>TIGR00763 lon ATP-dependent protease La

Probab=99.58  E-value=7.3e-14  Score=153.93  Aligned_cols=200  Identities=21%  Similarity=0.252  Sum_probs=133.8

Q ss_pred             CCCCChHHHHHHHHHHHHhhhcc--CCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVNN--ETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVN  271 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~--~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~  271 (490)
                      ++++|.++.++.+.+++......  ..+.+++|+||||||||++++++++.+.    ..++.+++....+...+...   
T Consensus       320 ~~~~G~~~~k~~i~~~~~~~~~~~~~~~~~lll~GppG~GKT~lAk~iA~~l~----~~~~~i~~~~~~~~~~i~g~---  392 (775)
T TIGR00763       320 EDHYGLKKVKERILEYLAVQKLRGKMKGPILCLVGPPGVGKTSLGKSIAKALN----RKFVRFSLGGVRDEAEIRGH---  392 (775)
T ss_pred             hhcCChHHHHHHHHHHHHHHHhhcCCCCceEEEECCCCCCHHHHHHHHHHHhc----CCeEEEeCCCcccHHHHcCC---
Confidence            77999999999999987654322  2445799999999999999999999985    56677776655443332110   


Q ss_pred             HhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCH----HHHHHhHhCCC------------CCCCcEEEE
Q psy200          272 ELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQ----TILYTIFEWPS------------IPGSKLVLV  335 (490)
Q Consensus       272 ~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~----~~L~~l~~~~~------------~~~~~vilI  335 (490)
                        ...+.|.....+.+.+..+.   ....||||||||.+....+    ++|..+++...            ..-++++||
T Consensus       393 --~~~~~g~~~g~i~~~l~~~~---~~~~villDEidk~~~~~~~~~~~aLl~~ld~~~~~~f~d~~~~~~~d~s~v~~I  467 (775)
T TIGR00763       393 --RRTYVGAMPGRIIQGLKKAK---TKNPLFLLDEIDKIGSSFRGDPASALLEVLDPEQNNAFSDHYLDVPFDLSKVIFI  467 (775)
T ss_pred             --CCceeCCCCchHHHHHHHhC---cCCCEEEEechhhcCCccCCCHHHHHHHhcCHHhcCccccccCCceeccCCEEEE
Confidence              11223333444444444332   2233899999999976432    56666654210            122578999


Q ss_pred             EecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHh-----ccC---CCCCCCHHHHHHHHHHHHHhhCC
Q psy200          336 GVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLK-----QTD---KFNMFNASALQLLAGKVAAVSGD  407 (490)
Q Consensus       336 ~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~-----~~~---~~~~~~~~~i~~i~~~i~~~~Gd  407 (490)
                      +++|.   .+.+.+.+.+||.    .|.|.+|+.++...|+..++.     ..+   ....++++++..|++... ...+
T Consensus       468 ~TtN~---~~~i~~~L~~R~~----vi~~~~~~~~e~~~I~~~~l~~~~~~~~~l~~~~~~~~~~~l~~i~~~~~-~e~g  539 (775)
T TIGR00763       468 ATANS---IDTIPRPLLDRME----VIELSGYTEEEKLEIAKKYLIPKALEDHGLKPDELKITDEALLLLIKYYT-REAG  539 (775)
T ss_pred             EecCC---chhCCHHHhCCee----EEecCCCCHHHHHHHHHHHHHHHHHHHcCCCcceEEECHHHHHHHHHhcC-hhcC
Confidence            99995   4567788999995    799999999999999877652     111   134689999999988322 2345


Q ss_pred             HHHHHH
Q psy200          408 IRKAID  413 (490)
Q Consensus       408 ~r~ai~  413 (490)
                      +|.+-.
T Consensus       540 ~R~l~r  545 (775)
T TIGR00763       540 VRNLER  545 (775)
T ss_pred             ChHHHH
Confidence            554443

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.

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

Probab=99.58  E-value=1.7e-13  Score=141.84  Aligned_cols=239  Identities=20%  Similarity=0.236  Sum_probs=159.1

Q ss_pred             hHHHhhcCCCCCCChHHHHHHHHHHHHhhh--ccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCH
Q psy200          185 KVEEKAKDSCELPGREVQLEGIRQFLLGHV--NNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNA  262 (490)
Q Consensus       185 ~~~~~~l~~~~lvgre~~~~~l~~~L~~~~--~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~  262 (490)
                      ..++..|. .+.+|.++..+++.++|.-..  ..-.+..++|+||||+|||+|++.||+.++    .+|+.+.....++.
T Consensus       315 ~~a~~iLd-~dHYGLekVKeRIlEyLAV~~l~~~~kGpILcLVGPPGVGKTSLgkSIA~al~----RkfvR~sLGGvrDE  389 (782)
T COG0466         315 KKAEKILD-KDHYGLEKVKERILEYLAVQKLTKKLKGPILCLVGPPGVGKTSLGKSIAKALG----RKFVRISLGGVRDE  389 (782)
T ss_pred             HHHHHHhc-ccccCchhHHHHHHHHHHHHHHhccCCCcEEEEECCCCCCchhHHHHHHHHhC----CCEEEEecCccccH
Confidence            44555666 899999999999999886432  223667899999999999999999999986    67888888888776


Q ss_pred             HHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccC----HHHHHHhHhCCC------------
Q psy200          263 ASVYETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRK----QTILYTIFEWPS------------  326 (490)
Q Consensus       263 ~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~----~~~L~~l~~~~~------------  326 (490)
                      .++-.+=     -.+.|.-...+.+.+.++   +-..-|++|||||.|...-    ..+|+..++..+            
T Consensus       390 AEIRGHR-----RTYIGamPGrIiQ~mkka---~~~NPv~LLDEIDKm~ss~rGDPaSALLEVLDPEQN~~F~DhYLev~  461 (782)
T COG0466         390 AEIRGHR-----RTYIGAMPGKIIQGMKKA---GVKNPVFLLDEIDKMGSSFRGDPASALLEVLDPEQNNTFSDHYLEVP  461 (782)
T ss_pred             HHhcccc-----ccccccCChHHHHHHHHh---CCcCCeEEeechhhccCCCCCChHHHHHhhcCHhhcCchhhccccCc
Confidence            5542110     022333344444444332   2334599999999997652    345655543221            


Q ss_pred             CCCCcEEEEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhcc-----C---CCCCCCHHHHHHHH
Q psy200          327 IPGSKLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQT-----D---KFNMFNASALQLLA  398 (490)
Q Consensus       327 ~~~~~vilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~-----~---~~~~~~~~~i~~i~  398 (490)
                      ..-+.|+||+++|.++   .+-.+|..|+.    +|.+..|+.+|-.+|.+.+|-..     +   ....+++++|..|.
T Consensus       462 yDLS~VmFiaTANsl~---tIP~PLlDRME----iI~lsgYt~~EKl~IAk~~LiPk~~~~~gL~~~el~i~d~ai~~iI  534 (782)
T COG0466         462 YDLSKVMFIATANSLD---TIPAPLLDRME----VIRLSGYTEDEKLEIAKRHLIPKQLKEHGLKKGELTITDEAIKDII  534 (782)
T ss_pred             cchhheEEEeecCccc---cCChHHhccee----eeeecCCChHHHHHHHHHhcchHHHHHcCCCccceeecHHHHHHHH
Confidence            2457899999999654   33445667774    89999999999888877665322     1   35679999999999


Q ss_pred             HHHHHhhC--CHHHHH-HHHHHHHHHHHhccccCCcc-cccCHHHHHHHHHH
Q psy200          399 GKVAAVSG--DIRKAI-DITNHLIDLTYDNVKENGEV-TGIGLKEVLGVISS  446 (490)
Q Consensus       399 ~~i~~~~G--d~r~ai-~ll~~a~~~a~~~~~~~~~~-~~It~~~v~~a~~~  446 (490)
                      +.+....|  ++.+-| .+|+.++.........   . -.|+..++.+-+..
T Consensus       535 ~~YTREAGVR~LeR~i~ki~RK~~~~i~~~~~k---~~~~i~~~~l~~yLG~  583 (782)
T COG0466         535 RYYTREAGVRNLEREIAKICRKAAKKILLKKEK---SIVKIDEKNLKKYLGV  583 (782)
T ss_pred             HHHhHhhhhhHHHHHHHHHHHHHHHHHHhcCcc---cceeeCHHHHHHHhCC
Confidence            86655555  343334 4666666443332211   1 25666677665543

>PRK07940 DNA polymerase III subunit delta'; Validated

Probab=99.58  E-value=6.7e-14  Score=141.32  Aligned_cols=199  Identities=16%  Similarity=0.248  Sum_probs=131.0

Q ss_pred             CCCCChHHHHHHHHHHHHhhhc------cCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVN------NETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYE  267 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~------~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~  267 (490)
                      ++++|+++.++.|..++.....      ..-++.++|+||+|+|||++|+.+++.+......   .-.|..+.+...+..
T Consensus         5 ~~IiGq~~~~~~L~~~i~~~~~~~~~~~~~l~ha~Lf~Gp~G~GKt~lA~~lA~~l~c~~~~---~~~Cg~C~~C~~~~~   81 (394)
T PRK07940          5 DDLVGQEAVVAELRAAARAARADVAAAGSGMTHAWLFTGPPGSGRSVAARAFAAALQCTDPD---EPGCGECRACRTVLA   81 (394)
T ss_pred             hhccChHHHHHHHHHHHHhccccccccCCCCCeEEEEECCCCCcHHHHHHHHHHHhCCCCCC---CCCCCCCHHHHHHhc
Confidence            6799999999999999975310      0146779999999999999999999987533211   112333322222211


Q ss_pred             HHHHHhc---CCCCCCcHHHHHHHHHHHHhc--CCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEEEecCCCC
Q psy200          268 TIVNELK---LKPGGKSERHQLGAILKYFDT--KHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVANALD  342 (490)
Q Consensus       268 ~i~~~l~---~~~~~~s~~~~~~~l~~~l~~--~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI~~tn~~~  342 (490)
                      .-.-++.   ........+++++.+..+...  .++..|+||||+|.|....++.|..+++.+  ....++|+++++   
T Consensus        82 ~~hpD~~~i~~~~~~i~i~~iR~l~~~~~~~p~~~~~kViiIDead~m~~~aanaLLk~LEep--~~~~~fIL~a~~---  156 (394)
T PRK07940         82 GTHPDVRVVAPEGLSIGVDEVRELVTIAARRPSTGRWRIVVIEDADRLTERAANALLKAVEEP--PPRTVWLLCAPS---  156 (394)
T ss_pred             CCCCCEEEeccccccCCHHHHHHHHHHHHhCcccCCcEEEEEechhhcCHHHHHHHHHHhhcC--CCCCeEEEEECC---
Confidence            1000110   011123455666555544322  245679999999999988888888887743  223445555554   


Q ss_pred             hhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHHHH
Q psy200          343 LTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDIT  415 (490)
Q Consensus       343 ~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll  415 (490)
                       .+.+.+.+++||.    .+.|.+++.+++..++....       .++++....++.   ...|++..++.++
T Consensus       157 -~~~llpTIrSRc~----~i~f~~~~~~~i~~~L~~~~-------~~~~~~a~~la~---~s~G~~~~A~~l~  214 (394)
T PRK07940        157 -PEDVLPTIRSRCR----HVALRTPSVEAVAEVLVRRD-------GVDPETARRAAR---ASQGHIGRARRLA  214 (394)
T ss_pred             -hHHChHHHHhhCe----EEECCCCCHHHHHHHHHHhc-------CCCHHHHHHHHH---HcCCCHHHHHHHh
Confidence             5777899999995    89999999999998887432       246777777765   6678888877654

>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=99.57  E-value=5e-14  Score=138.01  Aligned_cols=201  Identities=19%  Similarity=0.298  Sum_probs=129.9

Q ss_pred             hHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCc-eEEEEeccCCCCHHHHHHHHHHHhcCCC
Q psy200          199 REVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAF-KTIYINCNSVRNAASVYETIVNELKLKP  277 (490)
Q Consensus       199 re~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~-~~~~v~~~~~~~~~~l~~~i~~~l~~~~  277 (490)
                      |+.++++|.++|...  ....+.+.|+|++|+|||+||..+++.......| .++|+++....+...++..|+..|+...
T Consensus         1 re~~~~~l~~~L~~~--~~~~~~v~I~G~~G~GKT~LA~~~~~~~~~~~~f~~v~wv~~~~~~~~~~~~~~i~~~l~~~~   78 (287)
T PF00931_consen    1 REKEIEKLKDWLLDN--SNEVRVVAIVGMGGIGKTTLARQVARDLRIKNRFDGVIWVSLSKNPSLEQLLEQILRQLGEPD   78 (287)
T ss_dssp             -HHHHHHHHHHHHTT--TTSSEEEEEEESTTSSHHHHHHHHHCHHHHCCCCTEEEEEEEES-SCCHHHHHHHHHHHTCC-
T ss_pred             CHHHHHHHHHHhhCC--CCCeEEEEEEcCCcCCcceeeeecccccccccccccccccccccccccccccccccccccccc
Confidence            688999999999762  2677899999999999999999999885545666 5778888888788899999999998763


Q ss_pred             ----CCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEEEecCCCChhHhhhHHhhh
Q psy200          278 ----GGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVANALDLTDRMLPRLQA  353 (490)
Q Consensus       278 ----~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI~~tn~~~~~~~l~~~l~~  353 (490)
                          ...........+.+.+..  ++++||||+++....-  +.+...+.. ...++++  |.+|....+..    .+..
T Consensus        79 ~~~~~~~~~~~~~~~l~~~L~~--~~~LlVlDdv~~~~~~--~~l~~~~~~-~~~~~ki--lvTTR~~~v~~----~~~~  147 (287)
T PF00931_consen   79 SSISDPKDIEELQDQLRELLKD--KRCLLVLDDVWDEEDL--EELREPLPS-FSSGSKI--LVTTRDRSVAG----SLGG  147 (287)
T ss_dssp             STSSCCSSHHHHHHHHHHHHCC--TSEEEEEEEE-SHHHH---------HC-HHSS-EE--EEEESCGGGGT----THHS
T ss_pred             cccccccccccccccchhhhcc--ccceeeeeeecccccc--ccccccccc-ccccccc--ccccccccccc----cccc
Confidence                335677788888888774  4899999999986511  111111111 1123443  33453222211    1111


Q ss_pred             ccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHHHHHHHH
Q psy200          354 NVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITNHLI  419 (490)
Q Consensus       354 R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll~~a~  419 (490)
                      .    ...+.+.+++.++..++|.+......   ......++.+++.+...||+.+.++.++...+
T Consensus       148 ~----~~~~~l~~L~~~ea~~L~~~~~~~~~---~~~~~~~~~~~~~i~~~c~glPLal~~~a~~l  206 (287)
T PF00931_consen  148 T----DKVIELEPLSEEEALELFKKRAGRKE---SESPEDLEDLAKEIVEKCGGLPLALKLIASYL  206 (287)
T ss_dssp             C----EEEEECSS--HHHHHHHHHHHHTSHS-------TTSCTHHHHHHHHTTT-HHHHHHHHHHH
T ss_pred             c----cccccccccccccccccccccccccc---cccccccccccccccccccccccccccccccc
Confidence            1    14799999999999999999876542   11122223333444458999999999886655

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.

>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=99.57  E-value=2.5e-14  Score=122.94  Aligned_cols=119  Identities=26%  Similarity=0.425  Sum_probs=88.7

Q ss_pred             EEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEE
Q psy200          222 MYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFDTKHKSIL  301 (490)
Q Consensus       222 ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~v  301 (490)
                      |+|+||||+|||++++.+++.++    +.++.+++....+              ...+.....+...+.++... .+++|
T Consensus         1 ill~G~~G~GKT~l~~~la~~l~----~~~~~i~~~~~~~--------------~~~~~~~~~i~~~~~~~~~~-~~~~v   61 (132)
T PF00004_consen    1 ILLHGPPGTGKTTLARALAQYLG----FPFIEIDGSELIS--------------SYAGDSEQKIRDFFKKAKKS-AKPCV   61 (132)
T ss_dssp             EEEESSTTSSHHHHHHHHHHHTT----SEEEEEETTHHHT--------------SSTTHHHHHHHHHHHHHHHT-STSEE
T ss_pred             CEEECcCCCCeeHHHHHHHhhcc----ccccccccccccc--------------cccccccccccccccccccc-cccee
Confidence            68999999999999999999985    7889998876521              23334555666666665443 24799


Q ss_pred             EEEecCccccccC-----------HHHHHHhHhCCCCCCCcEEEEEecCCCChhHhhhHHhh-hccCCCCeeEEeC
Q psy200          302 LILDEIDALESRK-----------QTILYTIFEWPSIPGSKLVLVGVANALDLTDRMLPRLQ-ANVTLQPTLMNFA  365 (490)
Q Consensus       302 I~IDEid~l~~~~-----------~~~L~~l~~~~~~~~~~vilI~~tn~~~~~~~l~~~l~-~R~~~~~~~i~~~  365 (490)
                      |||||+|.+....           ...|...++.......++++|+++|.   .+.+.+.+. +||.   ..+.|+
T Consensus        62 l~iDe~d~l~~~~~~~~~~~~~~~~~~L~~~l~~~~~~~~~~~vI~ttn~---~~~i~~~l~~~rf~---~~i~~~  131 (132)
T PF00004_consen   62 LFIDEIDKLFPKSQPSSSSFEQRLLNQLLSLLDNPSSKNSRVIVIATTNS---PDKIDPALLRSRFD---RRIEFP  131 (132)
T ss_dssp             EEEETGGGTSHHCSTSSSHHHHHHHHHHHHHHHTTTTTSSSEEEEEEESS---GGGSCHHHHSTTSE---EEEEE-
T ss_pred             eeeccchhcccccccccccccccccceeeecccccccccccceeEEeeCC---hhhCCHhHHhCCCc---EEEEcC
Confidence            9999999998776           45666667666555678999999995   566777888 8886   355553

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 ....

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

Probab=99.57  E-value=1.7e-13  Score=149.72  Aligned_cols=236  Identities=16%  Similarity=0.195  Sum_probs=153.1

Q ss_pred             HHHhhcCCCCCCChHHHHHHHHHHHHhhhc--cCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHH
Q psy200          186 VEEKAKDSCELPGREVQLEGIRQFLLGHVN--NETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAA  263 (490)
Q Consensus       186 ~~~~~l~~~~lvgre~~~~~l~~~L~~~~~--~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~  263 (490)
                      .++..|. ++++|.++.++++.++|.....  ...+..++|+||||+|||++++.++..++    ..++.+++....+..
T Consensus       315 ~~~~~l~-~~~~g~~~vK~~i~~~l~~~~~~~~~~g~~i~l~GppG~GKTtl~~~ia~~l~----~~~~~i~~~~~~d~~  389 (784)
T PRK10787        315 QAQEILD-TDHYGLERVKDRILEYLAVQSRVNKIKGPILCLVGPPGVGKTSLGQSIAKATG----RKYVRMALGGVRDEA  389 (784)
T ss_pred             HHHHHhh-hhccCHHHHHHHHHHHHHHHHhcccCCCceEEEECCCCCCHHHHHHHHHHHhC----CCEEEEEcCCCCCHH
Confidence            3444444 7899999999999998874322  23566899999999999999999999875    456777766665544


Q ss_pred             HHHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccC----HHHHHHhHhCCC------------C
Q psy200          264 SVYETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRK----QTILYTIFEWPS------------I  327 (490)
Q Consensus       264 ~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~----~~~L~~l~~~~~------------~  327 (490)
                      .+...-.     .+.|.....+...+...   +....||+|||+|.+....    +++|+.+++...            .
T Consensus       390 ~i~g~~~-----~~~g~~~G~~~~~l~~~---~~~~~villDEidk~~~~~~g~~~~aLlevld~~~~~~~~d~~~~~~~  461 (784)
T PRK10787        390 EIRGHRR-----TYIGSMPGKLIQKMAKV---GVKNPLFLLDEIDKMSSDMRGDPASALLEVLDPEQNVAFSDHYLEVDY  461 (784)
T ss_pred             Hhccchh-----ccCCCCCcHHHHHHHhc---CCCCCEEEEEChhhcccccCCCHHHHHHHHhccccEEEEecccccccc
Confidence            3322110     12222223333333221   1123489999999998654    477887765321            1


Q ss_pred             CCCcEEEEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhc--------cCCCCCCCHHHHHHHHH
Q psy200          328 PGSKLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQ--------TDKFNMFNASALQLLAG  399 (490)
Q Consensus       328 ~~~~vilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~--------~~~~~~~~~~~i~~i~~  399 (490)
                      .-+++++|+++|..    .+.++|.+||.    .+.|.+|+.++..+|+++++..        ......+++++++.|++
T Consensus       462 dls~v~~i~TaN~~----~i~~aLl~R~~----ii~~~~~t~eek~~Ia~~~L~~k~~~~~~l~~~~l~i~~~ai~~ii~  533 (784)
T PRK10787        462 DLSDVMFVATSNSM----NIPAPLLDRME----VIRLSGYTEDEKLNIAKRHLLPKQIERNALKKGELTVDDSAIIGIIR  533 (784)
T ss_pred             cCCceEEEEcCCCC----CCCHHHhccee----eeecCCCCHHHHHHHHHHhhhHHHHHHhCCCCCeEEECHHHHHHHHH
Confidence            33789999999864    26788889996    7999999999999998887741        11345689999999997


Q ss_pred             HHHHhhCCHHHHHH----HHHHHHHHHHhccccCCcccccCHHHHHHHHH
Q psy200          400 KVAAVSGDIRKAID----ITNHLIDLTYDNVKENGEVTGIGLKEVLGVIS  445 (490)
Q Consensus       400 ~i~~~~Gd~r~ai~----ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~~  445 (490)
                      ... ..-+.|.+-.    +++.++......+.  ...-.|+.+++.+.+.
T Consensus       534 ~yt-~e~GaR~LeR~I~~i~r~~l~~~~~~~~--~~~v~v~~~~~~~~lg  580 (784)
T PRK10787        534 YYT-REAGVRSLEREISKLCRKAVKQLLLDKS--LKHIEINGDNLHDYLG  580 (784)
T ss_pred             hCC-cccCCcHHHHHHHHHHHHHHHHHHhcCC--CceeeecHHHHHHHhC
Confidence            322 2334444433    44444433222221  1124688888777665

>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=99.56  E-value=4.7e-14  Score=133.41  Aligned_cols=203  Identities=18%  Similarity=0.333  Sum_probs=108.1

Q ss_pred             CCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHH------
Q psy200          196 LPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETI------  269 (490)
Q Consensus       196 lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i------  269 (490)
                      |+||+++++.|.+++..    +....++|+||.|+|||+|++.+.+.+. ..++..+|+.+........ +..+      
T Consensus         1 F~gR~~el~~l~~~l~~----~~~~~~~l~G~rg~GKTsLl~~~~~~~~-~~~~~~~y~~~~~~~~~~~-~~~~~~~~~~   74 (234)
T PF01637_consen    1 FFGREKELEKLKELLES----GPSQHILLYGPRGSGKTSLLKEFINELK-EKGYKVVYIDFLEESNESS-LRSFIEETSL   74 (234)
T ss_dssp             S-S-HHHHHHHHHCHHH------SSEEEEEESTTSSHHHHHHHHHHHCT---EECCCHHCCTTBSHHHH-HHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHh----hcCcEEEEEcCCcCCHHHHHHHHHHHhh-hcCCcEEEEecccchhhhH-HHHHHHHHHH
Confidence            68999999999998864    5678999999999999999999999873 2223445555544432222 1111      


Q ss_pred             ----HHHhcC--CC---------CCCcHHHHHHHHHHHHhcCCCeEEEEEecCcccc-cc--CHH---HHHHhHhCCCCC
Q psy200          270 ----VNELKL--KP---------GGKSERHQLGAILKYFDTKHKSILLILDEIDALE-SR--KQT---ILYTIFEWPSIP  328 (490)
Q Consensus       270 ----~~~l~~--~~---------~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~-~~--~~~---~L~~l~~~~~~~  328 (490)
                          ...+..  ..         ...........+.+.+.+.+..+||+|||+|.+. ..  ...   .|..+++... .
T Consensus        75 ~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~~~~iiviDe~~~~~~~~~~~~~~~~~l~~~~~~~~-~  153 (234)
T PF01637_consen   75 ADELSEALGISIPSITLEKISKDLSEDSFSALERLLEKLKKKGKKVIIVIDEFQYLAIASEEDKDFLKSLRSLLDSLL-S  153 (234)
T ss_dssp             HCHCHHHHHHHCCTSTTEEEECTS-GG-G--HHHHHHHHHHCHCCEEEEEETGGGGGBCTTTTHHHHHHHHHHHHH----
T ss_pred             HHHHHHHHhhhcccccchhhhhcchhhHHHHHHHHHHHHHhcCCcEEEEEecHHHHhhcccchHHHHHHHHHHHhhcc-c
Confidence                111211  10         1112223333444445444445999999999999 22  233   3333333311 2


Q ss_pred             CCcEEEEEecCCCChhHhh---hHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhh
Q psy200          329 GSKLVLVGVANALDLTDRM---LPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVS  405 (490)
Q Consensus       329 ~~~vilI~~tn~~~~~~~l---~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~  405 (490)
                      ..++.+|.+.....+...+   ...+..|+.    .+.++|++.++..+++...+... ....++++.++.++.    .+
T Consensus       154 ~~~~~~v~~~S~~~~~~~~~~~~~~~~~~~~----~~~l~~l~~~e~~~~~~~~~~~~-~~~~~~~~~~~~i~~----~~  224 (234)
T PF01637_consen  154 QQNVSIVITGSSDSLMEEFLDDKSPLFGRFS----HIELKPLSKEEAREFLKELFKEL-IKLPFSDEDIEEIYS----LT  224 (234)
T ss_dssp             -TTEEEEEEESSHHHHHHTT-TTSTTTT-------EEEE----HHHHHHHHHHHHHCC-------HHHHHHHHH----HH
T ss_pred             cCCceEEEECCchHHHHHhhcccCccccccc----eEEEeeCCHHHHHHHHHHHHHHh-hcccCCHHHHHHHHH----Hh
Confidence            2333333333222222221   223445554    69999999999999999987765 111358888888876    77


Q ss_pred             CCHHHHHHH
Q psy200          406 GDIRKAIDI  414 (490)
Q Consensus       406 Gd~r~ai~l  414 (490)
                      |+.+..|+.
T Consensus       225 gG~P~~l~~  233 (234)
T PF01637_consen  225 GGNPRYLQE  233 (234)
T ss_dssp             TT-HHHHHH
T ss_pred             CCCHHHHhc
Confidence            777766653

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

>TIGR02974 phageshock_pspF psp operon transcriptional activator PspF

Probab=99.56  E-value=4.3e-14  Score=140.21  Aligned_cols=213  Identities=16%  Similarity=0.167  Sum_probs=144.7

Q ss_pred             CCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcC
Q psy200          196 LPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKL  275 (490)
Q Consensus       196 lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~  275 (490)
                      ++|....+..+.+.+...  ......|+|+|++||||+++|++++.... ..+-+|+.+||.... ...+-..++..-..
T Consensus         1 liG~S~~m~~~~~~~~~~--a~~~~pVLI~GE~GtGK~~lAr~iH~~s~-r~~~pfv~vnc~~~~-~~~l~~~lfG~~~g   76 (329)
T TIGR02974         1 LIGESNAFLEVLEQVSRL--APLDRPVLIIGERGTGKELIAARLHYLSK-RWQGPLVKLNCAALS-ENLLDSELFGHEAG   76 (329)
T ss_pred             CCcCCHHHHHHHHHHHHH--hCCCCCEEEECCCCChHHHHHHHHHHhcC-ccCCCeEEEeCCCCC-hHHHHHHHhccccc
Confidence            567778888888888774  35678999999999999999999976542 344589999999864 22222233222211


Q ss_pred             CCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCHHHHHHhHhCCCC--------CCCcEEEEEecCCCChh---
Q psy200          276 KPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPSI--------PGSKLVLVGVANALDLT---  344 (490)
Q Consensus       276 ~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~--------~~~~vilI~~tn~~~~~---  344 (490)
                      .+.|... .....+..+  .   .-+||||||+.|....|..|..+++....        ....+.+|++++.. +.   
T Consensus        77 ~~~ga~~-~~~G~~~~a--~---gGtL~Ldei~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiI~at~~~-l~~~~  149 (329)
T TIGR02974        77 AFTGAQK-RHQGRFERA--D---GGTLFLDELATASLLVQEKLLRVIEYGEFERVGGSQTLQVDVRLVCATNAD-LPALA  149 (329)
T ss_pred             cccCccc-ccCCchhhC--C---CCEEEeCChHhCCHHHHHHHHHHHHcCcEEecCCCceeccceEEEEechhh-HHHHh
Confidence            2222111 011112211  1   23899999999999999988888764321        13467888888632 11   


Q ss_pred             --HhhhHHhhhccCCCCeeEEeCCCC--HHHHHHHHHHHHhcc----CCC--CCCCHHHHHHHHHHHHHhhCCHHHHHHH
Q psy200          345 --DRMLPRLQANVTLQPTLMNFAPYS--REQILEIISQKLKQT----DKF--NMFNASALQLLAGKVAAVSGDIRKAIDI  414 (490)
Q Consensus       345 --~~l~~~l~~R~~~~~~~i~~~pls--~~e~~~il~~~l~~~----~~~--~~~~~~~i~~i~~~i~~~~Gd~r~ai~l  414 (490)
                        ..+.+.|..|+..  ..|.++|+.  .+|+..++.+++...    +..  ..+++++++.+..  +.|.||+|++.++
T Consensus       150 ~~g~fr~dL~~rl~~--~~i~lPpLReR~eDI~~L~~~fl~~~~~~~~~~~~~~ls~~a~~~L~~--y~WPGNvrEL~n~  225 (329)
T TIGR02974       150 AEGRFRADLLDRLAF--DVITLPPLRERQEDIMLLAEHFAIRMARELGLPLFPGFTPQAREQLLE--YHWPGNVRELKNV  225 (329)
T ss_pred             hcCchHHHHHHHhcc--hhcCCCchhhhhhhHHHHHHHHHHHHHHHhCCCCCCCcCHHHHHHHHh--CCCCchHHHHHHH
Confidence              1344667777743  368999998  678887777766543    223  4689999999998  8899999999999


Q ss_pred             HHHHHHHHH
Q psy200          415 TNHLIDLTY  423 (490)
Q Consensus       415 l~~a~~~a~  423 (490)
                      +++++..+.
T Consensus       226 i~~~~~~~~  234 (329)
T TIGR02974       226 VERSVYRHG  234 (329)
T ss_pred             HHHHHHhCC
Confidence            999987764

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

>KOG2035|consensus

Probab=99.56  E-value=1.1e-13  Score=127.75  Aligned_cols=217  Identities=17%  Similarity=0.203  Sum_probs=146.2

Q ss_pred             CCCCcchHHHhhcCCCCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccC
Q psy200          179 FSEDKPKVEEKAKDSCELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNS  258 (490)
Q Consensus       179 ~~~~~~~~~~~~l~~~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~  258 (490)
                      .|.++|.+...    +.+.++++....|.....    .+...++++|||.|.||-|.+.++.+++-. .++.-+.+....
T Consensus         2 LWvdkyrpksl----~~l~~~~e~~~~Lksl~~----~~d~PHll~yGPSGaGKKTrimclL~elYG-~gveklki~~~t   72 (351)
T KOG2035|consen    2 LWVDKYRPKSL----DELIYHEELANLLKSLSS----TGDFPHLLVYGPSGAGKKTRIMCLLRELYG-VGVEKLKIETRT   72 (351)
T ss_pred             cchhhcCcchh----hhcccHHHHHHHHHHhcc----cCCCCeEEEECCCCCCchhhHHHHHHHHhC-CCchheeeeeEE
Confidence            58889998887    889999988877777654    356789999999999999999999999842 111000000000


Q ss_pred             CCCH--HHH-----HHHHHHHhcCCCCCCcHH-HHHHHHHHHH-------hcCCCeEEEEEecCccccccCHHHHHHhHh
Q psy200          259 VRNA--ASV-----YETIVNELKLKPGGKSER-HQLGAILKYF-------DTKHKSILLILDEIDALESRKQTILYTIFE  323 (490)
Q Consensus       259 ~~~~--~~l-----~~~i~~~l~~~~~~~s~~-~~~~~l~~~l-------~~~~~~~vI~IDEid~l~~~~~~~L~~l~~  323 (490)
                      +.++  +.+     -+...-++.....|..-. -+.+.+.+..       .......|++|-|+|.|....|.+|++.++
T Consensus        73 ~~tpS~kklEistvsS~yHlEitPSDaG~~DRvViQellKevAQt~qie~~~qr~fKvvvi~ead~LT~dAQ~aLRRTME  152 (351)
T KOG2035|consen   73 FTTPSKKKLEISTVSSNYHLEITPSDAGNYDRVVIQELLKEVAQTQQIETQGQRPFKVVVINEADELTRDAQHALRRTME  152 (351)
T ss_pred             EecCCCceEEEEEecccceEEeChhhcCcccHHHHHHHHHHHHhhcchhhccccceEEEEEechHhhhHHHHHHHHHHHH
Confidence            0000  000     000000000011111111 1112222211       112345699999999999999999999998


Q ss_pred             CCCCCCCcEEEEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHH
Q psy200          324 WPSIPGSKLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAA  403 (490)
Q Consensus       324 ~~~~~~~~vilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~  403 (490)
                      .. ....++|++|-+     ..++.+++++||-    .+.++.++++|+..++...+.+++  ..+..+.+..|++   .
T Consensus       153 kY-s~~~RlIl~cns-----~SriIepIrSRCl----~iRvpaps~eeI~~vl~~v~~kE~--l~lp~~~l~rIa~---k  217 (351)
T KOG2035|consen  153 KY-SSNCRLILVCNS-----TSRIIEPIRSRCL----FIRVPAPSDEEITSVLSKVLKKEG--LQLPKELLKRIAE---K  217 (351)
T ss_pred             HH-hcCceEEEEecC-----cccchhHHhhhee----EEeCCCCCHHHHHHHHHHHHHHhc--ccCcHHHHHHHHH---H
Confidence            54 356777776544     4778899999995    799999999999999999999984  5577888999988   8


Q ss_pred             hhCCHHHHHHHHHHHH
Q psy200          404 VSGDIRKAIDITNHLI  419 (490)
Q Consensus       404 ~~Gd~r~ai~ll~~a~  419 (490)
                      ++||+|.||-+|+.+.
T Consensus       218 S~~nLRrAllmlE~~~  233 (351)
T KOG2035|consen  218 SNRNLRRALLMLEAVR  233 (351)
T ss_pred             hcccHHHHHHHHHHHH
Confidence            8999999998777654

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

Probab=99.54  E-value=2.9e-13  Score=143.90  Aligned_cols=210  Identities=17%  Similarity=0.173  Sum_probs=151.0

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhc------CCceEEEEeccCCCCHHHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIK------DAFKTIYINCNSVRNAASVYE  267 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~------~~~~~~~v~~~~~~~~~~l~~  267 (490)
                      +.++||+++++++.+.|..    ...++-+|+|+||+|||.++..+|..+...      .+..++.++...+        
T Consensus       170 DPvIGRd~EI~r~iqIL~R----R~KNNPvLiGEpGVGKTAIvEGLA~rIv~g~VP~~L~~~~i~sLD~g~L--------  237 (786)
T COG0542         170 DPVIGRDEEIRRTIQILSR----RTKNNPVLVGEPGVGKTAIVEGLAQRIVNGDVPESLKDKRIYSLDLGSL--------  237 (786)
T ss_pred             CCCcChHHHHHHHHHHHhc----cCCCCCeEecCCCCCHHHHHHHHHHHHhcCCCCHHHcCCEEEEecHHHH--------
Confidence            8999999999999999975    455566778999999999999999998522      1234444443322        


Q ss_pred             HHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCHH---H--HHHhHhCCCCCCCcEEEEEecCCCC
Q psy200          268 TIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQT---I--LYTIFEWPSIPGSKLVLVGVANALD  342 (490)
Q Consensus       268 ~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~~---~--L~~l~~~~~~~~~~vilI~~tn~~~  342 (490)
                          ..+..+.|..++.+...+.+ +.+.+ ++||||||+|.+.+.+..   .  ..+++ .+....+.+.+||+|+..+
T Consensus       238 ----vAGakyRGeFEeRlk~vl~e-v~~~~-~vILFIDEiHtiVGAG~~~G~a~DAaNiL-KPaLARGeL~~IGATT~~E  310 (786)
T COG0542         238 ----VAGAKYRGEFEERLKAVLKE-VEKSK-NVILFIDEIHTIVGAGATEGGAMDAANLL-KPALARGELRCIGATTLDE  310 (786)
T ss_pred             ----hccccccCcHHHHHHHHHHH-HhcCC-CeEEEEechhhhcCCCcccccccchhhhh-HHHHhcCCeEEEEeccHHH
Confidence                11335566656666655555 44434 899999999999766421   1  12222 3445677899999998665


Q ss_pred             hhHhh--hHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhcc--CCCCCCCHHHHHHHHHHHHHhhCC---HHHHHHHH
Q psy200          343 LTDRM--LPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQT--DKFNMFNASALQLLAGKVAAVSGD---IRKAIDIT  415 (490)
Q Consensus       343 ~~~~l--~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~--~~~~~~~~~~i~~i~~~i~~~~Gd---~r~ai~ll  415 (490)
                      +...+  +++|.+||.    .+.++.++.++...||+..-..+  .+...++++++...+.....+--|   +.+||+++
T Consensus       311 YRk~iEKD~AL~RRFQ----~V~V~EPs~e~ti~ILrGlk~~yE~hH~V~i~D~Al~aAv~LS~RYI~dR~LPDKAIDLi  386 (786)
T COG0542         311 YRKYIEKDAALERRFQ----KVLVDEPSVEDTIAILRGLKERYEAHHGVRITDEALVAAVTLSDRYIPDRFLPDKAIDLL  386 (786)
T ss_pred             HHHHhhhchHHHhcCc----eeeCCCCCHHHHHHHHHHHHHHHHHccCceecHHHHHHHHHHHHhhcccCCCCchHHHHH
Confidence            54444  578999996    89999999999999987544433  245679999999998866665554   56899999


Q ss_pred             HHHHHHHHhcc
Q psy200          416 NHLIDLTYDNV  426 (490)
Q Consensus       416 ~~a~~~a~~~~  426 (490)
                      ..|......+.
T Consensus       387 DeA~a~~~l~~  397 (786)
T COG0542         387 DEAGARVRLEI  397 (786)
T ss_pred             HHHHHHHHhcc
Confidence            99987776654

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

Probab=99.54  E-value=7e-13  Score=122.66  Aligned_cols=191  Identities=18%  Similarity=0.214  Sum_probs=133.1

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHh
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNEL  273 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l  273 (490)
                      ++|+|-+.+.+.|.+.....+.+.+.+++||+|++|||||++++++++++.. .+.+++.+.-..+.+            
T Consensus        27 ~~L~Gie~Qk~~l~~Nt~~Fl~G~pannvLL~G~rGtGKSSlVkall~~y~~-~GLRlIev~k~~L~~------------   93 (249)
T PF05673_consen   27 DDLIGIERQKEALIENTEQFLQGLPANNVLLWGARGTGKSSLVKALLNEYAD-QGLRLIEVSKEDLGD------------   93 (249)
T ss_pred             HHhcCHHHHHHHHHHHHHHHHcCCCCcceEEecCCCCCHHHHHHHHHHHHhh-cCceEEEECHHHhcc------------
Confidence            7899999999999999999999999999999999999999999999998863 347888885443322            


Q ss_pred             cCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCcccccc-CHHHHHHhHhCC-CCCCCcEEEEEecCCCChh-------
Q psy200          274 KLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESR-KQTILYTIFEWP-SIPGSKLVLVGVANALDLT-------  344 (490)
Q Consensus       274 ~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~-~~~~L~~l~~~~-~~~~~~vilI~~tn~~~~~-------  344 (490)
                              ...+.+    .+.....++|||+||+-.=... .-..|..+++=. .....++++.+++|+-.+.       
T Consensus        94 --------l~~l~~----~l~~~~~kFIlf~DDLsFe~~d~~yk~LKs~LeGgle~~P~NvliyATSNRRHLv~E~~~d~  161 (249)
T PF05673_consen   94 --------LPELLD----LLRDRPYKFILFCDDLSFEEGDTEYKALKSVLEGGLEARPDNVLIYATSNRRHLVPESFSDR  161 (249)
T ss_pred             --------HHHHHH----HHhcCCCCEEEEecCCCCCCCcHHHHHHHHHhcCccccCCCcEEEEEecchhhccchhhhhc
Confidence                    222222    2333456899999997532211 234566666533 3457789999999933221       


Q ss_pred             -----------HhhhH--HhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhC--CHH
Q psy200          345 -----------DRMLP--RLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSG--DIR  409 (490)
Q Consensus       345 -----------~~l~~--~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~G--d~r  409 (490)
                                 +.+.+  .|..|||+   .|.|.+++.++..+|+.+.+...  ...++++.+..-|...+...|  .-|
T Consensus       162 ~~~~~~eih~~d~~eEklSLsDRFGL---~l~F~~~~q~~YL~IV~~~~~~~--g~~~~~e~l~~~Al~wa~~rg~RSGR  236 (249)
T PF05673_consen  162 EDIQDDEIHPSDTIEEKLSLSDRFGL---WLSFYPPDQEEYLAIVRHYAERY--GLELDEEELRQEALQWALRRGGRSGR  236 (249)
T ss_pred             cCCCccccCcchHHHHHHhHHHhCCc---EEEecCCCHHHHHHHHHHHHHHc--CCCCCHHHHHHHHHHHHHHcCCCCHH
Confidence                       11222  57889997   89999999999999999999877  355665555544443333344  344


Q ss_pred             HHHHH
Q psy200          410 KAIDI  414 (490)
Q Consensus       410 ~ai~l  414 (490)
                      -|-+.
T Consensus       237 tA~QF  241 (249)
T PF05673_consen  237 TARQF  241 (249)
T ss_pred             HHHHH
Confidence            44443

>PRK04132 replication factor C small subunit; Provisional

Probab=99.53  E-value=3.5e-13  Score=146.12  Aligned_cols=164  Identities=19%  Similarity=0.226  Sum_probs=126.3

Q ss_pred             EEEEC--CCCCcHHHHHHHHHHHhhhc-CCceEEEEeccCCCCHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHhc---
Q psy200          222 MYISG--PPGTGKSASLNLLVSRAEIK-DAFKTIYINCNSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFDT---  295 (490)
Q Consensus       222 ill~G--ppGtGKTtla~~l~~~l~~~-~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~---  295 (490)
                      -++.|  |.+.||||+|+++++++... -+..++++|++.....                    +.+++.+.++...   
T Consensus       567 ~~~~G~lPh~lGKTT~A~ala~~l~g~~~~~~~lElNASd~rgi--------------------d~IR~iIk~~a~~~~~  626 (846)
T PRK04132        567 NFIGGNLPTVLHNTTAALALARELFGENWRHNFLELNASDERGI--------------------NVIREKVKEFARTKPI  626 (846)
T ss_pred             hhhcCCCCCcccHHHHHHHHHHhhhcccccCeEEEEeCCCcccH--------------------HHHHHHHHHHHhcCCc
Confidence            34568  99999999999999997321 2357899999875332                    2333333322211   


Q ss_pred             -CCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHH
Q psy200          296 -KHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILE  374 (490)
Q Consensus       296 -~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~  374 (490)
                       +.+..||||||+|.|....|++|+.+++.+   ...+.||++||.   ...+.+.+++||.    .+.|.+++.+++..
T Consensus       627 ~~~~~KVvIIDEaD~Lt~~AQnALLk~lEep---~~~~~FILi~N~---~~kIi~tIrSRC~----~i~F~~ls~~~i~~  696 (846)
T PRK04132        627 GGASFKIIFLDEADALTQDAQQALRRTMEMF---SSNVRFILSCNY---SSKIIEPIQSRCA----IFRFRPLRDEDIAK  696 (846)
T ss_pred             CCCCCEEEEEECcccCCHHHHHHHHHHhhCC---CCCeEEEEEeCC---hhhCchHHhhhce----EEeCCCCCHHHHHH
Confidence             123569999999999998999999998743   345667777773   5677899999995    89999999999999


Q ss_pred             HHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHHHHHHHHH
Q psy200          375 IISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITNHLID  420 (490)
Q Consensus       375 il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll~~a~~  420 (490)
                      .|...+..+  ...++++++..|++   .+.||+|.++++|+.+..
T Consensus       697 ~L~~I~~~E--gi~i~~e~L~~Ia~---~s~GDlR~AIn~Lq~~~~  737 (846)
T PRK04132        697 RLRYIAENE--GLELTEEGLQAILY---IAEGDMRRAINILQAAAA  737 (846)
T ss_pred             HHHHHHHhc--CCCCCHHHHHHHHH---HcCCCHHHHHHHHHHHHH
Confidence            999988876  35578999999987   889999999999988764

>KOG2004|consensus

Probab=99.53  E-value=4.2e-13  Score=138.11  Aligned_cols=200  Identities=20%  Similarity=0.254  Sum_probs=137.7

Q ss_pred             HHhhcCCCCCCChHHHHHHHHHHHHhhhcc--CCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHH
Q psy200          187 EEKAKDSCELPGREVQLEGIRQFLLGHVNN--ETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAAS  264 (490)
Q Consensus       187 ~~~~l~~~~lvgre~~~~~l~~~L~~~~~~--~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~  264 (490)
                      ++..|. ++.+|-++..+++.++|.-....  -.++.++++||||+|||++++.||..++    ..|+.++...+.+..+
T Consensus       405 Ak~iLd-eDHYgm~dVKeRILEfiAV~kLrgs~qGkIlCf~GPPGVGKTSI~kSIA~ALn----RkFfRfSvGG~tDvAe  479 (906)
T KOG2004|consen  405 AKEILD-EDHYGMEDVKERILEFIAVGKLRGSVQGKILCFVGPPGVGKTSIAKSIARALN----RKFFRFSVGGMTDVAE  479 (906)
T ss_pred             HHHhhc-ccccchHHHHHHHHHHHHHHhhcccCCCcEEEEeCCCCCCcccHHHHHHHHhC----CceEEEeccccccHHh
Confidence            344444 89999999999999998644322  2678899999999999999999999986    5678887777766544


Q ss_pred             HHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccC----HHHHHHhHhCCC------------CC
Q psy200          265 VYETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRK----QTILYTIFEWPS------------IP  328 (490)
Q Consensus       265 l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~----~~~L~~l~~~~~------------~~  328 (490)
                      +-.+=     -.+.|.-...+.+.+...   +-..-+++|||||.+....    ..+|+.+++..+            ..
T Consensus       480 IkGHR-----RTYVGAMPGkiIq~LK~v---~t~NPliLiDEvDKlG~g~qGDPasALLElLDPEQNanFlDHYLdVp~D  551 (906)
T KOG2004|consen  480 IKGHR-----RTYVGAMPGKIIQCLKKV---KTENPLILIDEVDKLGSGHQGDPASALLELLDPEQNANFLDHYLDVPVD  551 (906)
T ss_pred             hcccc-----eeeeccCChHHHHHHHhh---CCCCceEEeehhhhhCCCCCCChHHHHHHhcChhhccchhhhccccccc
Confidence            32110     012223333333333321   1224489999999997542    345666554322            13


Q ss_pred             CCcEEEEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhcc--------CCCCCCCHHHHHHHHHH
Q psy200          329 GSKLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQT--------DKFNMFNASALQLLAGK  400 (490)
Q Consensus       329 ~~~vilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~--------~~~~~~~~~~i~~i~~~  400 (490)
                      -++|+|||++|.   .+.+-+.|+.|+.    .|.+..|..+|-.+|.+.+|-..        .....++++++..|.+.
T Consensus       552 LSkVLFicTAN~---idtIP~pLlDRME----vIelsGYv~eEKv~IA~~yLip~a~~~~gl~~e~v~is~~al~~lI~~  624 (906)
T KOG2004|consen  552 LSKVLFICTANV---IDTIPPPLLDRME----VIELSGYVAEEKVKIAERYLIPQALKDCGLKPEQVKISDDALLALIER  624 (906)
T ss_pred             hhheEEEEeccc---cccCChhhhhhhh----eeeccCccHHHHHHHHHHhhhhHHHHHcCCCHHhcCccHHHHHHHHHH
Confidence            578999999994   5666778889985    89999999999998887776433        23466888888888875


Q ss_pred             HHHhhC
Q psy200          401 VAAVSG  406 (490)
Q Consensus       401 i~~~~G  406 (490)
                      +....|
T Consensus       625 YcrEaG  630 (906)
T KOG2004|consen  625 YCREAG  630 (906)
T ss_pred             HHHHHh
Confidence            544444

>COG2204 AtoC Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]

Probab=99.53  E-value=6.1e-14  Score=141.75  Aligned_cols=217  Identities=19%  Similarity=0.256  Sum_probs=153.4

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHh
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNEL  273 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l  273 (490)
                      ..++|+...+++|.+.+.+.  ....-.|+|+|+.||||-.+|++|.+. ....+-+|+.+||..++ ..-+-++++..-
T Consensus       141 ~~liG~S~am~~l~~~i~kv--A~s~a~VLI~GESGtGKElvAr~IH~~-S~R~~~PFVavNcaAip-~~l~ESELFGhe  216 (464)
T COG2204         141 GELVGESPAMQQLRRLIAKV--APSDASVLITGESGTGKELVARAIHQA-SPRAKGPFIAVNCAAIP-ENLLESELFGHE  216 (464)
T ss_pred             CCceecCHHHHHHHHHHHHH--hCCCCCEEEECCCCCcHHHHHHHHHhh-CcccCCCceeeecccCC-HHHHHHHhhccc
Confidence            78999999999999999874  466789999999999999999999554 33445689999999973 222222333322


Q ss_pred             cCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCHHHHHHhHhCCCC--------CCCcEEEEEecCCCChhH
Q psy200          274 KLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPSI--------PGSKLVLVGVANALDLTD  345 (490)
Q Consensus       274 ~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~--------~~~~vilI~~tn~~~~~~  345 (490)
                      .+.+.|..... ...|+.+  .+|   .||||||..|.-.-|..|+..++....        -...+.||++||.. +.+
T Consensus       217 kGAFTGA~~~r-~G~fE~A--~GG---TLfLDEI~~mpl~~Q~kLLRvLqe~~~~rvG~~~~i~vdvRiIaaT~~d-L~~  289 (464)
T COG2204         217 KGAFTGAITRR-IGRFEQA--NGG---TLFLDEIGEMPLELQVKLLRVLQEREFERVGGNKPIKVDVRIIAATNRD-LEE  289 (464)
T ss_pred             ccCcCCccccc-CcceeEc--CCc---eEEeeccccCCHHHHHHHHHHHHcCeeEecCCCcccceeeEEEeecCcC-HHH
Confidence            22233221111 1122211  112   999999999999888888888764422        24567899999842 322


Q ss_pred             -----hhhHHhhhccCCCCeeEEeCCCC--HHHHHHHHHHHHhcc-----CCCCCCCHHHHHHHHHHHHHhhCCHHHHHH
Q psy200          346 -----RMLPRLQANVTLQPTLMNFAPYS--REQILEIISQKLKQT-----DKFNMFNASALQLLAGKVAAVSGDIRKAID  413 (490)
Q Consensus       346 -----~l~~~l~~R~~~~~~~i~~~pls--~~e~~~il~~~l~~~-----~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~  413 (490)
                           ++.+.|+.|+..  -.|.++|+-  .+++-.++.+++.+.     .....+++++++.+..  +.|.||+|++.|
T Consensus       290 ~v~~G~FReDLyyRLnV--~~i~iPpLRER~EDIp~L~~hfl~~~~~~~~~~~~~~s~~a~~~L~~--y~WPGNVREL~N  365 (464)
T COG2204         290 EVAAGRFREDLYYRLNV--VPLRLPPLRERKEDIPLLAEHFLKRFAAELGRPPKGFSPEALAALLA--YDWPGNVRELEN  365 (464)
T ss_pred             HHHcCCcHHHHHhhhcc--ceecCCcccccchhHHHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHh--CCCChHHHHHHH
Confidence                 234677778764  367778886  567777777766554     2346799999999987  899999999999


Q ss_pred             HHHHHHHHHHhc
Q psy200          414 ITNHLIDLTYDN  425 (490)
Q Consensus       414 ll~~a~~~a~~~  425 (490)
                      ++++++.++...
T Consensus       366 ~ver~~il~~~~  377 (464)
T COG2204         366 VVERAVILSEGP  377 (464)
T ss_pred             HHHHHHhcCCcc
Confidence            999998877654

>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN

Probab=99.52  E-value=1.2e-12  Score=126.26  Aligned_cols=206  Identities=11%  Similarity=0.156  Sum_probs=133.6

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHH--------HHhcC---CCCCCcHHHH-H
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIV--------NELKL---KPGGKSERHQ-L  286 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~--------~~l~~---~~~~~s~~~~-~  286 (490)
                      +.+++|+|+||||||++|+++++.++    ..++.++|.......+++....        ..+..   ...+...... .
T Consensus        21 g~~vLL~G~~GtGKT~lA~~la~~lg----~~~~~i~~~~~~~~~dllg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   96 (262)
T TIGR02640        21 GYPVHLRGPAGTGKTTLAMHVARKRD----RPVMLINGDAELTTSDLVGSYAGYTRKKVHDQFIHNVVKLEDIVRQNWVD   96 (262)
T ss_pred             CCeEEEEcCCCCCHHHHHHHHHHHhC----CCEEEEeCCccCCHHHHhhhhcccchhhHHHHHHHHhhhhhcccceeecC
Confidence            57899999999999999999998764    6788899987666665543321        00000   0000000000 0


Q ss_pred             HHHHHHHhcCCCeEEEEEecCccccccCHHHHHHhHhCCC--C-----------CCCcEEEEEecCCCC--hhHhhhHHh
Q psy200          287 GAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPS--I-----------PGSKLVLVGVANALD--LTDRMLPRL  351 (490)
Q Consensus       287 ~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~--~-----------~~~~vilI~~tn~~~--~~~~l~~~l  351 (490)
                      ..+..+...   ..+|+|||++.+....+..|..+++...  .           .+..+.+|+++|..+  ....+.+.+
T Consensus        97 g~l~~A~~~---g~~lllDEi~r~~~~~q~~Ll~~Le~~~~~i~~~~~~~~~i~~~~~frvIaTsN~~~~~g~~~l~~aL  173 (262)
T TIGR02640        97 NRLTLAVRE---GFTLVYDEFTRSKPETNNVLLSVFEEGVLELPGKRGTSRYVDVHPEFRVIFTSNPVEYAGVHETQDAL  173 (262)
T ss_pred             chHHHHHHc---CCEEEEcchhhCCHHHHHHHHHHhcCCeEEccCCCCCCceEecCCCCEEEEeeCCccccceecccHHH
Confidence            112222322   2399999999999888888888875321  0           123677888998542  223446778


Q ss_pred             hhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhh--C-----CHHHHHHHHHHHHHHHHh
Q psy200          352 QANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVS--G-----DIRKAIDITNHLIDLTYD  424 (490)
Q Consensus       352 ~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~--G-----d~r~ai~ll~~a~~~a~~  424 (490)
                      .+||.    .+.+..++.++..+|+..++.       +.++.++.+.+.+....  +     ++|.+|.+++.+...+. 
T Consensus       174 ~~R~~----~i~i~~P~~~~e~~Il~~~~~-------~~~~~~~~iv~~~~~~R~~~~~~~~~~r~~i~~~~~~~~~~~-  241 (262)
T TIGR02640       174 LDRLI----TIFMDYPDIDTETAILRAKTD-------VAEDSAATIVRLVREFRASGDEITSGLRASLMIAEVATQQDI-  241 (262)
T ss_pred             HhhcE----EEECCCCCHHHHHHHHHHhhC-------CCHHHHHHHHHHHHHHHhhCCccCCcHHHHHHHHHHHHHcCC-
Confidence            88985    799999999999999988652       35666666665443322  1     37777777666654432 


Q ss_pred             ccccCCcccccCHHHHHHHHHHhccC
Q psy200          425 NVKENGEVTGIGLKEVLGVISSVYCT  450 (490)
Q Consensus       425 ~~~~~~~~~~It~~~v~~a~~~~~~~  450 (490)
                             ...++.++|.++...+..+
T Consensus       242 -------~~~~~~~~~~~~~~~~~~~  260 (262)
T TIGR02640       242 -------PVDVDDEDFVDLCIDILAS  260 (262)
T ss_pred             -------CCCCCcHHHHHHHHHHhcc
Confidence                   3468899999998888754

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).

>KOG0735|consensus

Probab=99.52  E-value=5.2e-13  Score=137.20  Aligned_cols=192  Identities=18%  Similarity=0.235  Sum_probs=134.6

Q ss_pred             CCCCChHHHHHHHHHHHHhhhcc---------CCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVNN---------ETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAAS  264 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~---------~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~  264 (490)
                      +++.|-.+..+.|.+.+..-.+.         ....+||||||||||||.||.+++....    +.|+.+-++++     
T Consensus       667 ~digg~~~~k~~l~~~i~~P~kyp~if~~~plr~~~giLLyGppGcGKT~la~a~a~~~~----~~fisvKGPEl-----  737 (952)
T KOG0735|consen  667 EDIGGLFEAKKVLEEVIEWPSKYPQIFANCPLRLRTGILLYGPPGCGKTLLASAIASNSN----LRFISVKGPEL-----  737 (952)
T ss_pred             eecccHHHHHHHHHHHHhccccchHHHhhCCcccccceEEECCCCCcHHHHHHHHHhhCC----eeEEEecCHHH-----
Confidence            78899998888888887654221         1346899999999999999999998854    77777755433     


Q ss_pred             HHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccC--------HHHHHHhH-hCCCC-CCCcEEE
Q psy200          265 VYETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRK--------QTILYTIF-EWPSI-PGSKLVL  334 (490)
Q Consensus       265 l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~--------~~~L~~l~-~~~~~-~~~~vil  334 (490)
                       +.        ++.|.+++.+++.|.++..  .+|||||+||+|.+..++        .....+++ ++... .-..+.+
T Consensus       738 -L~--------KyIGaSEq~vR~lF~rA~~--a~PCiLFFDEfdSiAPkRGhDsTGVTDRVVNQlLTelDG~Egl~GV~i  806 (952)
T KOG0735|consen  738 -LS--------KYIGASEQNVRDLFERAQS--AKPCILFFDEFDSIAPKRGHDSTGVTDRVVNQLLTELDGAEGLDGVYI  806 (952)
T ss_pred             -HH--------HHhcccHHHHHHHHHHhhc--cCCeEEEeccccccCcccCCCCCCchHHHHHHHHHhhccccccceEEE
Confidence             22        4567889999999988765  579999999999998663        22333433 22222 2345777


Q ss_pred             EEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhC-CHHHHH
Q psy200          335 VGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSG-DIRKAI  412 (490)
Q Consensus       335 I~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~G-d~r~ai  412 (490)
                      +++|.+.|+.+   +++. |-|.-...+..+.++..+..+|++......   ..-++..++.++.+..+++| |+..++
T Consensus       807 ~aaTsRpdliD---pALL-RpGRlD~~v~C~~P~~~eRl~il~~ls~s~---~~~~~vdl~~~a~~T~g~tgADlq~ll  878 (952)
T KOG0735|consen  807 LAATSRPDLID---PALL-RPGRLDKLVYCPLPDEPERLEILQVLSNSL---LKDTDVDLECLAQKTDGFTGADLQSLL  878 (952)
T ss_pred             EEecCCccccC---Hhhc-CCCccceeeeCCCCCcHHHHHHHHHHhhcc---CCccccchHHHhhhcCCCchhhHHHHH
Confidence            78887766544   4443 223223578899999999999998765543   33456678899987777777 454443

>KOG0730|consensus

Probab=99.52  E-value=4.1e-13  Score=137.68  Aligned_cols=218  Identities=17%  Similarity=0.230  Sum_probs=151.6

Q ss_pred             CCCCChHHHHHHHHHHHHhhhc---------cCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVN---------NETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAAS  264 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~---------~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~  264 (490)
                      ..+.|....+..+...+...+.         ...++.+++|||||+|||.++++|+++..    ..++.+|++..     
T Consensus       184 ~~~gg~~~~~~~i~e~v~~pl~~~~~~~s~g~~~prg~Ll~gppg~Gkt~l~~aVa~e~~----a~~~~i~~pel-----  254 (693)
T KOG0730|consen  184 DDIGGLKRQLSVIRELVELPLRHPALFKSIGIKPPRGLLLYGPPGTGKTFLVRAVANEYG----AFLFLINGPEL-----  254 (693)
T ss_pred             cccchhHHHHHHHHHHHHhhhcchhhhhhcCCCCCCCccccCCCCCChHHHHHHHHHHhC----ceeEecccHHH-----
Confidence            3566677777777666554322         24678999999999999999999999864    56677776543     


Q ss_pred             HHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccC----------HHHHHHhHhCCCCCCCcEEE
Q psy200          265 VYETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRK----------QTILYTIFEWPSIPGSKLVL  334 (490)
Q Consensus       265 l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~----------~~~L~~l~~~~~~~~~~vil  334 (490)
                       +.        .+.|++...+++.|+++.+.. -|.+|||||+|.+...+          -..|+.++++.. ...++++
T Consensus       255 -i~--------k~~gEte~~LR~~f~~a~k~~-~psii~IdEld~l~p~r~~~~~~e~Rv~sqlltL~dg~~-~~~~viv  323 (693)
T KOG0730|consen  255 -IS--------KFPGETESNLRKAFAEALKFQ-VPSIIFIDELDALCPKREGADDVESRVVSQLLTLLDGLK-PDAKVIV  323 (693)
T ss_pred             -HH--------hcccchHHHHHHHHHHHhccC-CCeeEeHHhHhhhCCcccccchHHHHHHHHHHHHHhhCc-CcCcEEE
Confidence             11        456678889999999887642 28999999999998642          134556666543 5678999


Q ss_pred             EEecCCCChhHhhhHHhhh-ccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHH
Q psy200          335 VGVANALDLTDRMLPRLQA-NVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAID  413 (490)
Q Consensus       335 I~~tn~~~~~~~l~~~l~~-R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~  413 (490)
                      ++++|+.   +.+++.+++ ||.   ..+.+.-++.++..+|++..+....  . .++..+..++...+++.|  ..+-.
T Consensus       324 l~atnrp---~sld~alRRgRfd---~ev~IgiP~~~~RldIl~~l~k~~~--~-~~~~~l~~iA~~thGyvG--aDL~~  392 (693)
T KOG0730|consen  324 LAATNRP---DSLDPALRRGRFD---REVEIGIPGSDGRLDILRVLTKKMN--L-LSDVDLEDIAVSTHGYVG--ADLAA  392 (693)
T ss_pred             EEecCCc---cccChhhhcCCCc---ceeeecCCCchhHHHHHHHHHHhcC--C-cchhhHHHHHHHccchhH--HHHHH
Confidence            9999864   455666764 676   5899999999999999998887762  2 256778888873333333  12234


Q ss_pred             HHHHHHHHHHhccccCCcccccCHHHHHHHHHHhccCcc
Q psy200          414 ITNHLIDLTYDNVKENGEVTGIGLKEVLGVISSVYCTSQ  452 (490)
Q Consensus       414 ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~~~~~~~~~  452 (490)
                      +|..|...+.++          +++++..|+..+.+...
T Consensus       393 l~~ea~~~~~r~----------~~~~~~~A~~~i~psa~  421 (693)
T KOG0730|consen  393 LCREASLQATRR----------TLEIFQEALMGIRPSAL  421 (693)
T ss_pred             HHHHHHHHHhhh----------hHHHHHHHHhcCCchhh
Confidence            666665555444          35666666666655444

>PRK11608 pspF phage shock protein operon transcriptional activator; Provisional

Probab=99.51  E-value=1.3e-13  Score=136.98  Aligned_cols=215  Identities=17%  Similarity=0.165  Sum_probs=146.2

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHh
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNEL  273 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l  273 (490)
                      +.++|+...+.++.+.+....  ....+|+|+|++||||+++|+++.... ...+-+++.++|.... ...+-..++..-
T Consensus         6 ~~liG~S~~~~~~~~~i~~~a--~~~~pVlI~GE~GtGK~~lA~~iH~~s-~r~~~pfv~v~c~~~~-~~~~~~~lfg~~   81 (326)
T PRK11608          6 DNLLGEANSFLEVLEQVSRLA--PLDKPVLIIGERGTGKELIASRLHYLS-SRWQGPFISLNCAALN-ENLLDSELFGHE   81 (326)
T ss_pred             CccEECCHHHHHHHHHHHHHh--CCCCCEEEECCCCCcHHHHHHHHHHhC-CccCCCeEEEeCCCCC-HHHHHHHHcccc
Confidence            679999999999999988753  557899999999999999999997543 2334589999999874 333333333222


Q ss_pred             cCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCHHHHHHhHhCCCC--------CCCcEEEEEecCCCChh-
Q psy200          274 KLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPSI--------PGSKLVLVGVANALDLT-  344 (490)
Q Consensus       274 ~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~--------~~~~vilI~~tn~~~~~-  344 (490)
                      ...+.|.... ....+..  .. +  -+||||||+.|....|..|..+++....        ....+.+|++++.. +. 
T Consensus        82 ~~~~~g~~~~-~~g~l~~--a~-g--GtL~l~~i~~L~~~~Q~~L~~~l~~~~~~~~g~~~~~~~~~RiI~~s~~~-l~~  154 (326)
T PRK11608         82 AGAFTGAQKR-HPGRFER--AD-G--GTLFLDELATAPMLVQEKLLRVIEYGELERVGGSQPLQVNVRLVCATNAD-LPA  154 (326)
T ss_pred             ccccCCcccc-cCCchhc--cC-C--CeEEeCChhhCCHHHHHHHHHHHhcCcEEeCCCCceeeccEEEEEeCchh-HHH
Confidence            1111111111 1112221  11 2  2899999999999999999888764321        12357777777632 21 


Q ss_pred             ----HhhhHHhhhccCCCCeeEEeCCCC--HHHHHHHHHHHHhcc----CCC--CCCCHHHHHHHHHHHHHhhCCHHHHH
Q psy200          345 ----DRMLPRLQANVTLQPTLMNFAPYS--REQILEIISQKLKQT----DKF--NMFNASALQLLAGKVAAVSGDIRKAI  412 (490)
Q Consensus       345 ----~~l~~~l~~R~~~~~~~i~~~pls--~~e~~~il~~~l~~~----~~~--~~~~~~~i~~i~~~i~~~~Gd~r~ai  412 (490)
                          ..+.+.+..|+..  ..|.++|+.  .+|+..++.+++...    +..  ..+++++++.+..  +.|.||++++-
T Consensus       155 l~~~g~f~~dL~~~l~~--~~i~lPpLReR~eDI~~L~~~fl~~~~~~~~~~~~~~~s~~al~~L~~--y~WPGNvrEL~  230 (326)
T PRK11608        155 MVAEGKFRADLLDRLAF--DVVQLPPLRERQSDIMLMAEHFAIQMCRELGLPLFPGFTERARETLLN--YRWPGNIRELK  230 (326)
T ss_pred             HHHcCCchHHHHHhcCC--CEEECCChhhhhhhHHHHHHHHHHHHHHHhCCCCCCCCCHHHHHHHHh--CCCCcHHHHHH
Confidence                1234667777743  379999997  467777777665433    222  3589999999998  89999999999


Q ss_pred             HHHHHHHHHHH
Q psy200          413 DITNHLIDLTY  423 (490)
Q Consensus       413 ~ll~~a~~~a~  423 (490)
                      +++++++..+.
T Consensus       231 ~vl~~a~~~~~  241 (326)
T PRK11608        231 NVVERSVYRHG  241 (326)
T ss_pred             HHHHHHHHhcC
Confidence            99999987654

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

Probab=99.50  E-value=3.9e-13  Score=145.79  Aligned_cols=213  Identities=16%  Similarity=0.203  Sum_probs=143.6

Q ss_pred             CCCCChHHHHHHHHHHHHhhhc-----cCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVN-----NETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYET  268 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~-----~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~  268 (490)
                      ..++|+++.++.|...+..+..     ..+.+.++|+||+|||||.+|+.+++.+.    ..++.++|..+..... ...
T Consensus       458 ~~ViGQ~~ai~~l~~~i~~~~~gl~~~~kp~~~~Lf~GP~GvGKT~lAk~LA~~l~----~~~i~id~se~~~~~~-~~~  532 (758)
T PRK11034        458 MLVFGQDKAIEALTEAIKMSRAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSKALG----IELLRFDMSEYMERHT-VSR  532 (758)
T ss_pred             ceEeCcHHHHHHHHHHHHHHhccccCCCCCcceEEEECCCCCCHHHHHHHHHHHhC----CCcEEeechhhccccc-HHH
Confidence            6799999999999999986532     12345799999999999999999999884    5678888877643222 122


Q ss_pred             HHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCHHHHHHhHhCCCC--------CCCcEEEEEecCC
Q psy200          269 IVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPSI--------PGSKLVLVGVANA  340 (490)
Q Consensus       269 i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~--------~~~~vilI~~tn~  340 (490)
                      +   ++.+ .|.........+.+++.. ....|||||||+.+....++.|+++++....        .-.++++|+++|.
T Consensus       533 L---iG~~-~gyvg~~~~g~L~~~v~~-~p~sVlllDEieka~~~v~~~LLq~ld~G~ltd~~g~~vd~rn~iiI~TsN~  607 (758)
T PRK11034        533 L---IGAP-PGYVGFDQGGLLTDAVIK-HPHAVLLLDEIEKAHPDVFNLLLQVMDNGTLTDNNGRKADFRNVVLVMTTNA  607 (758)
T ss_pred             H---cCCC-CCcccccccchHHHHHHh-CCCcEEEeccHhhhhHHHHHHHHHHHhcCeeecCCCceecCCCcEEEEeCCc
Confidence            2   1221 111111111233344433 3357999999999998888889888874321        1246788888882


Q ss_pred             C---------C-------------hhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhcc-------CCCCCCCH
Q psy200          341 L---------D-------------LTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQT-------DKFNMFNA  391 (490)
Q Consensus       341 ~---------~-------------~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~-------~~~~~~~~  391 (490)
                      -         .             +...+.|.|..|+.   .++.|+|++.+++.+|+...+...       +....+++
T Consensus       608 g~~~~~~~~~g~~~~~~~~~~~~~~~~~f~pefl~Rid---~ii~f~~L~~~~l~~I~~~~l~~~~~~l~~~~i~l~~~~  684 (758)
T PRK11034        608 GVRETERKSIGLIHQDNSTDAMEEIKKIFTPEFRNRLD---NIIWFDHLSTDVIHQVVDKFIVELQAQLDQKGVSLEVSQ  684 (758)
T ss_pred             CHHHHhhcccCcccchhhHHHHHHHHHhcCHHHHccCC---EEEEcCCCCHHHHHHHHHHHHHHHHHHHHHCCCCceECH
Confidence            1         0             01224467777876   589999999999999987665432       56778999


Q ss_pred             HHHHHHHHHHHHhhCCHHHHHHHHHHHH
Q psy200          392 SALQLLAGKVAAVSGDIRKAIDITNHLI  419 (490)
Q Consensus       392 ~~i~~i~~~i~~~~Gd~r~ai~ll~~a~  419 (490)
                      ++++.|++..+....+.|.+-.++++-+
T Consensus       685 ~~~~~l~~~~~~~~~GAR~l~r~i~~~l  712 (758)
T PRK11034        685 EARDWLAEKGYDRAMGARPMARVIQDNL  712 (758)
T ss_pred             HHHHHHHHhCCCCCCCCchHHHHHHHHH
Confidence            9999999855555555565555444443

>COG3829 RocR Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]

Probab=99.50  E-value=1.4e-13  Score=138.94  Aligned_cols=231  Identities=16%  Similarity=0.181  Sum_probs=160.1

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHH-HHHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVY-ETIVNE  272 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~-~~i~~~  272 (490)
                      ++++|...++.++.+.+..  .......|+|.|+.||||-.+|+++.+. ....+-+|+.+||..++  ..++ ++++..
T Consensus       245 ~~Iig~S~~m~~~~~~akr--~A~tdstVLi~GESGTGKElfA~~IH~~-S~R~~~PFIaiNCaAiP--e~LlESELFGy  319 (560)
T COG3829         245 DDIIGESPAMLRVLELAKR--IAKTDSTVLILGESGTGKELFARAIHNL-SPRANGPFIAINCAAIP--ETLLESELFGY  319 (560)
T ss_pred             hhhccCCHHHHHHHHHHHh--hcCCCCcEEEecCCCccHHHHHHHHHhc-CcccCCCeEEEecccCC--HHHHHHHHhCc
Confidence            7899999999888888876  3567789999999999999999999654 34556699999999973  3333 334333


Q ss_pred             hcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCHHHHHHhHhCCC--------CCCCcEEEEEecCCCChh
Q psy200          273 LKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPS--------IPGSKLVLVGVANALDLT  344 (490)
Q Consensus       273 l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~--------~~~~~vilI~~tn~~~~~  344 (490)
                      -.+.+.|....--...|+.  ..+|   .||||||..|.-.-|..|++.++...        .....|.+|++||.. +.
T Consensus       320 e~GAFTGA~~~GK~GlfE~--A~gG---TLFLDEIgempl~LQaKLLRVLQEkei~rvG~t~~~~vDVRIIAATN~n-L~  393 (560)
T COG3829         320 EKGAFTGASKGGKPGLFEL--ANGG---TLFLDEIGEMPLPLQAKLLRVLQEKEIERVGGTKPIPVDVRIIAATNRN-LE  393 (560)
T ss_pred             CCccccccccCCCCcceee--ccCC---eEEehhhccCCHHHHHHHHHHHhhceEEecCCCCceeeEEEEEeccCcC-HH
Confidence            3334444332212222222  1122   99999999999888888877765321        235678999999843 22


Q ss_pred             Hh-----hhHHhhhccCCCCeeEEeCCCC--HHHHHHHHHHHHhcc----CCC-CCCCHHHHHHHHHHHHHhhCCHHHHH
Q psy200          345 DR-----MLPRLQANVTLQPTLMNFAPYS--REQILEIISQKLKQT----DKF-NMFNASALQLLAGKVAAVSGDIRKAI  412 (490)
Q Consensus       345 ~~-----l~~~l~~R~~~~~~~i~~~pls--~~e~~~il~~~l~~~----~~~-~~~~~~~i~~i~~~i~~~~Gd~r~ai  412 (490)
                      +.     +-+.|+.|++.  ..|.++|+-  ++++..+...++.+.    +.. ..++++++..+.+  +.|.||+|++-
T Consensus       394 ~~i~~G~FReDLYYRLNV--~~i~iPPLReR~eDI~~L~~~Fl~k~s~~~~~~v~~ls~~a~~~L~~--y~WPGNVRELe  469 (560)
T COG3829         394 KMIAEGTFREDLYYRLNV--IPITIPPLRERKEDIPLLAEYFLDKFSRRYGRNVKGLSPDALALLLR--YDWPGNVRELE  469 (560)
T ss_pred             HHHhcCcchhhheeeece--eeecCCCcccCcchHHHHHHHHHHHHHHHcCCCcccCCHHHHHHHHh--CCCCchHHHHH
Confidence            22     33567777764  356777775  567777766666543    323 3489999999988  89999999999


Q ss_pred             HHHHHHHHHHHhccccCCcccccCHHHHH-HHHHH
Q psy200          413 DITNHLIDLTYDNVKENGEVTGIGLKEVL-GVISS  446 (490)
Q Consensus       413 ~ll~~a~~~a~~~~~~~~~~~~It~~~v~-~a~~~  446 (490)
                      |++++++.++....       .|+.+|+- ..+..
T Consensus       470 NviER~v~~~~~~~-------~I~~~~lp~~~l~~  497 (560)
T COG3829         470 NVIERAVNLVESDG-------LIDADDLPAFALEE  497 (560)
T ss_pred             HHHHHHHhccCCcc-------eeehhhcchhhhcc
Confidence            99999998665555       47777765 44444

>TIGR02329 propionate_PrpR propionate catabolism operon regulatory protein PrpR

Probab=99.50  E-value=2.6e-13  Score=141.96  Aligned_cols=232  Identities=18%  Similarity=0.198  Sum_probs=153.9

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHh
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNEL  273 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l  273 (490)
                      ++++|....+..+.+.+...  .....+|+|+|++||||+++|+.+++... ..+.+|+.+||..+.. ..+-..++..-
T Consensus       212 ~~iiG~S~~m~~~~~~i~~~--A~~~~pVLI~GE~GTGKe~lA~~IH~~S~-r~~~pfv~inC~~l~e-~lleseLFG~~  287 (526)
T TIGR02329       212 DDLLGASAPMEQVRALVRLY--ARSDATVLILGESGTGKELVAQAIHQLSG-RRDFPFVAINCGAIAE-SLLEAELFGYE  287 (526)
T ss_pred             hheeeCCHHHHHHHHHHHHH--hCCCCcEEEECCCCcCHHHHHHHHHHhcC-cCCCCEEEeccccCCh-hHHHHHhcCCc
Confidence            66999999999999988763  34578999999999999999999976542 3456899999998742 22222222221


Q ss_pred             cCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCHHHHHHhHhCCCC--------CCCcEEEEEecCCCChhH
Q psy200          274 KLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPSI--------PGSKLVLVGVANALDLTD  345 (490)
Q Consensus       274 ~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~--------~~~~vilI~~tn~~~~~~  345 (490)
                      .+.+.|.........|+.+  .   .-.||||||+.|....|..|..+++....        ....+.+|++++.. +.+
T Consensus       288 ~gaftga~~~~~~Gl~e~A--~---gGTLfLdeI~~Lp~~~Q~~Ll~~L~~~~~~r~g~~~~~~~dvRiIaat~~~-l~~  361 (526)
T TIGR02329       288 EGAFTGARRGGRTGLIEAA--H---RGTLFLDEIGEMPLPLQTRLLRVLEEREVVRVGGTEPVPVDVRVVAATHCA-LTT  361 (526)
T ss_pred             ccccccccccccccchhhc--C---CceEEecChHhCCHHHHHHHHHHHhcCcEEecCCCceeeecceEEeccCCC-HHH
Confidence            1222221111111122211  1   22899999999999999999888764321        12345677777632 211


Q ss_pred             -----hhhHHhhhccCCCCeeEEeCCCC--HHHHHHHHHHHHhccC--CCCCCCHHHHHH-------HHHHHHHhhCCHH
Q psy200          346 -----RMLPRLQANVTLQPTLMNFAPYS--REQILEIISQKLKQTD--KFNMFNASALQL-------LAGKVAAVSGDIR  409 (490)
Q Consensus       346 -----~l~~~l~~R~~~~~~~i~~~pls--~~e~~~il~~~l~~~~--~~~~~~~~~i~~-------i~~~i~~~~Gd~r  409 (490)
                           .+.+.+..|+..  ..|.++|+.  .+|+..++.+++....  ....+++++++.       +..  +.|.||+|
T Consensus       362 ~v~~g~fr~dL~~rL~~--~~I~lPPLReR~eDI~~L~~~fl~~~~~~~~~~~~~~a~~~~~~~~~~L~~--y~WPGNvr  437 (526)
T TIGR02329       362 AVQQGRFRRDLFYRLSI--LRIALPPLRERPGDILPLAAEYLVQAAAALRLPDSEAAAQVLAGVADPLQR--YPWPGNVR  437 (526)
T ss_pred             HhhhcchhHHHHHhcCC--cEEeCCCchhchhHHHHHHHHHHHHHHHHcCCCCCHHHHHHhHHHHHHHHh--CCCCchHH
Confidence                 234456666643  479999998  4688888777776541  123588898887       665  78999999


Q ss_pred             HHHHHHHHHHHHHHhccccCCcccccCHHHHHHHH
Q psy200          410 KAIDITNHLIDLTYDNVKENGEVTGIGLKEVLGVI  444 (490)
Q Consensus       410 ~ai~ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~  444 (490)
                      ++-+++++++..+....     ...|+.+++....
T Consensus       438 EL~nvier~~i~~~~~~-----~~~I~~~~l~~~~  467 (526)
T TIGR02329       438 ELRNLVERLALELSAMP-----AGALTPDVLRALA  467 (526)
T ss_pred             HHHHHHHHHHHhcccCC-----CCccCHHHhhhhc
Confidence            99999999987664322     2368888876544

At least five distinct pathways exists for the catabolism of propionate by way of propionyl-CoA. Members of this family represent the transcriptional regulatory protein PrpR, whose gene is found in most cases divergently transcribed from an operon for the methylcitric acid cycle of propionate catabolism. 2-methylcitric acid, a catabolite by this pathway, is a coactivator of PrpR.

>COG1221 PspF Transcriptional regulators containing an AAA-type ATPase domain and a DNA-binding domain [Transcription / Signal transduction mechanisms]

Probab=99.50  E-value=2.4e-13  Score=135.20  Aligned_cols=219  Identities=20%  Similarity=0.247  Sum_probs=151.5

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHh
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNEL  273 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l  273 (490)
                      ..++|.....+++.+.+..  ......+|+|+|++||||+.+|+.++........-+|+.+||..+...-.... ++..-
T Consensus        78 ~~LIG~~~~~~~~~eqik~--~ap~~~~vLi~GetGtGKel~A~~iH~~s~r~~~~PFI~~NCa~~~en~~~~e-LFG~~  154 (403)
T COG1221          78 DDLIGESPSLQELREQIKA--YAPSGLPVLIIGETGTGKELFARLIHALSARRAEAPFIAFNCAAYSENLQEAE-LFGHE  154 (403)
T ss_pred             hhhhccCHHHHHHHHHHHh--hCCCCCcEEEecCCCccHHHHHHHHHHhhhcccCCCEEEEEHHHhCcCHHHHH-Hhccc
Confidence            7899999999999998887  45677899999999999999999998433221456899999999854332222 33333


Q ss_pred             cCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCHHHHHHhHhCCC--------CCCCcEEEEEecCCCChhH
Q psy200          274 KLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPS--------IPGSKLVLVGVANALDLTD  345 (490)
Q Consensus       274 ~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~--------~~~~~vilI~~tn~~~~~~  345 (490)
                      .+.+.|. ...-...|+.+ .  ++  .||+|||+.|....|..|+.+++...        .....|.+||+|+. ++.+
T Consensus       155 kGaftGa-~~~k~Glfe~A-~--GG--tLfLDEI~~LP~~~Q~kLl~~le~g~~~rvG~~~~~~~dVRli~AT~~-~l~~  227 (403)
T COG1221         155 KGAFTGA-QGGKAGLFEQA-N--GG--TLFLDEIHRLPPEGQEKLLRVLEEGEYRRVGGSQPRPVDVRLICATTE-DLEE  227 (403)
T ss_pred             cceeecc-cCCcCchheec-C--CC--EEehhhhhhCCHhHHHHHHHHHHcCceEecCCCCCcCCCceeeecccc-CHHH
Confidence            3333331 11111222221 1  22  99999999999999999999987532        23567889998873 3455


Q ss_pred             hhhH--HhhhccCCCCeeEEeCCCC--HHHHHHHHHHHHhcc----CCC-CCCCHHHHHHHHHHHHHhhCCHHHHHHHHH
Q psy200          346 RMLP--RLQANVTLQPTLMNFAPYS--REQILEIISQKLKQT----DKF-NMFNASALQLLAGKVAAVSGDIRKAIDITN  416 (490)
Q Consensus       346 ~l~~--~l~~R~~~~~~~i~~~pls--~~e~~~il~~~l~~~----~~~-~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll~  416 (490)
                      .+..  .+.+|+..  ..|.++|+.  .+|+..++.+++..+    +.. ....++++..+..  +.+.||+|++.|+++
T Consensus       228 ~~~~g~dl~~rl~~--~~I~LPpLrER~~Di~~L~e~Fl~~~~~~l~~~~~~~~~~a~~~L~~--y~~pGNirELkN~Ve  303 (403)
T COG1221         228 AVLAGADLTRRLNI--LTITLPPLRERKEDILLLAEHFLKSEARRLGLPLSVDSPEALRALLA--YDWPGNIRELKNLVE  303 (403)
T ss_pred             HHHhhcchhhhhcC--ceecCCChhhchhhHHHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHh--CCCCCcHHHHHHHHH
Confidence            5555  56554332  378888887  457777766666554    222 2334577887776  778999999999999


Q ss_pred             HHHHHHHhcc
Q psy200          417 HLIDLTYDNV  426 (490)
Q Consensus       417 ~a~~~a~~~~  426 (490)
                      +++..+...+
T Consensus       304 ~~~~~~~~~~  313 (403)
T COG1221         304 RAVAQASGEG  313 (403)
T ss_pred             HHHHHhcccc
Confidence            9998886554

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

Probab=99.49  E-value=8.8e-13  Score=133.88  Aligned_cols=227  Identities=17%  Similarity=0.222  Sum_probs=135.5

Q ss_pred             CCCCChHHHHHHHHHHHHhhhc---c---------CCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCC
Q psy200          194 CELPGREVQLEGIRQFLLGHVN---N---------ETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRN  261 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~---~---------~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~  261 (490)
                      +.++|++..++.|...+.+...   .         ....+++|+||+|||||++|+.++..+.    .+++.+++..+..
T Consensus        71 ~~ViGq~~ak~~l~~av~~~~~r~~~~~~~~~~~~~~~~~iLl~Gp~GtGKT~lAr~lA~~l~----~pf~~id~~~l~~  146 (412)
T PRK05342         71 QYVIGQERAKKVLSVAVYNHYKRLRHGDKKDDDVELQKSNILLIGPTGSGKTLLAQTLARILD----VPFAIADATTLTE  146 (412)
T ss_pred             hHeeChHHHHHHHHHHHHHHHHhhhcccccccccccCCceEEEEcCCCCCHHHHHHHHHHHhC----CCceecchhhccc
Confidence            6799999999988777643211   1         1347899999999999999999998874    5677777765421


Q ss_pred             HHHHHHHHHHHhcCCCCCCcHHHHHHHHHHH----HhcCCCeEEEEEecCcccccc--------------CHHHHHHhHh
Q psy200          262 AASVYETIVNELKLKPGGKSERHQLGAILKY----FDTKHKSILLILDEIDALESR--------------KQTILYTIFE  323 (490)
Q Consensus       262 ~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~----l~~~~~~~vI~IDEid~l~~~--------------~~~~L~~l~~  323 (490)
                      .             .+.|.....+...+...    +.. ..+.||||||||.+...              .|..|+.+++
T Consensus       147 ~-------------gyvG~d~e~~l~~l~~~~~~~~~~-a~~gIi~iDEIdkl~~~~~~~~~~~d~s~~~vQ~~LL~~Le  212 (412)
T PRK05342        147 A-------------GYVGEDVENILLKLLQAADYDVEK-AQRGIVYIDEIDKIARKSENPSITRDVSGEGVQQALLKILE  212 (412)
T ss_pred             C-------------CcccchHHHHHHHHHHhccccHHH-cCCcEEEEechhhhccccCCCCcCCCcccHHHHHHHHHHHh
Confidence            1             12223333322221111    111 23569999999999754              3567777775


Q ss_pred             CCC----------CCCCcEEEEEecCC--------CC-------------------------------hhHh--------
Q psy200          324 WPS----------IPGSKLVLVGVANA--------LD-------------------------------LTDR--------  346 (490)
Q Consensus       324 ~~~----------~~~~~vilI~~tn~--------~~-------------------------------~~~~--------  346 (490)
                      -..          .....+++|.++|.        ..                               +...        
T Consensus       213 g~~~~v~~~gg~~~~~~~~~~i~t~nilfi~~Gaf~g~~~~~~~r~~~~~~gf~~~~~~~~~~~~~~~~~~~~~~~dL~~  292 (412)
T PRK05342        213 GTVASVPPQGGRKHPQQEFIQVDTTNILFICGGAFDGLEKIIKQRLGKKGIGFGAEVKSKKEKRTEGELLKQVEPEDLIK  292 (412)
T ss_pred             cCeEEeCCCCCcCcCCCCeEEeccCCceeeecccccCcHHHHHHHHhhcccCCccccccccccchhHHHHHhcCHHHHHH
Confidence            210          11122333333331        00                               0000        


Q ss_pred             --hhHHhhhccCCCCeeEEeCCCCHHHHHHHHHH----H-------HhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHH
Q psy200          347 --MLPRLQANVTLQPTLMNFAPYSREQILEIISQ----K-------LKQTDKFNMFNASALQLLAGKVAAVSGDIRKAID  413 (490)
Q Consensus       347 --l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~----~-------l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~  413 (490)
                        +.|.|..|+.   .++.|.+++.+++.+|+..    .       +...+....+++++++.|++..+....+.|.+-.
T Consensus       293 ~gf~PEflgRld---~iv~f~~L~~~~L~~Il~~~~~~l~~q~~~~l~~~~i~L~~t~~al~~Ia~~~~~~~~GAR~Lrr  369 (412)
T PRK05342        293 FGLIPEFIGRLP---VVATLEELDEEALVRILTEPKNALVKQYQKLFEMDGVELEFTDEALEAIAKKAIERKTGARGLRS  369 (412)
T ss_pred             HhhhHHHhCCCC---eeeecCCCCHHHHHHHHHHHHHHHHHHHHHHHHhCCcEEEECHHHHHHHHHhCCCCCCCCchHHH
Confidence              2455666766   4899999999999999873    2       2223456679999999999865555556666555


Q ss_pred             HHHHHHHHHHhccc--cCCcccccCHHHHH
Q psy200          414 ITNHLIDLTYDNVK--ENGEVTGIGLKEVL  441 (490)
Q Consensus       414 ll~~a~~~a~~~~~--~~~~~~~It~~~v~  441 (490)
                      ++++.+.-...+--  .....-.|+.+.|.
T Consensus       370 iie~~l~~~~~~~p~~~~~~~v~I~~~~v~  399 (412)
T PRK05342        370 ILEEILLDVMFELPSREDVEKVVITKEVVE  399 (412)
T ss_pred             HHHHHhHHHHHhccccCCCceEEECHHHhc
Confidence            55555443322211  11112357777664

>TIGR01817 nifA Nif-specific regulatory protein

Probab=99.49  E-value=1.3e-13  Score=146.47  Aligned_cols=225  Identities=16%  Similarity=0.184  Sum_probs=152.1

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHh
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNEL  273 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l  273 (490)
                      +.++|....+.++.+.+...  ......|+|+|++||||+++|++|++... ..+-+++.+||..+.. ..+-..++..-
T Consensus       196 ~~liG~s~~~~~~~~~~~~~--a~~~~pvli~Ge~GtGK~~lA~~ih~~s~-r~~~pfv~i~c~~~~~-~~~~~~lfg~~  271 (534)
T TIGR01817       196 DGIIGKSPAMRQVVDQARVV--ARSNSTVLLRGESGTGKELIAKAIHYLSP-RAKRPFVKVNCAALSE-TLLESELFGHE  271 (534)
T ss_pred             CceEECCHHHHHHHHHHHHH--hCcCCCEEEECCCCccHHHHHHHHHHhCC-CCCCCeEEeecCCCCH-HHHHHHHcCCC
Confidence            68999999999999988874  35677999999999999999999977643 2345899999998733 22222222111


Q ss_pred             cCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCHHHHHHhHhCCCC--------CCCcEEEEEecCCCChhH
Q psy200          274 KLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPSI--------PGSKLVLVGVANALDLTD  345 (490)
Q Consensus       274 ~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~--------~~~~vilI~~tn~~~~~~  345 (490)
                      ...+.+... .....+..  .   ..-+||||||+.|....|..|..+++....        ....+.+|++++.. +.+
T Consensus       272 ~~~~~~~~~-~~~g~~~~--a---~~GtL~ldei~~L~~~~Q~~Ll~~l~~~~~~~~~~~~~~~~~~riI~~s~~~-l~~  344 (534)
T TIGR01817       272 KGAFTGAIA-QRKGRFEL--A---DGGTLFLDEIGEISPAFQAKLLRVLQEGEFERVGGNRTLKVDVRLVAATNRD-LEE  344 (534)
T ss_pred             CCccCCCCc-CCCCcccc--c---CCCeEEEechhhCCHHHHHHHHHHHhcCcEEECCCCceEeecEEEEEeCCCC-HHH
Confidence            111111100 00001111  1   123899999999999999989888764321        11357788877632 211


Q ss_pred             -----hhhHHhhhccCCCCeeEEeCCCC--HHHHHHHHHHHHhcc----CCCCCCCHHHHHHHHHHHHHhhCCHHHHHHH
Q psy200          346 -----RMLPRLQANVTLQPTLMNFAPYS--REQILEIISQKLKQT----DKFNMFNASALQLLAGKVAAVSGDIRKAIDI  414 (490)
Q Consensus       346 -----~l~~~l~~R~~~~~~~i~~~pls--~~e~~~il~~~l~~~----~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~l  414 (490)
                           .+.+.|..|+..  ..|.++|+.  .+++..++.+++...    +....+++++++.+..  +.|.||+|++.++
T Consensus       345 ~~~~~~f~~~L~~rl~~--~~i~lPpLreR~eDi~~L~~~~l~~~~~~~~~~~~~s~~a~~~L~~--~~WPGNvrEL~~v  420 (534)
T TIGR01817       345 AVAKGEFRADLYYRINV--VPIFLPPLRERREDIPLLAEAFLEKFNRENGRPLTITPSAIRVLMS--CKWPGNVRELENC  420 (534)
T ss_pred             HHHcCCCCHHHHHHhcC--CeeeCCCcccccccHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHh--CCCCChHHHHHHH
Confidence                 234566667653  368899998  678887777776543    2236799999999998  7899999999999


Q ss_pred             HHHHHHHHHhccccCCcccccCHHHHH
Q psy200          415 TNHLIDLTYDNVKENGEVTGIGLKEVL  441 (490)
Q Consensus       415 l~~a~~~a~~~~~~~~~~~~It~~~v~  441 (490)
                      +++++..+.  +      ..|+.+++.
T Consensus       421 ~~~a~~~~~--~------~~I~~~~l~  439 (534)
T TIGR01817       421 LERTATLSR--S------GTITRSDFS  439 (534)
T ss_pred             HHHHHHhCC--C------CcccHHHCc
Confidence            999986653  2      357777764

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.

>PRK13531 regulatory ATPase RavA; Provisional

Probab=99.48  E-value=2.3e-12  Score=130.86  Aligned_cols=230  Identities=14%  Similarity=0.119  Sum_probs=146.6

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHH-HHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETI-VNE  272 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i-~~~  272 (490)
                      ..|+|+++.++.+...+.      .+.+++|+||||||||++|++++..+....  .|.++.|.-. ++.+++..+ +..
T Consensus        20 ~~i~gre~vI~lll~aal------ag~hVLL~GpPGTGKT~LAraLa~~~~~~~--~F~~~~~~ft-tp~DLfG~l~i~~   90 (498)
T PRK13531         20 KGLYERSHAIRLCLLAAL------SGESVFLLGPPGIAKSLIARRLKFAFQNAR--AFEYLMTRFS-TPEEVFGPLSIQA   90 (498)
T ss_pred             hhccCcHHHHHHHHHHHc------cCCCEEEECCCChhHHHHHHHHHHHhcccC--cceeeeeeec-CcHHhcCcHHHhh
Confidence            889999999988887774      378999999999999999999998765322  3344443311 233332211 011


Q ss_pred             hcCCCCCCcHHHHHHHHHHHHhcC-CCeEEEEEecCccccccCHHHHHHhHhCCCC--------CCCcEEEEEecCCCCh
Q psy200          273 LKLKPGGKSERHQLGAILKYFDTK-HKSILLILDEIDALESRKQTILYTIFEWPSI--------PGSKLVLVGVANALDL  343 (490)
Q Consensus       273 l~~~~~~~s~~~~~~~l~~~l~~~-~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~--------~~~~vilI~~tn~~~~  343 (490)
                      +..  .        ..+.....+. ...-+||+|||+.+....|..|...++....        ...+++ ++++|...-
T Consensus        91 ~~~--~--------g~f~r~~~G~L~~A~lLfLDEI~rasp~~QsaLLeam~Er~~t~g~~~~~lp~rfi-v~ATN~LPE  159 (498)
T PRK13531         91 LKD--E--------GRYQRLTSGYLPEAEIVFLDEIWKAGPAILNTLLTAINERRFRNGAHEEKIPMRLL-VTASNELPE  159 (498)
T ss_pred             hhh--c--------CchhhhcCCccccccEEeecccccCCHHHHHHHHHHHHhCeEecCCeEEeCCCcEE-EEECCCCcc
Confidence            000  0        0111111110 0122999999999999999999888854321        122333 444564322


Q ss_pred             hHhhhHHhhhccCCCCeeEEeCCCC-HHHHHHHHHHHHhc-c--------------------CCCCCCCHHHHHHHHHHH
Q psy200          344 TDRMLPRLQANVTLQPTLMNFAPYS-REQILEIISQKLKQ-T--------------------DKFNMFNASALQLLAGKV  401 (490)
Q Consensus       344 ~~~l~~~l~~R~~~~~~~i~~~pls-~~e~~~il~~~l~~-~--------------------~~~~~~~~~~i~~i~~~i  401 (490)
                      ...+.+.+..||.   ..+.+++++ .++..++|...... .                    -....+++.+++.|.+.+
T Consensus       160 ~g~~leAL~DRFl---iri~vp~l~~~~~e~~lL~~~~~~~~~~~~~~~vis~eel~~lq~~v~~V~v~d~v~eyI~~L~  236 (498)
T PRK13531        160 ADSSLEALYDRML---IRLWLDKVQDKANFRSMLTSQQDENDNPVPASLQITDEEYQQWQKEIGKITLPDHVFELIFQLR  236 (498)
T ss_pred             cCCchHHhHhhEE---EEEECCCCCchHHHHHHHHcccccccCCCcccCCCCHHHHHHHHHHhcceeCCHHHHHHHHHHH
Confidence            2345667888885   379999997 45667777653211 0                    123456777777777755


Q ss_pred             HH---hh----CCHHHHHHHHHHHHHHHHhccccCCcccccCHHHHHHHHHHhccCcc
Q psy200          402 AA---VS----GDIRKAIDITNHLIDLTYDNVKENGEVTGIGLKEVLGVISSVYCTSQ  452 (490)
Q Consensus       402 ~~---~~----Gd~r~ai~ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~~~~~~~~~  452 (490)
                      ..   ..    -..|..+.+++.+-..|...|     ...|+.+|+. .+..+..++.
T Consensus       237 ~~lr~~r~~~~~SpR~~~~l~~~akA~A~l~G-----R~~V~p~Dv~-ll~~vL~HRl  288 (498)
T PRK13531        237 QQLDALPNAPYVSDRRWKKAIRLLQASAFFSG-----RDAIAPIDLI-LLKDCLWHDA  288 (498)
T ss_pred             HHHhcCCCCCCcCcHHHHHHHHHHHHHHHHCC-----CCCCCHHHHH-HhHHHhccCH
Confidence            42   11    357888999888888999999     7899999999 7777765544

>PRK05022 anaerobic nitric oxide reductase transcription regulator; Provisional

Probab=99.48  E-value=6.5e-13  Score=139.98  Aligned_cols=217  Identities=16%  Similarity=0.224  Sum_probs=150.0

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHh
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNEL  273 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l  273 (490)
                      ..++|+...++++.+.+...  ......|+|+|++||||+++|++++.... ..+-+++.+||..+.. ..+-..++...
T Consensus       187 ~~iig~s~~~~~~~~~i~~~--a~~~~pVlI~Ge~GtGK~~~A~~ih~~s~-r~~~p~v~v~c~~~~~-~~~e~~lfG~~  262 (509)
T PRK05022        187 GEMIGQSPAMQQLKKEIEVV--AASDLNVLILGETGVGKELVARAIHAASP-RADKPLVYLNCAALPE-SLAESELFGHV  262 (509)
T ss_pred             CceeecCHHHHHHHHHHHHH--hCCCCcEEEECCCCccHHHHHHHHHHhCC-cCCCCeEEEEcccCCh-HHHHHHhcCcc
Confidence            67999999999999999874  45678999999999999999999987643 3445899999998853 22222333222


Q ss_pred             cCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCHHHHHHhHhCCCC--------CCCcEEEEEecCCCChhH
Q psy200          274 KLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPSI--------PGSKLVLVGVANALDLTD  345 (490)
Q Consensus       274 ~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~--------~~~~vilI~~tn~~~~~~  345 (490)
                      ...+.+.... ....+..  .. +  -+||||||+.|....|..|..+++....        ....+.+|++++.. +.+
T Consensus       263 ~g~~~ga~~~-~~g~~~~--a~-g--GtL~ldeI~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiI~~t~~~-l~~  335 (509)
T PRK05022        263 KGAFTGAISN-RSGKFEL--AD-G--GTLFLDEIGELPLALQAKLLRVLQYGEIQRVGSDRSLRVDVRVIAATNRD-LRE  335 (509)
T ss_pred             ccccCCCccc-CCcchhh--cC-C--CEEEecChhhCCHHHHHHHHHHHhcCCEeeCCCCcceecceEEEEecCCC-HHH
Confidence            2222222111 1112221  11 2  2899999999999889888888754321        12467788888643 212


Q ss_pred             -----hhhHHhhhccCCCCeeEEeCCCC--HHHHHHHHHHHHhcc----C-CCCCCCHHHHHHHHHHHHHhhCCHHHHHH
Q psy200          346 -----RMLPRLQANVTLQPTLMNFAPYS--REQILEIISQKLKQT----D-KFNMFNASALQLLAGKVAAVSGDIRKAID  413 (490)
Q Consensus       346 -----~l~~~l~~R~~~~~~~i~~~pls--~~e~~~il~~~l~~~----~-~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~  413 (490)
                           .+.+.+..|+..  ..|.++|+.  .+|+..++.+++.+.    + ....+++++++.+..  +.|.||+|++-+
T Consensus       336 ~~~~~~f~~dL~~rl~~--~~i~lPpLreR~eDI~~L~~~fl~~~~~~~~~~~~~~s~~a~~~L~~--y~WPGNvrEL~~  411 (509)
T PRK05022        336 EVRAGRFRADLYHRLSV--FPLSVPPLRERGDDVLLLAGYFLEQNRARLGLRSLRLSPAAQAALLA--YDWPGNVRELEH  411 (509)
T ss_pred             HHHcCCccHHHHhcccc--cEeeCCCchhchhhHHHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHh--CCCCCcHHHHHH
Confidence                 244566666653  368899997  467777766665543    2 345799999999998  889999999999


Q ss_pred             HHHHHHHHHHhc
Q psy200          414 ITNHLIDLTYDN  425 (490)
Q Consensus       414 ll~~a~~~a~~~  425 (490)
                      ++++|+..+...
T Consensus       412 ~i~ra~~~~~~~  423 (509)
T PRK05022        412 VISRAALLARAR  423 (509)
T ss_pred             HHHHHHHhcCCC
Confidence            999998877654

>COG3267 ExeA Type II secretory pathway, component ExeA (predicted ATPase) [Intracellular trafficking and secretion]

Probab=99.48  E-value=9.8e-12  Score=114.49  Aligned_cols=209  Identities=19%  Similarity=0.321  Sum_probs=147.8

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCCCCCCcHH----HHHHHHHHHH
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKPGGKSER----HQLGAILKYF  293 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~~~s~~----~~~~~l~~~l  293 (490)
                      ..+.+.++|+-|+|||.+.+++...+. .....+++++.... +...+...|+.++..... ....    .....+....
T Consensus        50 ~qg~~~vtGevGsGKTv~~Ral~~s~~-~d~~~~v~i~~~~~-s~~~~~~ai~~~l~~~p~-~~~~~~~e~~~~~L~al~  126 (269)
T COG3267          50 GQGILAVTGEVGSGKTVLRRALLASLN-EDQVAVVVIDKPTL-SDATLLEAIVADLESQPK-VNVNAVLEQIDRELAALV  126 (269)
T ss_pred             CCceEEEEecCCCchhHHHHHHHHhcC-CCceEEEEecCcch-hHHHHHHHHHHHhccCcc-chhHHHHHHHHHHHHHHH
Confidence            345788999999999999996666554 44455567766655 667788888888876322 2233    3334455555


Q ss_pred             hcCCCeEEEEEecCccccccCHHHHHHhHhCCCCCC--CcEEEEEecCCC-ChhHhhhHHhhhccCCCCeeEEeCCCCHH
Q psy200          294 DTKHKSILLILDEIDALESRKQTILYTIFEWPSIPG--SKLVLVGVANAL-DLTDRMLPRLQANVTLQPTLMNFAPYSRE  370 (490)
Q Consensus       294 ~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~--~~vilI~~tn~~-~~~~~l~~~l~~R~~~~~~~i~~~pls~~  370 (490)
                      +++++++++++||++.+.....+.|..+.+......  -.++++|-+.-. ++....+..+..|+.+   .|.+.|++.+
T Consensus       127 ~~g~r~v~l~vdEah~L~~~~le~Lrll~nl~~~~~~~l~ivL~Gqp~L~~~lr~~~l~e~~~R~~i---r~~l~P~~~~  203 (269)
T COG3267         127 KKGKRPVVLMVDEAHDLNDSALEALRLLTNLEEDSSKLLSIVLIGQPKLRPRLRLPVLRELEQRIDI---RIELPPLTEA  203 (269)
T ss_pred             HhCCCCeEEeehhHhhhChhHHHHHHHHHhhcccccCceeeeecCCcccchhhchHHHHhhhheEEE---EEecCCcChH
Confidence            666677999999999999888777777765543333  346777665411 1222225677788873   4999999999


Q ss_pred             HHHHHHHHHHhccC-CCCCCCHHHHHHHHHHHHHhhCCHHHHHH-HHHHHHHHHHhccccCCcccccCHHHHH
Q psy200          371 QILEIISQKLKQTD-KFNMFNASALQLLAGKVAAVSGDIRKAID-ITNHLIDLTYDNVKENGEVTGIGLKEVL  441 (490)
Q Consensus       371 e~~~il~~~l~~~~-~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~-ll~~a~~~a~~~~~~~~~~~~It~~~v~  441 (490)
                      +...+|+++++..+ .+..++++++..++.   ...| ++.++| ++..|...|...+     ...|+...+.
T Consensus       204 ~t~~yl~~~Le~a~~~~~l~~~~a~~~i~~---~sqg-~P~lin~~~~~Al~~a~~a~-----~~~v~~a~~~  267 (269)
T COG3267         204 ETGLYLRHRLEGAGLPEPLFSDDALLLIHE---ASQG-IPRLINNLATLALDAAYSAG-----EDGVSEAEIK  267 (269)
T ss_pred             HHHHHHHHHHhccCCCcccCChhHHHHHHH---Hhcc-chHHHHHHHHHHHHHHHHcC-----CCccchhhcc
Confidence            99999999999874 456789999999987   4455 666665 8888888888877     5667666543

>PRK07471 DNA polymerase III subunit delta'; Validated

Probab=99.48  E-value=2.7e-12  Score=128.73  Aligned_cols=201  Identities=14%  Similarity=0.174  Sum_probs=126.9

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCc--e------EEEEeccCCCCHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAF--K------TIYINCNSVRNAASV  265 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~--~------~~~v~~~~~~~~~~l  265 (490)
                      ++++|+++.++.|...+..   +.-++.++|+||+|+||+++|.++++.+-.....  .      .....|..+.....+
T Consensus        19 ~~iiGq~~~~~~L~~~~~~---~rl~HA~Lf~Gp~G~GK~~lA~~~A~~Llc~~~~~~~~~~~~~~~l~~~~~c~~c~~i   95 (365)
T PRK07471         19 TALFGHAAAEAALLDAYRS---GRLHHAWLIGGPQGIGKATLAYRMARFLLATPPPGGDGAVPPPTSLAIDPDHPVARRI   95 (365)
T ss_pred             hhccChHHHHHHHHHHHHc---CCCCceEEEECCCCCCHHHHHHHHHHHHhCCCCCCCCccccccccccCCCCChHHHHH
Confidence            7899999999999888864   3456679999999999999999999998533210  0      000002211111111


Q ss_pred             HHHHHHH---hcC--CC------CCCcHHHHHHHHHHHHh--cCCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcE
Q psy200          266 YETIVNE---LKL--KP------GGKSERHQLGAILKYFD--TKHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKL  332 (490)
Q Consensus       266 ~~~i~~~---l~~--~~------~~~s~~~~~~~l~~~l~--~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~v  332 (490)
                      ...-.-+   +..  ..      .....+++++.......  ..+++.||||||+|.+....++.|..+++.+   ....
T Consensus        96 ~~~~HPDl~~i~~~~~~~~~~~~~~I~VdqiR~l~~~~~~~~~~~~~kVviIDead~m~~~aanaLLK~LEep---p~~~  172 (365)
T PRK07471         96 AAGAHGGLLTLERSWNEKGKRLRTVITVDEVRELISFFGLTAAEGGWRVVIVDTADEMNANAANALLKVLEEP---PARS  172 (365)
T ss_pred             HccCCCCeEEEecccccccccccccccHHHHHHHHHHhCcCcccCCCEEEEEechHhcCHHHHHHHHHHHhcC---CCCe
Confidence            0000000   000  01      11234555443332211  1356789999999999988888888887743   2344


Q ss_pred             EEEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHH
Q psy200          333 VLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAI  412 (490)
Q Consensus       333 ilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai  412 (490)
                      ++|.+++.   .+.+.+.+++||.    .+.|.+++.+++..++......      ..++.+..+++   ...|+++.++
T Consensus       173 ~~IL~t~~---~~~llpti~SRc~----~i~l~~l~~~~i~~~L~~~~~~------~~~~~~~~l~~---~s~Gsp~~Al  236 (365)
T PRK07471        173 LFLLVSHA---PARLLPTIRSRCR----KLRLRPLAPEDVIDALAAAGPD------LPDDPRAALAA---LAEGSVGRAL  236 (365)
T ss_pred             EEEEEECC---chhchHHhhccce----EEECCCCCHHHHHHHHHHhccc------CCHHHHHHHHH---HcCCCHHHHH
Confidence            44445553   3456788999995    8999999999999999875422      24444455554   5678899988


Q ss_pred             HHHH
Q psy200          413 DITN  416 (490)
Q Consensus       413 ~ll~  416 (490)
                      .+++
T Consensus       237 ~ll~  240 (365)
T PRK07471        237 RLAG  240 (365)
T ss_pred             HHhc
Confidence            8764

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

Probab=99.47  E-value=4.8e-12  Score=126.12  Aligned_cols=150  Identities=15%  Similarity=0.226  Sum_probs=103.6

Q ss_pred             EEEEEecCccccccC------------HHHHHHhHhCC-------CCCCCcEEEEEecCCC-ChhHhhhHHhhhccCCCC
Q psy200          300 ILLILDEIDALESRK------------QTILYTIFEWP-------SIPGSKLVLVGVANAL-DLTDRMLPRLQANVTLQP  359 (490)
Q Consensus       300 ~vI~IDEid~l~~~~------------~~~L~~l~~~~-------~~~~~~vilI~~tn~~-~~~~~l~~~l~~R~~~~~  359 (490)
                      -||||||||.+....            |..|+.+++-.       .....+++|||..-.. .-+..+.|.|..||..  
T Consensus       251 GIVfiDEiDKIa~~~~~~~~DvS~eGVQ~~LLki~EG~~v~~k~~~i~T~~ILFI~~GAF~~~kp~DlIPEl~GR~Pi--  328 (443)
T PRK05201        251 GIVFIDEIDKIAARGGSSGPDVSREGVQRDLLPLVEGSTVSTKYGMVKTDHILFIASGAFHVSKPSDLIPELQGRFPI--  328 (443)
T ss_pred             CEEEEEcchhhcccCCCCCCCCCccchhcccccccccceeeecceeEECCceeEEecCCcCCCChhhccHHHhCccce--
Confidence            399999999997442            44454444321       1234677888766421 2245578999999985  


Q ss_pred             eeEEeCCCCHHHHHHHHHH----HH-------hccCCCCCCCHHHHHHHHHHHHH-----hhCCHHHHHHHHHHHHHHHH
Q psy200          360 TLMNFAPYSREQILEIISQ----KL-------KQTDKFNMFNASALQLLAGKVAA-----VSGDIRKAIDITNHLIDLTY  423 (490)
Q Consensus       360 ~~i~~~pls~~e~~~il~~----~l-------~~~~~~~~~~~~~i~~i~~~i~~-----~~Gd~r~ai~ll~~a~~~a~  423 (490)
                       ++.|.+++.+++..||..    .+       ..++....|++++++.||+....     ..-+.|.+-.++++.+.-+.
T Consensus       329 -~v~L~~L~~~dL~~ILteP~nsLikQy~~Lf~~egv~L~Ftd~Al~~IA~~A~~~N~~~~~iGAR~LrtI~E~~L~d~~  407 (443)
T PRK05201        329 -RVELDALTEEDFVRILTEPKASLIKQYQALLATEGVTLEFTDDAIRRIAEIAYQVNEKTENIGARRLHTVMEKLLEDIS  407 (443)
T ss_pred             -EEECCCCCHHHHHHHhcCChhHHHHHHHHHHhhcCcEEEEcHHHHHHHHHHHHHhcccccccchhhHHHHHHHHHHHHh
Confidence             899999999999998832    22       22356678999999999997766     35678888888888886665


Q ss_pred             hcccc-CCcccccCHHHHHHHHHHhccCcc
Q psy200          424 DNVKE-NGEVTGIGLKEVLGVISSVYCTSQ  452 (490)
Q Consensus       424 ~~~~~-~~~~~~It~~~v~~a~~~~~~~~~  452 (490)
                      -+... ....-.|+.+.|...+..+.....
T Consensus       408 Fe~p~~~~~~v~I~~~~V~~~l~~l~~~~D  437 (443)
T PRK05201        408 FEAPDMSGETVTIDAAYVDEKLGDLVKDED  437 (443)
T ss_pred             ccCCCCCCCEEEECHHHHHHHHHHHHhcCC
Confidence            43321 112346888999888888765433

>PRK15424 propionate catabolism operon regulatory protein PrpR; Provisional

Probab=99.47  E-value=3.8e-13  Score=140.51  Aligned_cols=230  Identities=19%  Similarity=0.228  Sum_probs=149.4

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHh-------hhcCCceEEEEeccCCCCHHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRA-------EIKDAFKTIYINCNSVRNAASVY  266 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l-------~~~~~~~~~~v~~~~~~~~~~l~  266 (490)
                      ++++|....++++.+.+...  ......|+|+|++||||+++|+.+.+.+       ....+.+|+.+||..+.. ..+-
T Consensus       219 ~~iiG~S~~m~~~~~~i~~~--A~s~~pVLI~GE~GTGKe~~A~~IH~~~~~~~~~~S~r~~~pfv~inCaal~e-~lle  295 (538)
T PRK15424        219 GDLLGQSPQMEQVRQTILLY--ARSSAAVLIQGETGTGKELAAQAIHREYFARHDARQGKKSHPFVAVNCGAIAE-SLLE  295 (538)
T ss_pred             hheeeCCHHHHHHHHHHHHH--hCCCCcEEEECCCCCCHHHHHHHHHHhhcccccccCccCCCCeEEeecccCCh-hhHH
Confidence            56999999999999988763  3457899999999999999999998762       223456899999998743 2222


Q ss_pred             HHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCHHHHHHhHhCCCC--------CCCcEEEEEec
Q psy200          267 ETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPSI--------PGSKLVLVGVA  338 (490)
Q Consensus       267 ~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~--------~~~~vilI~~t  338 (490)
                      ..++..-.+.+.|.........|+.  ..   .-.||||||+.|....|..|..+++....        ....+.+|++|
T Consensus       296 seLFG~~~gaftga~~~~~~Gl~e~--A~---gGTLfLdeI~~Lp~~~Q~kLl~~L~e~~~~r~G~~~~~~~dvRiIaat  370 (538)
T PRK15424        296 AELFGYEEGAFTGSRRGGRAGLFEI--AH---GGTLFLDEIGEMPLPLQTRLLRVLEEKEVTRVGGHQPVPVDVRVISAT  370 (538)
T ss_pred             HHhcCCccccccCccccccCCchhc--cC---CCEEEEcChHhCCHHHHHHHHhhhhcCeEEecCCCceeccceEEEEec
Confidence            2222211111221110011112221  11   12899999999999999989888764321        13456788888


Q ss_pred             CCCChhH-----hhhHHhhhccCCCCeeEEeCCCC--HHHHHHHHHHHHhcc--CCCCCCCHHHH-------HHHHHHHH
Q psy200          339 NALDLTD-----RMLPRLQANVTLQPTLMNFAPYS--REQILEIISQKLKQT--DKFNMFNASAL-------QLLAGKVA  402 (490)
Q Consensus       339 n~~~~~~-----~l~~~l~~R~~~~~~~i~~~pls--~~e~~~il~~~l~~~--~~~~~~~~~~i-------~~i~~~i~  402 (490)
                      +.. +..     .+.+.+..|+..  ..|.++|+.  .+|+..++.+++.+.  .....++++++       +.+..  +
T Consensus       371 ~~~-L~~~v~~g~Fr~dL~yrL~~--~~I~lPPLReR~eDI~~L~~~fl~~~~~~~~~~~~~~a~~~~~~a~~~L~~--y  445 (538)
T PRK15424        371 HCD-LEEDVRQGRFRRDLFYRLSI--LRLQLPPLRERVADILPLAESFLKQSLAALSAPFSAALRQGLQQCETLLLH--Y  445 (538)
T ss_pred             CCC-HHHHHhcccchHHHHHHhcC--CeecCCChhhchhHHHHHHHHHHHHHHHHcCCCCCHHHHHhhHHHHHHHHh--C
Confidence            632 222     133456666653  478899997  468888888777653  11234677766       34443  6


Q ss_pred             HhhCCHHHHHHHHHHHHHHHHhccccCCcccccCHHHHH
Q psy200          403 AVSGDIRKAIDITNHLIDLTYDNVKENGEVTGIGLKEVL  441 (490)
Q Consensus       403 ~~~Gd~r~ai~ll~~a~~~a~~~~~~~~~~~~It~~~v~  441 (490)
                      .|.||+|++-+++++++.++....     ...|+.+++.
T Consensus       446 ~WPGNvREL~nvier~~i~~~~~~-----~~~i~~~~l~  479 (538)
T PRK15424        446 DWPGNVRELRNLMERLALFLSVEP-----TPDLTPQFLQ  479 (538)
T ss_pred             CCCchHHHHHHHHHHHHHhcCCCC-----cCccCHHHhh
Confidence            799999999999999987655332     2456766654

>KOG0651|consensus

Probab=99.47  E-value=2.5e-13  Score=127.40  Aligned_cols=221  Identities=14%  Similarity=0.145  Sum_probs=142.8

Q ss_pred             CCCCChHHHHHHHHHHHHhhhc---------cCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVN---------NETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAAS  264 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~---------~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~  264 (490)
                      +.+-|...++.++.+.+.-.+.         -..+.+++||||||+|||.++++|+..++    +.++.+..+.+     
T Consensus       132 ~~~ggl~~qirelre~ielpl~np~lf~rvgIk~Pkg~ll~GppGtGKTlla~~Vaa~mg----~nfl~v~ss~l-----  202 (388)
T KOG0651|consen  132 ENVGGLFYQIRELREVIELPLTNPELFLRVGIKPPKGLLLYGPPGTGKTLLARAVAATMG----VNFLKVVSSAL-----  202 (388)
T ss_pred             HHhCChHHHHHHHHhheEeeccCchhccccCCCCCceeEEeCCCCCchhHHHHHHHHhcC----CceEEeeHhhh-----
Confidence            5677777777777775543322         23678999999999999999999999986    55566644433     


Q ss_pred             HHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccC--------H---HHHHHhHh-CC-CCCCCc
Q psy200          265 VYETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRK--------Q---TILYTIFE-WP-SIPGSK  331 (490)
Q Consensus       265 l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~--------~---~~L~~l~~-~~-~~~~~~  331 (490)
                               ...+.|++..-+++.+..+..  ..+|+|||||||.+.+..        +   ..|.++++ |. .....+
T Consensus       203 ---------v~kyiGEsaRlIRemf~yA~~--~~pciifmdeiDAigGRr~se~Ts~dreiqrTLMeLlnqmdgfd~l~r  271 (388)
T KOG0651|consen  203 ---------VDKYIGESARLIRDMFRYARE--VIPCIIFMDEIDAIGGRRFSEGTSSDREIQRTLMELLNQMDGFDTLHR  271 (388)
T ss_pred             ---------hhhhcccHHHHHHHHHHHHhh--hCceEEeehhhhhhccEEeccccchhHHHHHHHHHHHHhhccchhccc
Confidence                     225666777777777776655  558999999999987552        2   33444432 21 224568


Q ss_pred             EEEEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHH
Q psy200          332 LVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKA  411 (490)
Q Consensus       332 vilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~a  411 (490)
                      +-+|+++|+.+   .++++|.+ -+.-...+..+-++......+++-......+...++.+++-.+.+   .. |+. ..
T Consensus       272 Vk~ImatNrpd---tLdpaLlR-pGRldrk~~iPlpne~~r~~I~Kih~~~i~~~Geid~eaivK~~d---~f-~ga-d~  342 (388)
T KOG0651|consen  272 VKTIMATNRPD---TLDPALLR-PGRLDRKVEIPLPNEQARLGILKIHVQPIDFHGEIDDEAILKLVD---GF-NGA-DL  342 (388)
T ss_pred             ccEEEecCCcc---ccchhhcC-CccccceeccCCcchhhceeeEeeccccccccccccHHHHHHHHh---cc-ChH-HH
Confidence            88999999654   34444432 121113455555555555555544433334456678888777765   22 322 25


Q ss_pred             HHHHHHHHHHHHhccccCCcccccCHHHHHHHHHHhc
Q psy200          412 IDITNHLIDLTYDNVKENGEVTGIGLKEVLGVISSVY  448 (490)
Q Consensus       412 i~ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~~~~~  448 (490)
                      .+.|..|-..|..+.     ...+-.+++..++.+..
T Consensus       343 rn~~tEag~Fa~~~~-----~~~vl~Ed~~k~vrk~~  374 (388)
T KOG0651|consen  343 RNVCTEAGMFAIPEE-----RDEVLHEDFMKLVRKQA  374 (388)
T ss_pred             hhhcccccccccchh-----hHHHhHHHHHHHHHHHH
Confidence            678888887776665     45788899998887764

>TIGR00390 hslU ATP-dependent protease HslVU, ATPase subunit

Probab=99.47  E-value=1.2e-11  Score=123.14  Aligned_cols=151  Identities=15%  Similarity=0.213  Sum_probs=104.6

Q ss_pred             eEEEEEecCccccccC------------HHHHHHhHhCC-------CCCCCcEEEEEecCCCC-hhHhhhHHhhhccCCC
Q psy200          299 SILLILDEIDALESRK------------QTILYTIFEWP-------SIPGSKLVLVGVANALD-LTDRMLPRLQANVTLQ  358 (490)
Q Consensus       299 ~~vI~IDEid~l~~~~------------~~~L~~l~~~~-------~~~~~~vilI~~tn~~~-~~~~l~~~l~~R~~~~  358 (490)
                      .-||||||||.+....            |..|+.+++-.       .....+++|||..-... -+..+.|.|..||.. 
T Consensus       248 ~GIVfiDEiDKIa~~~~~~~~DvS~eGVQ~~LLkilEGt~v~~k~~~v~T~~ILFI~~GAF~~~kp~DlIPEl~GR~Pi-  326 (441)
T TIGR00390       248 SGIIFIDEIDKIAKKGESSGADVSREGVQRDLLPIVEGSTVNTKYGMVKTDHILFIAAGAFQLAKPSDLIPELQGRFPI-  326 (441)
T ss_pred             CCEEEEEchhhhcccCCCCCCCCCccchhccccccccCceeeecceeEECCceeEEecCCcCCCChhhccHHHhCccce-
Confidence            3499999999998542            44555554321       22345777887664221 245578999999985 


Q ss_pred             CeeEEeCCCCHHHHHHHHH----HH-------HhccCCCCCCCHHHHHHHHHHHHH-----hhCCHHHHHHHHHHHHHHH
Q psy200          359 PTLMNFAPYSREQILEIIS----QK-------LKQTDKFNMFNASALQLLAGKVAA-----VSGDIRKAIDITNHLIDLT  422 (490)
Q Consensus       359 ~~~i~~~pls~~e~~~il~----~~-------l~~~~~~~~~~~~~i~~i~~~i~~-----~~Gd~r~ai~ll~~a~~~a  422 (490)
                        +..|.+++.+++..||.    ..       +..++....|++++++.|++....     ..-+.|.+-.++++.+.-+
T Consensus       327 --~v~L~~L~~edL~rILteP~nsLikQy~~Lf~~egv~L~Ftd~Al~~IA~~A~~~N~~~~~iGAR~LrtilE~~l~d~  404 (441)
T TIGR00390       327 --RVELQALTTDDFERILTEPKNSLIKQYKALMKTEGVNIEFSDEAIKRIAELAYNVNEKTENIGARRLHTVLERLLEDI  404 (441)
T ss_pred             --EEECCCCCHHHHHHHhcCChhHHHHHHHHHHhhcCcEEEEeHHHHHHHHHHHHHhcccccccchhhHHHHHHHHHHHH
Confidence              89999999999998872    12       233356678999999999997765     3567888888888887665


Q ss_pred             Hhcccc-CCcccccCHHHHHHHHHHhccCcc
Q psy200          423 YDNVKE-NGEVTGIGLKEVLGVISSVYCTSQ  452 (490)
Q Consensus       423 ~~~~~~-~~~~~~It~~~v~~a~~~~~~~~~  452 (490)
                      .-+... ....-.|+.+.|...+..+.....
T Consensus       405 ~fe~p~~~~~~v~I~~~~V~~~l~~~~~~~D  435 (441)
T TIGR00390       405 SFEAPDLSGQNITIDADYVSKKLGALVADED  435 (441)
T ss_pred             HhcCCCCCCCEEEECHHHHHhHHHHHHhcCC
Confidence            544321 122346899999998888775543

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.

>TIGR00678 holB DNA polymerase III, delta' subunit

Probab=99.46  E-value=2.6e-12  Score=117.81  Aligned_cols=172  Identities=14%  Similarity=0.226  Sum_probs=106.6

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHH---hcCCCCCCcHHHHHHHHHHHH
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNE---LKLKPGGKSERHQLGAILKYF  293 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~---l~~~~~~~s~~~~~~~l~~~l  293 (490)
                      .-++.++|+||+|+|||++++.+++.+.......  ...|....+...+...-..+   +.......+.+.+.+.+..+.
T Consensus        12 ~~~~~~L~~G~~G~gkt~~a~~~~~~l~~~~~~~--~~~c~~~~~c~~~~~~~~~d~~~~~~~~~~~~~~~i~~i~~~~~   89 (188)
T TIGR00678        12 RLAHAYLFAGPEGVGKELLALALAKALLCEQPGG--GEPCGECPSCRLIEAGNHPDLHRLEPEGQSIKVDQVRELVEFLS   89 (188)
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHHcCCCCCC--CCCCCCCHHHHHHHcCCCCcEEEeccccCcCCHHHHHHHHHHHc
Confidence            3457799999999999999999999985321100  00111110000000000000   000001123445544443322


Q ss_pred             h--cCCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHH
Q psy200          294 D--TKHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQ  371 (490)
Q Consensus       294 ~--~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e  371 (490)
                      .  ..+...||||||+|.+....++.|..+++..   ....++|.+++.   ...+.+.+++|+.    .+.|.|++.++
T Consensus        90 ~~~~~~~~kviiide~~~l~~~~~~~Ll~~le~~---~~~~~~il~~~~---~~~l~~~i~sr~~----~~~~~~~~~~~  159 (188)
T TIGR00678        90 RTPQESGRRVVIIEDAERMNEAAANALLKTLEEP---PPNTLFILITPS---PEKLLPTIRSRCQ----VLPFPPLSEEA  159 (188)
T ss_pred             cCcccCCeEEEEEechhhhCHHHHHHHHHHhcCC---CCCeEEEEEECC---hHhChHHHHhhcE----EeeCCCCCHHH
Confidence            2  1245779999999999887788888887653   234445555552   2677889999985    89999999999


Q ss_pred             HHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHH
Q psy200          372 ILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKA  411 (490)
Q Consensus       372 ~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~a  411 (490)
                      +.+++...    +    +++++++.+++   ...|++|.+
T Consensus       160 ~~~~l~~~----g----i~~~~~~~i~~---~~~g~~r~~  188 (188)
T TIGR00678       160 LLQWLIRQ----G----ISEEAAELLLA---LAGGSPGAA  188 (188)
T ss_pred             HHHHHHHc----C----CCHHHHHHHHH---HcCCCcccC
Confidence            99999875    1    67888999887   667887753

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.

>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=99.45  E-value=6.3e-12  Score=122.19  Aligned_cols=109  Identities=23%  Similarity=0.276  Sum_probs=71.8

Q ss_pred             eEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEEEecCCC-------C--hhHhhhHHhhhccCCCCeeEEeCCCCH
Q psy200          299 SILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVANAL-------D--LTDRMLPRLQANVTLQPTLMNFAPYSR  369 (490)
Q Consensus       299 ~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI~~tn~~-------~--~~~~l~~~l~~R~~~~~~~i~~~pls~  369 (490)
                      |-||||||+|.|.-.....|.+.++..   -+++ +|.+||+-       +  .+.-+-..|.+|+-    .|...||+.
T Consensus       279 pGVLFIDEvHmLDiEcFsfLnralEs~---~sPi-iIlATNRg~~~irGt~~~sphGiP~DlLDRll----II~t~py~~  350 (398)
T PF06068_consen  279 PGVLFIDEVHMLDIECFSFLNRALESE---LSPI-IILATNRGITKIRGTDIISPHGIPLDLLDRLL----IIRTKPYSE  350 (398)
T ss_dssp             E-EEEEESGGGSBHHHHHHHHHHHTST---T--E-EEEEES-SEEE-BTTS-EEETT--HHHHTTEE----EEEE----H
T ss_pred             cceEEecchhhccHHHHHHHHHHhcCC---CCcE-EEEecCceeeeccCccCcCCCCCCcchHhhcE----EEECCCCCH
Confidence            569999999999877667777777633   2344 44556622       1  11222335667774    899999999


Q ss_pred             HHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHHHHHHHH
Q psy200          370 EQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITNHLI  419 (490)
Q Consensus       370 ~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll~~a~  419 (490)
                      +|+.+|+.-++..+  ...+++++++.+.+  .+..-++|++++++.-|-
T Consensus       351 ~ei~~Il~iR~~~E--~v~i~~~al~~L~~--ig~~~SLRYAiqLi~~a~  396 (398)
T PF06068_consen  351 EEIKQILKIRAKEE--DVEISEDALDLLTK--IGVETSLRYAIQLITPAS  396 (398)
T ss_dssp             HHHHHHHHHHHHHC--T--B-HHHHHHHHH--HHHHS-HHHHHHCHHHHH
T ss_pred             HHHHHHHHhhhhhh--cCcCCHHHHHHHHH--HhhhccHHHHHHhhhhhh
Confidence            99999999999998  57899999999997  456778999999886553

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.

>KOG0732|consensus

Probab=99.45  E-value=3.1e-12  Score=138.62  Aligned_cols=249  Identities=17%  Similarity=0.173  Sum_probs=167.8

Q ss_pred             CCCCChHHHHHHHHHHHHhhhc---------cCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCC-ceEEEEeccCCCCHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVN---------NETSGSMYISGPPGTGKSASLNLLVSRAEIKDA-FKTIYINCNSVRNAA  263 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~---------~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~-~~~~~v~~~~~~~~~  263 (490)
                      +.+.|.+..+..|++.+...+.         -.++++++++||||||||..|++++..+....+ +.+..-...      
T Consensus       265 d~vggl~~~i~~LKEmVl~PLlyPE~f~~~~itpPrgvL~~GppGTGkTl~araLa~~~s~~~~kisffmrkga------  338 (1080)
T KOG0732|consen  265 DSVGGLENYINQLKEMVLLPLLYPEFFDNFNITPPRGVLFHGPPGTGKTLMARALAAACSRGNRKISFFMRKGA------  338 (1080)
T ss_pred             cccccHHHHHHHHHHHHHhHhhhhhHhhhcccCCCcceeecCCCCCchhHHHHhhhhhhcccccccchhhhcCc------
Confidence            7899999999999886654432         236889999999999999999999998752211 111111111      


Q ss_pred             HHHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccC---HH--------HHHHhHhCCCCCCCcE
Q psy200          264 SVYETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRK---QT--------ILYTIFEWPSIPGSKL  332 (490)
Q Consensus       264 ~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~---~~--------~L~~l~~~~~~~~~~v  332 (490)
                              +.-..|.|....++.-.|+++.+  ..|.|||+||||-|....   |+        .|+.+++ .....+++
T Consensus       339 --------D~lskwvgEaERqlrllFeeA~k--~qPSIIffdeIdGlapvrSskqEqih~SIvSTLLaLmd-GldsRgqV  407 (1080)
T KOG0732|consen  339 --------DCLSKWVGEAERQLRLLFEEAQK--TQPSIIFFDEIDGLAPVRSSKQEQIHASIVSTLLALMD-GLDSRGQV  407 (1080)
T ss_pred             --------hhhccccCcHHHHHHHHHHHHhc--cCceEEeccccccccccccchHHHhhhhHHHHHHHhcc-CCCCCCce
Confidence                    11126777888888888887766  579999999999887553   22        3344443 23357899


Q ss_pred             EEEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHH
Q psy200          333 VLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAI  412 (490)
Q Consensus       333 ilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai  412 (490)
                      +|||+||+.+   .+++.+++ -+.....+.|.-++.+...+|+.-+-..-  ...+....+..+++.   +.|....-|
T Consensus       408 vvigATnRpd---a~dpaLRR-Pgrfdref~f~lp~~~ar~~Il~Ihtrkw--~~~i~~~l~~~la~~---t~gy~gaDl  478 (1080)
T KOG0732|consen  408 VVIGATNRPD---AIDPALRR-PGRFDREFYFPLPDVDARAKILDIHTRKW--EPPISRELLLWLAEE---TSGYGGADL  478 (1080)
T ss_pred             EEEcccCCcc---ccchhhcC-CcccceeEeeeCCchHHHHHHHHHhccCC--CCCCCHHHHHHHHHh---ccccchHHH
Confidence            9999999764   44555532 23223589999999999999987665544  356788888999883   444433334


Q ss_pred             -HHHHHHHHHHHhccccC-----------CcccccCHHHHHHHHHHhccCccccccccccCCCChHhHHHH
Q psy200          413 -DITNHLIDLTYDNVKEN-----------GEVTGIGLKEVLGVISSVYCTSQSLHCSKDEDSFPLQQKLAL  471 (490)
Q Consensus       413 -~ll~~a~~~a~~~~~~~-----------~~~~~It~~~v~~a~~~~~~~~~~~~~~~~l~~L~~~qk~vL  471 (490)
                       .+|..|...+.++....           .....|...+|..|+..+++....   ...+.+-|+...+++
T Consensus       479 kaLCTeAal~~~~r~~Pq~y~s~~kl~~d~~~ikV~~~~f~~A~~~i~ps~~R---~~~~~s~Pl~~~~~~  546 (1080)
T KOG0732|consen  479 KALCTEAALIALRRSFPQIYSSSDKLLIDVALIKVEVRDFVEAMSRITPSSRR---SSVIFSRPLSTYLKP  546 (1080)
T ss_pred             HHHHHHHhhhhhccccCeeecccccccccchhhhhhhHhhhhhhhccCCCCCc---cccCCCCCCCcceec
Confidence             48888888887665433           123348889999999998876552   245555555544433

>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional

Probab=99.44  E-value=1.5e-12  Score=137.29  Aligned_cols=225  Identities=12%  Similarity=0.146  Sum_probs=147.5

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHh
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNEL  273 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l  273 (490)
                      +.++|....+.++.+.+...  ......|+|+|++||||+++|+++.... ....-+++.+||..+.. ..+-..++...
T Consensus       204 ~~~ig~s~~~~~~~~~~~~~--A~~~~pvlI~GE~GtGK~~lA~aiH~~s-~r~~~pfv~inca~~~~-~~~e~elFG~~  279 (520)
T PRK10820        204 SQIVAVSPKMRQVVEQARKL--AMLDAPLLITGDTGTGKDLLAYACHLRS-PRGKKPFLALNCASIPD-DVVESELFGHA  279 (520)
T ss_pred             cceeECCHHHHHHHHHHHHH--hCCCCCEEEECCCCccHHHHHHHHHHhC-CCCCCCeEEeccccCCH-HHHHHHhcCCC
Confidence            68999999988888888764  3457789999999999999999986543 23445789999998752 22222332211


Q ss_pred             cCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCHHHHHHhHhCCCC--------CCCcEEEEEecCCC--Ch
Q psy200          274 KLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPSI--------PGSKLVLVGVANAL--DL  343 (490)
Q Consensus       274 ~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~--------~~~~vilI~~tn~~--~~  343 (490)
                      ...+.+.. ......|..  ..   .-+||||||+.|....|..|..+++....        ....+.+|++++..  ++
T Consensus       280 ~~~~~~~~-~~~~g~~e~--a~---~GtL~LdeI~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~vRiI~st~~~l~~l  353 (520)
T PRK10820        280 PGAYPNAL-EGKKGFFEQ--AN---GGSVLLDEIGEMSPRMQAKLLRFLNDGTFRRVGEDHEVHVDVRVICATQKNLVEL  353 (520)
T ss_pred             CCCcCCcc-cCCCChhhh--cC---CCEEEEeChhhCCHHHHHHHHHHHhcCCcccCCCCcceeeeeEEEEecCCCHHHH
Confidence            11111110 000111221  11   22899999999999989888888764311        12456777777532  11


Q ss_pred             hH--hhhHHhhhccCCCCeeEEeCCCCH--HHHHHHHHHHHhcc----CC-CCCCCHHHHHHHHHHHHHhhCCHHHHHHH
Q psy200          344 TD--RMLPRLQANVTLQPTLMNFAPYSR--EQILEIISQKLKQT----DK-FNMFNASALQLLAGKVAAVSGDIRKAIDI  414 (490)
Q Consensus       344 ~~--~l~~~l~~R~~~~~~~i~~~pls~--~e~~~il~~~l~~~----~~-~~~~~~~~i~~i~~~i~~~~Gd~r~ai~l  414 (490)
                      ..  .+.+.+..|+..  ..|.++|+..  +++..++.+++...    +. ...+++++++.+..  +.|.||+|++-++
T Consensus       354 ~~~g~f~~dL~~rL~~--~~i~lPpLreR~~Di~~L~~~fl~~~~~~~g~~~~~ls~~a~~~L~~--y~WPGNvreL~nv  429 (520)
T PRK10820        354 VQKGEFREDLYYRLNV--LTLNLPPLRDRPQDIMPLTELFVARFADEQGVPRPKLAADLNTVLTR--YGWPGNVRQLKNA  429 (520)
T ss_pred             HHcCCccHHHHhhcCe--eEEeCCCcccChhHHHHHHHHHHHHHHHHcCCCCCCcCHHHHHHHhc--CCCCCHHHHHHHH
Confidence            11  234567777653  4788999974  56776665555433    22 34689999999987  7899999999999


Q ss_pred             HHHHHHHHHhccccCCcccccCHHHH
Q psy200          415 TNHLIDLTYDNVKENGEVTGIGLKEV  440 (490)
Q Consensus       415 l~~a~~~a~~~~~~~~~~~~It~~~v  440 (490)
                      +.+|+..+..        ..|+.+++
T Consensus       430 l~~a~~~~~~--------~~i~~~~~  447 (520)
T PRK10820        430 IYRALTQLEG--------YELRPQDI  447 (520)
T ss_pred             HHHHHHhCCC--------CcccHHHc
Confidence            9999876542        24666664

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

Probab=99.44  E-value=3.3e-12  Score=140.15  Aligned_cols=212  Identities=17%  Similarity=0.267  Sum_probs=143.1

Q ss_pred             CCCCChHHHHHHHHHHHHhhhc-----cCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVN-----NETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYET  268 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~-----~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~  268 (490)
                      +.++|+++.++.|...+.....     ..+.+.++++||+|||||.+|+.+++.+.    ..++.++++.+...... ..
T Consensus       454 ~~v~GQ~~ai~~l~~~i~~~~~g~~~~~~p~~~~lf~Gp~GvGKT~lA~~la~~l~----~~~~~~d~se~~~~~~~-~~  528 (731)
T TIGR02639       454 AKIFGQDEAIDSLVSSIKRSRAGLGNPNKPVGSFLFTGPTGVGKTELAKQLAEALG----VHLERFDMSEYMEKHTV-SR  528 (731)
T ss_pred             cceeCcHHHHHHHHHHHHHHhcCCCCCCCCceeEEEECCCCccHHHHHHHHHHHhc----CCeEEEeCchhhhcccH-HH
Confidence            8899999999999998875321     11334689999999999999999999884    46788887765432211 11


Q ss_pred             HHHHhcCC--CCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCHHHHHHhHhCCCC--------CCCcEEEEEec
Q psy200          269 IVNELKLK--PGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPSI--------PGSKLVLVGVA  338 (490)
Q Consensus       269 i~~~l~~~--~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~--------~~~~vilI~~t  338 (490)
                      +   ++.+  +.|...   ...+.+++.. ....|||||||+.+....++.|+++++....        .-.+.++|+++
T Consensus       529 l---ig~~~gyvg~~~---~~~l~~~~~~-~p~~VvllDEieka~~~~~~~Ll~~ld~g~~~d~~g~~vd~~~~iii~Ts  601 (731)
T TIGR02639       529 L---IGAPPGYVGFEQ---GGLLTEAVRK-HPHCVLLLDEIEKAHPDIYNILLQVMDYATLTDNNGRKADFRNVILIMTS  601 (731)
T ss_pred             H---hcCCCCCcccch---hhHHHHHHHh-CCCeEEEEechhhcCHHHHHHHHHhhccCeeecCCCcccCCCCCEEEECC
Confidence            1   1211  112111   1233344433 3457999999999988888899988874421        12357788888


Q ss_pred             CCC--C--------------------hhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhcc-------CCCCCC
Q psy200          339 NAL--D--------------------LTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQT-------DKFNMF  389 (490)
Q Consensus       339 n~~--~--------------------~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~-------~~~~~~  389 (490)
                      |.-  .                    +...+.|.|..|+.   .++.|.|++.+++.+|+...+...       +....+
T Consensus       602 n~g~~~~~~~~~~f~~~~~~~~~~~~~~~~f~pef~~Rid---~Vi~F~pLs~e~l~~Iv~~~L~~l~~~l~~~~~~l~i  678 (731)
T TIGR02639       602 NAGASEMSKPPIGFGSENVESKSDKAIKKLFSPEFRNRLD---AIIHFNPLSEEVLEKIVQKFVDELSKQLNEKNIKLEL  678 (731)
T ss_pred             CcchhhhhhccCCcchhhhHHHHHHHHHhhcChHHHhcCC---eEEEcCCCCHHHHHHHHHHHHHHHHHHHHhCCCeEEe
Confidence            731  0                    01123466777887   589999999999999998877542       335678


Q ss_pred             CHHHHHHHHHHHHHhhCCHHHHHHHHHHHHH
Q psy200          390 NASALQLLAGKVAAVSGDIRKAIDITNHLID  420 (490)
Q Consensus       390 ~~~~i~~i~~~i~~~~Gd~r~ai~ll~~a~~  420 (490)
                      ++++++.|+++.+....+.|.+-.+++..+.
T Consensus       679 ~~~a~~~La~~~~~~~~GaR~l~r~i~~~~~  709 (731)
T TIGR02639       679 TDDAKKYLAEKGYDEEFGARPLARVIQEEIK  709 (731)
T ss_pred             CHHHHHHHHHhCCCcccCchHHHHHHHHHhH
Confidence            9999999998655555566766655555443

>PRK13407 bchI magnesium chelatase subunit I; Provisional

Probab=99.42  E-value=7.3e-12  Score=123.58  Aligned_cols=245  Identities=18%  Similarity=0.205  Sum_probs=150.6

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCC---CHHHH-HHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVR---NAASV-YETI  269 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~---~~~~l-~~~i  269 (490)
                      ..++|+++.++.+.-.+..    ...+++||+|+||+|||++++++++-+..........+++....   +.... ...+
T Consensus         8 ~~i~Gq~~~~~~l~~~~~~----~~~~~vLl~G~pG~gKT~lar~la~llP~~~~~e~~~~~~~~~~~~~~~~~~~~~~~   83 (334)
T PRK13407          8 SAIVGQEEMKQAMVLTAID----PGIGGVLVFGDRGTGKSTAVRALAALLPLIKAVEGCPVNSARPEDCPEWAHVSSTTM   83 (334)
T ss_pred             HHhCCHHHHHHHHHHHHhc----cCCCcEEEEcCCCCCHHHHHHHHHHHCCCcchhcccccccCcccCCcccccccCCcc
Confidence            5689999998877654421    23478999999999999999999998731110001111111000   00000 0000


Q ss_pred             HHH---hcCCCCCCcHHHHHH--HHHHHH-------hcC----CCeEEEEEecCccccccCHHHHHHhHhCCCC------
Q psy200          270 VNE---LKLKPGGKSERHQLG--AILKYF-------DTK----HKSILLILDEIDALESRKQTILYTIFEWPSI------  327 (490)
Q Consensus       270 ~~~---l~~~~~~~s~~~~~~--~l~~~l-------~~~----~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~------  327 (490)
                      ...   +.....+.+.+.+..  .+...+       ..+    ...-+|||||++.+....|..|...++....      
T Consensus        84 ~~~~~p~~~~p~~~t~~~l~G~~d~~~~l~~g~~~~~~G~l~~A~~GiL~lDEInrl~~~~q~~Lle~mee~~v~v~r~G  163 (334)
T PRK13407         84 IERPTPVVDLPLGVTEDRVVGALDIERALTRGEKAFEPGLLARANRGYLYIDEVNLLEDHIVDLLLDVAQSGENVVEREG  163 (334)
T ss_pred             cccCCccccCCCCCCcceeecchhhhhhhhcCCeeecCCceEEcCCCeEEecChHhCCHHHHHHHHHHHHcCCeEEEECC
Confidence            000   000001111111111  011111       100    1113899999999999999999888864431      


Q ss_pred             ----CCCcEEEEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCH-HHHHHHHHHHHhcc-------------------
Q psy200          328 ----PGSKLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSR-EQILEIISQKLKQT-------------------  383 (490)
Q Consensus       328 ----~~~~vilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~-~e~~~il~~~l~~~-------------------  383 (490)
                          ...+++++++.|..+  ..+.+.+..||.+   .+.+.++.. ++..+++.......                   
T Consensus       164 ~~~~~p~rfiviAt~NP~e--~~l~~aLldRF~~---~v~v~~~~~~~e~~~il~~~~~~~~~~~~~~~~~~~~~~~~~~  238 (334)
T PRK13407        164 LSIRHPARFVLVGSGNPEE--GELRPQLLDRFGL---SVEVRSPRDVETRVEVIRRRDAYDADHDAFMAKWGAEDMQLRG  238 (334)
T ss_pred             eEEecCCCEEEEecCCccc--CCCCHHHHhhcce---EEEcCCCCcHHHHHHHHHHhhcccccchhhhccccccccCCHH
Confidence                346889999888543  2356678889885   677777765 67677776543210                   


Q ss_pred             --------CCCCCCCHHHHHHHHHHHHHhh-CCHHHHHHHHHHHHHHHHhccccCCcccccCHHHHHHHHHHhccCcc
Q psy200          384 --------DKFNMFNASALQLLAGKVAAVS-GDIRKAIDITNHLIDLTYDNVKENGEVTGIGLKEVLGVISSVYCTSQ  452 (490)
Q Consensus       384 --------~~~~~~~~~~i~~i~~~i~~~~-Gd~r~ai~ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~~~~~~~~~  452 (490)
                              -....++++.++++++.+.... .+.|..+.+++.|...|..++     ...|+.+||..+..-+...+.
T Consensus       239 ~i~~a~~~~~~V~v~~~~~~yi~~l~~~~~~~s~Ra~i~l~~aA~a~A~l~G-----r~~V~~~Di~~~~~~vl~hR~  311 (334)
T PRK13407        239 RILGARARLPQLKTPNTVLHDCAALCIALGSDGLRGELTLLRAARALAAFEG-----AEAVGRSHLRSVATMALSHRL  311 (334)
T ss_pred             HHHHHHHhcCCcccCHHHHHHHHHHHHHHCCCCchHHHHHHHHHHHHHHHcC-----CCeeCHHHHHHHHHHhhhhhc
Confidence                    1235678888998888665554 478888889999999999999     779999999998877776655

>PRK15429 formate hydrogenlyase transcriptional activator FhlA; Provisional

Probab=99.42  E-value=3.6e-12  Score=139.30  Aligned_cols=215  Identities=16%  Similarity=0.239  Sum_probs=145.9

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHh
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNEL  273 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l  273 (490)
                      .+++|+...+..+.+.+...  .....+|+|+|++|||||++|++++.... ..+.+++.++|.... ...+-..++...
T Consensus       376 ~~liG~S~~~~~~~~~~~~~--a~~~~pVLI~GE~GTGK~~lA~~ih~~s~-r~~~~~v~i~c~~~~-~~~~~~~lfg~~  451 (686)
T PRK15429        376 GEIIGRSEAMYSVLKQVEMV--AQSDSTVLILGETGTGKELIARAIHNLSG-RNNRRMVKMNCAAMP-AGLLESDLFGHE  451 (686)
T ss_pred             cceeecCHHHHHHHHHHHHH--hCCCCCEEEECCCCcCHHHHHHHHHHhcC-CCCCCeEEEecccCC-hhHhhhhhcCcc
Confidence            57999999999998888764  34567999999999999999999977642 345689999999874 233333333322


Q ss_pred             cCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCHHHHHHhHhCCCC--------CCCcEEEEEecCCCChhH
Q psy200          274 KLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPSI--------PGSKLVLVGVANALDLTD  345 (490)
Q Consensus       274 ~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~--------~~~~vilI~~tn~~~~~~  345 (490)
                      ...+.+.... ....+.  ...   .-+||||||+.|....|..|..+++....        ....+.+|++++.. +..
T Consensus       452 ~~~~~g~~~~-~~g~le--~a~---~GtL~Ldei~~L~~~~Q~~L~~~l~~~~~~~~g~~~~~~~~~RiI~~t~~~-l~~  524 (686)
T PRK15429        452 RGAFTGASAQ-RIGRFE--LAD---KSSLFLDEVGDMPLELQPKLLRVLQEQEFERLGSNKIIQTDVRLIAATNRD-LKK  524 (686)
T ss_pred             cccccccccc-hhhHHH--hcC---CCeEEEechhhCCHHHHHHHHHHHHhCCEEeCCCCCcccceEEEEEeCCCC-HHH
Confidence            2222221111 112222  111   23999999999999989988888754321        12467788877632 211


Q ss_pred             -----hhhHHhhhccCCCCeeEEeCCCC--HHHHHHHHHHHHhcc----CCC-CCCCHHHHHHHHHHHHHhhCCHHHHHH
Q psy200          346 -----RMLPRLQANVTLQPTLMNFAPYS--REQILEIISQKLKQT----DKF-NMFNASALQLLAGKVAAVSGDIRKAID  413 (490)
Q Consensus       346 -----~l~~~l~~R~~~~~~~i~~~pls--~~e~~~il~~~l~~~----~~~-~~~~~~~i~~i~~~i~~~~Gd~r~ai~  413 (490)
                           .+...+..|+..  ..|.++|+.  .+|+..++.+++.+.    +.. ..+++++++.+..  +.|.||+|++-+
T Consensus       525 ~~~~~~f~~~L~~~l~~--~~i~lPpLreR~~Di~~L~~~~l~~~~~~~~~~~~~~s~~al~~L~~--y~WPGNvrEL~~  600 (686)
T PRK15429        525 MVADREFRSDLYYRLNV--FPIHLPPLRERPEDIPLLVKAFTFKIARRMGRNIDSIPAETLRTLSN--MEWPGNVRELEN  600 (686)
T ss_pred             HHHcCcccHHHHhccCe--eEEeCCChhhhHhHHHHHHHHHHHHHHHHcCCCCCCcCHHHHHHHHh--CCCCCcHHHHHH
Confidence                 233446666543  468899987  467777777665543    222 2489999999987  899999999999


Q ss_pred             HHHHHHHHHH
Q psy200          414 ITNHLIDLTY  423 (490)
Q Consensus       414 ll~~a~~~a~  423 (490)
                      ++++++..+.
T Consensus       601 ~i~~a~~~~~  610 (686)
T PRK15429        601 VIERAVLLTR  610 (686)
T ss_pred             HHHHHHHhCC
Confidence            9999987654

>PRK07399 DNA polymerase III subunit delta'; Validated

Probab=99.42  E-value=2.6e-11  Score=119.29  Aligned_cols=203  Identities=14%  Similarity=0.252  Sum_probs=128.5

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCC--------------ceEEEEeccCC
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDA--------------FKTIYINCNSV  259 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~--------------~~~~~v~~~~~  259 (490)
                      ++++|++..++.|...+..   +.-++.+|++||.|+||+++|.++++.+.....              -.+.++.....
T Consensus         4 ~~iiGq~~~~~~L~~~i~~---~rl~ha~Lf~G~~G~Gk~~~A~~~a~~llc~~~c~~c~~~~~~~~~hPDl~~i~p~~~   80 (314)
T PRK07399          4 ANLIGQPLAIELLTAAIKQ---NRIAPAYLFAGPEGVGRKLAALCFIEGLLSQGSPSKNIRRRLEEGNHPDLLWVEPTYQ   80 (314)
T ss_pred             HHhCCHHHHHHHHHHHHHh---CCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCCcHhcccccCCCCCEEEEecccc
Confidence            5799999999999998864   345789999999999999999999998753220              01222221100


Q ss_pred             CCHHHHHHHHHHHhcC--C-CCCCcHHHHHHHHHHHHhc---CCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEE
Q psy200          260 RNAASVYETIVNELKL--K-PGGKSERHQLGAILKYFDT---KHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLV  333 (490)
Q Consensus       260 ~~~~~l~~~i~~~l~~--~-~~~~s~~~~~~~l~~~l~~---~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vi  333 (490)
                      .....+-.......+.  . ......+++++.. +.+..   .+...|+|||++|.|....++.|+.+++.+.  ..  +
T Consensus        81 ~~g~~~~~~~~~~~~~~~~~~~~I~id~ir~i~-~~l~~~p~~~~~kVvII~~ae~m~~~aaNaLLK~LEEPp--~~--~  155 (314)
T PRK07399         81 HQGKLITASEAEEAGLKRKAPPQIRLEQIREIK-RFLSRPPLEAPRKVVVIEDAETMNEAAANALLKTLEEPG--NG--T  155 (314)
T ss_pred             ccccccchhhhhhccccccccccCcHHHHHHHH-HHHccCcccCCceEEEEEchhhcCHHHHHHHHHHHhCCC--CC--e
Confidence            0000000000011110  0 0112234444332 22221   2456799999999999888899999888653  23  3


Q ss_pred             EEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHH
Q psy200          334 LVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAID  413 (490)
Q Consensus       334 lI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~  413 (490)
                      +|.+++   -.+++++.+++||.    .+.|.+++.+++.++|.......    ..+ .....++.   ...|+++.+++
T Consensus       156 fILi~~---~~~~Ll~TI~SRcq----~i~f~~l~~~~~~~~L~~~~~~~----~~~-~~~~~l~~---~a~Gs~~~al~  220 (314)
T PRK07399        156 LILIAP---SPESLLPTIVSRCQ----IIPFYRLSDEQLEQVLKRLGDEE----ILN-INFPELLA---LAQGSPGAAIA  220 (314)
T ss_pred             EEEEEC---ChHhCcHHHHhhce----EEecCCCCHHHHHHHHHHhhccc----cch-hHHHHHHH---HcCCCHHHHHH
Confidence            444454   25788999999995    89999999999999999864322    111 11344443   67899999998


Q ss_pred             HHHHHH
Q psy200          414 ITNHLI  419 (490)
Q Consensus       414 ll~~a~  419 (490)
                      +++...
T Consensus       221 ~l~~~~  226 (314)
T PRK07399        221 NIEQLQ  226 (314)
T ss_pred             HHHHHH
Confidence            776543

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

Probab=99.41  E-value=3e-12  Score=127.72  Aligned_cols=182  Identities=20%  Similarity=0.266  Sum_probs=120.3

Q ss_pred             CCCChHHHHHHHHHHHHhhhccCCCC-eEEEECCCCCcHHHHHHHHHHHhhhcC--------------------CceEEE
Q psy200          195 ELPGREVQLEGIRQFLLGHVNNETSG-SMYISGPPGTGKSASLNLLVSRAEIKD--------------------AFKTIY  253 (490)
Q Consensus       195 ~lvgre~~~~~l~~~L~~~~~~~~~~-~ill~GppGtGKTtla~~l~~~l~~~~--------------------~~~~~~  253 (490)
                      ++++.+..+.++..++..+   +... .++|+||+|+|||++|.++++.+....                    ...+++
T Consensus         2 ~~~~~~~~~~~l~~~~~~~---~~~~halL~~Gp~G~Gktt~a~~lA~~l~~~~~~~~~~~~~~~~~~~~~~~~~~d~le   78 (325)
T COG0470           2 ELVPWQEAVKRLLVQALES---GRLPHALLFYGPPGVGKTTAALALAKELLCENPTGLLPCGHCRSCKLIPAGNHPDFLE   78 (325)
T ss_pred             CcccchhHHHHHHHHHHhc---CCCCceeeeeCCCCCCHHHHHHHHHHHHhCCCcccCCcccchhhhhHHhhcCCCceEE
Confidence            5788888888888888742   3344 499999999999999999999986322                    124555


Q ss_pred             EeccCCCCHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHhc--CCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCc
Q psy200          254 INCNSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFDT--KHKSILLILDEIDALESRKQTILYTIFEWPSIPGSK  331 (490)
Q Consensus       254 v~~~~~~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~--~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~  331 (490)
                      ++.+......                ...+.+.+........  .++..||||||+|.|....++++...++.   +..+
T Consensus        79 l~~s~~~~~~----------------i~~~~vr~~~~~~~~~~~~~~~kviiidead~mt~~A~nallk~lEe---p~~~  139 (325)
T COG0470          79 LNPSDLRKID----------------IIVEQVRELAEFLSESPLEGGYKVVIIDEADKLTEDAANALLKTLEE---PPKN  139 (325)
T ss_pred             ecccccCCCc----------------chHHHHHHHHHHhccCCCCCCceEEEeCcHHHHhHHHHHHHHHHhcc---CCCC
Confidence            5544432210                1122232222222222  25677999999999999888888888774   3456


Q ss_pred             EEEEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHH
Q psy200          332 LVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKA  411 (490)
Q Consensus       332 vilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~a  411 (490)
                      ..+|.++|   ....+.+.+++||.    .+.|.|++.........             ++.+..+..   ...||+|.+
T Consensus       140 ~~~il~~n---~~~~il~tI~SRc~----~i~f~~~~~~~~i~~~e-------------~~~l~~i~~---~~~gd~r~~  196 (325)
T COG0470         140 TRFILITN---DPSKILPTIRSRCQ----RIRFKPPSRLEAIAWLE-------------DQGLEEIAA---VAEGDARKA  196 (325)
T ss_pred             eEEEEEcC---Chhhccchhhhcce----eeecCCchHHHHHHHhh-------------ccchhHHHH---HHHHHHHcC
Confidence            66666677   46778889999996    89999943332222211             344455544   577888888


Q ss_pred             HHHHHHHHHH
Q psy200          412 IDITNHLIDL  421 (490)
Q Consensus       412 i~ll~~a~~~  421 (490)
                      ++.++.+...
T Consensus       197 i~~lq~~~~~  206 (325)
T COG0470         197 INPLQALAAL  206 (325)
T ss_pred             CCHHHHHHHh
Confidence            8877665443

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=99.41  E-value=4.1e-12  Score=140.44  Aligned_cols=215  Identities=18%  Similarity=0.251  Sum_probs=142.7

Q ss_pred             CCCCChHHHHHHHHHHHHhhhcc----C-CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVNN----E-TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYET  268 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~----~-~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~  268 (490)
                      ..++|++..++.+.+.+.....+    . +.+.++++||+|+|||.+|+++++.+.. ..-.++.++++.+....... .
T Consensus       566 ~~v~GQ~~Av~~v~~~i~~~~~gl~~~~~p~~~~lf~Gp~GvGKT~lA~~La~~l~~-~~~~~~~~dmse~~~~~~~~-~  643 (852)
T TIGR03345       566 ERVIGQDHALEAIAERIRTARAGLEDPRKPLGVFLLVGPSGVGKTETALALAELLYG-GEQNLITINMSEFQEAHTVS-R  643 (852)
T ss_pred             CeEcChHHHHHHHHHHHHHHhcCCCCCCCCceEEEEECCCCCCHHHHHHHHHHHHhC-CCcceEEEeHHHhhhhhhhc-c
Confidence            88999999999999998764221    1 2245899999999999999999998842 22356777766653322111 1


Q ss_pred             HHHHhcCC--CCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCHHHHHHhHhCCCCC--------CCcEEEEEec
Q psy200          269 IVNELKLK--PGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPSIP--------GSKLVLVGVA  338 (490)
Q Consensus       269 i~~~l~~~--~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~--------~~~vilI~~t  338 (490)
                      +   ++.+  +.|...   ...|.+++.. ....||+||||+.+....++.|+++++.....        -.+.++|+++
T Consensus       644 l---~g~~~gyvg~~~---~g~L~~~v~~-~p~svvllDEieka~~~v~~~Llq~ld~g~l~d~~Gr~vd~~n~iiI~TS  716 (852)
T TIGR03345       644 L---KGSPPGYVGYGE---GGVLTEAVRR-KPYSVVLLDEVEKAHPDVLELFYQVFDKGVMEDGEGREIDFKNTVILLTS  716 (852)
T ss_pred             c---cCCCCCcccccc---cchHHHHHHh-CCCcEEEEechhhcCHHHHHHHHHHhhcceeecCCCcEEeccccEEEEeC
Confidence            1   1211  112111   1123344443 45679999999998887788888888754311        1467888888


Q ss_pred             CCC---------C-----------------hhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhcc--------C
Q psy200          339 NAL---------D-----------------LTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQT--------D  384 (490)
Q Consensus       339 n~~---------~-----------------~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~--------~  384 (490)
                      |.-         +                 +...+.+.|.+|+.    .+.|.|++.+++.+|+...+...        +
T Consensus       717 Nlg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~PEflnRi~----iI~F~pLs~e~l~~Iv~~~L~~l~~rl~~~~g  792 (852)
T TIGR03345       717 NAGSDLIMALCADPETAPDPEALLEALRPELLKVFKPAFLGRMT----VIPYLPLDDDVLAAIVRLKLDRIARRLKENHG  792 (852)
T ss_pred             CCchHHHHHhccCcccCcchHHHHHHHHHHHHHhccHHHhccee----EEEeCCCCHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            821         0                 00113466777774    79999999999999988766542        3


Q ss_pred             CCCCCCHHHHHHHHHHHHHhhCCHHHHHHHHHHHHHH
Q psy200          385 KFNMFNASALQLLAGKVAAVSGDIRKAIDITNHLIDL  421 (490)
Q Consensus       385 ~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll~~a~~~  421 (490)
                      ....+++++++.|++..+....|.|.+.++++.-+..
T Consensus       793 i~l~i~d~a~~~La~~g~~~~~GAR~L~r~Ie~~i~~  829 (852)
T TIGR03345       793 AELVYSEALVEHIVARCTEVESGARNIDAILNQTLLP  829 (852)
T ss_pred             ceEEECHHHHHHHHHHcCCCCCChHHHHHHHHHHHHH
Confidence            3456899999999984333334788888877775543

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.

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=99.41  E-value=7.3e-12  Score=139.42  Aligned_cols=218  Identities=17%  Similarity=0.209  Sum_probs=146.3

Q ss_pred             CCCCChHHHHHHHHHHHHhhhcc-----CCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVNN-----ETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYET  268 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~-----~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~  268 (490)
                      ..++|++..++.|...+.....+     .+...++|+||+|||||++|+++++.+.. ....+++++|+.+..... ...
T Consensus       565 ~~v~GQ~~av~~v~~~i~~~~~gl~~~~~p~~~~Lf~Gp~GvGKt~lA~~La~~l~~-~~~~~i~~d~s~~~~~~~-~~~  642 (852)
T TIGR03346       565 ERVVGQDEAVEAVSDAIRRSRAGLSDPNRPIGSFLFLGPTGVGKTELAKALAEFLFD-DEDAMVRIDMSEYMEKHS-VAR  642 (852)
T ss_pred             cccCCChHHHHHHHHHHHHHhccCCCCCCCCeEEEEEcCCCCCHHHHHHHHHHHhcC-CCCcEEEEechhhcccch-HHH
Confidence            78999999999999999864321     13457889999999999999999988742 334778888887643222 122


Q ss_pred             HHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCHHHHHHhHhCCCC--------CCCcEEEEEecCC
Q psy200          269 IVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPSI--------PGSKLVLVGVANA  340 (490)
Q Consensus       269 i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~--------~~~~vilI~~tn~  340 (490)
                      ++   +.+.......+ ...|.+.+.. ....|||||||+.+....++.|+++++....        .-.+.+||+++|.
T Consensus       643 l~---g~~~g~~g~~~-~g~l~~~v~~-~p~~vlllDeieka~~~v~~~Ll~~l~~g~l~d~~g~~vd~rn~iiI~TSn~  717 (852)
T TIGR03346       643 LI---GAPPGYVGYEE-GGQLTEAVRR-KPYSVVLFDEVEKAHPDVFNVLLQVLDDGRLTDGQGRTVDFRNTVIIMTSNL  717 (852)
T ss_pred             hc---CCCCCccCccc-ccHHHHHHHc-CCCcEEEEeccccCCHHHHHHHHHHHhcCceecCCCeEEecCCcEEEEeCCc
Confidence            21   11111011111 1223333333 3346999999999998888999998865421        1245678888884


Q ss_pred             C-----C-----------------hhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhcc-------CCCCCCCH
Q psy200          341 L-----D-----------------LTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQT-------DKFNMFNA  391 (490)
Q Consensus       341 ~-----~-----------------~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~-------~~~~~~~~  391 (490)
                      -     +                 +...+.+.|..|+.   .++.|.|++.+++.+|+...+...       +....+++
T Consensus       718 g~~~~~~~~~~~~~~~~~~~~~~~~~~~F~pel~~Rid---~IivF~PL~~e~l~~I~~l~L~~l~~~l~~~~~~l~i~~  794 (852)
T TIGR03346       718 GSQFIQELAGGDDYEEMREAVMEVLRAHFRPEFLNRID---EIVVFHPLGREQIARIVEIQLGRLRKRLAERKITLELSD  794 (852)
T ss_pred             chHhHhhhcccccHHHHHHHHHHHHHhhcCHHHhcCcC---eEEecCCcCHHHHHHHHHHHHHHHHHHHHHCCCeecCCH
Confidence            1     1                 01112356667776   589999999999998877665432       23467899


Q ss_pred             HHHHHHHHHHHHhhCCHHHHHHHHHHHHHH
Q psy200          392 SALQLLAGKVAAVSGDIRKAIDITNHLIDL  421 (490)
Q Consensus       392 ~~i~~i~~~i~~~~Gd~r~ai~ll~~a~~~  421 (490)
                      ++++.|++.-+...+++|.+-+++++.+..
T Consensus       795 ~a~~~L~~~~~~~~~gaR~L~~~i~~~i~~  824 (852)
T TIGR03346       795 AALDFLAEAGYDPVYGARPLKRAIQREIEN  824 (852)
T ss_pred             HHHHHHHHhCCCCCCCchhHHHHHHHHHHH
Confidence            999999984434478999888887777644

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.

>CHL00081 chlI Mg-protoporyphyrin IX chelatase

Probab=99.41  E-value=2.2e-11  Score=120.43  Aligned_cols=244  Identities=18%  Similarity=0.189  Sum_probs=158.8

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHh
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNEL  273 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l  273 (490)
                      ..++|+++.+..|...+.    ....++++|.|++|||||++++.+++.+....-...-.++|... ++..+...+....
T Consensus        17 ~~ivGq~~~k~al~~~~~----~p~~~~vli~G~~GtGKs~~ar~~~~~l~~~~~~~~~pf~~~p~-~p~~~~~~~~~~~   91 (350)
T CHL00081         17 TAIVGQEEMKLALILNVI----DPKIGGVMIMGDRGTGKSTTIRALVDLLPEIEVVKDDPFNSHPS-DPELMSDEVREAI   91 (350)
T ss_pred             HHHhChHHHHHHHHHhcc----CCCCCeEEEEcCCCCCHHHHHHHHHHHHhhcCccCCCCCCCCCC-Chhhhchhhhhhh
Confidence            678999988877766654    35567899999999999999999988775221110001122222 2222222222111


Q ss_pred             c-----------CC----CCCCcHHHHHHH--HHHHHhcC-----------CCeEEEEEecCccccccCHHHHHHhHhCC
Q psy200          274 K-----------LK----PGGKSERHQLGA--ILKYFDTK-----------HKSILLILDEIDALESRKQTILYTIFEWP  325 (490)
Q Consensus       274 ~-----------~~----~~~~s~~~~~~~--l~~~l~~~-----------~~~~vI~IDEid~l~~~~~~~L~~l~~~~  325 (490)
                      .           .+    ..+.+.+.++.-  +...+..+           ...-+|+|||++.+....|..|...++..
T Consensus        92 ~~~~~~~~~~~~~~~~~lp~~~ted~l~G~iD~~~al~~g~~~~~~GlL~~A~~GiL~lDEInrL~~~~Q~~LLeam~e~  171 (350)
T CHL00081         92 QNGETIETEKIKIPMVDLPLGATEDRVCGTIDIEKALTEGVKAFEPGLLAKANRGILYVDEVNLLDDHLVDILLDSAASG  171 (350)
T ss_pred             cccccccceeccccceecCCCCchhhccCcccHHHHhhcCcccccCCeeeecCCCEEEecChHhCCHHHHHHHHHHHHhC
Confidence            0           00    112233332221  11111110           11239999999999999999988887542


Q ss_pred             C----------CCCCcEEEEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCC-HHHHHHHHHHHHhcc-----------
Q psy200          326 S----------IPGSKLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYS-REQILEIISQKLKQT-----------  383 (490)
Q Consensus       326 ~----------~~~~~vilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls-~~e~~~il~~~l~~~-----------  383 (490)
                      .          ....++++|++.|..+  ..+.+.+..||.+   .+.+..++ .++..+++.+.....           
T Consensus       172 ~~~ier~G~s~~~p~rfiviaT~np~e--g~l~~~LldRf~l---~i~l~~~~~~~~e~~il~~~~~~~~~~~~~~~~~~  246 (350)
T CHL00081        172 WNTVEREGISIRHPARFVLVGSGNPEE--GELRPQLLDRFGM---HAEIRTVKDPELRVKIVEQRTSFDKNPQEFREKYE  246 (350)
T ss_pred             CeEEeeCCeeeecCCCEEEEeccCccc--CCCCHHHHHHhCc---eeecCCCCChHHHHHHHHhhhccccChhhhhhhhc
Confidence            1          1246788888888542  2466788889986   68888887 477777776643210           


Q ss_pred             ----------------CCCCCCCHHHHHHHHHHHHHhhC-CHHHHHHHHHHHHHHHHhccccCCcccccCHHHHHHHHHH
Q psy200          384 ----------------DKFNMFNASALQLLAGKVAAVSG-DIRKAIDITNHLIDLTYDNVKENGEVTGIGLKEVLGVISS  446 (490)
Q Consensus       384 ----------------~~~~~~~~~~i~~i~~~i~~~~G-d~r~ai~ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~~~  446 (490)
                                      -....+++..++.|++.+....- +.|..|.+++-|..+|..+|     ...|+.+||..++.-
T Consensus       247 ~~~~~~~~~I~~ar~~~~~V~v~~~~~~yi~~l~~~~~~~s~Ra~i~l~raArA~Aal~G-----R~~V~pdDv~~~a~~  321 (350)
T CHL00081        247 ESQEELRSKIVAAQNLLPKVEIDYDLRVKISQICSELDVDGLRGDIVTNRAAKALAAFEG-----RTEVTPKDIFKVITL  321 (350)
T ss_pred             cccccCHHHHHHHHHhcCCCccCHHHHHHHHHHHHHHCCCCChHHHHHHHHHHHHHHHcC-----CCCCCHHHHHHHHHH
Confidence                            13456888899988886655442 68888999999999999999     789999999999999


Q ss_pred             hccCcc
Q psy200          447 VYCTSQ  452 (490)
Q Consensus       447 ~~~~~~  452 (490)
                      ++.++.
T Consensus       322 vL~HR~  327 (350)
T CHL00081        322 CLRHRL  327 (350)
T ss_pred             HHHHhC
Confidence            887776

>COG3604 FhlA Transcriptional regulator containing GAF, AAA-type ATPase, and DNA binding domains [Transcription / Signal transduction mechanisms]

Probab=99.41  E-value=1.4e-12  Score=130.11  Aligned_cols=214  Identities=17%  Similarity=0.229  Sum_probs=143.8

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHh
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNEL  273 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l  273 (490)
                      ..++|+...+.++.+.+.-  -....-.|||.|+.||||-.+|++|.+ +....+-+++++||..+.. .-+-++++..-
T Consensus       223 ~~iIG~S~am~~ll~~i~~--VA~Sd~tVLi~GETGtGKElvAraIH~-~S~R~~kPfV~~NCAAlPe-sLlESELFGHe  298 (550)
T COG3604         223 GGIIGRSPAMRQLLKEIEV--VAKSDSTVLIRGETGTGKELVARAIHQ-LSPRRDKPFVKLNCAALPE-SLLESELFGHE  298 (550)
T ss_pred             ccceecCHHHHHHHHHHHH--HhcCCCeEEEecCCCccHHHHHHHHHh-hCcccCCCceeeeccccch-HHHHHHHhccc
Confidence            6899999999999998875  345678999999999999999999955 4444555899999999742 11223333333


Q ss_pred             cCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCHHHHHHhHhCCCC--------CCCcEEEEEecCCCChhH
Q psy200          274 KLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPSI--------PGSKLVLVGVANALDLTD  345 (490)
Q Consensus       274 ~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~--------~~~~vilI~~tn~~~~~~  345 (490)
                      .+.+.|.... -...|+  +..+|   .||+|||..|.-.-|..|...++....        -...|.+|++||+. +..
T Consensus       299 KGAFTGA~~~-r~GrFE--lAdGG---TLFLDEIGelPL~lQaKLLRvLQegEieRvG~~r~ikVDVRiIAATNRD-L~~  371 (550)
T COG3604         299 KGAFTGAINT-RRGRFE--LADGG---TLFLDEIGELPLALQAKLLRVLQEGEIERVGGDRTIKVDVRVIAATNRD-LEE  371 (550)
T ss_pred             ccccccchhc-cCccee--ecCCC---eEechhhccCCHHHHHHHHHHHhhcceeecCCCceeEEEEEEEeccchh-HHH
Confidence            3333222110 001111  11122   899999999998888877777654422        24567899999943 222


Q ss_pred             -----hhhHHhhhccCCCCeeEEeCCCC--HHHHHHHHHHHHh----ccCC-CCCCCHHHHHHHHHHHHHhhCCHHHHHH
Q psy200          346 -----RMLPRLQANVTLQPTLMNFAPYS--REQILEIISQKLK----QTDK-FNMFNASALQLLAGKVAAVSGDIRKAID  413 (490)
Q Consensus       346 -----~l~~~l~~R~~~~~~~i~~~pls--~~e~~~il~~~l~----~~~~-~~~~~~~~i~~i~~~i~~~~Gd~r~ai~  413 (490)
                           ++-..++.|+..  ..|.++|+-  .+++--+..+++.    +.+. ...+++++++.+.+  +.|.||+|.+.+
T Consensus       372 ~V~~G~FRaDLYyRLsV--~Pl~lPPLRER~~DIplLA~~Fle~~~~~~gr~~l~ls~~Al~~L~~--y~wPGNVRELen  447 (550)
T COG3604         372 MVRDGEFRADLYYRLSV--FPLELPPLRERPEDIPLLAGYFLEKFRRRLGRAILSLSAEALELLSS--YEWPGNVRELEN  447 (550)
T ss_pred             HHHcCcchhhhhhcccc--cccCCCCcccCCccHHHHHHHHHHHHHHhcCCcccccCHHHHHHHHc--CCCCCcHHHHHH
Confidence                 233456667664  256677775  3344433333332    2243 57799999999998  889999999999


Q ss_pred             HHHHHHHHH
Q psy200          414 ITNHLIDLT  422 (490)
Q Consensus       414 ll~~a~~~a  422 (490)
                      ++++|+.+|
T Consensus       448 ~veRavlla  456 (550)
T COG3604         448 VVERAVLLA  456 (550)
T ss_pred             HHHHHHHHh
Confidence            999999988

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

Probab=99.41  E-value=9.5e-12  Score=125.65  Aligned_cols=215  Identities=17%  Similarity=0.240  Sum_probs=133.6

Q ss_pred             HhhcCCCCCCChHHHHHHHHHHHHhhhcc------C--------CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEE
Q psy200          188 EKAKDSCELPGREVQLEGIRQFLLGHVNN------E--------TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIY  253 (490)
Q Consensus       188 ~~~l~~~~lvgre~~~~~l~~~L~~~~~~------~--------~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~  253 (490)
                      ...|. +.++|+++.++.|...+.+....      .        ...+++|+||+|+|||++|+.++..+.    .+++.
T Consensus        72 ~~~L~-~~ViGQe~A~~~l~~av~~h~~~~~~~~~~~~~~~~~~~~~~iLL~GP~GsGKT~lAraLA~~l~----~pf~~  146 (413)
T TIGR00382        72 KAHLD-EYVIGQEQAKKVLSVAVYNHYKRLNFEKNKKSDNGVELSKSNILLIGPTGSGKTLLAQTLARILN----VPFAI  146 (413)
T ss_pred             HHHhc-ceecCHHHHHHHHHHHHHHHHhhhccccccccccccccCCceEEEECCCCcCHHHHHHHHHHhcC----CCeEE
Confidence            33444 78999999999998777432211      1        136899999999999999999998874    55666


Q ss_pred             EeccCCCCHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHH----HhcCCCeEEEEEecCccccc--------------cCH
Q psy200          254 INCNSVRNAASVYETIVNELKLKPGGKSERHQLGAILKY----FDTKHKSILLILDEIDALES--------------RKQ  315 (490)
Q Consensus       254 v~~~~~~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~----l~~~~~~~vI~IDEid~l~~--------------~~~  315 (490)
                      +++..+..             ..+.|.........+...    +.. ..+.+|||||+|.+..              .-|
T Consensus       147 ~da~~L~~-------------~gyvG~d~e~~L~~~~~~~~~~l~~-a~~gIV~lDEIdkl~~~~~~~s~~~dvsg~~vq  212 (413)
T TIGR00382       147 ADATTLTE-------------AGYVGEDVENILLKLLQAADYDVEK-AQKGIIYIDEIDKISRKSENPSITRDVSGEGVQ  212 (413)
T ss_pred             echhhccc-------------cccccccHHHHHHHHHHhCcccHHh-cccceEEecccchhchhhccccccccccchhHH
Confidence            66654311             012333332222221111    111 2345999999999975              236


Q ss_pred             HHHHHhHhCCC----------CCCCcEEEEEecCCC-----------------------C--------------hh----
Q psy200          316 TILYTIFEWPS----------IPGSKLVLVGVANAL-----------------------D--------------LT----  344 (490)
Q Consensus       316 ~~L~~l~~~~~----------~~~~~vilI~~tn~~-----------------------~--------------~~----  344 (490)
                      ..|+++++-..          .....+++|.++|-.                       .              +.    
T Consensus       213 ~~LL~iLeG~~~~v~~~~gr~~~~~~~i~i~TsNilfi~~Gaf~g~~~i~~~r~~~~~~gf~~~~~~~~~~~~~~~~~~~  292 (413)
T TIGR00382       213 QALLKIIEGTVANVPPQGGRKHPYQEFIQIDTSNILFICGGAFVGLEKIIKKRTGKSSIGFGAEVKKKSKEKADLLRQVE  292 (413)
T ss_pred             HHHHHHhhccceecccCCCccccCCCeEEEEcCCceeeecccccChHHHHHHHhhhccccccccccccchhhHHHHHHHH
Confidence            67777764111          112345566555530                       0              00    


Q ss_pred             -----H-hhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHH----Hh-------ccCCCCCCCHHHHHHHHHHHHHhhCC
Q psy200          345 -----D-RMLPRLQANVTLQPTLMNFAPYSREQILEIISQK----LK-------QTDKFNMFNASALQLLAGKVAAVSGD  407 (490)
Q Consensus       345 -----~-~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~----l~-------~~~~~~~~~~~~i~~i~~~i~~~~Gd  407 (490)
                           . .+.|.|..|+.   .++.|.|++.+++.+|+...    +.       ..+....+++++++.|++..+...-+
T Consensus       293 ~~dl~~~g~~PEflgRld---~Iv~f~pL~~~~L~~Il~~~~n~l~kq~~~~l~~~gi~L~~t~~a~~~Ia~~~~~~~~G  369 (413)
T TIGR00382       293 PEDLVKFGLIPEFIGRLP---VIATLEKLDEEALIAILTKPKNALVKQYQALFKMDNVELDFEEEALKAIAKKALERKTG  369 (413)
T ss_pred             HHHHHHHhhHHHHhCCCC---eEeecCCCCHHHHHHHHHHHHHHHHHHHHHHhccCCeEEEECHHHHHHHHHhCCCCCCC
Confidence                 0 13466667776   47899999999999998653    22       12455678999999999865555566


Q ss_pred             HHHHHHHHHHHHHHHHh
Q psy200          408 IRKAIDITNHLIDLTYD  424 (490)
Q Consensus       408 ~r~ai~ll~~a~~~a~~  424 (490)
                      .|.+-.++++.+.-...
T Consensus       370 AR~Lr~iie~~l~~~m~  386 (413)
T TIGR00382       370 ARGLRSIVEGLLLDVMF  386 (413)
T ss_pred             chHHHHHHHHhhHHHHh
Confidence            77776677776654443

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.

>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional

Probab=99.40  E-value=1.3e-12  Score=141.81  Aligned_cols=225  Identities=17%  Similarity=0.202  Sum_probs=152.9

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHh
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNEL  273 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l  273 (490)
                      +.++|....+.++.+.+....  .....|+|+|++||||+++|+++++... ..+-+|+.+||..+.. ..+..+++...
T Consensus       325 ~~l~g~s~~~~~~~~~~~~~a--~~~~pvli~Ge~GtGK~~~A~~ih~~s~-r~~~pfv~vnc~~~~~-~~~~~elfg~~  400 (638)
T PRK11388        325 DHMPQDSPQMRRLIHFGRQAA--KSSFPVLLCGEEGVGKALLAQAIHNESE-RAAGPYIAVNCQLYPD-EALAEEFLGSD  400 (638)
T ss_pred             cceEECCHHHHHHHHHHHHHh--CcCCCEEEECCCCcCHHHHHHHHHHhCC-ccCCCeEEEECCCCCh-HHHHHHhcCCC
Confidence            679999999999888888753  4566799999999999999999977642 2345889999998843 33333333222


Q ss_pred             cCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCHHHHHHhHhCCCCC--------CCcEEEEEecCCCChhH
Q psy200          274 KLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPSIP--------GSKLVLVGVANALDLTD  345 (490)
Q Consensus       274 ~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~--------~~~vilI~~tn~~~~~~  345 (490)
                      .    +.........|..  .   ..-+||||||+.|....|..|..+++.....        ...+.+|++++.. +..
T Consensus       401 ~----~~~~~~~~g~~~~--a---~~GtL~ldei~~l~~~~Q~~Ll~~l~~~~~~~~~~~~~~~~~~riI~~t~~~-l~~  470 (638)
T PRK11388        401 R----TDSENGRLSKFEL--A---HGGTLFLEKVEYLSPELQSALLQVLKTGVITRLDSRRLIPVDVRVIATTTAD-LAM  470 (638)
T ss_pred             C----cCccCCCCCceeE--C---CCCEEEEcChhhCCHHHHHHHHHHHhcCcEEeCCCCceEEeeEEEEEeccCC-HHH
Confidence            1    1100000001111  1   1238999999999999999998888644211        1256788887632 211


Q ss_pred             -----hhhHHhhhccCCCCeeEEeCCCCH--HHHHHHHHHHHhcc----CCCCCCCHHHHHHHHHHHHHhhCCHHHHHHH
Q psy200          346 -----RMLPRLQANVTLQPTLMNFAPYSR--EQILEIISQKLKQT----DKFNMFNASALQLLAGKVAAVSGDIRKAIDI  414 (490)
Q Consensus       346 -----~l~~~l~~R~~~~~~~i~~~pls~--~e~~~il~~~l~~~----~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~l  414 (490)
                           .+.+.+..|+..  ..|.++|+..  +|+..++.+++...    +....+++++++.+.+  +.|.||+|++.++
T Consensus       471 ~~~~~~f~~dL~~~l~~--~~i~lPpLreR~~Di~~L~~~~l~~~~~~~~~~~~~s~~a~~~L~~--y~WPGNvreL~~~  546 (638)
T PRK11388        471 LVEQNRFSRQLYYALHA--FEITIPPLRMRREDIPALVNNKLRSLEKRFSTRLKIDDDALARLVS--YRWPGNDFELRSV  546 (638)
T ss_pred             HHhcCCChHHHhhhhce--eEEeCCChhhhhhHHHHHHHHHHHHHHHHhCCCCCcCHHHHHHHHc--CCCCChHHHHHHH
Confidence                 233456666543  4788999974  57777777766543    2234689999999998  8899999999999


Q ss_pred             HHHHHHHHHhccccCCcccccCHHHHHHHH
Q psy200          415 TNHLIDLTYDNVKENGEVTGIGLKEVLGVI  444 (490)
Q Consensus       415 l~~a~~~a~~~~~~~~~~~~It~~~v~~a~  444 (490)
                      +++++..+.  +      ..|+.+++...+
T Consensus       547 l~~~~~~~~--~------~~i~~~~lp~~~  568 (638)
T PRK11388        547 IENLALSSD--N------GRIRLSDLPEHL  568 (638)
T ss_pred             HHHHHHhCC--C------CeecHHHCchhh
Confidence            999886542  2      358888876555

>PRK05564 DNA polymerase III subunit delta'; Validated

Probab=99.39  E-value=2.7e-11  Score=120.12  Aligned_cols=180  Identities=15%  Similarity=0.144  Sum_probs=121.5

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcC----CceEEEEeccCCCCHHHHHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKD----AFKTIYINCNSVRNAASVYETI  269 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~----~~~~~~v~~~~~~~~~~l~~~i  269 (490)
                      ++++|++..++.+..++..   +.-++.++++||.|+|||++|+.+++.+.+..    ...+..+....           
T Consensus         4 ~~i~g~~~~~~~l~~~~~~---~~~~ha~Lf~G~~G~Gk~~la~~~a~~l~c~~~~~~h~D~~~~~~~~-----------   69 (313)
T PRK05564          4 HTIIGHENIKNRIKNSIIK---NRFSHAHIIVGEDGIGKSLLAKEIALKILGKSQQREYVDIIEFKPIN-----------   69 (313)
T ss_pred             hhccCcHHHHHHHHHHHHc---CCCCceEEeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCeEEecccc-----------
Confidence            6789999999999888863   34556778999999999999999999874221    11222332110           


Q ss_pred             HHHhcCCCCCCcHHHHHHHHHHHHhc--CCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEEEecCCCChhHhh
Q psy200          270 VNELKLKPGGKSERHQLGAILKYFDT--KHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVANALDLTDRM  347 (490)
Q Consensus       270 ~~~l~~~~~~~s~~~~~~~l~~~l~~--~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI~~tn~~~~~~~l  347 (490)
                             ....+.+++++.+......  .++..|+|||++|.|....++.|...++.+   ....++|.+++   -.+.+
T Consensus        70 -------~~~i~v~~ir~~~~~~~~~p~~~~~kv~iI~~ad~m~~~a~naLLK~LEep---p~~t~~il~~~---~~~~l  136 (313)
T PRK05564         70 -------KKSIGVDDIRNIIEEVNKKPYEGDKKVIIIYNSEKMTEQAQNAFLKTIEEP---PKGVFIILLCE---NLEQI  136 (313)
T ss_pred             -------CCCCCHHHHHHHHHHHhcCcccCCceEEEEechhhcCHHHHHHHHHHhcCC---CCCeEEEEEeC---ChHhC
Confidence                   1112345555544432211  245679999999999988888888887743   33444444443   24688


Q ss_pred             hHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHH
Q psy200          348 LPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAID  413 (490)
Q Consensus       348 ~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~  413 (490)
                      .+.+++||.    .+.|.+++.+++..++...+.      .++++.++.++.   ...|....++.
T Consensus       137 l~TI~SRc~----~~~~~~~~~~~~~~~l~~~~~------~~~~~~~~~l~~---~~~g~~~~a~~  189 (313)
T PRK05564        137 LDTIKSRCQ----IYKLNRLSKEEIEKFISYKYN------DIKEEEKKSAIA---FSDGIPGKVEK  189 (313)
T ss_pred             cHHHHhhce----eeeCCCcCHHHHHHHHHHHhc------CCCHHHHHHHHH---HcCCCHHHHHH
Confidence            899999995    899999999999998877543      246666666654   33444665554

>KOG0742|consensus

Probab=99.39  E-value=1.7e-11  Score=118.94  Aligned_cols=164  Identities=16%  Similarity=0.275  Sum_probs=104.5

Q ss_pred             CCCCChHHHHHHHHHHHHhhhc----cCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVN----NETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETI  269 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~----~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i  269 (490)
                      +.++-+-....+|..+.....+    ....++|++|||||||||+.++.++.+-+    ..+..+.+...          
T Consensus       355 ~~ViL~psLe~Rie~lA~aTaNTK~h~apfRNilfyGPPGTGKTm~ArelAr~SG----lDYA~mTGGDV----------  420 (630)
T KOG0742|consen  355 EGVILHPSLEKRIEDLAIATANTKKHQAPFRNILFYGPPGTGKTMFARELARHSG----LDYAIMTGGDV----------  420 (630)
T ss_pred             CCeecCHHHHHHHHHHHHHhcccccccchhhheeeeCCCCCCchHHHHHHHhhcC----CceehhcCCCc----------
Confidence            4556554444444444332211    22557999999999999999999998754    44444443332          


Q ss_pred             HHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccC---------HHHHHHhHhCCCCCCCcEEEEEecCC
Q psy200          270 VNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRK---------QTILYTIFEWPSIPGSKLVLVGVANA  340 (490)
Q Consensus       270 ~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~---------~~~L~~l~~~~~~~~~~vilI~~tn~  340 (490)
                            ...|...-.....+-+..++..+-++|||||+|.+....         ...|..++=........|+++.++|.
T Consensus       421 ------APlG~qaVTkiH~lFDWakkS~rGLllFIDEADAFLceRnktymSEaqRsaLNAlLfRTGdqSrdivLvlAtNr  494 (630)
T KOG0742|consen  421 ------APLGAQAVTKIHKLFDWAKKSRRGLLLFIDEADAFLCERNKTYMSEAQRSALNALLFRTGDQSRDIVLVLATNR  494 (630)
T ss_pred             ------cccchHHHHHHHHHHHHHhhcccceEEEehhhHHHHHHhchhhhcHHHHHHHHHHHHHhcccccceEEEeccCC
Confidence                  111111222223333444555778999999999986442         23444433222234557888888985


Q ss_pred             CChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhcc
Q psy200          341 LDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQT  383 (490)
Q Consensus       341 ~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~  383 (490)
                         +..++..+.+|+.   ..+.|+-+..+|..++|..++.++
T Consensus       495 ---pgdlDsAV~DRid---e~veFpLPGeEERfkll~lYlnky  531 (630)
T KOG0742|consen  495 ---PGDLDSAVNDRID---EVVEFPLPGEEERFKLLNLYLNKY  531 (630)
T ss_pred             ---ccchhHHHHhhhh---heeecCCCChHHHHHHHHHHHHHH
Confidence               3455667777877   689999999999999999888776

>KOG0744|consensus

Probab=99.38  E-value=1.1e-11  Score=117.02  Aligned_cols=171  Identities=19%  Similarity=0.306  Sum_probs=118.1

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccC----------CCCeEEEECCCCCcHHHHHHHHHHHhhhc--CC---ceEEEEeccC
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNE----------TSGSMYISGPPGTGKSASLNLLVSRAEIK--DA---FKTIYINCNS  258 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~----------~~~~ill~GppGtGKTtla~~l~~~l~~~--~~---~~~~~v~~~~  258 (490)
                      +.++.-.+.+++|..+....+.-.          -.+.++++||||||||+|++++++.+...  ..   -..+++||..
T Consensus       142 EsLiyds~lK~~ll~Ya~s~l~fsek~vntnlIt~NRliLlhGPPGTGKTSLCKaLaQkLSIR~~~~y~~~~liEinshs  221 (423)
T KOG0744|consen  142 ESLIYDSNLKERLLSYAASALLFSEKKVNTNLITWNRLILLHGPPGTGKTSLCKALAQKLSIRTNDRYYKGQLIEINSHS  221 (423)
T ss_pred             HHHhhcccHHHHHHHHHHHHHHHHhcCCCCceeeeeeEEEEeCCCCCChhHHHHHHHHhheeeecCccccceEEEEehhH
Confidence            345555566667777665443211          34689999999999999999999998632  11   2466776544


Q ss_pred             CCCHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCH---------------HH-HHHhH
Q psy200          259 VRNAASVYETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQ---------------TI-LYTIF  322 (490)
Q Consensus       259 ~~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~---------------~~-L~~l~  322 (490)
                            +++.++.+     .|.-...+++.+.+.++..+.-++++|||++.|...+.               ++ |.++-
T Consensus       222 ------LFSKWFsE-----SgKlV~kmF~kI~ELv~d~~~lVfvLIDEVESLa~aR~s~~S~~EpsDaIRvVNalLTQlD  290 (423)
T KOG0744|consen  222 ------LFSKWFSE-----SGKLVAKMFQKIQELVEDRGNLVFVLIDEVESLAAARTSASSRNEPSDAIRVVNALLTQLD  290 (423)
T ss_pred             ------HHHHHHhh-----hhhHHHHHHHHHHHHHhCCCcEEEEEeHHHHHHHHHHHhhhcCCCCchHHHHHHHHHHHHH
Confidence                  34433322     23346667778888887778899999999999964431               12 22222


Q ss_pred             hCCCCCCCcEEEEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhcc
Q psy200          323 EWPSIPGSKLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQT  383 (490)
Q Consensus       323 ~~~~~~~~~vilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~  383 (490)
                      .+  ....+|++++++|   +.+.++-++.+|.+.   ..++.|++...+.+|++..+...
T Consensus       291 rl--K~~~NvliL~TSN---l~~siD~AfVDRADi---~~yVG~Pt~~ai~~IlkscieEL  343 (423)
T KOG0744|consen  291 RL--KRYPNVLILATSN---LTDSIDVAFVDRADI---VFYVGPPTAEAIYEILKSCIEEL  343 (423)
T ss_pred             Hh--ccCCCEEEEeccc---hHHHHHHHhhhHhhh---eeecCCccHHHHHHHHHHHHHHH
Confidence            22  2356788888888   778888888899875   78899999999999998776554

>KOG0735|consensus

Probab=99.38  E-value=2.1e-11  Score=125.65  Aligned_cols=203  Identities=15%  Similarity=0.212  Sum_probs=139.0

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHhc--
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFDT--  295 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~--  295 (490)
                      ..++++|+|++|+|||.|++++++++..+..+.+.+++|+...                  +.+.+.+.+.+...+..  
T Consensus       430 ~~~~Ill~G~~GsGKT~L~kal~~~~~k~~~~hv~~v~Cs~l~------------------~~~~e~iQk~l~~vfse~~  491 (952)
T KOG0735|consen  430 RHGNILLNGPKGSGKTNLVKALFDYYSKDLIAHVEIVSCSTLD------------------GSSLEKIQKFLNNVFSEAL  491 (952)
T ss_pred             ccccEEEeCCCCCCHhHHHHHHHHHhccccceEEEEEechhcc------------------chhHHHHHHHHHHHHHHHH
Confidence            5679999999999999999999999986666688889998763                  23455555555555533  


Q ss_pred             CCCeEEEEEecCccccccC-----H---------HHHHHhHhCCCCCCCcEEEEEecCCCChhHhhhHHhhh--ccCCCC
Q psy200          296 KHKSILLILDEIDALESRK-----Q---------TILYTIFEWPSIPGSKLVLVGVANALDLTDRMLPRLQA--NVTLQP  359 (490)
Q Consensus       296 ~~~~~vI~IDEid~l~~~~-----~---------~~L~~l~~~~~~~~~~vilI~~tn~~~~~~~l~~~l~~--R~~~~~  359 (490)
                      ...|.||++|++|.|.+..     |         ..|++++......+..+.||++.+..   ..+.+.+.+  +|.   
T Consensus       492 ~~~PSiIvLDdld~l~~~s~~e~~q~~~~~~rla~flnqvi~~y~~~~~~ia~Iat~qe~---qtl~~~L~s~~~Fq---  565 (952)
T KOG0735|consen  492 WYAPSIIVLDDLDCLASASSNENGQDGVVSERLAAFLNQVIKIYLKRNRKIAVIATGQEL---QTLNPLLVSPLLFQ---  565 (952)
T ss_pred             hhCCcEEEEcchhhhhccCcccCCcchHHHHHHHHHHHHHHHHHHccCcEEEEEEechhh---hhcChhhcCccceE---
Confidence            2568999999999998731     1         23333333333355677888888743   222332222  344   


Q ss_pred             eeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCC-HHHHHHHHHHHHHHHHhccccCCcccccCHH
Q psy200          360 TLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGD-IRKAIDITNHLIDLTYDNVKENGEVTGIGLK  438 (490)
Q Consensus       360 ~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd-~r~ai~ll~~a~~~a~~~~~~~~~~~~It~~  438 (490)
                      ..+.++++...+..+||.+.+.+..  .....+.++.++.   .+.|- ++.+.-++++|+..|..+.-... ...++.+
T Consensus       566 ~~~~L~ap~~~~R~~IL~~~~s~~~--~~~~~~dLd~ls~---~TEGy~~~DL~ifVeRai~~a~leris~~-~klltke  639 (952)
T KOG0735|consen  566 IVIALPAPAVTRRKEILTTIFSKNL--SDITMDDLDFLSV---KTEGYLATDLVIFVERAIHEAFLERISNG-PKLLTKE  639 (952)
T ss_pred             EEEecCCcchhHHHHHHHHHHHhhh--hhhhhHHHHHHHH---hcCCccchhHHHHHHHHHHHHHHHHhccC-cccchHH
Confidence            5899999999999999999998762  3345666777765   44453 44444578888877773321111 2378899


Q ss_pred             HHHHHHHHhccC
Q psy200          439 EVLGVISSVYCT  450 (490)
Q Consensus       439 ~v~~a~~~~~~~  450 (490)
                      +|.+++.+..+.
T Consensus       640 ~f~ksL~~F~P~  651 (952)
T KOG0735|consen  640 LFEKSLKDFVPL  651 (952)
T ss_pred             HHHHHHHhcChH
Confidence            999999987653

>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=99.38  E-value=1.2e-11  Score=107.72  Aligned_cols=148  Identities=22%  Similarity=0.277  Sum_probs=91.5

Q ss_pred             CChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCC
Q psy200          197 PGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLK  276 (490)
Q Consensus       197 vgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~  276 (490)
                      +|++.++..+...+..    ...++++|+|++|+|||++++.+++.+. ..+..++++++............+...    
T Consensus         1 ~~~~~~~~~i~~~~~~----~~~~~v~i~G~~G~GKT~l~~~i~~~~~-~~~~~v~~~~~~~~~~~~~~~~~~~~~----   71 (151)
T cd00009           1 VGQEEAIEALREALEL----PPPKNLLLYGPPGTGKTTLARAIANELF-RPGAPFLYLNASDLLEGLVVAELFGHF----   71 (151)
T ss_pred             CchHHHHHHHHHHHhC----CCCCeEEEECCCCCCHHHHHHHHHHHhh-cCCCCeEEEehhhhhhhhHHHHHhhhh----
Confidence            3677777777777743    4577999999999999999999999874 234678888876653322211110000    


Q ss_pred             CCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCHHHHHHhHhCCCCC---CCcEEEEEecCCCChhHhhhHHhhh
Q psy200          277 PGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPSIP---GSKLVLVGVANALDLTDRMLPRLQA  353 (490)
Q Consensus       277 ~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~---~~~vilI~~tn~~~~~~~l~~~l~~  353 (490)
                               ............++.+|+|||++.+.......+..++......   ...+.+|++++.... ..+...+.+
T Consensus        72 ---------~~~~~~~~~~~~~~~~lilDe~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~ii~~~~~~~~-~~~~~~~~~  141 (151)
T cd00009          72 ---------LVRLLFELAEKAKPGVLFIDEIDSLSRGAQNALLRVLETLNDLRIDRENVRVIGATNRPLL-GDLDRALYD  141 (151)
T ss_pred             ---------hHhHHHHhhccCCCeEEEEeChhhhhHHHHHHHHHHHHhcCceeccCCCeEEEEecCcccc-CCcChhHHh
Confidence                     0111111222345779999999998554455555555543321   356777777774432 355667778


Q ss_pred             ccCCCCeeEEeCC
Q psy200          354 NVTLQPTLMNFAP  366 (490)
Q Consensus       354 R~~~~~~~i~~~p  366 (490)
                      ||.   ..+.+++
T Consensus       142 r~~---~~i~~~~  151 (151)
T cd00009         142 RLD---IRIVIPL  151 (151)
T ss_pred             hhc---cEeecCC
Confidence            875   2566553

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.

>TIGR02030 BchI-ChlI magnesium chelatase ATPase subunit I

Probab=99.38  E-value=2.6e-11  Score=119.91  Aligned_cols=244  Identities=17%  Similarity=0.183  Sum_probs=152.3

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCH--HHHHHHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNA--ASVYETIVN  271 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~--~~l~~~i~~  271 (490)
                      ..++|+++.+..|.-.+-    ....++++|.|++|+||||+++.++..+.......-...+|......  ..-+.....
T Consensus         4 ~~ivgq~~~~~al~~~~~----~~~~g~vli~G~~G~gKttl~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~   79 (337)
T TIGR02030         4 TAIVGQDEMKLALLLNVI----DPKIGGVMVMGDRGTGKSTAVRALAALLPEIKAVAGCPFNSSPSDPEMMCEEVRIRVD   79 (337)
T ss_pred             cccccHHHHHHHHHHHhc----CCCCCeEEEEcCCCCCHHHHHHHHHHhhcccccccCCCCCCCCCCccccChHHhhhhh
Confidence            468999998877655443    24567899999999999999999988763111000001111110000  000000000


Q ss_pred             ---H----------hcCCCCCCcHHHHHHH--HHHHHhc-----------CCCeEEEEEecCccccccCHHHHHHhHhCC
Q psy200          272 ---E----------LKLKPGGKSERHQLGA--ILKYFDT-----------KHKSILLILDEIDALESRKQTILYTIFEWP  325 (490)
Q Consensus       272 ---~----------l~~~~~~~s~~~~~~~--l~~~l~~-----------~~~~~vI~IDEid~l~~~~~~~L~~l~~~~  325 (490)
                         .          ...+ .+.+.+.+...  +...+..           ....-+|||||++.+....|..|...++..
T Consensus        80 ~~~~~~~~~~~~~~~~lP-~~~t~d~l~G~~d~~~~l~~g~~~~~~GlL~~A~~GvL~lDEi~~L~~~~Q~~Ll~~l~~g  158 (337)
T TIGR02030        80 SQEPLSIIKKPVPVVDLP-LGATEDRVCGTLDIERALTEGVKAFEPGLLARANRGILYIDEVNLLEDHLVDVLLDVAASG  158 (337)
T ss_pred             cccccccccCCCCcCCCC-CCCcccceecchhHhhHhhcCCEEeecCcceeccCCEEEecChHhCCHHHHHHHHHHHHhC
Confidence               0          0000 01111111111  1111100           011238999999999998899888887543


Q ss_pred             C----------CCCCcEEEEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCH-HHHHHHHHHHHhcc-----------
Q psy200          326 S----------IPGSKLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSR-EQILEIISQKLKQT-----------  383 (490)
Q Consensus       326 ~----------~~~~~vilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~-~e~~~il~~~l~~~-----------  383 (490)
                      .          ....++++|++.|..+  ..+.+.+.+||.+   .+.+.++.. ++..+++.......           
T Consensus       159 ~~~v~r~G~~~~~~~r~iviat~np~e--g~l~~~LldRf~l---~i~l~~p~~~eer~eIL~~~~~~~~~~~~~~~~~~  233 (337)
T TIGR02030       159 WNVVEREGISIRHPARFVLVGSGNPEE--GELRPQLLDRFGL---HAEIRTVRDVELRVEIVERRTEYDADPHAFCEKWQ  233 (337)
T ss_pred             CeEEEECCEEEEcCCCEEEEecccccc--CCCCHHHHhhcce---EEECCCCCCHHHHHHHHHhhhhcccCchhhhhhhh
Confidence            2          1246788888887542  2466788899985   677877765 67677776632210           


Q ss_pred             ----------------CCCCCCCHHHHHHHHHHHHHhhC-CHHHHHHHHHHHHHHHHhccccCCcccccCHHHHHHHHHH
Q psy200          384 ----------------DKFNMFNASALQLLAGKVAAVSG-DIRKAIDITNHLIDLTYDNVKENGEVTGIGLKEVLGVISS  446 (490)
Q Consensus       384 ----------------~~~~~~~~~~i~~i~~~i~~~~G-d~r~ai~ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~~~  446 (490)
                                      -....+++++++.+++.+..... +.|..+.+++-|...|..++     ...|+.+||..++.-
T Consensus       234 ~e~~~~~~~I~~a~~~~~~V~v~d~~~~~i~~l~~~~~~~s~Ra~i~l~raArA~Aal~G-----R~~V~~dDv~~~a~~  308 (337)
T TIGR02030       234 TEQEALQAKIVNAQNLLPQVTIPYDVLVKVAELCAELDVDGLRGELTLNRAAKALAAFEG-----RTEVTVDDIRRVAVL  308 (337)
T ss_pred             hhhhcCHHHHHHHHHHhccCcCCHHHHHHHHHHHHHHCCCCCcHHHHHHHHHHHHHHHcC-----CCCCCHHHHHHHHHH
Confidence                            13455788889998886666554 57999999999999999999     789999999999999


Q ss_pred             hccCcc
Q psy200          447 VYCTSQ  452 (490)
Q Consensus       447 ~~~~~~  452 (490)
                      ++..+.
T Consensus       309 vL~HR~  314 (337)
T TIGR02030       309 ALRHRL  314 (337)
T ss_pred             HHHHhC
Confidence            887766

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.

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

Probab=99.38  E-value=3.4e-12  Score=109.63  Aligned_cols=119  Identities=26%  Similarity=0.436  Sum_probs=87.1

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhc----CCceEEEEeccCCCCHHHHHHHHHHHhcCCCCC-CcHHHHHHHHHHH
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIK----DAFKTIYINCNSVRNAASVYETIVNELKLKPGG-KSERHQLGAILKY  292 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~----~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~~-~s~~~~~~~l~~~  292 (490)
                      ..+.++|+|++|+|||++++.+++.+...    .+..+++++|....+...++..|+..++..... .+..++.+.+.+.
T Consensus         3 ~~~~~~i~G~~G~GKT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~l~~~~~~~   82 (131)
T PF13401_consen    3 SQRILVISGPPGSGKTTLIKRLARQLNAEAEIKNHPDVIYVNCPSSRTPRDFAQEILEALGLPLKSRQTSDELRSLLIDA   82 (131)
T ss_dssp             ----EEEEE-TTSSHHHHHHHHHHHHHHHHHHCCCEEEEEEEHHHHSSHHHHHHHHHHHHT-SSSSTS-HHHHHHHHHHH
T ss_pred             CCcccEEEcCCCCCHHHHHHHHHHHhHHhhhccCCCcEEEEEeCCCCCHHHHHHHHHHHhCccccccCCHHHHHHHHHHH
Confidence            35789999999999999999999987521    157889999999889999999999999876654 5778888888888


Q ss_pred             HhcCCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEEEecC
Q psy200          293 FDTKHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVAN  339 (490)
Q Consensus       293 l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI~~tn  339 (490)
                      +...+ ..+|+|||+|.+.  ....+..+..+....+..++++|..+
T Consensus        83 l~~~~-~~~lviDe~~~l~--~~~~l~~l~~l~~~~~~~vvl~G~~~  126 (131)
T PF13401_consen   83 LDRRR-VVLLVIDEADHLF--SDEFLEFLRSLLNESNIKVVLVGTPE  126 (131)
T ss_dssp             HHHCT-EEEEEEETTHHHH--THHHHHHHHHHTCSCBEEEEEEESST
T ss_pred             HHhcC-CeEEEEeChHhcC--CHHHHHHHHHHHhCCCCeEEEEEChh
Confidence            87643 4799999999985  24444444444445566777777664

>PRK10865 protein disaggregation chaperone; Provisional

Probab=99.38  E-value=1.3e-11  Score=136.93  Aligned_cols=214  Identities=16%  Similarity=0.191  Sum_probs=139.9

Q ss_pred             CCCCChHHHHHHHHHHHHhhhcc----C-CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVNN----E-TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYET  268 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~----~-~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~  268 (490)
                      ..++|++..++.|...+.....+    . +.+.++|+||+|+|||++|+++++.+. .....+++++|..+.... ....
T Consensus       568 ~~viGQ~~ai~~l~~~i~~~~~gl~~~~~p~~~~Lf~Gp~G~GKT~lA~aLa~~l~-~~~~~~i~id~se~~~~~-~~~~  645 (857)
T PRK10865        568 HRVIGQNEAVEAVSNAIRRSRAGLSDPNRPIGSFLFLGPTGVGKTELCKALANFMF-DSDDAMVRIDMSEFMEKH-SVSR  645 (857)
T ss_pred             CeEeCCHHHHHHHHHHHHHHHhcccCCCCCCceEEEECCCCCCHHHHHHHHHHHhh-cCCCcEEEEEhHHhhhhh-hHHH
Confidence            78999999999999999865321    1 225789999999999999999998874 223467888887653221 1112


Q ss_pred             HHHHhcCC--CCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCHHHHHHhHhCCCC--------CCCcEEEEEec
Q psy200          269 IVNELKLK--PGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPSI--------PGSKLVLVGVA  338 (490)
Q Consensus       269 i~~~l~~~--~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~--------~~~~vilI~~t  338 (490)
                      +   ++.+  +.|...   ...+.+.+.. ....||||||++.+....++.|+++++....        .-.+.++|+++
T Consensus       646 L---iG~~pgy~g~~~---~g~l~~~v~~-~p~~vLllDEieka~~~v~~~Ll~ile~g~l~d~~gr~vd~rn~iiI~TS  718 (857)
T PRK10865        646 L---VGAPPGYVGYEE---GGYLTEAVRR-RPYSVILLDEVEKAHPDVFNILLQVLDDGRLTDGQGRTVDFRNTVVIMTS  718 (857)
T ss_pred             H---hCCCCcccccch---hHHHHHHHHh-CCCCeEEEeehhhCCHHHHHHHHHHHhhCceecCCceEEeecccEEEEeC
Confidence            2   2221  111111   1223343432 2346999999999988888999988864321        12345678888


Q ss_pred             CCC-Ch-------------h--------HhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhcc-------CCCCCC
Q psy200          339 NAL-DL-------------T--------DRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQT-------DKFNMF  389 (490)
Q Consensus       339 n~~-~~-------------~--------~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~-------~~~~~~  389 (490)
                      |.- +.             .        ..+.+.|..|+.   ..+.|.|++.+++..|+...+...       +....+
T Consensus       719 N~g~~~~~~~~~~~~~~~~~~~~~~~~~~~f~PELlnRld---~iivF~PL~~edl~~Iv~~~L~~l~~rl~~~gi~l~i  795 (857)
T PRK10865        719 NLGSDLIQERFGELDYAHMKELVLGVVSHNFRPEFINRID---EVVVFHPLGEQHIASIAQIQLQRLYKRLEERGYEIHI  795 (857)
T ss_pred             CcchHHHHHhccccchHHHHHHHHHHHcccccHHHHHhCC---eeEecCCCCHHHHHHHHHHHHHHHHHHHHhCCCcCcC
Confidence            741 10             1        113467788886   489999999999999988776542       334568


Q ss_pred             CHHHHHHHHHHHHHhhCCHHHHHHHHHHHH
Q psy200          390 NASALQLLAGKVAAVSGDIRKAIDITNHLI  419 (490)
Q Consensus       390 ~~~~i~~i~~~i~~~~Gd~r~ai~ll~~a~  419 (490)
                      ++++++.|++.-+....+.|.+-+++++-+
T Consensus       796 s~~al~~L~~~gy~~~~GARpL~r~I~~~i  825 (857)
T PRK10865        796 SDEALKLLSENGYDPVYGARPLKRAIQQQI  825 (857)
T ss_pred             CHHHHHHHHHcCCCccCChHHHHHHHHHHH
Confidence            999999999743333345666555555443

>KOG2680|consensus

Probab=99.37  E-value=5.5e-11  Score=111.14  Aligned_cols=135  Identities=16%  Similarity=0.184  Sum_probs=98.7

Q ss_pred             eEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEEEecCCC---------ChhHhhhHHhhhccCCCCeeEEeCCCCH
Q psy200          299 SILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVANAL---------DLTDRMLPRLQANVTLQPTLMNFAPYSR  369 (490)
Q Consensus       299 ~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI~~tn~~---------~~~~~l~~~l~~R~~~~~~~i~~~pls~  369 (490)
                      |-||||||+|.|.-.....|...++-   .-+++++ .+||+-         .-+.-+--.+..|.-    +|...||+.
T Consensus       289 pGVLFIDEvHMLDIEcFsFlNrAlE~---d~~Piii-maTNrgit~iRGTn~~SphGiP~D~lDR~l----II~t~py~~  360 (454)
T KOG2680|consen  289 PGVLFIDEVHMLDIECFSFLNRALEN---DMAPIII-MATNRGITRIRGTNYRSPHGIPIDLLDRML----IISTQPYTE  360 (454)
T ss_pred             cceEEEeeehhhhhHHHHHHHHHhhh---ccCcEEE-EEcCCceEEeecCCCCCCCCCcHHHhhhhh----eeecccCcH
Confidence            66999999999976655556555542   2234444 445521         111112223444543    799999999


Q ss_pred             HHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHhccccCCcccccCHHHHHHHHHHhcc
Q psy200          370 EQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITNHLIDLTYDNVKENGEVTGIGLKEVLGVISSVYC  449 (490)
Q Consensus       370 ~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~~~~~~  449 (490)
                      +++.+||..+|..+  +..+++++++.+..  .+..-.+|++++++.-+...+.++.     ...+..+|+.++..-++.
T Consensus       361 ~d~~~IL~iRc~EE--dv~m~~~A~d~Lt~--i~~~tsLRYai~Lit~a~~~~~krk-----~~~v~~~di~r~y~LFlD  431 (454)
T KOG2680|consen  361 EDIKKILRIRCQEE--DVEMNPDALDLLTK--IGEATSLRYAIHLITAASLVCLKRK-----GKVVEVDDIERVYRLFLD  431 (454)
T ss_pred             HHHHHHHHhhhhhh--ccccCHHHHHHHHH--hhhhhhHHHHHHHHHHHHHHHHHhc-----CceeehhHHHHHHHHHhh
Confidence            99999999999987  67889999999986  3445689999999999998888887     678999999999887664


Q ss_pred             C
Q psy200          450 T  450 (490)
Q Consensus       450 ~  450 (490)
                      .
T Consensus       432 ~  432 (454)
T KOG2680|consen  432 E  432 (454)
T ss_pred             h
Confidence            3

>KOG4658|consensus

Probab=99.36  E-value=3.1e-11  Score=133.24  Aligned_cols=198  Identities=21%  Similarity=0.312  Sum_probs=143.4

Q ss_pred             CChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhh-hcCCc-eEEEEeccCCCCHHHHHHHHHHHhc
Q psy200          197 PGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAE-IKDAF-KTIYINCNSVRNAASVYETIVNELK  274 (490)
Q Consensus       197 vgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~-~~~~~-~~~~v~~~~~~~~~~l~~~i~~~l~  274 (490)
                      ||.+..++.+...|..    ...+.+-|||.+|+|||||++.+.+... ....| .++|+..+...+...++.+|+..++
T Consensus       161 VG~e~~~~kl~~~L~~----d~~~iv~i~GMGGvGKTTL~~qi~N~~~~v~~~Fd~~iWV~VSk~f~~~~iq~~Il~~l~  236 (889)
T KOG4658|consen  161 VGLETMLEKLWNRLME----DDVGIVGIYGMGGVGKTTLARQIFNKFDEVGNHFDGVIWVVVSKEFTTRKIQQTILERLG  236 (889)
T ss_pred             ccHHHHHHHHHHHhcc----CCCCEEEEECCCcccHHHHHHHHhcccchhcccCceEEEEEEcccccHHhHHHHHHHHhc
Confidence            9999999999998864    4448999999999999999999999986 56677 5778888888899999999999887


Q ss_pred             CC---CCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCHHHHHHhHhCCC---CCCCcEEEEEecCCCChhHhhh
Q psy200          275 LK---PGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPS---IPGSKLVLVGVANALDLTDRML  348 (490)
Q Consensus       275 ~~---~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~---~~~~~vilI~~tn~~~~~~~l~  348 (490)
                      ..   +......+....+.+.++  +++++|++||||.=..      +..+..+.   ..++++++  +|...+.-... 
T Consensus       237 ~~~~~~~~~~~~~~~~~i~~~L~--~krfllvLDDIW~~~d------w~~I~~~~p~~~~g~Kvvl--TTRs~~V~~~~-  305 (889)
T KOG4658|consen  237 LLDEEWEDKEEDELASKLLNLLE--GKRFLLVLDDIWEEVD------WDKIGVPFPSRENGSKVVL--TTRSEEVCGRA-  305 (889)
T ss_pred             cCCcccchhhHHHHHHHHHHHhc--cCceEEEEeccccccc------HHhcCCCCCCccCCeEEEE--EeccHhhhhcc-
Confidence            63   332233566667777776  6789999999998432      33333322   22344444  44322222211 


Q ss_pred             HHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHHHHHHHH
Q psy200          349 PRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITNHLI  419 (490)
Q Consensus       349 ~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll~~a~  419 (490)
                            .+. ...+.+..++.++.|.++.+......   .-+...+..+++.++..||+++.|++++..++
T Consensus       306 ------m~~-~~~~~v~~L~~~eaW~LF~~~v~~~~---~~~~~~i~~lak~v~~kC~GLPLAl~viG~~m  366 (889)
T KOG4658|consen  306 ------MGV-DYPIEVECLTPEEAWDLFQKKVGPNT---LGSHPDIEELAKEVAEKCGGLPLALNVLGGLL  366 (889)
T ss_pred             ------ccC-CccccccccCccccHHHHHHhhcccc---ccccccHHHHHHHHHHHhCChHHHHHHHHHHh
Confidence                  221 23688999999999999999875541   11212389999999999999999999887764

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

Probab=99.35  E-value=1.4e-11  Score=131.16  Aligned_cols=216  Identities=18%  Similarity=0.214  Sum_probs=148.6

Q ss_pred             CCCCChHHHHHHHHHHHHhhhc-----cCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVN-----NETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYET  268 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~-----~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~  268 (490)
                      ..++|+++.+..|...+...-.     ..+.+.+++.||.|+|||-||++++..+... .-..+.++.+.+.....+   
T Consensus       491 ~rViGQd~AV~avs~aIrraRaGL~dp~rPigsFlF~GPTGVGKTELAkaLA~~Lfg~-e~aliR~DMSEy~EkHsV---  566 (786)
T COG0542         491 KRVIGQDEAVEAVSDAIRRARAGLGDPNRPIGSFLFLGPTGVGKTELAKALAEALFGD-EQALIRIDMSEYMEKHSV---  566 (786)
T ss_pred             cceeChHHHHHHHHHHHHHHhcCCCCCCCCceEEEeeCCCcccHHHHHHHHHHHhcCC-CccceeechHHHHHHHHH---
Confidence            8999999999999999986532     2245688899999999999999999998522 235677766655332222   


Q ss_pred             HHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCHHHHHHhHhCCCC--------CCCcEEEEEecCC
Q psy200          269 IVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPSI--------PGSKLVLVGVANA  340 (490)
Q Consensus       269 i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~--------~~~~vilI~~tn~  340 (490)
                       ..-++.+..-...++ -..|.+++.+ +..+||++|||+.-...-.+.|+++++-...        .-.+.++|+++|-
T Consensus       567 -SrLIGaPPGYVGyee-GG~LTEaVRr-~PySViLlDEIEKAHpdV~nilLQVlDdGrLTD~~Gr~VdFrNtiIImTSN~  643 (786)
T COG0542         567 -SRLIGAPPGYVGYEE-GGQLTEAVRR-KPYSVILLDEIEKAHPDVFNLLLQVLDDGRLTDGQGRTVDFRNTIIIMTSNA  643 (786)
T ss_pred             -HHHhCCCCCCceecc-ccchhHhhhc-CCCeEEEechhhhcCHHHHHHHHHHhcCCeeecCCCCEEecceeEEEEeccc
Confidence             112233222122222 3455566654 3467999999999988888889998875422        1235688888881


Q ss_pred             C---------C--------hhHh--------hhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhcc-------CCCCC
Q psy200          341 L---------D--------LTDR--------MLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQT-------DKFNM  388 (490)
Q Consensus       341 ~---------~--------~~~~--------l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~-------~~~~~  388 (490)
                      -         +        +.+.        +.|.|..|+.   .+|.|.+++.+++.+|+...+...       +....
T Consensus       644 Gs~~i~~~~~~~~~~~~~~~~~~v~~~l~~~F~PEFLNRid---~II~F~~L~~~~l~~Iv~~~L~~l~~~L~~~~i~l~  720 (786)
T COG0542         644 GSEEILRDADGDDFADKEALKEAVMEELKKHFRPEFLNRID---EIIPFNPLSKEVLERIVDLQLNRLAKRLAERGITLE  720 (786)
T ss_pred             chHHHHhhccccccchhhhHHHHHHHHHHhhCCHHHHhhcc---cEEeccCCCHHHHHHHHHHHHHHHHHHHHhCCceEE
Confidence            0         0        0011        2355666776   589999999999999877665443       45667


Q ss_pred             CCHHHHHHHHHHHHHhhCCHHHHHHHHHHHH
Q psy200          389 FNASALQLLAGKVAAVSGDIRKAIDITNHLI  419 (490)
Q Consensus       389 ~~~~~i~~i~~~i~~~~Gd~r~ai~ll~~a~  419 (490)
                      +++++.++|+++.+....+.|-+..++++-+
T Consensus       721 ~s~~a~~~l~~~gyd~~~GARpL~R~Iq~~i  751 (786)
T COG0542         721 LSDEAKDFLAEKGYDPEYGARPLRRAIQQEI  751 (786)
T ss_pred             ECHHHHHHHHHhccCCCcCchHHHHHHHHHH
Confidence            8999999999977777777777766665544

>TIGR02442 Cob-chelat-sub cobaltochelatase subunit

Probab=99.35  E-value=6.6e-11  Score=127.56  Aligned_cols=244  Identities=17%  Similarity=0.194  Sum_probs=147.4

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCC------CCHHHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSV------RNAASVYE  267 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~------~~~~~l~~  267 (490)
                      ..++|++..+..|.-.+.    ....++|+|+|++|+|||++|+.+++.+..-....-..++|...      .....+..
T Consensus         4 ~~ivGq~~~~~al~~~av----~~~~g~vli~G~~GtgKs~lar~l~~~lp~~~~~~~~~~~c~p~~~~~~~~~~~~~~~   79 (633)
T TIGR02442         4 TAIVGQEDLKLALLLNAV----DPRIGGVLIRGEKGTAKSTAARGLAALLPPIDVVAGCPFSCDPDDPEEWCEECRRKYR   79 (633)
T ss_pred             chhcChHHHHHHHHHHhh----CCCCCeEEEEcCCCCcHHHHHHHHHHhCCCceeccCCcCCCCCCCccccChhhhhccc
Confidence            468999988866655443    23457799999999999999999988762000000001111110      00000000


Q ss_pred             HHHHH----hcCCCCCCcHHHHHHH--HHHHHhc------C-----CCeEEEEEecCccccccCHHHHHHhHhCCC----
Q psy200          268 TIVNE----LKLKPGGKSERHQLGA--ILKYFDT------K-----HKSILLILDEIDALESRKQTILYTIFEWPS----  326 (490)
Q Consensus       268 ~i~~~----l~~~~~~~s~~~~~~~--l~~~l~~------~-----~~~~vI~IDEid~l~~~~~~~L~~l~~~~~----  326 (490)
                      . ...    +.....+.+...++..  +...+..      .     ...-+||||||+.|....|+.|+.+++...    
T Consensus        80 ~-~~~~~~pfv~~p~~~t~~~l~G~~d~~~~l~~g~~~~~~G~L~~A~~GiL~lDEi~~l~~~~q~~Ll~~le~g~~~v~  158 (633)
T TIGR02442        80 P-SEQRPVPFVNLPLGATEDRVVGSLDIERALREGEKAFQPGLLAEAHRGILYIDEVNLLDDHLVDVLLDAAAMGVNRVE  158 (633)
T ss_pred             c-cccCCCCeeeCCCCCcHHHcCCcccHHHHhhcCCeeecCcceeecCCCeEEeChhhhCCHHHHHHHHHHHhcCCEEEE
Confidence            0 000    0000011111111110  1111110      0     112399999999999999999998886432    


Q ss_pred             ------CCCCcEEEEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCC-HHHHHHHHHHHHhc-----------------
Q psy200          327 ------IPGSKLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYS-REQILEIISQKLKQ-----------------  382 (490)
Q Consensus       327 ------~~~~~vilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls-~~e~~~il~~~l~~-----------------  382 (490)
                            ....++++|+++|..+  ..+.+.|.+||++   .+.+.++. .++..+++.+.+..                 
T Consensus       159 r~g~~~~~~~~~~lIat~np~e--g~l~~~L~dR~~l---~i~v~~~~~~~~~~~il~~~~~~~~~~~~~~~~~~~~~~~  233 (633)
T TIGR02442       159 REGLSVSHPARFVLIGTMNPEE--GDLRPQLLDRFGL---CVDVAAPRDPEERVEIIRRRLAFDADPEAFAARWAAEQEE  233 (633)
T ss_pred             ECCceeeecCCeEEEEecCCCC--CCCCHHHHhhcce---EEEccCCCchHHHHHHHHHHHhhccCcHHHHHHhhhhHHH
Confidence                  1235789999988542  2355778889985   56666654 45555555432210                 


Q ss_pred             ----------cCCCCCCCHHHHHHHHHHHHHhhC-CHHHHHHHHHHHHHHHHhccccCCcccccCHHHHHHHHHHhccCc
Q psy200          383 ----------TDKFNMFNASALQLLAGKVAAVSG-DIRKAIDITNHLIDLTYDNVKENGEVTGIGLKEVLGVISSVYCTS  451 (490)
Q Consensus       383 ----------~~~~~~~~~~~i~~i~~~i~~~~G-d~r~ai~ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~~~~~~~~  451 (490)
                                ....+.+++++++.++.......- +.|..+.+++-|..+|..++     ...|+.+||..|+.-++..+
T Consensus       234 l~~~i~~ar~~~~~V~is~~~~~~l~~~~~~~~i~s~Ra~i~~~r~Ara~AaL~g-----r~~V~~~Dv~~A~~lvL~hR  308 (633)
T TIGR02442       234 LRNRIARARSLLPSVRISDSLIRFISELCIEFGVDGHRADIVMARAARALAALDG-----RRRVTAEDVREAAELVLPHR  308 (633)
T ss_pred             HHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHhCCCCccHHHHHHHHHHHHHHHcC-----CCcCCHHHHHHHHHHHhhhh
Confidence                      012356788888888886655443 58888999999999999999     78999999999999888665


Q ss_pred             c
Q psy200          452 Q  452 (490)
Q Consensus       452 ~  452 (490)
                      .
T Consensus       309 ~  309 (633)
T TIGR02442       309 R  309 (633)
T ss_pred             c
Confidence            5

A number of genomes (actinobacteria, cyanobacteria, betaproteobacteria and pseudomonads) which apparently biosynthesize B12, encode a cobN gene but are demonstrably lacking cobS and cobT. These genomes do, however contain a homolog (modelled here) of the magnesium chelatase subunits BchI/BchD family. Aside from the cyanobacteria (which have a separate magnesium chelatase trimer), these species do not make chlorins, so do not have any use for a magnesium chelatase. Furthermore, in nearly all cases the members of this family are proximal to either CobN itself or other genes involved in cobalt transport or B12 biosynthesis.

>PRK08058 DNA polymerase III subunit delta'; Validated

Probab=99.34  E-value=4.6e-11  Score=118.92  Aligned_cols=196  Identities=15%  Similarity=0.250  Sum_probs=123.0

Q ss_pred             CCCCC-hHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHH
Q psy200          194 CELPG-REVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNE  272 (490)
Q Consensus       194 ~~lvg-re~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~  272 (490)
                      +.++| ++..++.|...+..   +.-++.++|+||+|+||+++|+.+++.+........  ..|..+.+...+...-.-+
T Consensus         5 ~~i~~~q~~~~~~L~~~~~~---~~l~ha~Lf~G~~G~gk~~~a~~la~~l~c~~~~~~--~~cg~C~~c~~~~~~~hpD   79 (329)
T PRK08058          5 EQLTALQPVVVKMLQNSIAK---NRLSHAYLFEGAKGTGKKATALWLAKSLFCLERNGV--EPCGTCTNCKRIDSGNHPD   79 (329)
T ss_pred             HHHHhhHHHHHHHHHHHHHc---CCCCceEEEECCCCCCHHHHHHHHHHHHCCCCCCCC--CCCCcCHHHHHHhcCCCCC
Confidence            45667 88888888887753   345667799999999999999999998753221000  0122222211111100000


Q ss_pred             hc---CCCCCCcHHHHHHHHHHHHh--cCCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEEEecCCCChhHhh
Q psy200          273 LK---LKPGGKSERHQLGAILKYFD--TKHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVANALDLTDRM  347 (490)
Q Consensus       273 l~---~~~~~~s~~~~~~~l~~~l~--~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI~~tn~~~~~~~l  347 (490)
                      +.   ......+.+++++.......  ..+...|+||||+|.|....++.|...++.+   ...+++|.+++   -..++
T Consensus        80 ~~~i~~~~~~i~id~ir~l~~~~~~~~~~~~~kvviI~~a~~~~~~a~NaLLK~LEEP---p~~~~~Il~t~---~~~~l  153 (329)
T PRK08058         80 VHLVAPDGQSIKKDQIRYLKEEFSKSGVESNKKVYIIEHADKMTASAANSLLKFLEEP---SGGTTAILLTE---NKHQI  153 (329)
T ss_pred             EEEeccccccCCHHHHHHHHHHHhhCCcccCceEEEeehHhhhCHHHHHHHHHHhcCC---CCCceEEEEeC---ChHhC
Confidence            00   01111345566655544321  1245669999999999988888898888743   34555555554   25678


Q ss_pred             hHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHHHHH
Q psy200          348 LPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITN  416 (490)
Q Consensus       348 ~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll~  416 (490)
                      .+.+++||.    .+.|.+++.+++..++...    +    ++++....++.    ..|++..++.++.
T Consensus       154 l~TIrSRc~----~i~~~~~~~~~~~~~L~~~----g----i~~~~~~~l~~----~~g~~~~A~~l~~  206 (329)
T PRK08058        154 LPTILSRCQ----VVEFRPLPPESLIQRLQEE----G----ISESLATLLAG----LTNSVEEALALSE  206 (329)
T ss_pred             cHHHHhhce----eeeCCCCCHHHHHHHHHHc----C----CChHHHHHHHH----HcCCHHHHHHHhc
Confidence            899999996    8999999999998887642    1    45555545543    4688887776543

>TIGR00764 lon_rel lon-related putative ATP-dependent protease

Probab=99.34  E-value=9.9e-11  Score=125.01  Aligned_cols=241  Identities=15%  Similarity=0.158  Sum_probs=154.0

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHh
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNEL  273 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l  273 (490)
                      ++++|+++.++.+...+..      ..+++|+|+||||||++++++++.+....-+.++++..+.. +..+++..++..+
T Consensus        18 ~~viG~~~a~~~l~~a~~~------~~~~ll~G~pG~GKT~la~~la~~l~~~~~~~~~~~~n~~~-~~~~~~~~v~~~~   90 (608)
T TIGR00764        18 DQVIGQEEAVEIIKKAAKQ------KRNVLLIGEPGVGKSMLAKAMAELLPDEELEDILVYPNPED-PNMPRIVEVPAGE   90 (608)
T ss_pred             hhccCHHHHHHHHHHHHHc------CCCEEEECCCCCCHHHHHHHHHHHcCchhheeEEEEeCCCC-CchHHHHHHHHhh
Confidence            7899999999888777753      35888999999999999999999886332145566655544 3444444444433


Q ss_pred             cCC-----------------------------------------------------------------------------
Q psy200          274 KLK-----------------------------------------------------------------------------  276 (490)
Q Consensus       274 ~~~-----------------------------------------------------------------------------  276 (490)
                      +..                                                                             
T Consensus        91 g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~n~lv~~s~~~  170 (608)
T TIGR00764        91 GREIVEDYKKKAFKQPSSRNLLLFMIGFIVLSEYFLKNLPPNYLLAAVIAAALILLIFGFFIPRTSIMVPKLLVDNSGKK  170 (608)
T ss_pred             chHHHHHHHHHhhcccchhhHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHHHHhcccchhceeeeeecCCCCC
Confidence            210                                                                             


Q ss_pred             ------CCCCcHHHHHHHHHHH-Hh--------------c----CCCeEEEEEecCccccccCHHHHHHhHhCCC-----
Q psy200          277 ------PGGKSERHQLGAILKY-FD--------------T----KHKSILLILDEIDALESRKQTILYTIFEWPS-----  326 (490)
Q Consensus       277 ------~~~~s~~~~~~~l~~~-l~--------------~----~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~-----  326 (490)
                            ..+.+...+...++.. +.              .    ....-+|||||++.|....|..|.+.++...     
T Consensus       171 ~~P~v~~~~~~~~~L~G~i~~~~~~g~~g~~~~~~~~i~~G~L~~AngGtL~Ldei~~L~~~~q~~Ll~~L~~~~i~~~g  250 (608)
T TIGR00764       171 KAPFVDATGAHAGALLGDVRHDPFQGSGGLGTPAHERVEAGAIHRAHKGVLYIDEIKTMPLEVQQYLLTALQDKKFPITG  250 (608)
T ss_pred             CCCEEEeCCCChHHCccceeeccccCccccccCccccCCCCceEECCCCEEEEEChHhCCHHHHHHHHHHHHhCcEEecC
Confidence                  0000111111111100 00              0    0112499999999999878888888764321     


Q ss_pred             -------------CCCCcEEEEEecCCCChhHhhhHHhhhccCCCCeeEEeCC---CCHHHH---HHHHHHHHhccCCCC
Q psy200          327 -------------IPGSKLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAP---YSREQI---LEIISQKLKQTDKFN  387 (490)
Q Consensus       327 -------------~~~~~vilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~p---ls~~e~---~~il~~~l~~~~~~~  387 (490)
                                   .....+.+|+++|.. ....+.+.+++||..-...+.|+.   .+.+..   ..++.+.+...+...
T Consensus       251 ~~e~~~~~~~~~~~ip~dvrvIa~~~~~-~l~~l~~~l~~rf~~y~v~v~~~~~~~~~~e~~~~~~~~i~~~~~r~G~l~  329 (608)
T TIGR00764       251 QSENSSGAMVRTEPVPCDFILVASGNLD-DLEGMHPALRSRIRGYGYEVYMKDTMPDTPENRDKLVQFVAQEVKKDGRIP  329 (608)
T ss_pred             ccccccccccCCCCCccceEEEEECCHH-HHhhcCHHHHHHhcCCeEEEEeeccCCCCHHHHHHHHHHHHHHHHHhCCCC
Confidence                         113467888888853 344578889899861001345543   344443   455555555554445


Q ss_pred             CCCHHHHHHHHHHHHHhhC-------CHHHHHHHHHHHHHHHHhccccCCcccccCHHHHHHHHHHh
Q psy200          388 MFNASALQLLAGKVAAVSG-------DIRKAIDITNHLIDLTYDNVKENGEVTGIGLKEVLGVISSV  447 (490)
Q Consensus       388 ~~~~~~i~~i~~~i~~~~G-------d~r~ai~ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~~~~  447 (490)
                      .+++++++.+.+......|       ..|.+-++|+.|...|..++     ...|+.+||.+|+...
T Consensus       330 ~~s~~Av~~Li~~~~R~ag~r~~lsl~~R~L~~llR~A~~iA~~~~-----~~~I~~ehV~~Ai~~~  391 (608)
T TIGR00764       330 HFTRDAVEEIVREAQRRAGRKDHLTLRLRELGGLVRAAGDIAKSSG-----KVYVTAEHVLKAKKLA  391 (608)
T ss_pred             cCCHHHHHHHHHHHHHHHhcccccCCCHHHHHHHHHHHHHHHHhcC-----CceecHHHHHHHHHHH
Confidence            7899999999875544333       47888899999988888777     6789999999987754

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

>KOG0741|consensus

Probab=99.33  E-value=5.1e-12  Score=126.11  Aligned_cols=229  Identities=17%  Similarity=0.239  Sum_probs=139.7

Q ss_pred             CCCChHHHHHHHHHHHH-hhhc---------cCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHH
Q psy200          195 ELPGREVQLEGIRQFLL-GHVN---------NETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAAS  264 (490)
Q Consensus       195 ~lvgre~~~~~l~~~L~-~~~~---------~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~  264 (490)
                      .+-|.++++..+....- ..+.         -..-++++||||||||||.+||.+...+..+.   ---+|++++     
T Consensus       222 GIGGLd~EFs~IFRRAFAsRvFpp~vie~lGi~HVKGiLLyGPPGTGKTLiARqIGkMLNAre---PKIVNGPeI-----  293 (744)
T KOG0741|consen  222 GIGGLDKEFSDIFRRAFASRVFPPEVIEQLGIKHVKGILLYGPPGTGKTLIARQIGKMLNARE---PKIVNGPEI-----  293 (744)
T ss_pred             ccccchHHHHHHHHHHHHhhcCCHHHHHHcCccceeeEEEECCCCCChhHHHHHHHHHhcCCC---CcccCcHHH-----
Confidence            57788888888765221 1111         11346899999999999999999998875221   122444433     


Q ss_pred             HHHHHHHHhcCCCCCCcHHHHHHHHHHHHhc------CCCeEEEEEecCccccccC----------HHHHHHhHhCC-C-
Q psy200          265 VYETIVNELKLKPGGKSERHQLGAILKYFDT------KHKSILLILDEIDALESRK----------QTILYTIFEWP-S-  326 (490)
Q Consensus       265 l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~------~~~~~vI~IDEid~l~~~~----------~~~L~~l~~~~-~-  326 (490)
                       +.        ++.|++++.+++.|.++-+.      ...-.|||+||||.++..+          .....+|+... . 
T Consensus       294 -L~--------KYVGeSE~NvR~LFaDAEeE~r~~g~~SgLHIIIFDEiDAICKqRGS~~g~TGVhD~VVNQLLsKmDGV  364 (744)
T KOG0741|consen  294 -LN--------KYVGESEENVRKLFADAEEEQRRLGANSGLHIIIFDEIDAICKQRGSMAGSTGVHDTVVNQLLSKMDGV  364 (744)
T ss_pred             -HH--------HhhcccHHHHHHHHHhHHHHHHhhCccCCceEEEehhhHHHHHhcCCCCCCCCccHHHHHHHHHhcccH
Confidence             22        56778899999888876532      2457799999999998652          23344443221 1 


Q ss_pred             CCCCcEEEEEecCCCChhHhhhHHhh--hccCCCCeeEEeCCCCHHHHHHHH---HHHHhccCCCCCCCHHHHHHHHHHH
Q psy200          327 IPGSKLVLVGVANALDLTDRMLPRLQ--ANVTLQPTLMNFAPYSREQILEII---SQKLKQTDKFNMFNASALQLLAGKV  401 (490)
Q Consensus       327 ~~~~~vilI~~tn~~~~~~~l~~~l~--~R~~~~~~~i~~~pls~~e~~~il---~~~l~~~~~~~~~~~~~i~~i~~~i  401 (490)
                      ..--+++|||.||+.|+.+.   +|.  .|+.   -.+.+.-+++.-..+|+   .++++..  ...-++-.++.|+...
T Consensus       365 eqLNNILVIGMTNR~DlIDE---ALLRPGRlE---VqmEIsLPDE~gRlQIl~IHT~rMre~--~~l~~dVdl~elA~lT  436 (744)
T KOG0741|consen  365 EQLNNILVIGMTNRKDLIDE---ALLRPGRLE---VQMEISLPDEKGRLQILKIHTKRMREN--NKLSADVDLKELAALT  436 (744)
T ss_pred             HhhhcEEEEeccCchhhHHH---HhcCCCceE---EEEEEeCCCccCceEEEEhhhhhhhhc--CCCCCCcCHHHHHHHh
Confidence            12247999999998877554   222  2333   25666666666555444   4445444  1222334477777655


Q ss_pred             HHhhCCHHHHHHHHHHHHHHHHhccc-----cC-----CcccccCHHHHHHHHHHhccC
Q psy200          402 AAVSGDIRKAIDITNHLIDLTYDNVK-----EN-----GEVTGIGLKEVLGVISSVYCT  450 (490)
Q Consensus       402 ~~~~Gd~r~ai~ll~~a~~~a~~~~~-----~~-----~~~~~It~~~v~~a~~~~~~~  450 (490)
                      -..+|-  .+-.+++.|...|..+.-     ..     .+..+|+++||..|+.++.+.
T Consensus       437 KNfSGA--EleglVksA~S~A~nR~vk~~~~~~~~~~~~e~lkV~r~DFl~aL~dVkPA  493 (744)
T KOG0741|consen  437 KNFSGA--ELEGLVKSAQSFAMNRHVKAGGKVEVDPVAIENLKVTRGDFLNALEDVKPA  493 (744)
T ss_pred             cCCchh--HHHHHHHHHHHHHHHhhhccCcceecCchhhhheeecHHHHHHHHHhcCcc
Confidence            455552  222355556555544321     11     235689999999999988654

>KOG2543|consensus

Probab=99.33  E-value=1.4e-10  Score=112.30  Aligned_cols=215  Identities=20%  Similarity=0.287  Sum_probs=143.7

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHh
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNEL  273 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l  273 (490)
                      ..+.+|+.++..|...+.+.-. .-+.+++|+|..|||||.+++.+.+.+    +.+.+|++|-++.+...++..|+.++
T Consensus         6 ~~v~~Re~qi~~L~~Llg~~~~-~~PS~~~iyG~sgTGKT~~~r~~l~~~----n~~~vw~n~~ecft~~~lle~IL~~~   80 (438)
T KOG2543|consen    6 PNVPCRESQIRRLKSLLGNNSC-TIPSIVHIYGHSGTGKTYLVRQLLRKL----NLENVWLNCVECFTYAILLEKILNKS   80 (438)
T ss_pred             cCccchHHHHHHHHHHhCCCCc-ccceeEEEeccCCCchhHHHHHHHhhc----CCcceeeehHHhccHHHHHHHHHHHh
Confidence            6799999999999998865211 234567999999999999999999986    47889999999999999999999998


Q ss_pred             c-CCCCCCcHH----HH---HHHHHH--HHhcCCCeEEEEEecCccccccCHHHHHHhHhCC---CCCCCcEEEEEecCC
Q psy200          274 K-LKPGGKSER----HQ---LGAILK--YFDTKHKSILLILDEIDALESRKQTILYTIFEWP---SIPGSKLVLVGVANA  340 (490)
Q Consensus       274 ~-~~~~~~s~~----~~---~~~l~~--~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~---~~~~~~vilI~~tn~  340 (490)
                      . .+..|...+    .+   ...+.+  .....++.++||+|.+|.+.......|..++++.   ......++++.... 
T Consensus        81 ~~~d~dg~~~~~~~en~~d~i~~l~q~~~~t~~d~~~~liLDnad~lrD~~a~ll~~l~~L~el~~~~~i~iils~~~~-  159 (438)
T KOG2543|consen   81 QLADKDGDKVEGDAENFSDFIYLLVQWPAATNRDQKVFLILDNADALRDMDAILLQCLFRLYELLNEPTIVIILSAPSC-  159 (438)
T ss_pred             ccCCCchhhhhhHHHHHHHHHHHHHhhHHhhccCceEEEEEcCHHhhhccchHHHHHHHHHHHHhCCCceEEEEecccc-
Confidence            5 333333222    22   222332  1122346899999999999877766555555443   33333333333221 


Q ss_pred             CChhHhhhHHhhhccC-CCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHHHHHHHH
Q psy200          341 LDLTDRMLPRLQANVT-LQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITNHLI  419 (490)
Q Consensus       341 ~~~~~~l~~~l~~R~~-~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll~~a~  419 (490)
                          ..   ....+.+ ...-.++|+.|+.+++..|+.+--... ....+-...+..+..-.+..|+|++.+..++..++
T Consensus       160 ----e~---~y~~n~g~~~i~~l~fP~Ys~~e~~~Il~~~~p~~-r~~~~ya~fl~v~l~vF~~~crd~~eL~~~~~~~w  231 (438)
T KOG2543|consen  160 ----EK---QYLINTGTLEIVVLHFPQYSVEETQVILSRDNPGK-RKLDVYAQFLHVLLQVFYMACRDVNELRSLISLAW  231 (438)
T ss_pred             ----HH---HhhcccCCCCceEEecCCCCHHHHHHHHhcCCccc-cchHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH
Confidence                11   1111222 223479999999999999987632211 01111245566777777889999998888887777


Q ss_pred             HHH
Q psy200          420 DLT  422 (490)
Q Consensus       420 ~~a  422 (490)
                      -.-
T Consensus       232 pky  234 (438)
T KOG2543|consen  232 PKY  234 (438)
T ss_pred             Hhh
Confidence            543

>KOG1942|consensus

Probab=99.32  E-value=1e-10  Score=109.08  Aligned_cols=133  Identities=23%  Similarity=0.268  Sum_probs=97.9

Q ss_pred             eEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEEEecCC--------CCh--hHhhhHHhhhccCCCCeeEEeCCCC
Q psy200          299 SILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVANA--------LDL--TDRMLPRLQANVTLQPTLMNFAPYS  368 (490)
Q Consensus       299 ~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI~~tn~--------~~~--~~~l~~~l~~R~~~~~~~i~~~pls  368 (490)
                      |-||||||+|.|.-.....|...++..   - .-++|.++|+        .++  +.-+-+.+..|+-    +|...+|+
T Consensus       297 PGVLFIDEVhMLDiEcFTyL~kalES~---i-aPivifAsNrG~~~irGt~d~~sPhGip~dllDRl~----Iirt~~y~  368 (456)
T KOG1942|consen  297 PGVLFIDEVHMLDIECFTYLHKALESP---I-APIVIFASNRGMCTIRGTEDILSPHGIPPDLLDRLL----IIRTLPYD  368 (456)
T ss_pred             CcceEeeehhhhhhHHHHHHHHHhcCC---C-CceEEEecCCcceeecCCcCCCCCCCCCHHHhhhee----EEeeccCC
Confidence            669999999999765555566655532   1 2344455552        111  1122345666664    79999999


Q ss_pred             HHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHhccccCCcccccCHHHHHHHHHHhc
Q psy200          369 REQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITNHLIDLTYDNVKENGEVTGIGLKEVLGVISSVY  448 (490)
Q Consensus       369 ~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~~~~~  448 (490)
                      ++++.+|+..+...+  ...++++++..+++  .+..-.+|++++++.-|-.+|.-.+     ...|..+++.++-.-+.
T Consensus       369 ~~e~r~Ii~~Ra~~E--~l~~~e~a~~~l~~--~gt~tsLRy~vqLl~p~~~~ak~~g-----~~~i~v~dvee~~~Lf~  439 (456)
T KOG1942|consen  369 EEEIRQIIKIRAQVE--GLQVEEEALDLLAE--IGTSTSLRYAVQLLTPASILAKTNG-----RKEISVEDVEEVTELFL  439 (456)
T ss_pred             HHHHHHHHHHHHhhh--cceecHHHHHHHHh--hccchhHHHHHHhcCHHHHHHHHcC-----CceeecccHHHHHHHHH
Confidence            999999999999887  46789999999987  4556689999999999988999888     66888888888765444

>CHL00095 clpC Clp protease ATP binding subunit

Probab=99.32  E-value=5.3e-11  Score=132.17  Aligned_cols=214  Identities=14%  Similarity=0.142  Sum_probs=140.1

Q ss_pred             CCCCChHHHHHHHHHHHHhhhc----cC-CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVN----NE-TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYET  268 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~----~~-~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~  268 (490)
                      +.++|++..++.|...+.....    .. +...++++||+|+|||++|+++++.+.. ....++.++.+.+.....+ ..
T Consensus       509 ~~v~GQ~~ai~~l~~~i~~~~~gl~~~~~p~~~~lf~Gp~GvGKt~lA~~LA~~l~~-~~~~~~~~d~s~~~~~~~~-~~  586 (821)
T CHL00095        509 KRIIGQDEAVVAVSKAIRRARVGLKNPNRPIASFLFSGPTGVGKTELTKALASYFFG-SEDAMIRLDMSEYMEKHTV-SK  586 (821)
T ss_pred             CcCcChHHHHHHHHHHHHHHhhcccCCCCCceEEEEECCCCCcHHHHHHHHHHHhcC-CccceEEEEchhccccccH-HH
Confidence            8899999999999998875422    11 2346889999999999999999998742 2235677777665432222 11


Q ss_pred             HHHHhcCC--CCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCHHHHHHhHhCCCC--------CCCcEEEEEec
Q psy200          269 IVNELKLK--PGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPSI--------PGSKLVLVGVA  338 (490)
Q Consensus       269 i~~~l~~~--~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~--------~~~~vilI~~t  338 (490)
                      +   ++.+  +.|...   ...+.+.+.. ....||+|||++.+....++.|+++++....        .-.+.++|+++
T Consensus       587 l---~g~~~gyvg~~~---~~~l~~~~~~-~p~~VvllDeieka~~~v~~~Llq~le~g~~~d~~g~~v~~~~~i~I~Ts  659 (821)
T CHL00095        587 L---IGSPPGYVGYNE---GGQLTEAVRK-KPYTVVLFDEIEKAHPDIFNLLLQILDDGRLTDSKGRTIDFKNTLIIMTS  659 (821)
T ss_pred             h---cCCCCcccCcCc---cchHHHHHHh-CCCeEEEECChhhCCHHHHHHHHHHhccCceecCCCcEEecCceEEEEeC
Confidence            1   1211  111111   1123344433 3357999999999988888999998875421        23567888888


Q ss_pred             CCC-C----------h-----------------------hHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhcc-
Q psy200          339 NAL-D----------L-----------------------TDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQT-  383 (490)
Q Consensus       339 n~~-~----------~-----------------------~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~-  383 (490)
                      |.- +          +                       ...+.|.|.+|++   .++.|.|++.+++.+|+...+... 
T Consensus       660 n~g~~~i~~~~~~~gf~~~~~~~~~~~~~~~~~~~~~~~~~~f~peflnRid---~ii~F~pL~~~~l~~Iv~~~l~~l~  736 (821)
T CHL00095        660 NLGSKVIETNSGGLGFELSENQLSEKQYKRLSNLVNEELKQFFRPEFLNRLD---EIIVFRQLTKNDVWEIAEIMLKNLF  736 (821)
T ss_pred             CcchHHHHhhccccCCcccccccccccHHHHHHHHHHHHHHhcCHHHhccCC---eEEEeCCCCHHHHHHHHHHHHHHHH
Confidence            721 0          0                       0012345667775   589999999999999987766542 


Q ss_pred             ------CCCCCCCHHHHHHHHHHHHHhhCCHHHHHHHHHHHH
Q psy200          384 ------DKFNMFNASALQLLAGKVAAVSGDIRKAIDITNHLI  419 (490)
Q Consensus       384 ------~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll~~a~  419 (490)
                            +....+++++++.|++..+....+.|.+-.++++.+
T Consensus       737 ~rl~~~~i~l~~~~~~~~~La~~~~~~~~GAR~l~r~i~~~i  778 (821)
T CHL00095        737 KRLNEQGIQLEVTERIKTLLIEEGYNPLYGARPLRRAIMRLL  778 (821)
T ss_pred             HHHHHCCcEEEECHHHHHHHHHhcCCCCCChhhHHHHHHHHH
Confidence                  345678999999999854444445665555554444

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

Probab=99.32  E-value=1.1e-10  Score=106.17  Aligned_cols=175  Identities=15%  Similarity=0.226  Sum_probs=125.3

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHh
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNEL  273 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l  273 (490)
                      ..++|-+.+.+.|.+.-...+.+.+.+++||+|..||||++|++++.+++. ......++|+-..+              
T Consensus        60 ~~l~Gvd~qk~~L~~NT~~F~~G~pANnVLLwGaRGtGKSSLVKA~~~e~~-~~glrLVEV~k~dl--------------  124 (287)
T COG2607          60 ADLVGVDRQKEALVRNTEQFAEGLPANNVLLWGARGTGKSSLVKALLNEYA-DEGLRLVEVDKEDL--------------  124 (287)
T ss_pred             HHHhCchHHHHHHHHHHHHHHcCCcccceEEecCCCCChHHHHHHHHHHHH-hcCCeEEEEcHHHH--------------
Confidence            689999999999999999888888999999999999999999999999986 22346777742222              


Q ss_pred             cCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCcccccc-CHHHHHHhHhCC-CCCCCcEEEEEecCCCChhHh-----
Q psy200          274 KLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESR-KQTILYTIFEWP-SIPGSKLVLVGVANALDLTDR-----  346 (490)
Q Consensus       274 ~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~-~~~~L~~l~~~~-~~~~~~vilI~~tn~~~~~~~-----  346 (490)
                               ..+- .+.+.++....++|||.||+-.=.+. .-..|...++-. .....+|+|.+++|+-.+..+     
T Consensus       125 ---------~~Lp-~l~~~Lr~~~~kFIlFcDDLSFe~gd~~yK~LKs~LeG~ve~rP~NVl~YATSNRRHLl~e~~~dn  194 (287)
T COG2607         125 ---------ATLP-DLVELLRARPEKFILFCDDLSFEEGDDAYKALKSALEGGVEGRPANVLFYATSNRRHLLPEDMKDN  194 (287)
T ss_pred             ---------hhHH-HHHHHHhcCCceEEEEecCCCCCCCchHHHHHHHHhcCCcccCCCeEEEEEecCCcccccHhhhhC
Confidence                     1111 22333555577899999998654332 234555555433 334678888888885433221     


Q ss_pred             ------------hhH--HhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHH
Q psy200          347 ------------MLP--RLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLA  398 (490)
Q Consensus       347 ------------l~~--~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~  398 (490)
                                  +.+  .+..|||+   .+.|.|.+.++..+++.+.+.+.  .+.++++.++.=+
T Consensus       195 ~~~~~eih~~eaveEKlSlSDRFGL---wL~F~~~~Q~~YL~~V~~~a~~~--~l~~~~e~l~~eA  255 (287)
T COG2607         195 EGSTGEIHPSEAVEEKLSLSDRFGL---WLSFYPCDQDEYLKIVDHYAKHF--GLDISDEELHAEA  255 (287)
T ss_pred             CCcccccChhHHHHHhhchhhhcce---eecccCCCHHHHHHHHHHHHHHc--CCCCCHHHHHHHH
Confidence                        111  46779996   89999999999999999999887  4556665555544

>TIGR01650 PD_CobS cobaltochelatase, CobS subunit

Probab=99.29  E-value=6.7e-11  Score=115.12  Aligned_cols=185  Identities=15%  Similarity=0.137  Sum_probs=118.9

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHh
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNEL  273 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l  273 (490)
                      ..++-..+....+..++.      ..++++|.|+||||||++++.++..++    ++++.++|....+..+++....-.+
T Consensus        45 ~~y~f~~~~~~~vl~~l~------~~~~ilL~G~pGtGKTtla~~lA~~l~----~~~~rV~~~~~l~~~DliG~~~~~l  114 (327)
T TIGR01650        45 PAYLFDKATTKAICAGFA------YDRRVMVQGYHGTGKSTHIEQIAARLN----WPCVRVNLDSHVSRIDLVGKDAIVL  114 (327)
T ss_pred             CCccCCHHHHHHHHHHHh------cCCcEEEEeCCCChHHHHHHHHHHHHC----CCeEEEEecCCCChhhcCCCceeec
Confidence            345555555555555553      256899999999999999999999986    7788999988877665543311101


Q ss_pred             cCCCCCCcHHHHH-HHHHHHHhcCCCeEEEEEecCccccccCHHHHHHhHhCC------C-----CCCCcEEEEEecCCC
Q psy200          274 KLKPGGKSERHQL-GAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWP------S-----IPGSKLVLVGVANAL  341 (490)
Q Consensus       274 ~~~~~~~s~~~~~-~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~------~-----~~~~~vilI~~tn~~  341 (490)
                      .   .+.....+. ..|..+..   .+.+|++||++......+..|..+++..      .     ..+..+.+|++.|..
T Consensus       115 ~---~g~~~~~f~~GpL~~A~~---~g~illlDEin~a~p~~~~~L~~lLE~~~~l~i~~~~~~i~~hp~FrviAT~Np~  188 (327)
T TIGR01650       115 K---DGKQITEFRDGILPWALQ---HNVALCFDEYDAGRPDVMFVIQRVLEAGGKLTLLDQNRVIRAHPAFRLFATANTI  188 (327)
T ss_pred             c---CCcceeEEecCcchhHHh---CCeEEEechhhccCHHHHHHHHHHhccCCeEEECCCceEecCCCCeEEEEeeCCC
Confidence            0   011001111 11222222   3568999999999888888888777631      1     134578899999975


Q ss_pred             C---------hhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHH
Q psy200          342 D---------LTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAG  399 (490)
Q Consensus       342 ~---------~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~  399 (490)
                      +         -...+...+.+||.+   .+.++.++.++-.+|+.......  .....+..++.+.+
T Consensus       189 g~Gd~~G~y~Gt~~l~~A~lDRF~i---~~~~~Yp~~e~E~~Il~~~~~~~--~~~~~~~i~~~mV~  250 (327)
T TIGR01650       189 GLGDTTGLYHGTQQINQAQMDRWSI---VTTLNYLEHDNEAAIVLAKAKGF--DDTEGKDIINAMVR  250 (327)
T ss_pred             CcCCCCcceeeeecCCHHHHhheee---EeeCCCCCHHHHHHHHHhhccCC--CccchHHHHHHHHH
Confidence            4         134456788889963   56899999999999988765332  11123455555554

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.

>PRK05707 DNA polymerase III subunit delta'; Validated

Probab=99.28  E-value=2.3e-10  Score=113.25  Aligned_cols=179  Identities=15%  Similarity=0.167  Sum_probs=113.2

Q ss_pred             cCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHh---cCC--CCCCcHHHHHHHHH
Q psy200          216 NETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNEL---KLK--PGGKSERHQLGAIL  290 (490)
Q Consensus       216 ~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l---~~~--~~~~s~~~~~~~l~  290 (490)
                      +.-++.++|+||+|+|||++|+.+++.+......  -.-.|..+.+...+...-.-++   ...  ....+.+++++...
T Consensus        19 ~r~~ha~Lf~G~~G~GK~~~A~~~A~~llC~~~~--~~~~Cg~C~sC~~~~~g~HPD~~~i~~~~~~~~i~id~iR~l~~   96 (328)
T PRK05707         19 GRHPHAYLLHGPAGIGKRALAERLAAALLCEAPQ--GGGACGSCKGCQLLRAGSHPDNFVLEPEEADKTIKVDQVRELVS   96 (328)
T ss_pred             CCcceeeeeECCCCCCHHHHHHHHHHHHcCCCCC--CCCCCCCCHHHHHHhcCCCCCEEEEeccCCCCCCCHHHHHHHHH
Confidence            3456779999999999999999999998642211  0012333322222211000000   000  11245667776554


Q ss_pred             HHHhc--CCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCC
Q psy200          291 KYFDT--KHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYS  368 (490)
Q Consensus       291 ~~l~~--~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls  368 (490)
                      .....  .++..|+|||++|.|....++.|...++.+   ...+++|.+|+   -.+.+++.+++||.    .+.|.+++
T Consensus        97 ~~~~~~~~~~~kv~iI~~a~~m~~~aaNaLLK~LEEP---p~~~~fiL~t~---~~~~ll~TI~SRc~----~~~~~~~~  166 (328)
T PRK05707         97 FVVQTAQLGGRKVVLIEPAEAMNRNAANALLKSLEEP---SGDTVLLLISH---QPSRLLPTIKSRCQ----QQACPLPS  166 (328)
T ss_pred             HHhhccccCCCeEEEECChhhCCHHHHHHHHHHHhCC---CCCeEEEEEEC---ChhhCcHHHHhhce----eeeCCCcC
Confidence            44322  244567889999999999899998888754   34566666665   25678899999996    89999999


Q ss_pred             HHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHHHH
Q psy200          369 REQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDIT  415 (490)
Q Consensus       369 ~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll  415 (490)
                      .+++.+.|...+..      ..++....++.   ...|.+..++.++
T Consensus       167 ~~~~~~~L~~~~~~------~~~~~~~~~l~---la~Gsp~~A~~l~  204 (328)
T PRK05707        167 NEESLQWLQQALPE------SDERERIELLT---LAGGSPLRALQLH  204 (328)
T ss_pred             HHHHHHHHHHhccc------CChHHHHHHHH---HcCCCHHHHHHHH
Confidence            99999999875421      24444444443   4667777776554

>PRK10923 glnG nitrogen regulation protein NR(I); Provisional

Probab=99.28  E-value=3.7e-11  Score=126.15  Aligned_cols=228  Identities=16%  Similarity=0.225  Sum_probs=149.5

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHh
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNEL  273 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l  273 (490)
                      ..++|....+.++...+...  ......++|+|++||||+++|+++++... ..+.+++.++|..+ ....+-..++..-
T Consensus       138 ~~lig~s~~~~~l~~~~~~~--~~~~~~vli~Ge~GtGK~~lA~~ih~~s~-~~~~~~i~i~c~~~-~~~~~~~~lfg~~  213 (469)
T PRK10923        138 TDIIGEAPAMQDVFRIIGRL--SRSSISVLINGESGTGKELVAHALHRHSP-RAKAPFIALNMAAI-PKDLIESELFGHE  213 (469)
T ss_pred             ccceecCHHHHHHHHHHHHH--hccCCeEEEEeCCCCcHHHHHHHHHhcCC-CCCCCeEeeeCCCC-CHHHHHHHhcCCC
Confidence            56889888888888877653  34567899999999999999999977542 34458899999887 3232333332222


Q ss_pred             cCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCHHHHHHhHhCCCC--------CCCcEEEEEecCCCChhH
Q psy200          274 KLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPSI--------PGSKLVLVGVANALDLTD  345 (490)
Q Consensus       274 ~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~--------~~~~vilI~~tn~~~~~~  345 (490)
                      .+.+.+.... ....    +... ..-.|||||++.|....|..|..+++....        ....+.+|++++.. +.+
T Consensus       214 ~g~~~~~~~~-~~g~----~~~a-~~Gtl~l~~i~~l~~~~q~~L~~~l~~~~~~~~~~~~~~~~~~rii~~~~~~-l~~  286 (469)
T PRK10923        214 KGAFTGANTI-RQGR----FEQA-DGGTLFLDEIGDMPLDVQTRLLRVLADGQFYRVGGYAPVKVDVRIIAATHQN-LEQ  286 (469)
T ss_pred             CCCCCCCCcC-CCCC----eeEC-CCCEEEEeccccCCHHHHHHHHHHHhcCcEEeCCCCCeEEeeEEEEEeCCCC-HHH
Confidence            1111111100 0001    1111 122789999999999989888888764321        12345777777532 222


Q ss_pred             -----hhhHHhhhccCCCCeeEEeCCCC--HHHHHHHHHHHHhcc----CC-CCCCCHHHHHHHHHHHHHhhCCHHHHHH
Q psy200          346 -----RMLPRLQANVTLQPTLMNFAPYS--REQILEIISQKLKQT----DK-FNMFNASALQLLAGKVAAVSGDIRKAID  413 (490)
Q Consensus       346 -----~l~~~l~~R~~~~~~~i~~~pls--~~e~~~il~~~l~~~----~~-~~~~~~~~i~~i~~~i~~~~Gd~r~ai~  413 (490)
                           .+.+.+..|+..  ..|.++|+.  .+++..++.+++...    +. ...+++++++.+..  +.|.||+|++-+
T Consensus       287 ~~~~~~~~~~L~~~l~~--~~i~~PpLreR~~Di~~l~~~~l~~~~~~~~~~~~~~~~~a~~~L~~--~~wpgNv~eL~~  362 (469)
T PRK10923        287 RVQEGKFREDLFHRLNV--IRVHLPPLRERREDIPRLARHFLQVAARELGVEAKLLHPETEAALTR--LAWPGNVRQLEN  362 (469)
T ss_pred             HHHcCCchHHHHHHhcc--eeecCCCcccchhhHHHHHHHHHHHHHHHcCCCCCCcCHHHHHHHHh--CCCCChHHHHHH
Confidence                 234566677643  378889987  467777777766543    22 23589999999998  899999999999


Q ss_pred             HHHHHHHHHHhccccCCcccccCHHHHHHHH
Q psy200          414 ITNHLIDLTYDNVKENGEVTGIGLKEVLGVI  444 (490)
Q Consensus       414 ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~  444 (490)
                      ++++++..+..        ..|+.+++...+
T Consensus       363 ~i~~~~~~~~~--------~~i~~~~l~~~~  385 (469)
T PRK10923        363 TCRWLTVMAAG--------QEVLIQDLPGEL  385 (469)
T ss_pred             HHHHHHHhCCC--------CcccHHHCcHhh
Confidence            99999876642        247777765433

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

Probab=99.26  E-value=2.3e-11  Score=110.92  Aligned_cols=129  Identities=19%  Similarity=0.380  Sum_probs=72.0

Q ss_pred             CCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCC-----HHHHHHHH
Q psy200          195 ELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRN-----AASVYETI  269 (490)
Q Consensus       195 ~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~-----~~~l~~~i  269 (490)
                      .|+||++++++|..+|. ....+.++.++|+|++|+|||++++.++..+.....+ ++.++|.....     ...++..+
T Consensus         1 ~fvgR~~e~~~l~~~l~-~~~~~~~~~~ll~G~~G~GKT~ll~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~l   78 (185)
T PF13191_consen    1 QFVGREEEIERLRDLLD-AAQSGSPRNLLLTGESGSGKTSLLRALLDRLAERGGY-VISINCDDSERNPYSPFRSALRQL   78 (185)
T ss_dssp             --TT-HHHHHHHHHTTG-GTSS-----EEE-B-TTSSHHHHHHHHHHHHHHHT---EEEEEEETTTS-HHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHH-HHHcCCCcEEEEECCCCCCHHHHHHHHHHHHHhcCCE-EEEEEEeccccchhhHHHHHHHHH
Confidence            48999999999999997 5566778999999999999999999999998766445 77787777631     13334444


Q ss_pred             HHHhcCCCC------------------------------------CCcHHHHH----HHHHHHHhc---CCCeEEEEEec
Q psy200          270 VNELKLKPG------------------------------------GKSERHQL----GAILKYFDT---KHKSILLILDE  306 (490)
Q Consensus       270 ~~~l~~~~~------------------------------------~~s~~~~~----~~l~~~l~~---~~~~~vI~IDE  306 (490)
                      +.++.....                                    ........    ..+...+..   ..++++|+|||
T Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~vlviDd  158 (185)
T PF13191_consen   79 IDQLLDQSQATTRSPLREKLAASLDDDAADLLVLLPDLDRLEAASALDPDSLEDRLEELLREILRELAARRKPLVLVIDD  158 (185)
T ss_dssp             S------------------------------------------SS---HHHHH----HHHHHHHTTS-SE---EEEEEET
T ss_pred             HHHhhccccccccccccccccccccccccccccccccccccccccCCCHHHHHhHHHHHHHHHHHHHHhCCCeEEEEEeC
Confidence            333221100                                    00111112    334444322   13469999999


Q ss_pred             CccccccCHHHHHHhHhCC
Q psy200          307 IDALESRKQTILYTIFEWP  325 (490)
Q Consensus       307 id~l~~~~~~~L~~l~~~~  325 (490)
                      +|++....++.|..+++..
T Consensus       159 ~d~~~~~~~~~l~~l~~~~  177 (185)
T PF13191_consen  159 LDWADPASLDLLRALARRL  177 (185)
T ss_dssp             TTHHHTTHHHHHHH-----
T ss_pred             CCCCCcHHHHHHHhccccc
Confidence            9999888888887776644

>TIGR02915 PEP_resp_reg putative PEP-CTERM system response regulator

Probab=99.26  E-value=3.9e-11  Score=125.09  Aligned_cols=224  Identities=17%  Similarity=0.189  Sum_probs=144.0

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHh
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNEL  273 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l  273 (490)
                      ..++|....+..+...+...  ......++|+|++|+||+++|+.+..... ....+++.++|..+.. ..+-..++..-
T Consensus       139 ~~lig~s~~~~~l~~~i~~~--a~~~~~vli~Ge~GtGK~~lA~~ih~~s~-~~~~~~v~v~c~~~~~-~~~~~~lfg~~  214 (445)
T TIGR02915       139 RGLITSSPGMQKICRTIEKI--APSDITVLLLGESGTGKEVLARALHQLSD-RKDKRFVAINCAAIPE-NLLESELFGYE  214 (445)
T ss_pred             cceeecCHHHHHHHHHHHHH--hCCCCCEEEECCCCcCHHHHHHHHHHhCC-cCCCCeEEEECCCCCh-HHHHHHhcCCC
Confidence            45788888888888877653  34567899999999999999999976543 3345789999998732 22222222211


Q ss_pred             cCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCHHHHHHhHhCCCC--------CCCcEEEEEecCCCChhH
Q psy200          274 KLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPSI--------PGSKLVLVGVANALDLTD  345 (490)
Q Consensus       274 ~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~--------~~~~vilI~~tn~~~~~~  345 (490)
                      ...+.+.. ......+.    . ...-+||||||+.|....|..|..+++....        ....+.+|++++.. +..
T Consensus       215 ~~~~~~~~-~~~~g~~~----~-a~~gtl~l~~i~~l~~~~q~~l~~~l~~~~~~~~~~~~~~~~~~rii~~~~~~-l~~  287 (445)
T TIGR02915       215 KGAFTGAV-KQTLGKIE----Y-AHGGTLFLDEIGDLPLNLQAKLLRFLQERVIERLGGREEIPVDVRIVCATNQD-LKR  287 (445)
T ss_pred             CCCcCCCc-cCCCCcee----E-CCCCEEEEechhhCCHHHHHHHHHHHhhCeEEeCCCCceeeeceEEEEecCCC-HHH
Confidence            11111110 00001111    1 1123899999999999989888888764321        12356777777632 211


Q ss_pred             -----hhhHHhhhccCCCCeeEEeCCCC--HHHHHHHHHHHHhcc----CC-CCCCCHHHHHHHHHHHHHhhCCHHHHHH
Q psy200          346 -----RMLPRLQANVTLQPTLMNFAPYS--REQILEIISQKLKQT----DK-FNMFNASALQLLAGKVAAVSGDIRKAID  413 (490)
Q Consensus       346 -----~l~~~l~~R~~~~~~~i~~~pls--~~e~~~il~~~l~~~----~~-~~~~~~~~i~~i~~~i~~~~Gd~r~ai~  413 (490)
                           .+.+.+..|+..  ..|.++|+.  .+++..++.+++...    +. ...+++++++.+..  +.|.||+|++-+
T Consensus       288 ~~~~~~~~~~L~~~l~~--~~i~lPpLr~R~~Di~~l~~~~l~~~~~~~~~~~~~~~~~a~~~L~~--~~wpgNvreL~~  363 (445)
T TIGR02915       288 MIAEGTFREDLFYRIAE--ISITIPPLRSRDGDAVLLANAFLERFARELKRKTKGFTDDALRALEA--HAWPGNVRELEN  363 (445)
T ss_pred             HHHcCCccHHHHHHhcc--ceecCCCchhchhhHHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHh--CCCCChHHHHHH
Confidence                 233456566543  378888887  456766666665543    22 24689999999987  789999999999


Q ss_pred             HHHHHHHHHHhccccCCcccccCHHHH
Q psy200          414 ITNHLIDLTYDNVKENGEVTGIGLKEV  440 (490)
Q Consensus       414 ll~~a~~~a~~~~~~~~~~~~It~~~v  440 (490)
                      ++++|+..+..        ..|+.+++
T Consensus       364 ~i~~a~~~~~~--------~~i~~~~l  382 (445)
T TIGR02915       364 KVKRAVIMAEG--------NQITAEDL  382 (445)
T ss_pred             HHHHHHHhCCC--------CcccHHHc
Confidence            99999865542        24666665

Members of this protein family share full-length homology with (but do not include) the acetoacetate metabolism regulatory protein AtoC. These proteins have a Fis family DNA binding sequence (pfam02954), a response regulator receiver domain (pfam00072), and sigma-54 interaction domain (pfam00158).

>TIGR01818 ntrC nitrogen regulation protein NR(I)

Probab=99.24  E-value=1e-10  Score=122.58  Aligned_cols=228  Identities=17%  Similarity=0.223  Sum_probs=148.7

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHh
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNEL  273 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l  273 (490)
                      ..++|......++...+...  ......++|.|++||||+++++++..... .....++.++|... ....+-..++...
T Consensus       134 ~~lig~s~~~~~v~~~i~~~--a~~~~~vli~Ge~GtGK~~~A~~ih~~~~-~~~~~~~~~~c~~~-~~~~~~~~lfg~~  209 (463)
T TIGR01818       134 AELIGEAPAMQEVFRAIGRL--SRSDITVLINGESGTGKELVARALHRHSP-RANGPFIALNMAAI-PKDLIESELFGHE  209 (463)
T ss_pred             cceeecCHHHHHHHHHHHHH--hCcCCeEEEECCCCCCHHHHHHHHHHhCC-CCCCCeEEEeCCCC-CHHHHHHHhcCCC
Confidence            35777777777777777652  34566899999999999999999976543 33458899999987 2222222222211


Q ss_pred             cCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCHHHHHHhHhCCCC--------CCCcEEEEEecCCCChhH
Q psy200          274 KLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPSI--------PGSKLVLVGVANALDLTD  345 (490)
Q Consensus       274 ~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~--------~~~~vilI~~tn~~~~~~  345 (490)
                      ...+.+... .....    +.. ....+||||||+.|....|..|..+++....        ....+.+|++++.. +.+
T Consensus       210 ~~~~~~~~~-~~~g~----~~~-a~~gtl~l~ei~~l~~~~q~~ll~~l~~~~~~~~~~~~~~~~~~rii~~~~~~-l~~  282 (463)
T TIGR01818       210 KGAFTGANT-RRQGR----FEQ-ADGGTLFLDEIGDMPLDAQTRLLRVLADGEFYRVGGRTPIKVDVRIVAATHQN-LEA  282 (463)
T ss_pred             CCCCCCccc-CCCCc----EEE-CCCCeEEEEchhhCCHHHHHHHHHHHhcCcEEECCCCceeeeeeEEEEeCCCC-HHH
Confidence            111111110 00001    111 1123799999999999888888888764321        12355677777532 211


Q ss_pred             -----hhhHHhhhccCCCCeeEEeCCCC--HHHHHHHHHHHHhcc----CC-CCCCCHHHHHHHHHHHHHhhCCHHHHHH
Q psy200          346 -----RMLPRLQANVTLQPTLMNFAPYS--REQILEIISQKLKQT----DK-FNMFNASALQLLAGKVAAVSGDIRKAID  413 (490)
Q Consensus       346 -----~l~~~l~~R~~~~~~~i~~~pls--~~e~~~il~~~l~~~----~~-~~~~~~~~i~~i~~~i~~~~Gd~r~ai~  413 (490)
                           .+.+.+..|+..  ..|.++|+.  .+++..++.+++...    +. ...+++++++.+..  +.|.||+|++-+
T Consensus       283 ~~~~~~f~~~L~~rl~~--~~i~lPpLr~R~~Di~~l~~~~l~~~~~~~~~~~~~~~~~a~~~L~~--~~wpgNvreL~~  358 (463)
T TIGR01818       283 LVRQGKFREDLFHRLNV--IRIHLPPLRERREDIPRLARHFLALAARELDVEPKLLDPEALERLKQ--LRWPGNVRQLEN  358 (463)
T ss_pred             HHHcCCcHHHHHHHhCc--ceecCCCcccchhhHHHHHHHHHHHHHHHhCCCCCCcCHHHHHHHHh--CCCCChHHHHHH
Confidence                 233466666653  379999998  788888887776554    11 24689999999998  789999999999


Q ss_pred             HHHHHHHHHHhccccCCcccccCHHHHHHHH
Q psy200          414 ITNHLIDLTYDNVKENGEVTGIGLKEVLGVI  444 (490)
Q Consensus       414 ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~  444 (490)
                      ++++++..+..        ..|+.+++...+
T Consensus       359 ~~~~~~~~~~~--------~~i~~~~l~~~~  381 (463)
T TIGR01818       359 LCRWLTVMASG--------DEVLVSDLPAEL  381 (463)
T ss_pred             HHHHHHHhCCC--------CcccHHhchHHH
Confidence            99999876643        247777775444

This model represents NtrC, a DNA-binding response regulator that is phosphorylated by NtrB and interacts with sigma-54. NtrC usually controls the expression of glutamine synthase, GlnA, and may be called GlnL, GlnG, etc.

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

Probab=99.22  E-value=4.9e-10  Score=113.16  Aligned_cols=170  Identities=16%  Similarity=0.180  Sum_probs=106.6

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCc-eEEEEeccCCCCHHHHHHHHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAF-KTIYINCNSVRNAASVYETIVNE  272 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~-~~~~v~~~~~~~~~~l~~~i~~~  272 (490)
                      +++++.++.++.+...|..      .++++|+|+||||||++|+.+++.+.....+ .+.++......+..+++.    .
T Consensus       175 ~d~~i~e~~le~l~~~L~~------~~~iil~GppGtGKT~lA~~la~~l~~~~~~~~v~~VtFHpsySYeDFI~----G  244 (459)
T PRK11331        175 NDLFIPETTIETILKRLTI------KKNIILQGPPGVGKTFVARRLAYLLTGEKAPQRVNMVQFHQSYSYEDFIQ----G  244 (459)
T ss_pred             hcccCCHHHHHHHHHHHhc------CCCEEEECCCCCCHHHHHHHHHHHhcCCcccceeeEEeecccccHHHHhc----c
Confidence            6688889999888887753      6799999999999999999999988533222 333444443334333332    1


Q ss_pred             hcCCCCCCc--HHHHHHHHHHHHhcCCCeEEEEEecCccccccC-HHHHHHhHhCC-------------------CCCCC
Q psy200          273 LKLKPGGKS--ERHQLGAILKYFDTKHKSILLILDEIDALESRK-QTILYTIFEWP-------------------SIPGS  330 (490)
Q Consensus       273 l~~~~~~~s--~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~-~~~L~~l~~~~-------------------~~~~~  330 (490)
                      +.....+..  ..-+.+++..+.....++++|||||+++..-.. ...++.+++..                   .....
T Consensus       245 ~rP~~vgy~~~~G~f~~~~~~A~~~p~~~~vliIDEINRani~kiFGel~~lLE~~~rg~~~~v~l~y~e~d~e~f~iP~  324 (459)
T PRK11331        245 YRPNGVGFRRKDGIFYNFCQQAKEQPEKKYVFIIDEINRANLSKVFGEVMMLMEHDKRGENWSVPLTYSENDEERFYVPE  324 (459)
T ss_pred             cCCCCCCeEecCchHHHHHHHHHhcccCCcEEEEehhhccCHHHhhhhhhhhccccccccccceeeeccccccccccCCC
Confidence            111111111  123455555555544578999999999976432 33344444321                   12346


Q ss_pred             cEEEEEecCCCCh-hHhhhHHhhhccCCCCeeEEeCC-CCHHHHHHHHH
Q psy200          331 KLVLVGVANALDL-TDRMLPRLQANVTLQPTLMNFAP-YSREQILEIIS  377 (490)
Q Consensus       331 ~vilI~~tn~~~~-~~~l~~~l~~R~~~~~~~i~~~p-ls~~e~~~il~  377 (490)
                      ++.+||++|..|- ...++.++++||.    .+.+.| ++.....+++.
T Consensus       325 Nl~IIgTMNt~Drs~~~lD~AlrRRF~----fi~i~p~~~~~~~~~~l~  369 (459)
T PRK11331        325 NVYIIGLMNTADRSLAVVDYALRRRFS----FIDIEPGFDTPQFRNFLL  369 (459)
T ss_pred             CeEEEEecCccccchhhccHHHHhhhh----eEEecCCCChHHHHHHHH
Confidence            7899999996652 2346789999997    677777 55555555543

>PRK15115 response regulator GlrR; Provisional

Probab=99.21  E-value=1.3e-10  Score=121.20  Aligned_cols=228  Identities=18%  Similarity=0.245  Sum_probs=142.8

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHh
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNEL  273 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l  273 (490)
                      ..++|....+..+.+.+...  ......++|+|++|+||+++|+.+.+... ..+..++.++|.... ...+-..++...
T Consensus       134 ~~lig~s~~~~~~~~~~~~~--a~~~~~vli~Ge~GtGk~~lA~~ih~~s~-r~~~~f~~i~c~~~~-~~~~~~~lfg~~  209 (444)
T PRK15115        134 EAIVTRSPLMLRLLEQARMV--AQSDVSVLINGQSGTGKEILAQAIHNASP-RASKPFIAINCGALP-EQLLESELFGHA  209 (444)
T ss_pred             hcccccCHHHHHHHHHHHhh--ccCCCeEEEEcCCcchHHHHHHHHHHhcC-CCCCCeEEEeCCCCC-HHHHHHHhcCCC
Confidence            34677766666666555442  23456899999999999999999977543 334589999999873 222222222221


Q ss_pred             cCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCHHHHHHhHhCCCC--------CCCcEEEEEecCCCChhH
Q psy200          274 KLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPSI--------PGSKLVLVGVANALDLTD  345 (490)
Q Consensus       274 ~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~--------~~~~vilI~~tn~~~~~~  345 (490)
                      ...+.+... .....    +.. ...-+||||||+.|....|..|..+++....        ....+.+|++++. ++..
T Consensus       210 ~~~~~~~~~-~~~g~----~~~-a~~gtl~l~~i~~l~~~~q~~L~~~l~~~~~~~~g~~~~~~~~~rii~~~~~-~l~~  282 (444)
T PRK15115        210 RGAFTGAVS-NREGL----FQA-AEGGTLFLDEIGDMPAPLQVKLLRVLQERKVRPLGSNRDIDIDVRIISATHR-DLPK  282 (444)
T ss_pred             cCCCCCCcc-CCCCc----EEE-CCCCEEEEEccccCCHHHHHHHHHHHhhCCEEeCCCCceeeeeEEEEEeCCC-CHHH
Confidence            111111100 00001    111 1123899999999999999988888764321        1235678877763 2322


Q ss_pred             -----hhhHHhhhccCCCCeeEEeCCCCH--HHHHHHHHHHHhcc----CCC-CCCCHHHHHHHHHHHHHhhCCHHHHHH
Q psy200          346 -----RMLPRLQANVTLQPTLMNFAPYSR--EQILEIISQKLKQT----DKF-NMFNASALQLLAGKVAAVSGDIRKAID  413 (490)
Q Consensus       346 -----~l~~~l~~R~~~~~~~i~~~pls~--~e~~~il~~~l~~~----~~~-~~~~~~~i~~i~~~i~~~~Gd~r~ai~  413 (490)
                           .+.+.+..|+..  ..|.++|+..  +++..++.+.+...    +.. ..+++++++.+..  +.|.||+|++.+
T Consensus       283 ~~~~~~f~~~l~~~l~~--~~i~lPpLr~R~eDi~~l~~~~l~~~~~~~~~~~~~~~~~a~~~L~~--~~WpgNvreL~~  358 (444)
T PRK15115        283 AMARGEFREDLYYRLNV--VSLKIPALAERTEDIPLLANHLLRQAAERHKPFVRAFSTDAMKRLMT--ASWPGNVRQLVN  358 (444)
T ss_pred             HHHcCCccHHHHHhhce--eeecCCChHhccccHHHHHHHHHHHHHHHhCCCCCCcCHHHHHHHHh--CCCCChHHHHHH
Confidence                 223445555542  3688888873  56776666665543    212 3489999999997  889999999999


Q ss_pred             HHHHHHHHHHhccccCCcccccCHHHHHHHH
Q psy200          414 ITNHLIDLTYDNVKENGEVTGIGLKEVLGVI  444 (490)
Q Consensus       414 ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~  444 (490)
                      ++++++..+.  +      ..|+.+++...+
T Consensus       359 ~i~~~~~~~~--~------~~i~~~~l~~~~  381 (444)
T PRK15115        359 VIEQCVALTS--S------PVISDALVEQAL  381 (444)
T ss_pred             HHHHHHHhCC--C------CccChhhhhhhh
Confidence            9999986543  2      357777765443

>TIGR02031 BchD-ChlD magnesium chelatase ATPase subunit D

Probab=99.21  E-value=5.3e-10  Score=119.24  Aligned_cols=215  Identities=13%  Similarity=0.081  Sum_probs=139.6

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHH--HHHhcCCCCCCcHHHHHHHHHHHHh
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETI--VNELKLKPGGKSERHQLGAILKYFD  294 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i--~~~l~~~~~~~s~~~~~~~l~~~l~  294 (490)
                      ...++|+|.|++|||||++++++++.+..  ...|+.+.+..  +...++..+  ...+..   |.     ..+-.-.+.
T Consensus        14 p~~g~vLl~G~~GtgKs~lar~l~~~~~~--~~pfv~i~~~~--t~d~L~G~idl~~~~~~---g~-----~~~~~G~L~   81 (589)
T TIGR02031        14 PSLGGVAIRARAGTGKTALARALAEILPP--IMPFVELPLGV--TEDRLIGGIDVEESLAG---GQ-----RVTQPGLLD   81 (589)
T ss_pred             CCcceEEEEcCCCcHHHHHHHHHHHhCCc--CCCeEecCccc--chhhcccchhhhhhhhc---Cc-----ccCCCCCee
Confidence            34789999999999999999999887642  22456565321  222222211  000000   00     000000011


Q ss_pred             cCCCeEEEEEecCccccccCHHHHHHhHhCCCC----------CCCcEEEEEecCCCChhHhhhHHhhhccCCCCeeEEe
Q psy200          295 TKHKSILLILDEIDALESRKQTILYTIFEWPSI----------PGSKLVLVGVANALDLTDRMLPRLQANVTLQPTLMNF  364 (490)
Q Consensus       295 ~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~----------~~~~vilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~  364 (490)
                      . ...-+||||||+.+....|..|...++...+          ....+.||+++|..+....+.+.+..||.+   .+.+
T Consensus        82 ~-A~~GvL~lDEi~rl~~~~q~~Ll~al~~g~v~i~r~G~~~~~p~~f~lIAt~np~e~~g~L~~~LldRf~l---~v~~  157 (589)
T TIGR02031        82 E-APRGVLYVDMANLLDDGLSNRLLQALDEGVVIVEREGISVVHPAKFALIATYDPAEGGGGLPDHLLDRLAL---HVSL  157 (589)
T ss_pred             e-CCCCcEeccchhhCCHHHHHHHHHHHHcCCeEEEECCCceeecCceEEEEecCCccccCCCCHHHHHhccC---eeec
Confidence            1 1123999999999999999999998864421          135688999888654334667788899986   3444


Q ss_pred             CCC-CHHHHHHHHHHHHhc---------------------cCCCCCCCHHHHHHHHHHHHHhhC-CHHHHHHHHHHHHHH
Q psy200          365 APY-SREQILEIISQKLKQ---------------------TDKFNMFNASALQLLAGKVAAVSG-DIRKAIDITNHLIDL  421 (490)
Q Consensus       365 ~pl-s~~e~~~il~~~l~~---------------------~~~~~~~~~~~i~~i~~~i~~~~G-d~r~ai~ll~~a~~~  421 (490)
                      ..+ +.++..+|+...+..                     ......++++.++.|++....... +.|..+.+++-|...
T Consensus       158 ~~~~~~~er~eil~~~~~~~~~~~~~~~~~~~~~i~~ar~~~~~V~i~~~~~~~l~~~~~~~gv~s~Ra~i~~~r~ArA~  237 (589)
T TIGR02031       158 EDVASQDLRVEIVRRERCNEVFRMNDELELLRGQIEAARELLPQVTISAEQVKELVLTAASLGISGHRADLFAVRAAKAH  237 (589)
T ss_pred             CCCCCHHHHHHHHHHHHHhhhhhcchhhHHHHHHHHHHHHhcCCccCCHHHHHHHHHHHHHcCCCCccHHHHHHHHHHHH
Confidence            433 455556666554311                     123467889999998886655443 488889999999999


Q ss_pred             HHhccccCCcccccCHHHHHHHHHHhccCcc
Q psy200          422 TYDNVKENGEVTGIGLKEVLGVISSVYCTSQ  452 (490)
Q Consensus       422 a~~~~~~~~~~~~It~~~v~~a~~~~~~~~~  452 (490)
                      |..++     ...|+.+||..|+.-++.++.
T Consensus       238 Aal~g-----r~~V~~~Dv~~a~~lvl~hR~  263 (589)
T TIGR02031       238 AALHG-----RTEVTEEDLKLAVELVLLPRA  263 (589)
T ss_pred             HHHhC-----CCCCCHHHHHHHHHHHhhhhc
Confidence            99999     789999999999998876554

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. Unlike subunit I (TIGR02030), this subunit is not found in archaea.

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

Probab=99.21  E-value=5.2e-10  Score=111.70  Aligned_cols=165  Identities=19%  Similarity=0.197  Sum_probs=108.4

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHh
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNEL  273 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l  273 (490)
                      ..++|+++.+..+...+..      +++++|.|+||||||++++.++..++    ..++.++|.....+.+++....-..
T Consensus        24 ~~~~g~~~~~~~~l~a~~~------~~~vll~G~PG~gKT~la~~lA~~l~----~~~~~i~~t~~l~p~d~~G~~~~~~   93 (329)
T COG0714          24 KVVVGDEEVIELALLALLA------GGHVLLEGPPGVGKTLLARALARALG----LPFVRIQCTPDLLPSDLLGTYAYAA   93 (329)
T ss_pred             CeeeccHHHHHHHHHHHHc------CCCEEEECCCCccHHHHHHHHHHHhC----CCeEEEecCCCCCHHHhcCchhHhh
Confidence            4588888888777666643      77999999999999999999999986    7889999998888777654322211


Q ss_pred             cCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCHHHHHHhHhCC---------CCCCCcEEEEEecCCCCh-
Q psy200          274 KLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWP---------SIPGSKLVLVGVANALDL-  343 (490)
Q Consensus       274 ~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~---------~~~~~~vilI~~tn~~~~-  343 (490)
                      .....     ..+.+...-+-..-+ .++++|||+......+..|+..++..         ......+++|++.|..+. 
T Consensus        94 ~~~~~-----~~~~~~~gpl~~~~~-~ill~DEInra~p~~q~aLl~~l~e~~vtv~~~~~~~~~~~f~viaT~Np~e~~  167 (329)
T COG0714          94 LLLEP-----GEFRFVPGPLFAAVR-VILLLDEINRAPPEVQNALLEALEERQVTVPGLTTIRLPPPFIVIATQNPGEYE  167 (329)
T ss_pred             hhccC-----CeEEEecCCcccccc-eEEEEeccccCCHHHHHHHHHHHhCcEEEECCcCCcCCCCCCEEEEccCccccC
Confidence            10000     000000000000011 49999999999999999999887642         112356788888885432 


Q ss_pred             -hHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHH
Q psy200          344 -TDRMLPRLQANVTLQPTLMNFAPYSREQILEIIS  377 (490)
Q Consensus       344 -~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~  377 (490)
                       ...+.+.+.+||.+   .+.++.+..++...++.
T Consensus       168 g~~~l~eA~ldRf~~---~~~v~yp~~~~e~~~i~  199 (329)
T COG0714         168 GTYPLPEALLDRFLL---RIYVDYPDSEEEERIIL  199 (329)
T ss_pred             CCcCCCHHHHhhEEE---EEecCCCCchHHHHHHH
Confidence             34456788889863   68888884444343333

>TIGR00368 Mg chelatase-related protein

Probab=99.21  E-value=6.6e-10  Score=115.60  Aligned_cols=231  Identities=16%  Similarity=0.164  Sum_probs=139.0

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHH---HH
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYET---IV  270 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~---i~  270 (490)
                      .++.|++..++.+.-.+      ..+.+++|+|++|+|||++++.+...+.....-  ..+.+....+....+..   +.
T Consensus       192 ~dv~Gq~~~~~al~~aa------~~g~~vlliG~pGsGKTtlar~l~~llp~~~~~--~~le~~~i~s~~g~~~~~~~~~  263 (499)
T TIGR00368       192 KDIKGQQHAKRALEIAA------AGGHNLLLFGPPGSGKTMLASRLQGILPPLTNE--EAIETARIWSLVGKLIDRKQIK  263 (499)
T ss_pred             HHhcCcHHHHhhhhhhc------cCCCEEEEEecCCCCHHHHHHHHhcccCCCCCc--EEEeccccccchhhhccccccc
Confidence            67889888766555443      346789999999999999999998765422111  22333222221111000   00


Q ss_pred             -HHhcCCCCCCcHHHHH--------HHHHHHHhcCCCeEEEEEecCccccccCHHHHHHhHhCCCC----------CCCc
Q psy200          271 -NELKLKPGGKSERHQL--------GAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPSI----------PGSK  331 (490)
Q Consensus       271 -~~l~~~~~~~s~~~~~--------~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~----------~~~~  331 (490)
                       .-+.......+...+.        ..+.  +..   .-+|||||++.+....++.|++.++....          ...+
T Consensus       264 ~~Pf~~p~~s~s~~~~~ggg~~~~pG~i~--lA~---~GvLfLDEi~e~~~~~~~~L~~~LE~~~v~i~r~g~~~~~pa~  338 (499)
T TIGR00368       264 QRPFRSPHHSASKPALVGGGPIPLPGEIS--LAH---NGVLFLDELPEFKRSVLDALREPIEDGSISISRASAKIFYPAR  338 (499)
T ss_pred             cCCccccccccchhhhhCCccccchhhhh--ccC---CCeEecCChhhCCHHHHHHHHHHHHcCcEEEEecCcceeccCC
Confidence             0000000001111110        0111  111   23999999999998889999988764421          2357


Q ss_pred             EEEEEecCCC-----C---------------hhHhhhHHhhhccCCCCeeEEeCCCCHHHHH------------H-----
Q psy200          332 LVLVGVANAL-----D---------------LTDRMLPRLQANVTLQPTLMNFAPYSREQIL------------E-----  374 (490)
Q Consensus       332 vilI~~tn~~-----~---------------~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~------------~-----  374 (490)
                      +.+|+++|..     +               +..++...+.+||++   .+.+.+++.+++.            +     
T Consensus       339 frlIaa~Npcpcg~~~~~~~~c~c~~~~~~~y~~~is~pllDR~dl---~~~~~~~~~~~l~~~~~~e~s~~ir~rV~~A  415 (499)
T TIGR00368       339 FQLVAAMNPCPCGHYGGKNTHCRCSPQQISRYWNKLSGPFLDRIDL---SVEVPLLPPEKLLSTGSGESSAEVKQRVIKA  415 (499)
T ss_pred             eEEEEecCCcccCcCCCCcccccCCHHHHHHHhhhccHhHHhhCCE---EEEEcCCCHHHHhccCCCCCHHHHHHHHHHH
Confidence            8899988842     1               233567789999996   7888887655432            1     


Q ss_pred             --HHHHHHhcc---C-----------CCCCCCHHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHhccccCCcccccCHH
Q psy200          375 --IISQKLKQT---D-----------KFNMFNASALQLLAGKVAAVSGDIRKAIDITNHLIDLTYDNVKENGEVTGIGLK  438 (490)
Q Consensus       375 --il~~~l~~~---~-----------~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll~~a~~~a~~~~~~~~~~~~It~~  438 (490)
                        +...++...   .           ..+.+++++.+.+.+.+....=..|....+++-|..+|..++     ...|+.+
T Consensus       416 r~~q~~R~~~~~~~~~N~~l~~~~l~~~~~l~~~~~~~l~~a~~~~~lS~R~~~rilrvArTiAdL~g-----~~~i~~~  490 (499)
T TIGR00368       416 REIQNIRYEKFANINKNADLNSDEIEQFCKLSAIDANDLEGALNKLGLSSRATHRILKVARTIADLKE-----EKNISRE  490 (499)
T ss_pred             HHHHHHHhcCCCCCcccccCCHHHHHhhcCCCHHHHHHHHHHHHhcCCCchHHHHHHHHHHHHHhhcC-----CCCCCHH
Confidence              111222110   0           013456666666655444444578888899999999999999     7899999


Q ss_pred             HHHHHHH
Q psy200          439 EVLGVIS  445 (490)
Q Consensus       439 ~v~~a~~  445 (490)
                      ||.+|+.
T Consensus       491 hv~eA~~  497 (499)
T TIGR00368       491 HLAEAIE  497 (499)
T ss_pred             HHHHHHh
Confidence            9999984

The N-terminal end matches very strongly a pfam Mg_chelatase domain.

>PRK13765 ATP-dependent protease Lon; Provisional

Probab=99.20  E-value=8.8e-10  Score=117.37  Aligned_cols=239  Identities=17%  Similarity=0.187  Sum_probs=154.5

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHh
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNEL  273 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l  273 (490)
                      ++++|+++.++.|...+..      .++++|+|+||+|||++++++++.+....-..++|+..+.. +...++..+...+
T Consensus        31 ~~vigq~~a~~~L~~~~~~------~~~~l~~G~~G~GKttla~~l~~~l~~~~~~~~~~~~np~~-~~~~~~~~v~~~~  103 (637)
T PRK13765         31 DQVIGQEHAVEVIKKAAKQ------RRHVMMIGSPGTGKSMLAKAMAELLPKEELQDILVYPNPED-PNNPKIRTVPAGK  103 (637)
T ss_pred             HHcCChHHHHHHHHHHHHh------CCeEEEECCCCCcHHHHHHHHHHHcChHhHHHheEeeCCCc-chHHHHHHHHHhc
Confidence            7899999999988877753      35899999999999999999999875332234556555443 5555555554433


Q ss_pred             cCC-----------------------------------------------------------------------------
Q psy200          274 KLK-----------------------------------------------------------------------------  276 (490)
Q Consensus       274 ~~~-----------------------------------------------------------------------------  276 (490)
                      +..                                                                             
T Consensus       104 G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~nllv~ns~~~~aP  183 (637)
T PRK13765        104 GKQIVEAHKEEARKRNQMRNMLMMIIIAGIIGYAFIYAGQILWGIIAAGLIYMALRYFRPKEDAMVPKLLVNNADKKTAP  183 (637)
T ss_pred             CHHHHHHHHHHhhhhccccchhHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHhhCCcCceEEEEEEEeCCCCCCCC
Confidence            210                                                                             


Q ss_pred             ---CCCCcHHHHHHHHHHH------H-----h--c-----CCCeEEEEEecCccccccCHHHHHHhHhCCCC--------
Q psy200          277 ---PGGKSERHQLGAILKY------F-----D--T-----KHKSILLILDEIDALESRKQTILYTIFEWPSI--------  327 (490)
Q Consensus       277 ---~~~~s~~~~~~~l~~~------l-----~--~-----~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~--------  327 (490)
                         ....+..+++..++..      +     .  +     ....-+|||||++.|....|..|.++++....        
T Consensus       184 vi~~~~p~~~~LfG~i~~~~~~~Gg~~t~~~~~i~~G~L~kAnGGtL~LDei~~L~~~~q~~Llr~L~~~~i~i~g~~e~  263 (637)
T PRK13765        184 FVDATGAHAGALLGDVRHDPFQSGGLETPAHDRVEAGAIHKAHKGVLFIDEINTLDLESQQSLLTAMQEKKFPITGQSER  263 (637)
T ss_pred             EEEeCCCCHHHcCCccccccccccccccCccccCCCCceeECCCcEEEEeChHhCCHHHHHHHHHHHHhCCEEecccccc
Confidence               0001122222222100      0     0  0     01124899999999987778888877643221        


Q ss_pred             ----------CCCcEEEEEecCCCChhHhhhHHhhhccCCCCeeEEeCCC---CHHHHHHHHHHHHh---ccCCCCCCCH
Q psy200          328 ----------PGSKLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPY---SREQILEIISQKLK---QTDKFNMFNA  391 (490)
Q Consensus       328 ----------~~~~vilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pl---s~~e~~~il~~~l~---~~~~~~~~~~  391 (490)
                                -...+.+|++++. ++...+++.|..||..-...+.|..-   +.+....++.....   ..+....++.
T Consensus       264 ~~~~~~~~~~ip~dvrvI~a~~~-~ll~~~dpdL~~rfk~~~v~v~f~~~~~d~~e~~~~~~~~iaqe~~~~G~l~~f~~  342 (637)
T PRK13765        264 SSGAMVRTEPVPCDFIMVAAGNL-DALENMHPALRSRIKGYGYEVYMRDTMEDTPENRRKLVRFVAQEVKRDGKIPHFDR  342 (637)
T ss_pred             cccccCCCcceeeeeEEEEecCc-CHHHhhhHHHHHHhccCeEEEEcccccCCCHHHHHHHHHHHHHHhhhccCCCCCCH
Confidence                      1246688888886 45566678888887511024556543   35555555543332   2223457999


Q ss_pred             HHHHHHHHHHHHhhCC-------HHHHHHHHHHHHHHHHhccccCCcccccCHHHHHHHHH
Q psy200          392 SALQLLAGKVAAVSGD-------IRKAIDITNHLIDLTYDNVKENGEVTGIGLKEVLGVIS  445 (490)
Q Consensus       392 ~~i~~i~~~i~~~~Gd-------~r~ai~ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~~  445 (490)
                      +++..|.+......|+       .+.+.++++.|..+|..++     ...|+.+|+.+|+.
T Consensus       343 eAVa~LI~~~~R~ag~r~~lsl~~~~l~~l~r~a~~~a~~~~-----~~~i~~~~v~~a~~  398 (637)
T PRK13765        343 DAVEEIIREAKRRAGRKGHLTLKLRDLGGLVRVAGDIARSEG-----AELTTAEHVLEAKK  398 (637)
T ss_pred             HHHHHHHHHHHHHhCCccccccCHHHHHHHHHHHHHHHHhhc-----cceecHHHHHHHHH
Confidence            9999999988777776       6778889999999999888     67899999988874

>COG1239 ChlI Mg-chelatase subunit ChlI [Coenzyme metabolism]

Probab=99.19  E-value=1.5e-09  Score=107.23  Aligned_cols=239  Identities=17%  Similarity=0.194  Sum_probs=144.4

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEE---EeccCCCCHHHHHHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIY---INCNSVRNAASVYETIV  270 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~---v~~~~~~~~~~l~~~i~  270 (490)
                      .-++|.+.....|.-..    -...-+++||.|+.|+||||++++|+.-|.   ...++.   ++|... .+..+.....
T Consensus        17 ~aivGqd~lk~aL~l~a----v~P~iggvLI~G~kGtaKSt~~Rala~LLp---~~~~V~gc~f~cdP~-~P~~~c~~c~   88 (423)
T COG1239          17 TAIVGQDPLKLALGLNA----VDPQIGGALIAGEKGTAKSTLARALADLLP---EIEVVIGCPFNCDPD-DPEEMCDECR   88 (423)
T ss_pred             hhhcCchHHHHHHhhhh----cccccceeEEecCCCccHHHHHHHHHHhCC---ccceecCCCCCCCCC-ChhhhhHHHH
Confidence            45788877665443321    235678999999999999999999998874   333332   233332 2222222222


Q ss_pred             HH---hc------------CCCCCCcHHHHHHH--HHHHHhc-----------CCCeEEEEEecCccccccCHHHHHHhH
Q psy200          271 NE---LK------------LKPGGKSERHQLGA--ILKYFDT-----------KHKSILLILDEIDALESRKQTILYTIF  322 (490)
Q Consensus       271 ~~---l~------------~~~~~~s~~~~~~~--l~~~l~~-----------~~~~~vI~IDEid~l~~~~~~~L~~l~  322 (490)
                      ..   ..            ....+.+.+.+...  +.++++.           ..++-||+|||+..|...-++.|+..+
T Consensus        89 ~k~~e~~~~~~~~r~v~~v~lPl~ateDrvvGslDi~ka~~~g~~af~PGlLa~AnRGIlYvDEvnlL~d~lvd~LLd~a  168 (423)
T COG1239          89 AKGDELEWLPREKRKVPFVALPLGATEDRLVGSLDIEKALEEGPKAFQPGLLARANRGILYVDEVNLLDDHLVDALLDVA  168 (423)
T ss_pred             hhccccccccccceecceecCCCccchhhhccccCHHHHHhcCccccCCcchhhccCCEEEEeccccccHHHHHHHHHHH
Confidence            22   10            01112223322110  1111111           123449999999999999899998887


Q ss_pred             hCC----------CCCCCcEEEEEecCCCChhHhhhHHhhhccCCCCeeEEeCCC-CHHHHHHHHHHHHhcc--------
Q psy200          323 EWP----------SIPGSKLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPY-SREQILEIISQKLKQT--------  383 (490)
Q Consensus       323 ~~~----------~~~~~~vilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pl-s~~e~~~il~~~l~~~--------  383 (490)
                      ...          .....++++|+++|..  ...|.++|..||++   .+...++ +.++..+|+.+.+.-.        
T Consensus       169 aeG~n~vereGisi~hpa~fvligTmNPE--eGeLrpqLlDRfg~---~v~~~~~~~~~~rv~Ii~r~~~f~~~Pe~f~~  243 (423)
T COG1239         169 AEGVNDVEREGISIRHPARFLLIGTMNPE--EGELRPQLLDRFGL---EVDTHYPLDLEERVEIIRRRLAFEAVPEAFLE  243 (423)
T ss_pred             HhCCceeeeCceeeccCccEEEEeecCcc--ccccchhhHhhhcc---eeeccCCCCHHHHHHHHHHHHHhhcCcHHHHH
Confidence            653          1246789999999976  35677899999996   4555544 4666667666655422        


Q ss_pred             -------------------CCCCCCCHHHHHHHHHHHHHhh-CCHHHHHHHHHHHHHHHHhccccCCcccccCHHHHHHH
Q psy200          384 -------------------DKFNMFNASALQLLAGKVAAVS-GDIRKAIDITNHLIDLTYDNVKENGEVTGIGLKEVLGV  443 (490)
Q Consensus       384 -------------------~~~~~~~~~~i~~i~~~i~~~~-Gd~r~ai~ll~~a~~~a~~~~~~~~~~~~It~~~v~~a  443 (490)
                                         .....+++++...|+....... .+.|..+-+.+.+..+|...|     ...|+.+++..+
T Consensus       244 ~~~~~~~~lR~~ii~ar~~l~~V~l~~~~~~~ia~~~~~~~v~g~radi~~~r~a~a~aa~~G-----r~~v~~~Di~~a  318 (423)
T COG1239         244 KYADAQRALRARIIAARSLLSEVELDDDAETKIAELCARLAVDGHRADIVVVRAAKALAALRG-----RTEVEEEDIREA  318 (423)
T ss_pred             HHHHHHHHHHHHHHHHHhccccccCcHHHHHHHHHHHHHhccCCCchhhHHHHHHHHHHHhcC-----ceeeehhhHHHH
Confidence                               1334556666666665333322 235666667777777777777     667888888888


Q ss_pred             HHHhccC
Q psy200          444 ISSVYCT  450 (490)
Q Consensus       444 ~~~~~~~  450 (490)
                      +.-....
T Consensus       319 ~~l~l~h  325 (423)
T COG1239         319 AELALLH  325 (423)
T ss_pred             Hhhhhhh
Confidence            7765443

>PRK06871 DNA polymerase III subunit delta'; Validated

Probab=99.18  E-value=2.5e-09  Score=105.12  Aligned_cols=189  Identities=11%  Similarity=0.088  Sum_probs=115.8

Q ss_pred             HHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHh---cC-CC
Q psy200          202 QLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNEL---KL-KP  277 (490)
Q Consensus       202 ~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l---~~-~~  277 (490)
                      ..+.|...+..   +.-++.++|+||.|+||+++|+.+++.+.......  .-.|..+.+...+...-.-++   .. ..
T Consensus        10 ~~~~l~~~~~~---~rl~HA~Lf~G~~G~GK~~lA~~~A~~llC~~~~~--~~~Cg~C~sC~~~~~g~HPD~~~i~p~~~   84 (325)
T PRK06871         10 TYQQITQAFQQ---GLGHHALLFKADSGLGTEQLIRALAQWLMCQTPQG--DQPCGQCHSCHLFQAGNHPDFHILEPIDN   84 (325)
T ss_pred             HHHHHHHHHHc---CCcceeEEeECCCCCCHHHHHHHHHHHHcCCCCCC--CCCCCCCHHHHHHhcCCCCCEEEEccccC
Confidence            33445555542   34567888999999999999999999986432110  012333322222211000000   00 01


Q ss_pred             CCCcHHHHHHHHHHHHhc--CCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEEEecCCCChhHhhhHHhhhcc
Q psy200          278 GGKSERHQLGAILKYFDT--KHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVANALDLTDRMLPRLQANV  355 (490)
Q Consensus       278 ~~~s~~~~~~~l~~~l~~--~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI~~tn~~~~~~~l~~~l~~R~  355 (490)
                      ...+.+++++........  .++..|+|||++|.|....++.|...++.   +...+++|.+++   -.+++++.++|||
T Consensus        85 ~~I~id~iR~l~~~~~~~~~~g~~KV~iI~~a~~m~~~AaNaLLKtLEE---Pp~~~~fiL~t~---~~~~llpTI~SRC  158 (325)
T PRK06871         85 KDIGVDQVREINEKVSQHAQQGGNKVVYIQGAERLTEAAANALLKTLEE---PRPNTYFLLQAD---LSAALLPTIYSRC  158 (325)
T ss_pred             CCCCHHHHHHHHHHHhhccccCCceEEEEechhhhCHHHHHHHHHHhcC---CCCCeEEEEEEC---ChHhCchHHHhhc
Confidence            123566666654443322  35667999999999999889999888875   344556665564   3678899999999


Q ss_pred             CCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHHHH
Q psy200          356 TLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDIT  415 (490)
Q Consensus       356 ~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll  415 (490)
                      .    .+.|.+++.+++.+.|......       ++..+..++.   ...|.+-.++.++
T Consensus       159 ~----~~~~~~~~~~~~~~~L~~~~~~-------~~~~~~~~~~---l~~g~p~~A~~~~  204 (325)
T PRK06871        159 Q----TWLIHPPEEQQALDWLQAQSSA-------EISEILTALR---INYGRPLLALTFL  204 (325)
T ss_pred             e----EEeCCCCCHHHHHHHHHHHhcc-------ChHHHHHHHH---HcCCCHHHHHHHh
Confidence            6    8999999999999998875321       2223333333   3445565555543

>PRK07993 DNA polymerase III subunit delta'; Validated

Probab=99.18  E-value=5.1e-10  Score=111.06  Aligned_cols=188  Identities=14%  Similarity=0.144  Sum_probs=119.7

Q ss_pred             HHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcC--CC---
Q psy200          203 LEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKL--KP---  277 (490)
Q Consensus       203 ~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~--~~---  277 (490)
                      .+.+...+.   .+.-++.++|+||.|+||+++|.++++.+-....-.  .-.|..+.+...+...-.-++..  +.   
T Consensus        11 ~~~l~~~~~---~~rl~HA~Lf~G~~G~Gk~~lA~~~A~~LlC~~~~~--~~~Cg~C~sC~~~~~g~HPD~~~i~p~~~~   85 (334)
T PRK07993         11 YEQLVGSYQ---AGRGHHALLIQALPGMGDDALIYALSRWLMCQQPQG--HKSCGHCRGCQLMQAGTHPDYYTLTPEKGK   85 (334)
T ss_pred             HHHHHHHHH---cCCcceEEeeECCCCCCHHHHHHHHHHHHcCCCCCC--CCCCCCCHHHHHHHcCCCCCEEEEeccccc
Confidence            344444444   245677888999999999999999999985321100  01233332222221100000000  11   


Q ss_pred             CCCcHHHHHHHHHHHHhc--CCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEEEecCCCChhHhhhHHhhhcc
Q psy200          278 GGKSERHQLGAILKYFDT--KHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVANALDLTDRMLPRLQANV  355 (490)
Q Consensus       278 ~~~s~~~~~~~l~~~l~~--~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI~~tn~~~~~~~l~~~l~~R~  355 (490)
                      ...+.+++++........  .++..|+|||++|.|.....+.|..+++.+   ..+.+||.+++   -.+++++.++|||
T Consensus        86 ~~I~idqiR~l~~~~~~~~~~g~~kV~iI~~ae~m~~~AaNaLLKtLEEP---p~~t~fiL~t~---~~~~lLpTIrSRC  159 (334)
T PRK07993         86 SSLGVDAVREVTEKLYEHARLGGAKVVWLPDAALLTDAAANALLKTLEEP---PENTWFFLACR---EPARLLATLRSRC  159 (334)
T ss_pred             ccCCHHHHHHHHHHHhhccccCCceEEEEcchHhhCHHHHHHHHHHhcCC---CCCeEEEEEEC---ChhhChHHHHhcc
Confidence            124566776655544322  256779999999999998899999888754   44566665564   3688899999999


Q ss_pred             CCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHHHH
Q psy200          356 TLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDIT  415 (490)
Q Consensus       356 ~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll  415 (490)
                      .    .+.|.+++.+++...|....       .++++....+++   ...|++..|++++
T Consensus       160 q----~~~~~~~~~~~~~~~L~~~~-------~~~~~~a~~~~~---la~G~~~~Al~l~  205 (334)
T PRK07993        160 R----LHYLAPPPEQYALTWLSREV-------TMSQDALLAALR---LSAGAPGAALALL  205 (334)
T ss_pred             c----cccCCCCCHHHHHHHHHHcc-------CCCHHHHHHHHH---HcCCCHHHHHHHh
Confidence            6    79999999999998887531       245555555544   5667788777664

>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=99.18  E-value=9.8e-11  Score=104.33  Aligned_cols=155  Identities=19%  Similarity=0.289  Sum_probs=89.8

Q ss_pred             ChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHh---c
Q psy200          198 GREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNEL---K  274 (490)
Q Consensus       198 gre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l---~  274 (490)
                      |+++.++.|...+..   +.-++.++|+||.|+||+++|..+++.+-.......   .|....+...+...-..++   .
T Consensus         1 gq~~~~~~L~~~~~~---~~l~ha~L~~G~~g~gk~~~a~~~a~~ll~~~~~~~---~c~~c~~c~~~~~~~~~d~~~~~   74 (162)
T PF13177_consen    1 GQEEIIELLKNLIKS---GRLPHALLFHGPSGSGKKTLALAFARALLCSNPNED---PCGECRSCRRIEEGNHPDFIIIK   74 (162)
T ss_dssp             S-HHHHHHHHHHHHC---TC--SEEEEECSTTSSHHHHHHHHHHHHC-TT-CTT-----SSSHHHHHHHTT-CTTEEEEE
T ss_pred             CcHHHHHHHHHHHHc---CCcceeEEEECCCCCCHHHHHHHHHHHHcCCCCCCC---CCCCCHHHHHHHhccCcceEEEe
Confidence            677788887777763   345667899999999999999999998853221100   2222211111110000000   0


Q ss_pred             CCCC--CCcHHHHHHHHHHHHhc--CCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEEEecCCCChhHhhhHH
Q psy200          275 LKPG--GKSERHQLGAILKYFDT--KHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVANALDLTDRMLPR  350 (490)
Q Consensus       275 ~~~~--~~s~~~~~~~l~~~l~~--~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI~~tn~~~~~~~l~~~  350 (490)
                      ....  ....+++++........  .+..-|+||||+|.|....+++|+..++.+   ...+++|.+++   ..+++++.
T Consensus        75 ~~~~~~~i~i~~ir~i~~~~~~~~~~~~~KviiI~~ad~l~~~a~NaLLK~LEep---p~~~~fiL~t~---~~~~il~T  148 (162)
T PF13177_consen   75 PDKKKKSIKIDQIREIIEFLSLSPSEGKYKVIIIDEADKLTEEAQNALLKTLEEP---PENTYFILITN---NPSKILPT  148 (162)
T ss_dssp             TTTSSSSBSHHHHHHHHHHCTSS-TTSSSEEEEEETGGGS-HHHHHHHHHHHHST---TTTEEEEEEES----GGGS-HH
T ss_pred             cccccchhhHHHHHHHHHHHHHHHhcCCceEEEeehHhhhhHHHHHHHHHHhcCC---CCCEEEEEEEC---ChHHChHH
Confidence            0111  23456666444332221  245779999999999999999999999854   34555555565   36788999


Q ss_pred             hhhccCCCCeeEEeCCCC
Q psy200          351 LQANVTLQPTLMNFAPYS  368 (490)
Q Consensus       351 l~~R~~~~~~~i~~~pls  368 (490)
                      +++||.    .+.|.+++
T Consensus       149 I~SRc~----~i~~~~ls  162 (162)
T PF13177_consen  149 IRSRCQ----VIRFRPLS  162 (162)
T ss_dssp             HHTTSE----EEEE----
T ss_pred             HHhhce----EEecCCCC
Confidence            999995    89998875

...

>COG1220 HslU ATP-dependent protease HslVU (ClpYQ), ATPase subunit [Posttranslational modification, protein turnover, chaperones]

Probab=99.16  E-value=2.8e-09  Score=101.54  Aligned_cols=151  Identities=16%  Similarity=0.266  Sum_probs=101.3

Q ss_pred             eEEEEEecCccccccC------------HHHHHHhHhCC-------CCCCCcEEEEEecC-CCChhHhhhHHhhhccCCC
Q psy200          299 SILLILDEIDALESRK------------QTILYTIFEWP-------SIPGSKLVLVGVAN-ALDLTDRMLPRLQANVTLQ  358 (490)
Q Consensus       299 ~~vI~IDEid~l~~~~------------~~~L~~l~~~~-------~~~~~~vilI~~tn-~~~~~~~l~~~l~~R~~~~  358 (490)
                      .-+|||||||.+....            |.-|+-+++-.       ......++||++.. +..-+..+.|.|+.||.+ 
T Consensus       251 ~GIvFIDEIDKIa~~~~~g~~dvSREGVQRDlLPlvEGstV~TKyG~VkTdHILFIasGAFh~sKPSDLiPELQGRfPI-  329 (444)
T COG1220         251 NGIVFIDEIDKIAKRGGSGGPDVSREGVQRDLLPLVEGSTVSTKYGPVKTDHILFIASGAFHVAKPSDLIPELQGRFPI-  329 (444)
T ss_pred             cCeEEEehhhHHHhcCCCCCCCcchhhhcccccccccCceeeccccccccceEEEEecCceecCChhhcChhhcCCCce-
Confidence            4499999999997542            22222222211       12345677887664 334467788999999985 


Q ss_pred             CeeEEeCCCCHHHHHHHHHH-----------HHhccCCCCCCCHHHHHHHHHHHHHhhC-----CHHHHHHHHHHHHHHH
Q psy200          359 PTLMNFAPYSREQILEIISQ-----------KLKQTDKFNMFNASALQLLAGKVAAVSG-----DIRKAIDITNHLIDLT  422 (490)
Q Consensus       359 ~~~i~~~pls~~e~~~il~~-----------~l~~~~~~~~~~~~~i~~i~~~i~~~~G-----d~r~ai~ll~~a~~~a  422 (490)
                        ++.+.+++.+++..||..           .+..++....|++++|+.|++..+....     +.|++..++++.++-.
T Consensus       330 --RVEL~~Lt~~Df~rILtep~~sLikQY~aLlkTE~v~l~FtddaI~~iAeiA~~vN~~~ENIGARRLhTvlErlLedi  407 (444)
T COG1220         330 --RVELDALTKEDFERILTEPKASLIKQYKALLKTEGVELEFTDDAIKRIAEIAYQVNEKTENIGARRLHTVLERLLEDI  407 (444)
T ss_pred             --EEEcccCCHHHHHHHHcCcchHHHHHHHHHHhhcCeeEEecHHHHHHHHHHHHHhcccccchhHHHHHHHHHHHHHHh
Confidence              899999999999988642           2233356778999999999996655443     4788877888776543


Q ss_pred             H-hccccCCcccccCHHHHHHHHHHhccCcc
Q psy200          423 Y-DNVKENGEVTGIGLKEVLGVISSVYCTSQ  452 (490)
Q Consensus       423 ~-~~~~~~~~~~~It~~~v~~a~~~~~~~~~  452 (490)
                      . .-.....+.-.|+.+.|..-+.++..+..
T Consensus       408 SFeA~d~~g~~v~Id~~yV~~~l~~l~~n~D  438 (444)
T COG1220         408 SFEAPDMSGQKVTIDAEYVEEKLGDLVANED  438 (444)
T ss_pred             CccCCcCCCCeEEEcHHHHHHHHHHHhcccc
Confidence            2 21111123567999999999988876543

>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=99.15  E-value=1.3e-10  Score=103.84  Aligned_cols=135  Identities=18%  Similarity=0.206  Sum_probs=86.7

Q ss_pred             CCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcC
Q psy200          196 LPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKL  275 (490)
Q Consensus       196 lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~  275 (490)
                      ++|....+.++.+.+....  ....+|+|+|++||||+.+|+++++.. ...+-+|+.+||..+ +...+-.+++..-..
T Consensus         1 liG~s~~m~~~~~~~~~~a--~~~~pVlI~GE~GtGK~~lA~~IH~~s-~r~~~pfi~vnc~~~-~~~~~e~~LFG~~~~   76 (168)
T PF00158_consen    1 LIGESPAMKRLREQAKRAA--SSDLPVLITGETGTGKELLARAIHNNS-PRKNGPFISVNCAAL-PEELLESELFGHEKG   76 (168)
T ss_dssp             SS--SHHHHHHHHHHHHHT--TSTS-EEEECSTTSSHHHHHHHHHHCS-TTTTS-EEEEETTTS--HHHHHHHHHEBCSS
T ss_pred             CEeCCHHHHHHHHHHHHHh--CCCCCEEEEcCCCCcHHHHHHHHHHhh-hcccCCeEEEehhhh-hcchhhhhhhccccc
Confidence            5788888888888888743  456899999999999999999997743 234568999999987 444444445443322


Q ss_pred             CCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCHHHHHHhHhCCC--------CCCCcEEEEEecCC
Q psy200          276 KPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPS--------IPGSKLVLVGVANA  340 (490)
Q Consensus       276 ~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~--------~~~~~vilI~~tn~  340 (490)
                      .+.+..... ...|..+-.  |   +||||||+.|....|..|.++++...        ....++.+|++|+.
T Consensus        77 ~~~~~~~~~-~G~l~~A~~--G---tL~Ld~I~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiI~st~~  143 (168)
T PF00158_consen   77 AFTGARSDK-KGLLEQANG--G---TLFLDEIEDLPPELQAKLLRVLEEGKFTRLGSDKPVPVDVRIIASTSK  143 (168)
T ss_dssp             SSTTTSSEB-EHHHHHTTT--S---EEEEETGGGS-HHHHHHHHHHHHHSEEECCTSSSEEE--EEEEEEESS
T ss_pred             ccccccccc-CCceeeccc--e---EEeecchhhhHHHHHHHHHHHHhhchhccccccccccccceEEeecCc
Confidence            222221111 133333221  2   99999999999999999999886431        11347888888873

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 ....

>smart00350 MCM minichromosome maintenance proteins

Probab=99.15  E-value=1.5e-09  Score=114.45  Aligned_cols=232  Identities=15%  Similarity=0.184  Sum_probs=141.8

Q ss_pred             CCCCChHHHHHHHHHHHHhhhcc--------CCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVNN--------ETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASV  265 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~--------~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l  265 (490)
                      ..++|++.....+.-.|-.....        ...-++||+|+||+|||++++.+++...     ...|+..... +...+
T Consensus       203 p~i~G~~~~k~~l~l~l~gg~~~~~~~~~~~r~~~~vLL~G~pGtGKs~lar~l~~~~~-----r~~~~~~~~~-~~~~l  276 (509)
T smart00350      203 PSIYGHEDIKKAILLLLFGGVHKNLPDGMKIRGDINILLLGDPGTAKSQLLKYVEKTAP-----RAVYTTGKGS-SAVGL  276 (509)
T ss_pred             ccccCcHHHHHHHHHHHhCCCccccCCCccccccceEEEeCCCChhHHHHHHHHHHHcC-----cceEcCCCCC-CcCCc
Confidence            78999998876665555321100        0113899999999999999999988653     1123321100 10000


Q ss_pred             HHHHHHHhcCCCCCCcHHHHH-HHHHHHHhcCCCeEEEEEecCccccccCHHHHHHhHhCCCC----------CCCcEEE
Q psy200          266 YETIVNELKLKPGGKSERHQL-GAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPSI----------PGSKLVL  334 (490)
Q Consensus       266 ~~~i~~~l~~~~~~~s~~~~~-~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~----------~~~~vil  334 (490)
                      ....   +.....|.-  .+. ..+.  +..   .-+++|||++.+....|..|...++....          ...++.+
T Consensus       277 ~~~~---~~~~~~g~~--~~~~G~l~--~A~---~Gil~iDEi~~l~~~~q~~L~e~me~~~i~i~k~G~~~~l~~~~~v  346 (509)
T smart00350      277 TAAV---TRDPETREF--TLEGGALV--LAD---NGVCCIDEFDKMDDSDRTAIHEAMEQQTISIAKAGITTTLNARCSV  346 (509)
T ss_pred             cccc---eEccCcceE--EecCccEE--ecC---CCEEEEechhhCCHHHHHHHHHHHhcCEEEEEeCCEEEEecCCcEE
Confidence            0000   000000000  000 0000  111   22999999999999889999888764321          2367889


Q ss_pred             EEecCCCChh--------H--hhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhcc---------------------
Q psy200          335 VGVANALDLT--------D--RMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQT---------------------  383 (490)
Q Consensus       335 I~~tn~~~~~--------~--~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~---------------------  383 (490)
                      |+++|..+-.        +  .+.+.+.+||++  ..+.+++++.+.-.+++.+.+..+                     
T Consensus       347 iAa~NP~~g~y~~~~~~~~n~~l~~~lLsRFdL--i~~~~d~~~~~~d~~i~~~i~~~~~~~~~~~~~~~~~~~~~~~l~  424 (509)
T smart00350      347 LAAANPIGGRYDPKLTPEENIDLPAPILSRFDL--LFVVLDEVDEERDRELAKHVVDLHRYSHPEPDEADEVPISQEFLR  424 (509)
T ss_pred             EEEeCCCCcccCCCcChhhccCCChHHhCceee--EEEecCCCChHHHHHHHHHHHHhhcccCccccccccccCCHHHHH
Confidence            9999965321        1  356788899986  345556777776666666543211                     


Q ss_pred             -------C-CCCCCCHHHHHHHHHHHHHhhC-------------CHHHHHHHHHHHHHHHHhccccCCcccccCHHHHHH
Q psy200          384 -------D-KFNMFNASALQLLAGKVAAVSG-------------DIRKAIDITNHLIDLTYDNVKENGEVTGIGLKEVLG  442 (490)
Q Consensus       384 -------~-~~~~~~~~~i~~i~~~i~~~~G-------------d~r~ai~ll~~a~~~a~~~~~~~~~~~~It~~~v~~  442 (490)
                             . ....+++++.+.|.+.+.....             .+|.++.+++.|-..|..+.     ...|+.+|+..
T Consensus       425 ~yi~~ar~~~~P~ls~~~~~~i~~~y~~~R~~~~~~~~~~~~~~t~R~l~sliRla~A~A~l~~-----r~~V~~~Dv~~  499 (509)
T smart00350      425 KYIAYAREKIKPKLSEEAAEKLVKAYVDLRKEDSQSEARSSIPITVRQLESIIRLSEAHAKMRL-----SDVVEEADVEE  499 (509)
T ss_pred             HHHHHHHhcCCCCCCHHHHHHHHHHHHHhcccccccccccccCcCHHHHHHHHHHHHHHHHHcC-----CCccCHHHHHH
Confidence                   0 1245788888888775533221             47778889998988999998     78999999999


Q ss_pred             HHHHhc
Q psy200          443 VISSVY  448 (490)
Q Consensus       443 a~~~~~  448 (490)
                      |+.-+.
T Consensus       500 ai~l~~  505 (509)
T smart00350      500 AIRLLR  505 (509)
T ss_pred             HHHHHH
Confidence            987654

>PLN03210 Resistant to P

Probab=99.14  E-value=2e-09  Score=124.41  Aligned_cols=200  Identities=19%  Similarity=0.305  Sum_probs=120.3

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCc-eEEEEeccCCC---------C--
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAF-KTIYINCNSVR---------N--  261 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~-~~~~v~~~~~~---------~--  261 (490)
                      ++++|++..+++|..+|.-  .....+.+.|+|++|+||||+|+++++.+.  ..| ..++++.....         +  
T Consensus       184 ~~~vG~~~~l~~l~~lL~l--~~~~~~vvgI~G~gGiGKTTLA~~l~~~l~--~~F~g~vfv~~~~v~~~~~~~~~~~~~  259 (1153)
T PLN03210        184 EDFVGIEDHIAKMSSLLHL--ESEEVRMVGIWGSSGIGKTTIARALFSRLS--RQFQSSVFIDRAFISKSMEIYSSANPD  259 (1153)
T ss_pred             ccccchHHHHHHHHHHHcc--ccCceEEEEEEcCCCCchHHHHHHHHHHHh--hcCCeEEEeeccccccchhhccccccc
Confidence            6899999999999988853  345677899999999999999999999875  233 22333221000         0  


Q ss_pred             ----HHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEEEe
Q psy200          262 ----AASVYETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGV  337 (490)
Q Consensus       262 ----~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI~~  337 (490)
                          ...+...++.++-.... ...... ..+.+.+.  +++++|||||+|...  ..+.+....+|. ..+++||+  +
T Consensus       260 ~~~~~~~l~~~~l~~il~~~~-~~~~~~-~~~~~~L~--~krvLLVLDdv~~~~--~l~~L~~~~~~~-~~GsrIIi--T  330 (1153)
T PLN03210        260 DYNMKLHLQRAFLSEILDKKD-IKIYHL-GAMEERLK--HRKVLIFIDDLDDQD--VLDALAGQTQWF-GSGSRIIV--I  330 (1153)
T ss_pred             ccchhHHHHHHHHHHHhCCCC-cccCCH-HHHHHHHh--CCeEEEEEeCCCCHH--HHHHHHhhCccC-CCCcEEEE--E
Confidence                01122233333211110 101011 23333344  578999999998642  123333333332 23455544  3


Q ss_pred             cCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHHHHHH
Q psy200          338 ANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITNH  417 (490)
Q Consensus       338 tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll~~  417 (490)
                      |....+    .    ...+.. ..+.+..++.++.++++..++...    ...++.+..+++.++..+|+++.|+.++..
T Consensus       331 Trd~~v----l----~~~~~~-~~~~v~~l~~~ea~~LF~~~Af~~----~~~~~~~~~l~~~iv~~c~GLPLAl~vlgs  397 (1153)
T PLN03210        331 TKDKHF----L----RAHGID-HIYEVCLPSNELALEMFCRSAFKK----NSPPDGFMELASEVALRAGNLPLGLNVLGS  397 (1153)
T ss_pred             eCcHHH----H----HhcCCC-eEEEecCCCHHHHHHHHHHHhcCC----CCCcHHHHHHHHHHHHHhCCCcHHHHHHHH
Confidence            432111    1    111111 378999999999999999877543    123455777888888999999999988765


Q ss_pred             HH
Q psy200          418 LI  419 (490)
Q Consensus       418 a~  419 (490)
                      .+
T Consensus       398 ~L  399 (1153)
T PLN03210        398 YL  399 (1153)
T ss_pred             HH
Confidence            54

syringae 6; Provisional

>PRK11361 acetoacetate metabolism regulatory protein AtoC; Provisional

Probab=99.14  E-value=5.1e-10  Score=117.17  Aligned_cols=228  Identities=18%  Similarity=0.186  Sum_probs=143.8

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHh
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNEL  273 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l  273 (490)
                      ..++|.......+.+.+...  ......++|+|++|+||+++++.+..... .....++.++|..+. ...+-..++..-
T Consensus       143 ~~ii~~S~~~~~~~~~~~~~--a~~~~~vli~Ge~GtGK~~lA~~ih~~s~-~~~~~~~~i~c~~~~-~~~~~~~lfg~~  218 (457)
T PRK11361        143 GHILTNSPAMMDICKDTAKI--ALSQASVLISGESGTGKELIARAIHYNSR-RAKGPFIKVNCAALP-ESLLESELFGHE  218 (457)
T ss_pred             cceecccHHHhHHHHHHHHH--cCCCcEEEEEcCCCccHHHHHHHHHHhCC-CCCCCeEEEECCCCC-HHHHHHHhcCCC
Confidence            34777777777777666553  24567899999999999999999977543 234578999999874 222222222211


Q ss_pred             cCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCHHHHHHhHhCCCC--------CCCcEEEEEecCCCChhH
Q psy200          274 KLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPSI--------PGSKLVLVGVANALDLTD  345 (490)
Q Consensus       274 ~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~--------~~~~vilI~~tn~~~~~~  345 (490)
                      ...+.+..... ...    +... ..-+||||||+.|....|..|..+++....        ....+.+|++++.. +..
T Consensus       219 ~~~~~~~~~~~-~g~----~~~a-~~gtl~ld~i~~l~~~~q~~L~~~l~~~~~~~~~~~~~~~~~~rii~~t~~~-l~~  291 (457)
T PRK11361        219 KGAFTGAQTLR-QGL----FERA-NEGTLLLDEIGEMPLVLQAKLLRILQEREFERIGGHQTIKVDIRIIAATNRD-LQA  291 (457)
T ss_pred             CCCCCCCCCCC-CCc----eEEC-CCCEEEEechhhCCHHHHHHHHHHHhcCcEEeCCCCceeeeceEEEEeCCCC-HHH
Confidence            11111111000 001    1111 123899999999999989888888764321        12346788877632 211


Q ss_pred             -----hhhHHhhhccCCCCeeEEeCCCC--HHHHHHHHHHHHhcc----CC-CCCCCHHHHHHHHHHHHHhhCCHHHHHH
Q psy200          346 -----RMLPRLQANVTLQPTLMNFAPYS--REQILEIISQKLKQT----DK-FNMFNASALQLLAGKVAAVSGDIRKAID  413 (490)
Q Consensus       346 -----~l~~~l~~R~~~~~~~i~~~pls--~~e~~~il~~~l~~~----~~-~~~~~~~~i~~i~~~i~~~~Gd~r~ai~  413 (490)
                           .+.+.+..|+..  ..|.++|+.  .+++..++.+++...    +. ...+++++++.+..  +.|.||++++-+
T Consensus       292 ~~~~g~~~~~l~~~l~~--~~i~~ppLreR~~di~~l~~~~l~~~~~~~~~~~~~~~~~a~~~L~~--~~wpgNv~eL~~  367 (457)
T PRK11361        292 MVKEGTFREDLFYRLNV--IHLILPPLRDRREDISLLANHFLQKFSSENQRDIIDIDPMAMSLLTA--WSWPGNIRELSN  367 (457)
T ss_pred             HHHcCCchHHHHHHhcc--ceecCCChhhchhhHHHHHHHHHHHHHHHcCCCCCCcCHHHHHHHHc--CCCCCcHHHHHH
Confidence                 233455555543  368888887  466666665555443    22 24689999999987  889999999999


Q ss_pred             HHHHHHHHHHhccccCCcccccCHHHHHHHH
Q psy200          414 ITNHLIDLTYDNVKENGEVTGIGLKEVLGVI  444 (490)
Q Consensus       414 ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~  444 (490)
                      ++++++..+.  +      ..|+.+++...+
T Consensus       368 ~~~~~~~~~~--~------~~i~~~~l~~~~  390 (457)
T PRK11361        368 VIERAVVMNS--G------PIIFSEDLPPQI  390 (457)
T ss_pred             HHHHHHHhCC--C------CcccHHHChHhh
Confidence            9999886543  2      357777775433

>PRK08769 DNA polymerase III subunit delta'; Validated

Probab=99.13  E-value=4.5e-09  Score=103.20  Aligned_cols=185  Identities=15%  Similarity=0.100  Sum_probs=110.4

Q ss_pred             HHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHH-HHHH---hc-C
Q psy200          201 VQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYET-IVNE---LK-L  275 (490)
Q Consensus       201 ~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~-i~~~---l~-~  275 (490)
                      ...+.+...+..   +.-++.++|+||.|+||+++|.++++.+-.....     .|..... ..++.. -.-+   +. .
T Consensus        11 ~~~~~l~~~~~~---~rl~HA~Lf~Gp~G~GK~~lA~~lA~~LlC~~~~-----~~~~c~~-c~~~~~g~HPD~~~i~~~   81 (319)
T PRK08769         11 RAYDQTVAALDA---GRLGHGLLICGPEGLGKRAVALALAEHVLASGPD-----PAAAQRT-RQLIAAGTHPDLQLVSFI   81 (319)
T ss_pred             HHHHHHHHHHHc---CCcceeEeeECCCCCCHHHHHHHHHHHHhCCCCC-----CCCcchH-HHHHhcCCCCCEEEEecC
Confidence            444455555542   3455679999999999999999999988532210     0000000 000000 0000   00 0


Q ss_pred             CC-------CCCcHHHHHHHHHHHHhc--CCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEEEecCCCChhHh
Q psy200          276 KP-------GGKSERHQLGAILKYFDT--KHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVANALDLTDR  346 (490)
Q Consensus       276 ~~-------~~~s~~~~~~~l~~~l~~--~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI~~tn~~~~~~~  346 (490)
                      +.       .....+.+++........  .++..|+|||++|.|.....+.|.++++.+   ...++||.+++   -.++
T Consensus        82 p~~~~~k~~~~I~idqIR~l~~~~~~~p~~g~~kV~iI~~ae~m~~~AaNaLLKtLEEP---p~~~~fiL~~~---~~~~  155 (319)
T PRK08769         82 PNRTGDKLRTEIVIEQVREISQKLALTPQYGIAQVVIVDPADAINRAACNALLKTLEEP---SPGRYLWLISA---QPAR  155 (319)
T ss_pred             CCcccccccccccHHHHHHHHHHHhhCcccCCcEEEEeccHhhhCHHHHHHHHHHhhCC---CCCCeEEEEEC---Chhh
Confidence            00       012344555444333221  245679999999999998899999888754   33444444454   2677


Q ss_pred             hhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHHHH
Q psy200          347 MLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDIT  415 (490)
Q Consensus       347 l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll  415 (490)
                      +++.++|||.    .+.|.+++.+++...|...        .+++.....++.   ...|.+..++.++
T Consensus       156 lLpTIrSRCq----~i~~~~~~~~~~~~~L~~~--------~~~~~~a~~~~~---l~~G~p~~A~~~~  209 (319)
T PRK08769        156 LPATIRSRCQ----RLEFKLPPAHEALAWLLAQ--------GVSERAAQEALD---AARGHPGLAAQWL  209 (319)
T ss_pred             CchHHHhhhe----EeeCCCcCHHHHHHHHHHc--------CCChHHHHHHHH---HcCCCHHHHHHHh
Confidence            8999999996    8999999999999888752        134443444443   4566666666544

>KOG1968|consensus

Probab=99.13  E-value=1.2e-10  Score=126.83  Aligned_cols=216  Identities=18%  Similarity=0.187  Sum_probs=152.2

Q ss_pred             cCCCCcchHHHhhcCCCCCCChHHHHHHHHHHHHhhhcc-----------CCCC-eEEEECCCCCcHHHHHHHHHHHhhh
Q psy200          178 LFSEDKPKVEEKAKDSCELPGREVQLEGIRQFLLGHVNN-----------ETSG-SMYISGPPGTGKSASLNLLVSRAEI  245 (490)
Q Consensus       178 ~~~~~~~~~~~~~l~~~~lvgre~~~~~l~~~L~~~~~~-----------~~~~-~ill~GppGtGKTtla~~l~~~l~~  245 (490)
                      ..|.+.|++...    .++.|.......+..||..+-..           .... .++++|+||+|||+.+..++..++ 
T Consensus       308 ~~~~~k~~p~~~----k~~~~~~~~~~~~~~~l~~~k~~~~~sy~~~~~~ss~~~~~l~~G~pGigKT~~~h~~~k~~g-  382 (871)
T KOG1968|consen  308 AGWTEKYQPTSS----KALEGNASSSKKASKWLAKSKDKEKSSYKENEPDSSKKKALLLSGPPGIGKTTAAHKAAKELG-  382 (871)
T ss_pred             cccccccccccH----HhhhcccchhhhhhhHHHhhhccccccccccCcchhhHHHHHhcCCCCCCchhhHhhhhhhcc-
Confidence            478888888876    78888888888899999876110           0112 478999999999999999999976 


Q ss_pred             cCCceEEEEeccCCCCHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCHHHHHHhHhCC
Q psy200          246 KDAFKTIYINCNSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWP  325 (490)
Q Consensus       246 ~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~  325 (490)
                         +.++..|....++...+...+....+....    ..............+..+||++||+|-++..+...+..+..+.
T Consensus       383 ---~~v~E~Nas~~RSk~~l~~~~~~~~~s~si----~~~~~~~~~~~~~~~~~~vil~devD~~~~~dRg~v~~l~~l~  455 (871)
T KOG1968|consen  383 ---FKVVEKNASDVRSKKELLNKLGNATSSHSI----KGSKKKKGNRQSLNSDHFLILMDEVDGMFGEDRGGVSKLSSLC  455 (871)
T ss_pred             ---cceeecCccccccccHHHhhhhccccccch----hhhhcccccccccccceeEEEEeccccccchhhhhHHHHHHHH
Confidence               899999999998888877776665443222    1111111111111244669999999999985555555544433


Q ss_pred             CCCCCcEEEEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhh
Q psy200          326 SIPGSKLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVS  405 (490)
Q Consensus       326 ~~~~~~vilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~  405 (490)
                      .  ....-+|+++|..+++.  ...+.+.|    ..++|..++.+.+...+...+..+  ...++++.++.+..   ...
T Consensus       456 ~--ks~~Piv~~cndr~~p~--sr~~~~~~----~~l~f~kP~~~~i~~ri~si~~se--~~ki~~~~l~~~s~---~~~  522 (871)
T KOG1968|consen  456 K--KSSRPLVCTCNDRNLPK--SRALSRAC----SDLRFSKPSSELIRSRIMSICKSE--GIKISDDVLEEISK---LSG  522 (871)
T ss_pred             H--hccCCeEEEecCCCCcc--ccchhhhc----ceeeecCCcHHHHHhhhhhhhccc--ceecCcHHHHHHHH---hcc
Confidence            2  34455666677544333  12222222    269999999999999999999887  56689999999987   778


Q ss_pred             CCHHHHHHHHHHH
Q psy200          406 GDIRKAIDITNHL  418 (490)
Q Consensus       406 Gd~r~ai~ll~~a  418 (490)
                      ||+|+.|+.++.-
T Consensus       523 ~DiR~~i~~lq~~  535 (871)
T KOG1968|consen  523 GDIRQIIMQLQFW  535 (871)
T ss_pred             cCHHHHHHHHhhh
Confidence            9999999877665

>KOG0743|consensus

Probab=99.10  E-value=4e-09  Score=104.86  Aligned_cols=156  Identities=17%  Similarity=0.192  Sum_probs=103.4

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccC---------CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNE---------TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAAS  264 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~---------~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~  264 (490)
                      +.++--.+..+.|.+-|...+++.         =.++-|||||||||||+++.++|+.+.    |.+.-++.....+   
T Consensus       201 ~TlaMd~~~K~~I~~Dl~~F~k~k~~YkrvGkawKRGYLLYGPPGTGKSS~IaAmAn~L~----ydIydLeLt~v~~---  273 (457)
T KOG0743|consen  201 ETLAMDPDLKERIIDDLDDFIKGKDFYKRVGKAWKRGYLLYGPPGTGKSSFIAAMANYLN----YDIYDLELTEVKL---  273 (457)
T ss_pred             cccccChhHHHHHHHHHHHHHhcchHHHhcCcchhccceeeCCCCCCHHHHHHHHHhhcC----CceEEeeeccccC---
Confidence            556665555555555555444332         126899999999999999999999987    6665565544322   


Q ss_pred             HHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccC------------------HHHHHHhHhCC-
Q psy200          265 VYETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRK------------------QTILYTIFEWP-  325 (490)
Q Consensus       265 l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~------------------~~~L~~l~~~~-  325 (490)
                                       -.++    .+.+..-....||+|+|||.-....                  ...|+++++.. 
T Consensus       274 -----------------n~dL----r~LL~~t~~kSIivIEDIDcs~~l~~~~~~~~~~~~~~~~~VTlSGLLNfiDGlw  332 (457)
T KOG0743|consen  274 -----------------DSDL----RHLLLATPNKSILLIEDIDCSFDLRERRKKKKENFEGDLSRVTLSGLLNFLDGLW  332 (457)
T ss_pred             -----------------cHHH----HHHHHhCCCCcEEEEeecccccccccccccccccccCCcceeehHHhhhhhcccc
Confidence                             1123    3333333456799999999874321                  12455555532 


Q ss_pred             CCCCCcEEEEEecCCCChhHhhhHHhhh--ccCCCCeeEEeCCCCHHHHHHHHHHHHhcc
Q psy200          326 SIPGSKLVLVGVANALDLTDRMLPRLQA--NVTLQPTLMNFAPYSREQILEIISQKLKQT  383 (490)
Q Consensus       326 ~~~~~~vilI~~tn~~~~~~~l~~~l~~--R~~~~~~~i~~~pls~~e~~~il~~~l~~~  383 (490)
                      ...+.-=|+|.+||   ..++++|+|.+  |+.   .+|++.-=+.+..+.++.+++...
T Consensus       333 Sscg~ERIivFTTN---h~EkLDPALlRpGRmD---mhI~mgyCtf~~fK~La~nYL~~~  386 (457)
T KOG0743|consen  333 SSCGDERIIVFTTN---HKEKLDPALLRPGRMD---MHIYMGYCTFEAFKTLASNYLGIE  386 (457)
T ss_pred             ccCCCceEEEEecC---ChhhcCHhhcCCCcce---eEEEcCCCCHHHHHHHHHHhcCCC
Confidence            22223345667787   46788888887  555   479999999999999999998764

>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=99.09  E-value=4.1e-11  Score=104.12  Aligned_cols=122  Identities=21%  Similarity=0.296  Sum_probs=76.2

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeE
Q psy200          221 SMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFDTKHKSI  300 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~  300 (490)
                      +|+|+||||+|||++++.+++.+.    ..++.++|....+..+++..+.-. ... ......    .+..++   .+..
T Consensus         1 ~vlL~G~~G~GKt~l~~~la~~~~----~~~~~i~~~~~~~~~dl~g~~~~~-~~~-~~~~~~----~l~~a~---~~~~   67 (139)
T PF07728_consen    1 PVLLVGPPGTGKTTLARELAALLG----RPVIRINCSSDTTEEDLIGSYDPS-NGQ-FEFKDG----PLVRAM---RKGG   67 (139)
T ss_dssp             EEEEEESSSSSHHHHHHHHHHHHT----CEEEEEE-TTTSTHHHHHCEEET--TTT-TCEEE-----CCCTTH---HEEE
T ss_pred             CEEEECCCCCCHHHHHHHHHHHhh----cceEEEEeccccccccceeeeeec-ccc-cccccc----cccccc---ccee
Confidence            589999999999999999999984    678889999888877775432111 000 000000    001111   1477


Q ss_pred             EEEEecCccccccCHHHHHHhHhCCCC----------CCC------cEEEEEecCCCC-hhHhhhHHhhhcc
Q psy200          301 LLILDEIDALESRKQTILYTIFEWPSI----------PGS------KLVLVGVANALD-LTDRMLPRLQANV  355 (490)
Q Consensus       301 vI~IDEid~l~~~~~~~L~~l~~~~~~----------~~~------~vilI~~tn~~~-~~~~l~~~l~~R~  355 (490)
                      ++||||++......+..|..+++....          ...      .+.+|+++|..+ ....+.+++++||
T Consensus        68 il~lDEin~a~~~v~~~L~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~~ii~t~N~~~~~~~~l~~al~~Rf  139 (139)
T PF07728_consen   68 ILVLDEINRAPPEVLESLLSLLEERRIQLPEGGEEIKEPNNDLASPNFRIIATMNPRDKGRKELSPALLDRF  139 (139)
T ss_dssp             EEEESSCGG--HHHHHTTHHHHSSSEEEE-TSSSEEE--TT------EEEEEEESSST--TTTTCHHHHTT-
T ss_pred             EEEECCcccCCHHHHHHHHHHHhhCcccccCCCcEEecCcccccccceEEEEEEcCCCCCcCcCCHHHHhhC
Confidence            999999999886666667666543211          011      389999999766 4456778888886

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.

>PF05729 NACHT: NACHT domain

Probab=99.08  E-value=3.8e-09  Score=94.22  Aligned_cols=149  Identities=23%  Similarity=0.426  Sum_probs=88.2

Q ss_pred             CeEEEECCCCCcHHHHHHHHHHHhhhcCC-----ceEEEEeccCCCCHH---HHHHHHHHHhcCCCCCCcHHHHHHHHHH
Q psy200          220 GSMYISGPPGTGKSASLNLLVSRAEIKDA-----FKTIYINCNSVRNAA---SVYETIVNELKLKPGGKSERHQLGAILK  291 (490)
Q Consensus       220 ~~ill~GppGtGKTtla~~l~~~l~~~~~-----~~~~~v~~~~~~~~~---~l~~~i~~~l~~~~~~~s~~~~~~~l~~  291 (490)
                      +.++|+|++|+|||++++.++..+.....     ..++++++.......   .+...|...+...     .......+..
T Consensus         1 r~l~I~G~~G~GKStll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~-----~~~~~~~~~~   75 (166)
T PF05729_consen    1 RVLWISGEPGSGKSTLLRKLAQQLAEEEPPPSKFPYPFFFSLRDISDSNNSRSLADLLFDQLPES-----IAPIEELLQE   75 (166)
T ss_pred             CEEEEECCCCCChHHHHHHHHHHHHhcCcccccceEEEEEeehhhhhccccchHHHHHHHhhccc-----hhhhHHHHHH
Confidence            46899999999999999999998864331     234455555553322   2333333333221     1111222333


Q ss_pred             HHhcCCCeEEEEEecCccccccCHH--------HHHHhHhCCCCCCCcEEEEEecCCCChhHhhhHHhhhccCCCCeeEE
Q psy200          292 YFDTKHKSILLILDEIDALESRKQT--------ILYTIFEWPSIPGSKLVLVGVANALDLTDRMLPRLQANVTLQPTLMN  363 (490)
Q Consensus       292 ~l~~~~~~~vI~IDEid~l~~~~~~--------~L~~l~~~~~~~~~~vilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~  363 (490)
                      ... ...+++||||.+|.+......        .+..++......+.++++.+.+..   ...+...+.. .    ..+.
T Consensus        76 ~~~-~~~~~llilDglDE~~~~~~~~~~~~~~~~l~~l~~~~~~~~~~liit~r~~~---~~~~~~~~~~-~----~~~~  146 (166)
T PF05729_consen   76 LLE-KNKRVLLILDGLDELEEQDQSQERQRLLDLLSQLLPQALPPGVKLIITSRPRA---FPDLRRRLKQ-A----QILE  146 (166)
T ss_pred             HHH-cCCceEEEEechHhcccchhhhHHHHHHHHHHHHhhhccCCCCeEEEEEcCCh---HHHHHHhcCC-C----cEEE
Confidence            333 356889999999999875332        344444432234566666554431   1122222221 1    3799


Q ss_pred             eCCCCHHHHHHHHHHHHhc
Q psy200          364 FAPYSREQILEIISQKLKQ  382 (490)
Q Consensus       364 ~~pls~~e~~~il~~~l~~  382 (490)
                      +.+++.+++..++++.+..
T Consensus       147 l~~~~~~~~~~~~~~~f~~  165 (166)
T PF05729_consen  147 LEPFSEEDIKQYLRKYFSN  165 (166)
T ss_pred             ECCCCHHHHHHHHHHHhhc
Confidence            9999999999999988753

>PRK08116 hypothetical protein; Validated

Probab=99.06  E-value=2e-09  Score=103.79  Aligned_cols=150  Identities=18%  Similarity=0.190  Sum_probs=85.9

Q ss_pred             HHHHHHHHHHhhhcc-CCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCCCCCC
Q psy200          202 QLEGIRQFLLGHVNN-ETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKPGGK  280 (490)
Q Consensus       202 ~~~~l~~~L~~~~~~-~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~~~  280 (490)
                      .+..+..++..+... ..+.+++|+|++|+|||+|+.++++++... +..+++++      ..+++..+...+..... .
T Consensus        96 a~~~a~~y~~~~~~~~~~~~gl~l~G~~GtGKThLa~aia~~l~~~-~~~v~~~~------~~~ll~~i~~~~~~~~~-~  167 (268)
T PRK08116         96 AYKIARKYVKKFEEMKKENVGLLLWGSVGTGKTYLAACIANELIEK-GVPVIFVN------FPQLLNRIKSTYKSSGK-E  167 (268)
T ss_pred             HHHHHHHHHHHHHhhccCCceEEEECCCCCCHHHHHHHHHHHHHHc-CCeEEEEE------HHHHHHHHHHHHhcccc-c
Confidence            344555555544322 234579999999999999999999998643 56777775      34455555444332111 1


Q ss_pred             cHHHHHHHHHHHHhcCCCeEEEEEecCcc--ccccCHHHHHHhHhCCCCCCCcEEEEEecCC--CChhHhhhHHhhhccC
Q psy200          281 SERHQLGAILKYFDTKHKSILLILDEIDA--LESRKQTILYTIFEWPSIPGSKLVLVGVANA--LDLTDRMLPRLQANVT  356 (490)
Q Consensus       281 s~~~~~~~l~~~l~~~~~~~vI~IDEid~--l~~~~~~~L~~l~~~~~~~~~~vilI~~tn~--~~~~~~l~~~l~~R~~  356 (490)
                      ...++   + +.+..   .-+|||||++.  .....++.|+.+++.....+.+  +|.+||.  .++...+..++.+|+.
T Consensus       168 ~~~~~---~-~~l~~---~dlLviDDlg~e~~t~~~~~~l~~iin~r~~~~~~--~IiTsN~~~~eL~~~~~~ri~sRl~  238 (268)
T PRK08116        168 DENEI---I-RSLVN---ADLLILDDLGAERDTEWAREKVYNIIDSRYRKGLP--TIVTTNLSLEELKNQYGKRIYDRIL  238 (268)
T ss_pred             cHHHH---H-HHhcC---CCEEEEecccCCCCCHHHHHHHHHHHHHHHHCCCC--EEEECCCCHHHHHHHHhHHHHHHHH
Confidence            12222   2 22322   23999999954  3444567788887754333334  4444653  2444445567777742


Q ss_pred             CCCeeEEeCCCC
Q psy200          357 LQPTLMNFAPYS  368 (490)
Q Consensus       357 ~~~~~i~~~pls  368 (490)
                      -....+.|...+
T Consensus       239 e~~~~v~~~g~d  250 (268)
T PRK08116        239 EMCTPVENEGKS  250 (268)
T ss_pred             HcCEEEEeeCcC
Confidence            111357776655

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

Probab=99.04  E-value=1.2e-08  Score=96.72  Aligned_cols=213  Identities=16%  Similarity=0.249  Sum_probs=131.2

Q ss_pred             HhhcCCCCCCChHHHHHHHHHHHHhhhc----c-C------CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEec
Q psy200          188 EKAKDSCELPGREVQLEGIRQFLLGHVN----N-E------TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINC  256 (490)
Q Consensus       188 ~~~l~~~~lvgre~~~~~l~~~L~~~~~----~-~------~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~  256 (490)
                      +..|. +.++|++...+-|.-.+.+..+    . .      ...++++.||.|+|||.||+.+++.+.    ++|.-.++
T Consensus        56 k~~Ld-~YVIGQe~AKKvLsVAVYNHYKRl~~~~~~~dvEL~KSNILLiGPTGsGKTlLAqTLAk~Ln----VPFaiADA  130 (408)
T COG1219          56 KAHLD-EYVIGQEQAKKVLSVAVYNHYKRLNNKEDNDDVELSKSNILLIGPTGSGKTLLAQTLAKILN----VPFAIADA  130 (408)
T ss_pred             HHHhh-hheecchhhhceeeeeehhHHHHHhccCCCCceeeeeccEEEECCCCCcHHHHHHHHHHHhC----CCeeeccc
Confidence            33344 7788888877665443333211    0 1      235899999999999999999999986    67777776


Q ss_pred             cCCCCHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHhc---CCCeEEEEEecCccccccC--------------HHHHH
Q psy200          257 NSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFDT---KHKSILLILDEIDALESRK--------------QTILY  319 (490)
Q Consensus       257 ~~~~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~---~~~~~vI~IDEid~l~~~~--------------~~~L~  319 (490)
                      ..+...             .+.|...+++...|.++...   ...+-+|+|||||.+....              |.+|+
T Consensus       131 TtLTEA-------------GYVGEDVENillkLlqaadydV~rAerGIIyIDEIDKIarkSeN~SITRDVSGEGVQQALL  197 (408)
T COG1219         131 TTLTEA-------------GYVGEDVENILLKLLQAADYDVERAERGIIYIDEIDKIARKSENPSITRDVSGEGVQQALL  197 (408)
T ss_pred             cchhhc-------------cccchhHHHHHHHHHHHcccCHHHHhCCeEEEechhhhhccCCCCCcccccCchHHHHHHH
Confidence            655321             34555566655444433211   0123399999999997653              56777


Q ss_pred             HhHhCC------------------CCCCCcEEEEEecCCCCh-------------------------------hHh----
Q psy200          320 TIFEWP------------------SIPGSKLVLVGVANALDL-------------------------------TDR----  346 (490)
Q Consensus       320 ~l~~~~------------------~~~~~~vilI~~tn~~~~-------------------------------~~~----  346 (490)
                      .+++-.                  .....+++|||......+                               ...    
T Consensus       198 KiiEGTvasVPPqGGRKHP~Qe~iqvDT~NILFIcgGAF~GlekiI~~R~~~~~iGF~a~~~~~~~~~~~~~~l~~vepe  277 (408)
T COG1219         198 KIIEGTVASVPPQGGRKHPQQEFIQVDTSNILFICGGAFAGLEKIIKKRLGKKGIGFGAEVKSKSKKKEEGELLKQVEPE  277 (408)
T ss_pred             HHHcCceeccCCCCCCCCCccceEEEcccceeEEeccccccHHHHHHHhccCCcccccccccchhhhhhHHHHHHhcChH
Confidence            776421                  113456666654321111                               000    


Q ss_pred             ------hhHHhhhccCCCCeeEEeCCCCHHHHHHHHHH-----------HHhccCCCCCCCHHHHHHHHHHHHHhhCCHH
Q psy200          347 ------MLPRLQANVTLQPTLMNFAPYSREQILEIISQ-----------KLKQTDKFNMFNASALQLLAGKVAAVSGDIR  409 (490)
Q Consensus       347 ------l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~-----------~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r  409 (490)
                            +.|.+-.|+.   ..-.+.+++.+++..||..           .+...+....|+++++..|+++.....-+.|
T Consensus       278 DLvkFGLIPEfIGRlP---via~L~~Lde~aLv~ILtePkNAlvKQYq~Lf~~d~V~L~F~~~AL~~IA~~A~~rkTGAR  354 (408)
T COG1219         278 DLVKFGLIPEFIGRLP---VIATLEELDEDALVQILTEPKNALVKQYQKLFEMDGVELEFTEEALKAIAKKAIERKTGAR  354 (408)
T ss_pred             HHHHcCCcHHHhcccc---eeeehhhcCHHHHHHHHhcccHHHHHHHHHHhcccCceEEEcHHHHHHHHHHHHHhccchh
Confidence                  1244444554   3678899999998887642           2223355677999999999988766666666


Q ss_pred             HHHHHHHHHHHH
Q psy200          410 KAIDITNHLIDL  421 (490)
Q Consensus       410 ~ai~ll~~a~~~  421 (490)
                      .+-.+++..+.-
T Consensus       355 GLRsI~E~~lld  366 (408)
T COG1219         355 GLRSIIEELLLD  366 (408)
T ss_pred             HHHHHHHHHHHH
Confidence            665566655543

>PRK10365 transcriptional regulatory protein ZraR; Provisional

Probab=99.04  E-value=1.8e-09  Score=112.52  Aligned_cols=227  Identities=18%  Similarity=0.229  Sum_probs=141.1

Q ss_pred             CCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhc
Q psy200          195 ELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELK  274 (490)
Q Consensus       195 ~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~  274 (490)
                      .++|.......+...+..  .......++|+|.+|+||+++++++..... ....+++.++|.... ...+-..++..-.
T Consensus       140 ~lig~s~~~~~~~~~i~~--~~~~~~~vli~ge~g~gk~~~a~~ih~~s~-~~~~~~i~~~c~~~~-~~~~~~~lfg~~~  215 (441)
T PRK10365        140 GMVGKSPAMQHLLSEIAL--VAPSEATVLIHGDSGTGKELVARAIHASSA-RSEKPLVTLNCAALN-ESLLESELFGHEK  215 (441)
T ss_pred             ceEecCHHHHHHHHHHhh--ccCCCCeEEEEecCCCCHHHHHHHHHHcCC-CCCCCeeeeeCCCCC-HHHHHHHhcCCCC
Confidence            356666666666555543  234567899999999999999999976542 344588999999763 2222222222111


Q ss_pred             CCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCHHHHHHhHhCCCC--------CCCcEEEEEecCCCChhH-
Q psy200          275 LKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPSI--------PGSKLVLVGVANALDLTD-  345 (490)
Q Consensus       275 ~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~--------~~~~vilI~~tn~~~~~~-  345 (490)
                      +.+.+.... ....+.   ..  ..-+||||||+.|....|..|..+++....        ....+.+|++++.. +.. 
T Consensus       216 ~~~~~~~~~-~~g~~~---~a--~~gtl~ldei~~l~~~~q~~l~~~l~~~~~~~~~~~~~~~~~~rii~~t~~~-~~~~  288 (441)
T PRK10365        216 GAFTGADKR-REGRFV---EA--DGGTLFLDEIGDISPMMQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRD-LAAE  288 (441)
T ss_pred             CCcCCCCcC-CCCcee---EC--CCCEEEEeccccCCHHHHHHHHHHHccCcEEeCCCCceeeeceEEEEeCCCC-HHHH
Confidence            111111000 000111   11  133899999999999889888887764321        12346677777632 222 


Q ss_pred             ----hhhHHhhhccCCCCeeEEeCCCC--HHHHHHHHHHHHhcc----CC-CCCCCHHHHHHHHHHHHHhhCCHHHHHHH
Q psy200          346 ----RMLPRLQANVTLQPTLMNFAPYS--REQILEIISQKLKQT----DK-FNMFNASALQLLAGKVAAVSGDIRKAIDI  414 (490)
Q Consensus       346 ----~l~~~l~~R~~~~~~~i~~~pls--~~e~~~il~~~l~~~----~~-~~~~~~~~i~~i~~~i~~~~Gd~r~ai~l  414 (490)
                          .+.+.+..|+..  ..+.++|+.  .+++..++.+.+...    +. ...+++++++.+..  +.|.||+|++.++
T Consensus       289 ~~~~~~~~~l~~~l~~--~~i~~ppLreR~~Di~~l~~~~l~~~~~~~~~~~~~~~~~a~~~L~~--~~wpgN~reL~~~  364 (441)
T PRK10365        289 VNAGRFRQDLYYRLNV--VAIEVPSLRQRREDIPLLAGHFLQRFAERNRKAVKGFTPQAMDLLIH--YDWPGNIRELENA  364 (441)
T ss_pred             HHcCCchHHHHHHhcc--ceecCCChhhcchhHHHHHHHHHHHHHHHhCCCCCCcCHHHHHHHHh--CCCCCHHHHHHHH
Confidence                233455555543  367888887  346777766666543    21 23489999999987  7899999999999


Q ss_pred             HHHHHHHHHhccccCCcccccCHHHHHHHH
Q psy200          415 TNHLIDLTYDNVKENGEVTGIGLKEVLGVI  444 (490)
Q Consensus       415 l~~a~~~a~~~~~~~~~~~~It~~~v~~a~  444 (490)
                      +++++..+.  +      ..|+.+++...+
T Consensus       365 ~~~~~~~~~--~------~~i~~~~l~~~~  386 (441)
T PRK10365        365 VERAVVLLT--G------EYISERELPLAI  386 (441)
T ss_pred             HHHHHHhCC--C------CccchHhCchhh
Confidence            999886543  2      357777775443

>PRK09862 putative ATP-dependent protease; Provisional

Probab=99.03  E-value=4.7e-09  Score=108.81  Aligned_cols=232  Identities=15%  Similarity=0.162  Sum_probs=134.2

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHH---HH-
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYE---TI-  269 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~---~i-  269 (490)
                      .++.|+...++.+.-      ....+.+++|+|++|+|||++++.+...+.....-..  +.+..+.+......   .+ 
T Consensus       191 ~~v~Gq~~~~~al~l------aa~~G~~llliG~~GsGKTtLak~L~gllpp~~g~e~--le~~~i~s~~g~~~~~~~~~  262 (506)
T PRK09862        191 SDVIGQEQGKRGLEI------TAAGGHNLLLIGPPGTGKTMLASRINGLLPDLSNEEA--LESAAILSLVNAESVQKQWR  262 (506)
T ss_pred             EEEECcHHHHhhhhe------eccCCcEEEEECCCCCcHHHHHHHHhccCCCCCCcEE--EecchhhhhhccccccCCcC
Confidence            456677665554322      2245789999999999999999999876642211112  22222111100000   00 


Q ss_pred             HHHhcCCCCCCcHHHHHH--------HHHHHHhcCCCeEEEEEecCccccccCHHHHHHhHhCCCC----------CCCc
Q psy200          270 VNELKLKPGGKSERHQLG--------AILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPSI----------PGSK  331 (490)
Q Consensus       270 ~~~l~~~~~~~s~~~~~~--------~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~----------~~~~  331 (490)
                      ..-+..+.+..+...+..        .+.  +..   .-+|||||++.+....++.|.+.++....          ...+
T Consensus       263 ~rPfr~ph~~~s~~~l~GGg~~~~pG~l~--~A~---gGvLfLDEi~e~~~~~~~~L~~~LE~g~v~I~r~g~~~~~pa~  337 (506)
T PRK09862        263 QRPFRSPHHSASLTAMVGGGAIPGPGEIS--LAH---NGVLFLDELPEFERRTLDALREPIESGQIHLSRTRAKITYPAR  337 (506)
T ss_pred             CCCccCCCccchHHHHhCCCceehhhHhh--hcc---CCEEecCCchhCCHHHHHHHHHHHHcCcEEEecCCcceeccCC
Confidence            000111111122222111        111  111   22999999999998888888888754432          2467


Q ss_pred             EEEEEecCCCC------------------hhHhhhHHhhhccCCCCeeEEeCCCCHHH-------------HH-HHH---
Q psy200          332 LVLVGVANALD------------------LTDRMLPRLQANVTLQPTLMNFAPYSREQ-------------IL-EII---  376 (490)
Q Consensus       332 vilI~~tn~~~------------------~~~~l~~~l~~R~~~~~~~i~~~pls~~e-------------~~-~il---  376 (490)
                      +.+|+++|...                  +..++...+.+||++   .+.+++++.++             +. .++   
T Consensus       338 f~lIAa~NP~pcG~~~~~~c~c~~~~~~~Y~~~ls~plLDRfdL---~v~v~~~~~~~l~~~~~~~ess~~i~~rV~~ar  414 (506)
T PRK09862        338 FQLVAAMNPSPTGHYQGNHNRCTPEQTLRYLNRLSGPFLDRFDL---SLEIPLPPPGILSKTVVPGESSATVKQRVMAAR  414 (506)
T ss_pred             EEEEEeecCccceecCCCCCCcCHHHHHHHHhhCCHhHHhhccE---EEEeCCCCHHHHhcccCCCCChHHHHHHHhhHH
Confidence            89999998542                  113456788899986   67788774332             22 111   


Q ss_pred             ---HHH---Hhcc------CCCCCCCHHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHhccccCCcccccCHHHHHHHH
Q psy200          377 ---SQK---LKQT------DKFNMFNASALQLLAGKVAAVSGDIRKAIDITNHLIDLTYDNVKENGEVTGIGLKEVLGVI  444 (490)
Q Consensus       377 ---~~~---l~~~------~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~  444 (490)
                         ..+   +...      ...+.+++++.+.+........-..|....+++-|..+|..++     ...|+.+||.+|+
T Consensus       415 ~~q~~r~~~~n~~l~~~~l~~~~~l~~~~~~~l~~~~~~~~lS~Ra~~rlLrvARTiADL~g-----~~~V~~~hv~eAl  489 (506)
T PRK09862        415 ERQFKRQNKLNAWLDSPEIRQFCKLESEDARWLEETLIHLGLSIRAWQRLLKVARTIADIDQ-----SDIITRQHLQEAV  489 (506)
T ss_pred             HHHHHHHHHHhcccCHHHHHHHhCCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHcC-----CCCCCHHHHHHHH
Confidence               111   0000      0123455566555554333444468888899999999999999     7899999999999


Q ss_pred             HH
Q psy200          445 SS  446 (490)
Q Consensus       445 ~~  446 (490)
                      .=
T Consensus       490 ~y  491 (506)
T PRK09862        490 SY  491 (506)
T ss_pred             Hh
Confidence            63

>COG3283 TyrR Transcriptional regulator of aromatic amino acids metabolism [Transcription / Amino acid transport and metabolism]

Probab=99.02  E-value=2.6e-09  Score=102.41  Aligned_cols=213  Identities=15%  Similarity=0.183  Sum_probs=136.1

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHh
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNEL  273 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l  273 (490)
                      +.+++.....+.+.......  .--...++|.|+.||||-.+|++... .....+.+|+.+||..++... .-.+++   
T Consensus       204 ~~~v~~S~~mk~~v~qA~k~--AmlDAPLLI~GeTGTGKdLlAkaCH~-~S~R~~~pFlalNCA~lPe~~-aEsElF---  276 (511)
T COG3283         204 EQIVAVSPKMKHVVEQAQKL--AMLDAPLLITGETGTGKDLLAKACHL-ASPRHSKPFLALNCASLPEDA-AESELF---  276 (511)
T ss_pred             HHHhhccHHHHHHHHHHHHh--hccCCCeEEecCCCchHHHHHHHHhh-cCcccCCCeeEeecCCCchhH-hHHHHh---
Confidence            56777777777776655542  23456899999999999999998744 333455689999999985421 111111   


Q ss_pred             cCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCHHHHHHhHhCCC--------CCCCcEEEEEecCCC--Ch
Q psy200          274 KLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPS--------IPGSKLVLVGVANAL--DL  343 (490)
Q Consensus       274 ~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~--------~~~~~vilI~~tn~~--~~  343 (490)
                       +...|  .+....+|+.+-.  |   .+|+|||..|...-|..|..+++-..        .-...|.|||+|...  ++
T Consensus       277 -G~apg--~~gk~GffE~Ang--G---TVlLDeIgEmSp~lQaKLLRFL~DGtFRRVGee~Ev~vdVRVIcatq~nL~~l  348 (511)
T COG3283         277 -GHAPG--DEGKKGFFEQANG--G---TVLLDEIGEMSPRLQAKLLRFLNDGTFRRVGEDHEVHVDVRVICATQVNLVEL  348 (511)
T ss_pred             -cCCCC--CCCccchhhhccC--C---eEEeehhhhcCHHHHHHHHHHhcCCceeecCCcceEEEEEEEEecccccHHHH
Confidence             11111  1122233333221  2   89999999999988888888765331        234678899988521  11


Q ss_pred             hH--hhhHHhhhccCCCCeeEEeCCCC--HHHHHHHHHHHHhcc-----CCCCCCCHHHHHHHHHHHHHhhCCHHHHHHH
Q psy200          344 TD--RMLPRLQANVTLQPTLMNFAPYS--REQILEIISQKLKQT-----DKFNMFNASALQLLAGKVAAVSGDIRKAIDI  414 (490)
Q Consensus       344 ~~--~l~~~l~~R~~~~~~~i~~~pls--~~e~~~il~~~l~~~-----~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~l  414 (490)
                      .+  .+.+.+..|+..  ..+.++|+-  .+++..+.+.++.+.     -..+.++++.+..+.+  +.|.||+|++-|.
T Consensus       349 v~~g~fReDLfyRLNV--Ltl~~PpLRer~~di~pL~e~Fv~q~s~elg~p~pkl~~~~~~~L~~--y~WpGNVRqL~N~  424 (511)
T COG3283         349 VQKGKFREDLFYRLNV--LTLNLPPLRERPQDIMPLAELFVQQFSDELGVPRPKLAADLLTVLTR--YAWPGNVRQLKNA  424 (511)
T ss_pred             HhcCchHHHHHHHhhe--eeecCCccccCcccchHHHHHHHHHHHHHhCCCCCccCHHHHHHHHH--cCCCccHHHHHHH
Confidence            11  123455556652  256666665  234444433333322     2456789999999988  8999999999999


Q ss_pred             HHHHHHHHHhc
Q psy200          415 TNHLIDLTYDN  425 (490)
Q Consensus       415 l~~a~~~a~~~  425 (490)
                      +.+|+...+..
T Consensus       425 iyRA~s~~Eg~  435 (511)
T COG3283         425 IYRALTLLEGY  435 (511)
T ss_pred             HHHHHHHhccC
Confidence            99999887643

>PHA02244 ATPase-like protein

Probab=99.00  E-value=2.3e-08  Score=98.66  Aligned_cols=152  Identities=13%  Similarity=0.169  Sum_probs=93.3

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHh
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNEL  273 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l  273 (490)
                      ..+++....+..+...+..++.  ...+++|+||+|||||++|+++++.++    .+++.+++..  +...+.    ...
T Consensus        96 ~~~ig~sp~~~~~~~ri~r~l~--~~~PVLL~GppGtGKTtLA~aLA~~lg----~pfv~In~l~--d~~~L~----G~i  163 (383)
T PHA02244         96 TTKIASNPTFHYETADIAKIVN--ANIPVFLKGGAGSGKNHIAEQIAEALD----LDFYFMNAIM--DEFELK----GFI  163 (383)
T ss_pred             CcccCCCHHHHHHHHHHHHHHh--cCCCEEEECCCCCCHHHHHHHHHHHhC----CCEEEEecCh--HHHhhc----ccc
Confidence            4566666666555555554443  356899999999999999999999865    5667776321  111110    000


Q ss_pred             cCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCHHHHHHhHhCC--------CCCCCcEEEEEecCCCC--h
Q psy200          274 KLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWP--------SIPGSKLVLVGVANALD--L  343 (490)
Q Consensus       274 ~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~--------~~~~~~vilI~~tn~~~--~  343 (490)
                        ...+ .. . ...|..++..+   .+|||||++.+....+..|..+++..        ...+.++.+|+++|...  +
T Consensus       164 --~~~g-~~-~-dgpLl~A~~~G---gvLiLDEId~a~p~vq~~L~~lLd~r~l~l~g~~i~~h~~FRlIATsN~~~~G~  235 (383)
T PHA02244        164 --DANG-KF-H-ETPFYEAFKKG---GLFFIDEIDASIPEALIIINSAIANKFFDFADERVTAHEDFRVISAGNTLGKGA  235 (383)
T ss_pred             --cccc-cc-c-chHHHHHhhcC---CEEEEeCcCcCCHHHHHHHHHHhccCeEEecCcEEecCCCEEEEEeeCCCccCc
Confidence              0011 00 0 01233334332   39999999999877777777766421        11346788999998531  1


Q ss_pred             ------hHhhhHHhhhccCCCCeeEEeCCCCH
Q psy200          344 ------TDRMLPRLQANVTLQPTLMNFAPYSR  369 (490)
Q Consensus       344 ------~~~l~~~l~~R~~~~~~~i~~~pls~  369 (490)
                            ...+.+.+.+||.    .+.|..+..
T Consensus       236 ~~~y~G~k~L~~AllDRFv----~I~~dyp~~  263 (383)
T PHA02244        236 DHIYVARNKIDGATLDRFA----PIEFDYDEK  263 (383)
T ss_pred             ccccCCCcccCHHHHhhcE----EeeCCCCcH
Confidence                  2455788999996    788888764

>KOG0745|consensus

Probab=99.00  E-value=1.3e-08  Score=99.93  Aligned_cols=187  Identities=17%  Similarity=0.279  Sum_probs=121.8

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHhc---
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFDT---  295 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~---  295 (490)
                      ..+|||.||.|+|||.|++.+++-+.    ++|+-.+|..+...             .+.|+..+.+...|......   
T Consensus       226 KSNvLllGPtGsGKTllaqTLAr~ld----VPfaIcDcTtLTQA-------------GYVGeDVEsvi~KLl~~A~~nVe  288 (564)
T KOG0745|consen  226 KSNVLLLGPTGSGKTLLAQTLARVLD----VPFAICDCTTLTQA-------------GYVGEDVESVIQKLLQEAEYNVE  288 (564)
T ss_pred             cccEEEECCCCCchhHHHHHHHHHhC----CCeEEecccchhhc-------------ccccccHHHHHHHHHHHccCCHH
Confidence            35799999999999999999999875    88888999887321             23445555544433322110   


Q ss_pred             CCCeEEEEEecCccccccC--------------HHHHHHhHhCC-----C-------------CCCCcEEEEEecCCCCh
Q psy200          296 KHKSILLILDEIDALESRK--------------QTILYTIFEWP-----S-------------IPGSKLVLVGVANALDL  343 (490)
Q Consensus       296 ~~~~~vI~IDEid~l~~~~--------------~~~L~~l~~~~-----~-------------~~~~~vilI~~tn~~~~  343 (490)
                      ..+.-|+||||+|.+....              |..|+.+++-.     .             +...+|+||+..-..++
T Consensus       289 kAQqGIVflDEvDKi~~~~~~i~~~RDVsGEGVQQaLLKllEGtvVnVpeK~~~~~~rgd~vqiDTtnILFiasGAF~~L  368 (564)
T KOG0745|consen  289 KAQQGIVFLDEVDKITKKAESIHTSRDVSGEGVQQALLKLLEGTVVNVPEKGSRRKPRGDTVQIDTTNILFIASGAFVGL  368 (564)
T ss_pred             HHhcCeEEEehhhhhcccCccccccccccchhHHHHHHHHhcccEEcccCCCCCCCCCCCeEEEeccceEEEecccccch
Confidence            1123399999999997331              55666665411     0             12345666643321111


Q ss_pred             hHh-----------------------------------------------------hhHHhhhccCCCCeeEEeCCCCHH
Q psy200          344 TDR-----------------------------------------------------MLPRLQANVTLQPTLMNFAPYSRE  370 (490)
Q Consensus       344 ~~~-----------------------------------------------------l~~~l~~R~~~~~~~i~~~pls~~  370 (490)
                      ...                                                     |.|.|..||-   -.+.|.+++.+
T Consensus       369 dk~I~rR~~d~slGFg~~s~~~vr~~~~~~s~~~~~~~~~~~lL~~~~~~DLisfGmIPEfVGRfP---VlVplh~L~~~  445 (564)
T KOG0745|consen  369 DKIISRRLDDKSLGFGAPSSKGVRANMATKSGVENDAEKRDELLEKVESGDLISFGMIPEFVGRFP---VLVPLHSLDED  445 (564)
T ss_pred             HHHHHHhhcchhcccCCCCCccchhhcccccCcchhHHHHHHHHhhccccchhhhcCcHHHhcccc---eEeeccccCHH
Confidence            000                                                     2355566665   47899999999


Q ss_pred             HHHHHHHH-----------HHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHhc
Q psy200          371 QILEIISQ-----------KLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITNHLIDLTYDN  425 (490)
Q Consensus       371 e~~~il~~-----------~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll~~a~~~a~~~  425 (490)
                      ++..+|..           .+...+.+..|++++++.|+++.....-+.|.+-.+|+.++..++-+
T Consensus       446 ~Lv~VLtEPknaL~~Qyk~lf~~~nV~L~fTe~Al~~IAq~Al~r~TGARgLRsIlE~~Lleamfe  511 (564)
T KOG0745|consen  446 QLVRVLTEPKNALGKQYKKLFGMDNVELHFTEKALEAIAQLALKRKTGARGLRSILESLLLEAMFE  511 (564)
T ss_pred             HHHHHHhcchhhHHHHHHHHhccCCeeEEecHHHHHHHHHHHHhhccchHHHHHHHHHHHhhhccc
Confidence            98887642           22222455679999999999977777777888778888888777654

>PRK06090 DNA polymerase III subunit delta'; Validated

Probab=99.00  E-value=1.1e-08  Score=100.28  Aligned_cols=161  Identities=13%  Similarity=0.151  Sum_probs=102.6

Q ss_pred             HHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHh---cCC--
Q psy200          202 QLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNEL---KLK--  276 (490)
Q Consensus       202 ~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l---~~~--  276 (490)
                      ..+.+...+.   .+.-++.++|+||.|+||+++|+.+++.+-....-   ...|..+.+...+...-.-++   ...  
T Consensus        11 ~~~~l~~~~~---~~rl~hA~L~~G~~G~Gk~~lA~~~a~~llC~~~~---~~~Cg~C~sC~~~~~g~HPD~~~i~p~~~   84 (319)
T PRK06090         11 VWQNWKAGLD---AGRIPGALLLQSDEGLGVESLVELFSRALLCQNYQ---SEACGFCHSCELMQSGNHPDLHVIKPEKE   84 (319)
T ss_pred             HHHHHHHHHH---cCCcceeEeeECCCCCCHHHHHHHHHHHHcCCCCC---CCCCCCCHHHHHHHcCCCCCEEEEecCcC
Confidence            3344455443   24456789999999999999999999988533210   012333322222111100011   000  


Q ss_pred             CCCCcHHHHHHHHHHHHh--cCCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEEEecCCCChhHhhhHHhhhc
Q psy200          277 PGGKSERHQLGAILKYFD--TKHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVANALDLTDRMLPRLQAN  354 (490)
Q Consensus       277 ~~~~s~~~~~~~l~~~l~--~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI~~tn~~~~~~~l~~~l~~R  354 (490)
                      ....+.+++++.......  ..++..|+|||++|.|.....+.|...++.+   ..+.++|.+++   -.+++++.++||
T Consensus        85 ~~~I~vdqiR~l~~~~~~~~~~~~~kV~iI~~ae~m~~~AaNaLLKtLEEP---p~~t~fiL~t~---~~~~lLpTI~SR  158 (319)
T PRK06090         85 GKSITVEQIRQCNRLAQESSQLNGYRLFVIEPADAMNESASNALLKTLEEP---APNCLFLLVTH---NQKRLLPTIVSR  158 (319)
T ss_pred             CCcCCHHHHHHHHHHHhhCcccCCceEEEecchhhhCHHHHHHHHHHhcCC---CCCeEEEEEEC---ChhhChHHHHhc
Confidence            112345666554332221  1245679999999999998889998888754   44566666665   367889999999


Q ss_pred             cCCCCeeEEeCCCCHHHHHHHHHH
Q psy200          355 VTLQPTLMNFAPYSREQILEIISQ  378 (490)
Q Consensus       355 ~~~~~~~i~~~pls~~e~~~il~~  378 (490)
                      |.    .+.|.+++.+++.+.+..
T Consensus       159 Cq----~~~~~~~~~~~~~~~L~~  178 (319)
T PRK06090        159 CQ----QWVVTPPSTAQAMQWLKG  178 (319)
T ss_pred             ce----eEeCCCCCHHHHHHHHHH
Confidence            96    899999999999988865

>PRK06964 DNA polymerase III subunit delta'; Validated

Probab=98.99  E-value=6.6e-09  Score=102.93  Aligned_cols=153  Identities=13%  Similarity=0.079  Sum_probs=98.0

Q ss_pred             cCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHH-------------------------
Q psy200          216 NETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIV-------------------------  270 (490)
Q Consensus       216 ~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~-------------------------  270 (490)
                      +.-++.++|+||.|+||+++|+.+++.+....... ..-.|..+.+...+...-.                         
T Consensus        18 ~rl~ha~Lf~Gp~G~GK~~lA~~~A~~LlC~~~~~-~~~~Cg~C~~C~~~~~~~HPD~~~i~p~~~~~~~~~~~~~~~~~   96 (342)
T PRK06964         18 ARLPHALLLHGQAGIGKLDFAQHLAQGLLCETPQP-DGEPCGTCAACNWFAQGNHPDYRIVRPEALAAEAPGAADEAKEA   96 (342)
T ss_pred             CCcceEEEEECCCCCCHHHHHHHHHHHHcCCCCCC-CCCCCCCCHHHHHHHcCCCCCEEEEecccccccccccccccccc
Confidence            45678899999999999999999999886422100 0012222211111100000                         


Q ss_pred             --HHhcC----CCCCCcHHHHHHHHHHHHhc--CCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEEEecCCCC
Q psy200          271 --NELKL----KPGGKSERHQLGAILKYFDT--KHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVANALD  342 (490)
Q Consensus       271 --~~l~~----~~~~~s~~~~~~~l~~~l~~--~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI~~tn~~~  342 (490)
                        .+-+.    .......+++++........  .++..|+|||++|.|.....+.|+..++.   +...++||.+|+   
T Consensus        97 ~~~~~~~k~~~~~~~I~idqiR~l~~~~~~~~~~~~~kV~iI~~ae~m~~~AaNaLLKtLEE---Pp~~t~fiL~t~---  170 (342)
T PRK06964         97 DADEGGKKTKAPSKEIKIEQVRALLDFCGVGTHRGGARVVVLYPAEALNVAAANALLKTLEE---PPPGTVFLLVSA---  170 (342)
T ss_pred             hhhcccccccccccccCHHHHHHHHHHhccCCccCCceEEEEechhhcCHHHHHHHHHHhcC---CCcCcEEEEEEC---
Confidence              00000    00123456666554432211  25567999999999999888999888874   445566666665   


Q ss_pred             hhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHH
Q psy200          343 LTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQK  379 (490)
Q Consensus       343 ~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~  379 (490)
                      -.+.+++.+++||.    .+.|.+++.+++.+.|...
T Consensus       171 ~~~~LLpTI~SRcq----~i~~~~~~~~~~~~~L~~~  203 (342)
T PRK06964        171 RIDRLLPTILSRCR----QFPMTVPAPEAAAAWLAAQ  203 (342)
T ss_pred             ChhhCcHHHHhcCE----EEEecCCCHHHHHHHHHHc
Confidence            36888999999995    8999999999999998764

>KOG0736|consensus

Probab=98.97  E-value=2.4e-08  Score=104.48  Aligned_cols=253  Identities=15%  Similarity=0.193  Sum_probs=148.5

Q ss_pred             CCCChHHHHHHHHHHHHhhhccC-----CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHH
Q psy200          195 ELPGREVQLEGIRQFLLGHVNNE-----TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETI  269 (490)
Q Consensus       195 ~lvgre~~~~~l~~~L~~~~~~~-----~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i  269 (490)
                      ...+++..+..+..++......+     ....+||+|+||+|||+++++++.+++    ..++.++|.++..        
T Consensus       402 ~~~~~~~~~~~l~~vl~p~~~~s~~~~~~~~~vLLhG~~g~GK~t~V~~vas~lg----~h~~evdc~el~~--------  469 (953)
T KOG0736|consen  402 SPPGLEAKVLELVAVLSPQKQPSGALLTLNPSVLLHGPPGSGKTTVVRAVASELG----LHLLEVDCYELVA--------  469 (953)
T ss_pred             CCccchHHHHHHHHHhCcccCcchhccccceEEEEeCCCCCChHHHHHHHHHHhC----CceEeccHHHHhh--------
Confidence            34556666666677665432222     345789999999999999999999987    7889998887632        


Q ss_pred             HHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccC--------HHHHHHhHh--CCCCCCCcEEEEEecC
Q psy200          270 VNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRK--------QTILYTIFE--WPSIPGSKLVLVGVAN  339 (490)
Q Consensus       270 ~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~--------~~~L~~l~~--~~~~~~~~vilI~~tn  339 (490)
                            ...+.....+...+.++..  ..+.||||-.+|-+....        +..+..++.  .......+++|||+++
T Consensus       470 ------~s~~~~etkl~~~f~~a~~--~~pavifl~~~dvl~id~dgged~rl~~~i~~~ls~e~~~~~~~~~ivv~t~~  541 (953)
T KOG0736|consen  470 ------ESASHTETKLQAIFSRARR--CSPAVLFLRNLDVLGIDQDGGEDARLLKVIRHLLSNEDFKFSCPPVIVVATTS  541 (953)
T ss_pred             ------cccchhHHHHHHHHHHHhh--cCceEEEEeccceeeecCCCchhHHHHHHHHHHHhcccccCCCCceEEEEecc
Confidence                  2222344455555555544  468999999999886331        122223332  2333567899999987


Q ss_pred             CCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhh-CCHHHHHHHHHH-
Q psy200          340 ALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVS-GDIRKAIDITNH-  417 (490)
Q Consensus       340 ~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~-Gd~r~ai~ll~~-  417 (490)
                      ..+   .+-+.+++-|-   ..|.++-++++|..++|+.++....   .=.+..++.+++++.... |++..+..-+-+ 
T Consensus       542 s~~---~lp~~i~~~f~---~ei~~~~lse~qRl~iLq~y~~~~~---~n~~v~~k~~a~~t~gfs~~~L~~l~~~~s~~  612 (953)
T KOG0736|consen  542 SIE---DLPADIQSLFL---HEIEVPALSEEQRLEILQWYLNHLP---LNQDVNLKQLARKTSGFSFGDLEALVAHSSLA  612 (953)
T ss_pred             ccc---cCCHHHHHhhh---hhccCCCCCHHHHHHHHHHHHhccc---cchHHHHHHHHHhcCCCCHHHHHHHhcCchHH
Confidence            542   33334444333   3799999999999999999887651   112344555555332211 232222211101 


Q ss_pred             HHHHHHhcc-----------ccCCcccccCHHHHHHHHHHhccCc--------cccccccccCCCChHhHHHHHHHHH
Q psy200          418 LIDLTYDNV-----------KENGEVTGIGLKEVLGVISSVYCTS--------QSLHCSKDEDSFPLQQKLALASLLL  476 (490)
Q Consensus       418 a~~~a~~~~-----------~~~~~~~~It~~~v~~a~~~~~~~~--------~~~~~~~~l~~L~~~qk~vL~al~~  476 (490)
                      +....+..+           .+......|+.+||.++++++....        +..+.-+.+.+|..-...+|-.|-+
T Consensus       613 ~~~~i~~~~l~g~~~~~~~~~~~~~~~~l~~edf~kals~~~~~fs~aiGAPKIPnV~WdDVGGLeevK~eIldTIql  690 (953)
T KOG0736|consen  613 AKTRIKNKGLAGGLQEEDEGELCAAGFLLTEEDFDKALSRLQKEFSDAIGAPKIPNVSWDDVGGLEEVKTEILDTIQL  690 (953)
T ss_pred             HHHHHHhhcccccchhccccccccccceecHHHHHHHHHHHHHhhhhhcCCCCCCccchhcccCHHHHHHHHHHHhcC
Confidence            111111111           0002246799999999999653211        1112235666776666666665544

>PF14516 AAA_35: AAA-like domain

Probab=98.97  E-value=5.9e-08  Score=96.75  Aligned_cols=204  Identities=18%  Similarity=0.224  Sum_probs=124.9

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCC-----CHHHHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVR-----NAASVYET  268 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~-----~~~~l~~~  268 (490)
                      ...+.|...-+++.+.|.     .++..+.|.||..+|||+++..+.+.+.. .++.++++++....     +...++..
T Consensus        11 ~~Yi~R~~~e~~~~~~i~-----~~G~~~~I~apRq~GKTSll~~l~~~l~~-~~~~~v~id~~~~~~~~~~~~~~f~~~   84 (331)
T PF14516_consen   11 PFYIERPPAEQECYQEIV-----QPGSYIRIKAPRQMGKTSLLLRLLERLQQ-QGYRCVYIDLQQLGSAIFSDLEQFLRW   84 (331)
T ss_pred             CcccCchHHHHHHHHHHh-----cCCCEEEEECcccCCHHHHHHHHHHHHHH-CCCEEEEEEeecCCCcccCCHHHHHHH
Confidence            345667655566666664     34778999999999999999999988863 47888999987753     34556655


Q ss_pred             HHHHh----cCCC--------CCCcHHHHHHHHHHH-HhcCCCeEEEEEecCccccccC---HHHHHHhHhCCCC-----
Q psy200          269 IVNEL----KLKP--------GGKSERHQLGAILKY-FDTKHKSILLILDEIDALESRK---QTILYTIFEWPSI-----  327 (490)
Q Consensus       269 i~~~l----~~~~--------~~~s~~~~~~~l~~~-l~~~~~~~vI~IDEid~l~~~~---~~~L~~l~~~~~~-----  327 (490)
                      ++..+    +...        ...+...+..+|.+. +....+++||+|||||.+....   .+.+..+-.|...     
T Consensus        85 ~~~~i~~~L~l~~~l~~~w~~~~~~~~~~~~~~~~~ll~~~~~~lVL~iDEiD~l~~~~~~~~dF~~~LR~~~~~~~~~~  164 (331)
T PF14516_consen   85 FCEEISRQLKLDEKLDEYWDEEIGSKISCTEYFEEYLLKQIDKPLVLFIDEIDRLFEYPQIADDFFGLLRSWYEQRKNNP  164 (331)
T ss_pred             HHHHHHHHcCCChhHHHHHHHhcCChhhHHHHHHHHHHhcCCCCEEEEEechhhhccCcchHHHHHHHHHHHHHhcccCc
Confidence            55544    3321        011334455566654 3445789999999999998743   2222222222211     


Q ss_pred             CCCcE--EEEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhh
Q psy200          328 PGSKL--VLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVS  405 (490)
Q Consensus       328 ~~~~v--ilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~  405 (490)
                      .-.++  ++++.+.. ......   -.+-|.++ ..+.+++++.+|+..++..+      ...+++..++.|..    +.
T Consensus       165 ~~~~L~li~~~~t~~-~~~~~~---~~SPFNIg-~~i~L~~Ft~~ev~~L~~~~------~~~~~~~~~~~l~~----~t  229 (331)
T PF14516_consen  165 IWQKLRLILAGSTED-YIILDI---NQSPFNIG-QPIELPDFTPEEVQELAQRY------GLEFSQEQLEQLMD----WT  229 (331)
T ss_pred             ccceEEEEEecCccc-ccccCC---CCCCcccc-cceeCCCCCHHHHHHHHHhh------hccCCHHHHHHHHH----HH
Confidence            11234  44443321 111111   12334443 36999999999999988764      23367777777765    77


Q ss_pred             CCHHHHHH-HHHHH
Q psy200          406 GDIRKAID-ITNHL  418 (490)
Q Consensus       406 Gd~r~ai~-ll~~a  418 (490)
                      |+-+.+++ +|...
T Consensus       230 gGhP~Lv~~~~~~l  243 (331)
T PF14516_consen  230 GGHPYLVQKACYLL  243 (331)
T ss_pred             CCCHHHHHHHHHHH
Confidence            77777665 44433

>PRK12377 putative replication protein; Provisional

Probab=98.96  E-value=9.6e-09  Score=97.43  Aligned_cols=150  Identities=20%  Similarity=0.246  Sum_probs=87.5

Q ss_pred             ChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCCC
Q psy200          198 GREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKP  277 (490)
Q Consensus       198 gre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~  277 (490)
                      |....+..+..++..+..  ...+++|+|++|||||+|+.++++.+.. .+..+++++.      .+++..+-.....  
T Consensus        82 ~~~~a~~~a~~~a~~~~~--~~~~l~l~G~~GtGKThLa~AIa~~l~~-~g~~v~~i~~------~~l~~~l~~~~~~--  150 (248)
T PRK12377         82 GQRYALSQAKSIADELMT--GCTNFVFSGKPGTGKNHLAAAIGNRLLA-KGRSVIVVTV------PDVMSRLHESYDN--  150 (248)
T ss_pred             hHHHHHHHHHHHHHHHHh--cCCeEEEECCCCCCHHHHHHHHHHHHHH-cCCCeEEEEH------HHHHHHHHHHHhc--
Confidence            334455556666655432  3478999999999999999999999863 3456666643      3455544433321  


Q ss_pred             CCCcHHHHHHHHHHHHhcCCCeEEEEEecCccc--cccCHHHHHHhHhCCCCCCCcEEEEEecCC--CChhHhhhHHhhh
Q psy200          278 GGKSERHQLGAILKYFDTKHKSILLILDEIDAL--ESRKQTILYTIFEWPSIPGSKLVLVGVANA--LDLTDRMLPRLQA  353 (490)
Q Consensus       278 ~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l--~~~~~~~L~~l~~~~~~~~~~vilI~~tn~--~~~~~~l~~~l~~  353 (490)
                       +.....   .+. .+   .+.-||||||+...  ....++.|+.+++.-+.....+++  +||.  .++...+..++.+
T Consensus       151 -~~~~~~---~l~-~l---~~~dLLiIDDlg~~~~s~~~~~~l~~ii~~R~~~~~ptii--tSNl~~~~l~~~~~~ri~d  220 (248)
T PRK12377        151 -GQSGEK---FLQ-EL---CKVDLLVLDEIGIQRETKNEQVVLNQIIDRRTASMRSVGM--LTNLNHEAMSTLLGERVMD  220 (248)
T ss_pred             -cchHHH---HHH-Hh---cCCCEEEEcCCCCCCCCHHHHHHHHHHHHHHHhcCCCEEE--EcCCCHHHHHHHhhHHHHH
Confidence             111222   222 22   33559999999554  344577888888754433344444  4662  2344444556667


Q ss_pred             ccCCC-CeeEEeCCCC
Q psy200          354 NVTLQ-PTLMNFAPYS  368 (490)
Q Consensus       354 R~~~~-~~~i~~~pls  368 (490)
                      |+... ...+.|..-+
T Consensus       221 Rl~~~~~~~v~~~g~s  236 (248)
T PRK12377        221 RMTMNGGRWVNFNWES  236 (248)
T ss_pred             HHhhCCCeEEEeCCcC
Confidence            76432 2457776544

>COG3284 AcoR Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription]

Probab=98.95  E-value=2.1e-09  Score=110.98  Aligned_cols=213  Identities=16%  Similarity=0.186  Sum_probs=144.7

Q ss_pred             ChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCCC
Q psy200          198 GREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKP  277 (490)
Q Consensus       198 gre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~  277 (490)
                      +.+..++.+...+....  ...-.++|.|++|+||-.+++++.+.-.  ..-+++.+||..+.. .-+-++++..+.+.+
T Consensus       317 ~~d~s~a~l~rk~~rv~--~~~~pvll~GEtGtGKe~laraiH~~s~--~~gpfvAvNCaAip~-~liesELFGy~~Gaf  391 (606)
T COG3284         317 LLDPSRATLLRKAERVA--ATDLPVLLQGETGTGKEVLARAIHQNSE--AAGPFVAVNCAAIPE-ALIESELFGYVAGAF  391 (606)
T ss_pred             ccCHHHHHHHHHHHHHh--hcCCCeEecCCcchhHHHHHHHHHhccc--ccCCeEEEEeccchH-HhhhHHHhccCcccc
Confidence            45556666666665532  3456899999999999999999988765  334889999998742 222344444555555


Q ss_pred             CCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCHHHHHHhHhCCCC-------CCCcEEEEEecCCCChhH-----
Q psy200          278 GGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPSI-------PGSKLVLVGVANALDLTD-----  345 (490)
Q Consensus       278 ~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~-------~~~~vilI~~tn~~~~~~-----  345 (490)
                      .|...+.....+..+-.  +   .+|+|||..|.-.-|..|++.++...+       ....|-||++|+.. +..     
T Consensus       392 Tga~~kG~~g~~~~A~g--G---tlFldeIgd~p~~~Qs~LLrVl~e~~v~p~g~~~~~vdirvi~ath~d-l~~lv~~g  465 (606)
T COG3284         392 TGARRKGYKGKLEQADG--G---TLFLDEIGDMPLALQSRLLRVLQEGVVTPLGGTRIKVDIRVIAATHRD-LAQLVEQG  465 (606)
T ss_pred             ccchhccccccceecCC--C---ccHHHHhhhchHHHHHHHHHHHhhCceeccCCcceeEEEEEEeccCcC-HHHHHHcC
Confidence            55444444444443322  2   899999999999889988888764321       34567888888732 222     


Q ss_pred             hhhHHhhhccCCCCeeEEeCCCCH-HHHHHHHHHHHhcc-CCCCCCCHHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHH
Q psy200          346 RMLPRLQANVTLQPTLMNFAPYSR-EQILEIISQKLKQT-DKFNMFNASALQLLAGKVAAVSGDIRKAIDITNHLIDLTY  423 (490)
Q Consensus       346 ~l~~~l~~R~~~~~~~i~~~pls~-~e~~~il~~~l~~~-~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll~~a~~~a~  423 (490)
                      ++-+.++.|++.  ..|.++|+.. .+...+|.+.+.++ .....++++++..+..  +.|.||+|++.++++.+..++.
T Consensus       466 ~fredLyyrL~~--~~i~lP~lr~R~d~~~~l~~~~~~~~~~~~~l~~~~~~~l~~--~~WPGNirel~~v~~~~~~l~~  541 (606)
T COG3284         466 RFREDLYYRLNA--FVITLPPLRERSDRIPLLDRILKRENDWRLQLDDDALARLLA--YRWPGNIRELDNVIERLAALSD  541 (606)
T ss_pred             CchHHHHHHhcC--eeeccCchhcccccHHHHHHHHHHccCCCccCCHHHHHHHHh--CCCCCcHHHHHHHHHHHHHcCC
Confidence            234667777653  4788888863 34444444444444 3346789999998876  8899999999999999987776


Q ss_pred             hc
Q psy200          424 DN  425 (490)
Q Consensus       424 ~~  425 (490)
                      ..
T Consensus       542 ~g  543 (606)
T COG3284         542 GG  543 (606)
T ss_pred             CC
Confidence            44

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

Probab=98.95  E-value=2.9e-09  Score=92.38  Aligned_cols=136  Identities=23%  Similarity=0.323  Sum_probs=85.0

Q ss_pred             CChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCC
Q psy200          197 PGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLK  276 (490)
Q Consensus       197 vgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~  276 (490)
                      +|....++++.+.+...  ......|+|+|++||||+++|++++.... ...-.++.++|....                
T Consensus         1 vG~S~~~~~l~~~l~~~--a~~~~pvli~GE~GtGK~~~A~~lh~~~~-~~~~~~~~~~~~~~~----------------   61 (138)
T PF14532_consen    1 VGKSPAMRRLRRQLERL--AKSSSPVLITGEPGTGKSLLARALHRYSG-RANGPFIVIDCASLP----------------   61 (138)
T ss_dssp             --SCHHHHHHHHHHHHH--HCSSS-EEEECCTTSSHHHHHHCCHHTTT-TCCS-CCCCCHHCTC----------------
T ss_pred             CCCCHHHHHHHHHHHHH--hCCCCcEEEEcCCCCCHHHHHHHHHhhcC-ccCCCeEEechhhCc----------------
Confidence            46667777888888764  35678999999999999999999977643 122244445555431                


Q ss_pred             CCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEEEecCCCChhH--hhhHHhhhc
Q psy200          277 PGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVANALDLTD--RMLPRLQAN  354 (490)
Q Consensus       277 ~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI~~tn~~~~~~--~l~~~l~~R  354 (490)
                               .+.+..+     +.-.|+|+|++.|....|..|..++......+.++|+.+..+..++.+  .+.+.+..+
T Consensus        62 ---------~~~l~~a-----~~gtL~l~~i~~L~~~~Q~~L~~~l~~~~~~~~RlI~ss~~~l~~l~~~~~~~~~L~~~  127 (138)
T PF14532_consen   62 ---------AELLEQA-----KGGTLYLKNIDRLSPEAQRRLLDLLKRQERSNVRLIASSSQDLEELVEEGRFSPDLYYR  127 (138)
T ss_dssp             ---------HHHHHHC-----TTSEEEEECGCCS-HHHHHHHHHHHHHCTTTTSEEEEEECC-CCCHHHHSTHHHHHHHH
T ss_pred             ---------HHHHHHc-----CCCEEEECChHHCCHHHHHHHHHHHHhcCCCCeEEEEEeCCCHHHHhhccchhHHHHHH
Confidence                     1222221     223899999999999999999888865434455666655555444332  356778877


Q ss_pred             cCCCCeeEEeCCC
Q psy200          355 VTLQPTLMNFAPY  367 (490)
Q Consensus       355 ~~~~~~~i~~~pl  367 (490)
                      +..  ..|.++|+
T Consensus       128 l~~--~~i~lPpL  138 (138)
T PF14532_consen  128 LSQ--LEIHLPPL  138 (138)
T ss_dssp             CST--CEEEE---
T ss_pred             hCC--CEEeCCCC
Confidence            764  36777764

>PF13173 AAA_14: AAA domain

Probab=98.92  E-value=3.7e-09  Score=90.43  Aligned_cols=126  Identities=21%  Similarity=0.319  Sum_probs=76.3

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCC
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFDTKHK  298 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~  298 (490)
                      .+.++|+||+|+||||+++.+++.+.  ..-.++++++.........               ..+ +.+.+.+...  .+
T Consensus         2 ~~~~~l~G~R~vGKTtll~~~~~~~~--~~~~~~yi~~~~~~~~~~~---------------~~~-~~~~~~~~~~--~~   61 (128)
T PF13173_consen    2 RKIIILTGPRGVGKTTLLKQLAKDLL--PPENILYINFDDPRDRRLA---------------DPD-LLEYFLELIK--PG   61 (128)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHhc--ccccceeeccCCHHHHHHh---------------hhh-hHHHHHHhhc--cC
Confidence            46889999999999999999998874  3346788876654211000               000 2223333221  24


Q ss_pred             eEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHH
Q psy200          299 SILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQI  372 (490)
Q Consensus       299 ~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~  372 (490)
                      ..+|||||||.+.. ....+..+.+..  .+.++++.|... ..+.......+..|..    .+.+.|++-.|.
T Consensus        62 ~~~i~iDEiq~~~~-~~~~lk~l~d~~--~~~~ii~tgS~~-~~l~~~~~~~l~gr~~----~~~l~Plsf~E~  127 (128)
T PF13173_consen   62 KKYIFIDEIQYLPD-WEDALKFLVDNG--PNIKIILTGSSS-SLLSKDIAESLAGRVI----EIELYPLSFREF  127 (128)
T ss_pred             CcEEEEehhhhhcc-HHHHHHHHHHhc--cCceEEEEccch-HHHhhcccccCCCeEE----EEEECCCCHHHh
Confidence            67999999999863 445555555522  334555544432 1122233455666664    799999998774

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

Probab=98.92  E-value=1.9e-09  Score=107.93  Aligned_cols=229  Identities=15%  Similarity=0.135  Sum_probs=120.1

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHh
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNEL  273 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l  273 (490)
                      .+++|++..+..+.-..      -.+++++++||||||||++++.+..-+..-..-..++++         .+..+..++
T Consensus       179 ~DV~GQ~~AKrAleiAA------AGgHnLl~~GpPGtGKTmla~Rl~~lLPpls~~E~lE~s---------~I~s~~g~~  243 (490)
T COG0606         179 KDVKGQEQAKRALEIAA------AGGHNLLLVGPPGTGKTMLASRLPGLLPPLSIPEALEVS---------AIHSLAGDL  243 (490)
T ss_pred             hhhcCcHHHHHHHHHHH------hcCCcEEEecCCCCchHHhhhhhcccCCCCChHHHHHHH---------HHhhhcccc
Confidence            78999999988776655      347899999999999999999886655210000111110         000111111


Q ss_pred             ------------cCCCCCCcHHHHHHHHHHHHh---cCCCeEEEEEecCccccccCHHHHHHhHhCCCC----------C
Q psy200          274 ------------KLKPGGKSERHQLGAILKYFD---TKHKSILLILDEIDALESRKQTILYTIFEWPSI----------P  328 (490)
Q Consensus       274 ------------~~~~~~~s~~~~~~~l~~~l~---~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~----------~  328 (490)
                                  ..+.+..+...+..--....-   ..-..-||||||+..+.....+.|..-++-...          .
T Consensus       244 ~~~~~~~~~rPFr~PHHsaS~~aLvGGG~~p~PGeIsLAH~GVLFLDElpef~~~iLe~LR~PLE~g~i~IsRa~~~v~y  323 (490)
T COG0606         244 HEGCPLKIHRPFRAPHHSASLAALVGGGGVPRPGEISLAHNGVLFLDELPEFKRSILEALREPLENGKIIISRAGSKVTY  323 (490)
T ss_pred             cccCccceeCCccCCCccchHHHHhCCCCCCCCCceeeecCCEEEeeccchhhHHHHHHHhCccccCcEEEEEcCCeeEE
Confidence                        011111121111110000000   001133999999999877555555544432211          2


Q ss_pred             CCcEEEEEecC--------------------CCChhHhhhHHhhhccCCCCeeEEeCCCCHHHH-------------HH-
Q psy200          329 GSKLVLVGVAN--------------------ALDLTDRMLPRLQANVTLQPTLMNFAPYSREQI-------------LE-  374 (490)
Q Consensus       329 ~~~vilI~~tn--------------------~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~-------------~~-  374 (490)
                      ..+|.+|+++|                    ...+..++...+.+|+++   .+.++.++..+.             .+ 
T Consensus       324 pa~Fqlv~AmNpcpcG~~~~~~~~C~c~~~~~~~Y~~klSgp~lDRiDl---~vev~~~~~~e~~~~~~~~ess~~v~~r  400 (490)
T COG0606         324 PARFQLVAAMNPCPCGNLGAPLRRCPCSPRQIKRYLNKLSGPFLDRIDL---MVEVPRLSAGELIRQVPTGESSAGVRER  400 (490)
T ss_pred             eeeeEEhhhcCCCCccCCCCCCCCcCCCHHHHHHHHHHhhHHHHhhhhh---eecccCCCHHHhhcCCCCCCCcHHHHHH
Confidence            45677887777                    112445566788889886   566666653322             11 


Q ss_pred             HH------HHHHhccCCCCCCCHHHHHH-----------HHHHHHHhhCCHHHHHHHHHHHHHHHHhccccCCcccccCH
Q psy200          375 II------SQKLKQTDKFNMFNASALQL-----------LAGKVAAVSGDIRKAIDITNHLIDLTYDNVKENGEVTGIGL  437 (490)
Q Consensus       375 il------~~~l~~~~~~~~~~~~~i~~-----------i~~~i~~~~Gd~r~ai~ll~~a~~~a~~~~~~~~~~~~It~  437 (490)
                      ++      ..+..+.+....+....++.           +-..+....=..|..-.+++-|..+|..++     ...|..
T Consensus       401 Va~AR~~Q~~R~~~~~~Na~l~~~~l~k~~~L~~~~~~~L~~al~~~~lS~R~~~rILKvarTiADL~g-----~~~i~~  475 (490)
T COG0606         401 VAKAREAQIARAGRIGINAELSEEALRKFCALQREDADLLKAALERLGLSARAYHRILKVARTIADLEG-----SEQIER  475 (490)
T ss_pred             HHHHHHHHHHHhhccCcchhcCHHHHHHhcccCHhHHHHHHHHHHhcchhHHHHHHHHHHHhhhhcccC-----cchhhH
Confidence            11      11111100122233333333           332222233345555567777778888888     678888


Q ss_pred             HHHHHHHH
Q psy200          438 KEVLGVIS  445 (490)
Q Consensus       438 ~~v~~a~~  445 (490)
                      .|+.+|++
T Consensus       476 ~hl~eAi~  483 (490)
T COG0606         476 SHLAEAIS  483 (490)
T ss_pred             HHHHHHHh
Confidence            88888885

>PRK06835 DNA replication protein DnaC; Validated

Probab=98.90  E-value=2.2e-08  Score=99.07  Aligned_cols=147  Identities=16%  Similarity=0.197  Sum_probs=85.8

Q ss_pred             HHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCCCCCCc
Q psy200          202 QLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKPGGKS  281 (490)
Q Consensus       202 ~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~~~s  281 (490)
                      .++....|+....  ....+++|+|++|+|||+|+.++++++.. .++.++|++.      .+++..+...-. ..    
T Consensus       168 ~~~~~~~f~~~f~--~~~~~Lll~G~~GtGKThLa~aIa~~l~~-~g~~V~y~t~------~~l~~~l~~~~~-~~----  233 (329)
T PRK06835        168 ILEKCKNFIENFD--KNNENLLFYGNTGTGKTFLSNCIAKELLD-RGKSVIYRTA------DELIEILREIRF-NN----  233 (329)
T ss_pred             HHHHHHHHHHHHh--ccCCcEEEECCCCCcHHHHHHHHHHHHHH-CCCeEEEEEH------HHHHHHHHHHHh-cc----
Confidence            3344445665532  23488999999999999999999999853 3567888853      344444432110 10    


Q ss_pred             HHHHHHHHHHHHhcCCCeEEEEEecCcccccc--CHHHHHHhHhCCCCCCCcEEEEEecC--CCChhHhhhHHhhhccCC
Q psy200          282 ERHQLGAILKYFDTKHKSILLILDEIDALESR--KQTILYTIFEWPSIPGSKLVLVGVAN--ALDLTDRMLPRLQANVTL  357 (490)
Q Consensus       282 ~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~--~~~~L~~l~~~~~~~~~~vilI~~tn--~~~~~~~l~~~l~~R~~~  357 (490)
                      ..+....+.. +..   .-+|||||++.....  .++.|+.+++.....+..+|+  +||  ..++...+.+++.+|+..
T Consensus       234 ~~~~~~~~~~-l~~---~DLLIIDDlG~e~~t~~~~~~Lf~iin~R~~~~k~tIi--TSNl~~~el~~~~~eri~SRL~~  307 (329)
T PRK06835        234 DKELEEVYDL-LIN---CDLLIIDDLGTEKITEFSKSELFNLINKRLLRQKKMII--STNLSLEELLKTYSERISSRLLG  307 (329)
T ss_pred             chhHHHHHHH-hcc---CCEEEEeccCCCCCCHHHHHHHHHHHHHHHHCCCCEEE--ECCCCHHHHHHHHhHHHHHHHHc
Confidence            0111111222 222   339999999776433  456788887654333444433  455  234445556777888765


Q ss_pred             CCeeEEeCCCC
Q psy200          358 QPTLMNFAPYS  368 (490)
Q Consensus       358 ~~~~i~~~pls  368 (490)
                      ....+.|..-+
T Consensus       308 ~~~~i~~~G~d  318 (329)
T PRK06835        308 NFTLLKFYGED  318 (329)
T ss_pred             CCEEEEecCcC
Confidence            44567775433

>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=98.90  E-value=2e-07  Score=93.07  Aligned_cols=178  Identities=15%  Similarity=0.211  Sum_probs=105.6

Q ss_pred             HHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhc--CCceEEEEeccCCCCHHHH----HHHHHHHhc
Q psy200          201 VQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIK--DAFKTIYINCNSVRNAASV----YETIVNELK  274 (490)
Q Consensus       201 ~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~--~~~~~~~v~~~~~~~~~~l----~~~i~~~l~  274 (490)
                      .-.+.|.+.|... ....+..+.|+|+=|+|||++++.+.+++...  ..+.+++++++......++    +..|...+.
T Consensus         3 ~~a~~la~~I~~~-~~~~~~~IgL~G~WGsGKSs~l~~l~~~L~~~~~~~~~~i~fn~w~~~~~~~~~~~~~~~l~~~l~   81 (325)
T PF07693_consen    3 PYAKALAEIIKNP-DSDDPFVIGLYGEWGSGKSSFLNMLKEELKEDNKEKYIFIYFNAWEYDGEDDLWASFLEELFDQLE   81 (325)
T ss_pred             HHHHHHHHHHhcc-CCCCCeEEEEECCCCCCHHHHHHHHHHHHhcccccceeeEEEccccCCCcchHHHHHHHHHHHHHH
Confidence            4455666666541 11467788899999999999999999999744  4578899999988764444    444444332


Q ss_pred             CCC----------------------C-----CC----------------------------------------cHHHHHH
Q psy200          275 LKP----------------------G-----GK----------------------------------------SERHQLG  287 (490)
Q Consensus       275 ~~~----------------------~-----~~----------------------------------------s~~~~~~  287 (490)
                      ...                      .     ..                                        ...++..
T Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  161 (325)
T PF07693_consen   82 KHFGSKKIKLYAKKKLKSLKIKFKIKINLSKAIPLALIGLPALILAVAIAKLKAELKNAFKSLEEKFLKKLKKEVEELIS  161 (325)
T ss_pred             HhcCccchhHHHhhhhhhhhceeeeeeecceeehHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhHHhhhhhHHHHHHHH
Confidence            100                      0     00                                        0001222


Q ss_pred             HHHHHHhcCCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEEEecCCCChhHhhh-------------HHhhhc
Q psy200          288 AILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVANALDLTDRML-------------PRLQAN  354 (490)
Q Consensus       288 ~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI~~tn~~~~~~~l~-------------~~l~~R  354 (490)
                      .+.+.+...++++||||||+|++.......++..+.... ...++++|.+.+..-+...+.             .-+..-
T Consensus       162 ~~~~~l~~~~~~iViiIDdLDR~~~~~i~~~l~~ik~~~-~~~~i~~Il~~D~~~l~~ai~~~~~~~~~~~~~~~yLeKi  240 (325)
T PF07693_consen  162 KIKKKLKESKKRIVIIIDDLDRCSPEEIVELLEAIKLLL-DFPNIIFILAFDPEILEKAIEKNYGEGFDEIDGREYLEKI  240 (325)
T ss_pred             HHHHhhhcCCceEEEEEcchhcCCcHHHHHHHHHHHHhc-CCCCeEEEEEecHHHHHHHHHhhcCcccccccHHHHHHhh
Confidence            233333345779999999999997765444444443322 224566665555221111110             111112


Q ss_pred             cCCCCeeEEeCCCCHHHHHHHHHHHHhcc
Q psy200          355 VTLQPTLMNFAPYSREQILEIISQKLKQT  383 (490)
Q Consensus       355 ~~~~~~~i~~~pls~~e~~~il~~~l~~~  383 (490)
                      +.   ..+.+++++..++..++...+...
T Consensus       241 iq---~~~~lP~~~~~~~~~~~~~~~~~~  266 (325)
T PF07693_consen  241 IQ---VPFSLPPPSPSDLERYLNELLESL  266 (325)
T ss_pred             cC---eEEEeCCCCHHHHHHHHHHHHHHh
Confidence            22   368999999999998888775544

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 [].

>PRK13406 bchD magnesium chelatase subunit D; Provisional

Probab=98.89  E-value=7e-08  Score=102.29  Aligned_cols=209  Identities=11%  Similarity=0.047  Sum_probs=138.2

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCCCCCCcHHHHHHH----HH-HH
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKPGGKSERHQLGA----IL-KY  292 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~~~s~~~~~~~----l~-~~  292 (490)
                      ..++++|.|+.|+||+++++.+..-+..  ..+|+.+..  ..+...++..           ...+.....    +. -.
T Consensus        24 ~~gGv~i~g~~G~~ks~~~r~l~~llp~--~~p~r~~p~--~~t~~~L~Gg-----------~Dl~~~l~~g~~~~~pGl   88 (584)
T PRK13406         24 GLGGVVLRARAGPVRDRWLAALRALLPA--GTPLRRLPP--GIADDRLLGG-----------LDLAATLRAGRPVAQRGL   88 (584)
T ss_pred             ccceEEEEcCCCcHHHHHHHHHHHhcCC--CCCcccCCC--CCcHHHccCC-----------chHHhHhhcCCcCCCCCc
Confidence            5689999999999999999999887642  223332221  1122222111           000000000    00 00


Q ss_pred             HhcCCCeEEEEEecCccccccCHHHHHHhHhCCCC----------CCCcEEEEEecCCCChhHhhhHHhhhccCCCCeeE
Q psy200          293 FDTKHKSILLILDEIDALESRKQTILYTIFEWPSI----------PGSKLVLVGVANALDLTDRMLPRLQANVTLQPTLM  362 (490)
Q Consensus       293 l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~----------~~~~vilI~~tn~~~~~~~l~~~l~~R~~~~~~~i  362 (490)
                      +.. -..-||||||+..+....++.|.+.++...+          ...+|++|++.|..++..++-+.+..||++   .+
T Consensus        89 la~-Ah~GvL~lDe~n~~~~~~~~aLleame~G~vtIeR~G~s~~~Pa~F~LIat~~~~~~~~~L~~~lLDRf~l---~v  164 (584)
T PRK13406         89 LAE-ADGGVLVLAMAERLEPGTAARLAAALDTGEVRLERDGLALRLPARFGLVALDEGAEEDERAPAALADRLAF---HL  164 (584)
T ss_pred             eee-ccCCEEEecCcccCCHHHHHHHHHHHhCCcEEEEECCcEEecCCCcEEEecCCChhcccCCCHHhHhheEE---EE
Confidence            111 1123999999999999999999988775422          346889998755444556677889999996   78


Q ss_pred             EeCCCCHHHHH-------HHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhC-CHHHHHHHHHHHHHHHHhccccCCcccc
Q psy200          363 NFAPYSREQIL-------EIISQKLKQTDKFNMFNASALQLLAGKVAAVSG-DIRKAIDITNHLIDLTYDNVKENGEVTG  434 (490)
Q Consensus       363 ~~~pls~~e~~-------~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~G-d~r~ai~ll~~a~~~a~~~~~~~~~~~~  434 (490)
                      .+..++..+..       .++..+- .. ....++++.++.+++.+....- +.|..+.+++-|..+|..++     ...
T Consensus       165 ~v~~~~~~~~~~~~~~~~~I~~AR~-rl-~~v~v~~~~l~~i~~~~~~~gv~S~Ra~i~llraARa~AaL~G-----r~~  237 (584)
T PRK13406        165 DLDGLALRDAREIPIDADDIAAARA-RL-PAVGPPPEAIAALCAAAAALGIASLRAPLLALRAARAAAALAG-----RTA  237 (584)
T ss_pred             EcCCCChHHhcccCCCHHHHHHHHH-HH-ccCCCCHHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHHHHcC-----CCC
Confidence            88887765432       2222221 11 2467899999998875554432 78999999999999999999     789


Q ss_pred             cCHHHHHHHHHHhccCcc
Q psy200          435 IGLKEVLGVISSVYCTSQ  452 (490)
Q Consensus       435 It~~~v~~a~~~~~~~~~  452 (490)
                      |+.+||..|+.-++..+.
T Consensus       238 V~~~dv~~Aa~lvL~hR~  255 (584)
T PRK13406        238 VEEEDLALAARLVLAPRA  255 (584)
T ss_pred             CCHHHHHHHHHHHHHhhc
Confidence            999999999998875544

>PRK07952 DNA replication protein DnaC; Validated

Probab=98.87  E-value=2.4e-08  Score=94.50  Aligned_cols=148  Identities=20%  Similarity=0.256  Sum_probs=86.0

Q ss_pred             HHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCCCCCC
Q psy200          201 VQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKPGGK  280 (490)
Q Consensus       201 ~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~~~  280 (490)
                      ..+..+..++...  .....+++|+|++|||||+|+.++++++.. .+..++++      +..+++..+-..+..  ...
T Consensus        83 ~al~~a~~~~~~~--~~~~~~~~l~G~~GtGKThLa~aia~~l~~-~g~~v~~i------t~~~l~~~l~~~~~~--~~~  151 (244)
T PRK07952         83 NALSKARQYVEEF--DGNIASFIFSGKPGTGKNHLAAAICNELLL-RGKSVLII------TVADIMSAMKDTFSN--SET  151 (244)
T ss_pred             HHHHHHHHHHHhh--ccCCceEEEECCCCCCHHHHHHHHHHHHHh-cCCeEEEE------EHHHHHHHHHHHHhh--ccc
Confidence            3555556666542  122458999999999999999999999863 24566666      345555555444321  112


Q ss_pred             cHHHHHHHHHHHHhcCCCeEEEEEecCcccccc--CHHHHHHhHhCCCCCCCcEEEEEecCC--CChhHhhhHHhhhccC
Q psy200          281 SERHQLGAILKYFDTKHKSILLILDEIDALESR--KQTILYTIFEWPSIPGSKLVLVGVANA--LDLTDRMLPRLQANVT  356 (490)
Q Consensus       281 s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~--~~~~L~~l~~~~~~~~~~vilI~~tn~--~~~~~~l~~~l~~R~~  356 (490)
                      +...+.+.    +.   +.-+|||||++.....  ..+.|+.+++.-+.....+++  +||.  .++...+..++.+|+.
T Consensus       152 ~~~~~l~~----l~---~~dlLvIDDig~~~~s~~~~~~l~~Ii~~Ry~~~~~tii--tSNl~~~~l~~~~g~ri~sRl~  222 (244)
T PRK07952        152 SEEQLLND----LS---NVDLLVIDEIGVQTESRYEKVIINQIVDRRSSSKRPTGM--LTNSNMEEMTKLLGERVMDRMR  222 (244)
T ss_pred             cHHHHHHH----hc---cCCEEEEeCCCCCCCCHHHHHHHHHHHHHHHhCCCCEEE--eCCCCHHHHHHHhChHHHHHHH
Confidence            22222222    32   2449999999987644  245677787644333334444  4662  2444445566667763


Q ss_pred             -CCCeeEEeCCCC
Q psy200          357 -LQPTLMNFAPYS  368 (490)
Q Consensus       357 -~~~~~i~~~pls  368 (490)
                       -+...+.|+--+
T Consensus       223 ~~~~~~i~f~~~s  235 (244)
T PRK07952        223 LGNSLWVIFNWDS  235 (244)
T ss_pred             HCCceEEEeeCCc
Confidence             223466776433

>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=98.86  E-value=1e-09  Score=99.76  Aligned_cols=133  Identities=18%  Similarity=0.203  Sum_probs=67.1

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHH-
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNE-  272 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~-  272 (490)
                      .+++|++..+..|.-...      .+++++|+||||+|||++|+.+..-+..-..-.  .+....+.+.....  .... 
T Consensus         3 ~dI~GQe~aKrAL~iAAa------G~h~lLl~GppGtGKTmlA~~l~~lLP~l~~~e--~le~~~i~s~~~~~--~~~~~   72 (206)
T PF01078_consen    3 SDIVGQEEAKRALEIAAA------GGHHLLLIGPPGTGKTMLARRLPSLLPPLTEEE--ALEVSKIYSVAGLG--PDEGL   72 (206)
T ss_dssp             CCSSSTHHHHHHHHHHHH------CC--EEEES-CCCTHHHHHHHHHHCS--CCEEC--CESS--S-TT---S-----EE
T ss_pred             hhhcCcHHHHHHHHHHHc------CCCCeEEECCCCCCHHHHHHHHHHhCCCCchHH--HhhhccccccccCC--CCCce
Confidence            578999998877766653      257999999999999999999987663111000  01111111111100  0000 


Q ss_pred             -----hcCCCCCCcHHHHHHHHHH------HHhcCCCeEEEEEecCccccccCHHHHHHhHhCCCC----------CCCc
Q psy200          273 -----LKLKPGGKSERHQLGAILK------YFDTKHKSILLILDEIDALESRKQTILYTIFEWPSI----------PGSK  331 (490)
Q Consensus       273 -----l~~~~~~~s~~~~~~~l~~------~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~----------~~~~  331 (490)
                           +..+....+...+..--..      .+..   .-||||||+..+.....+.|++.++...+          ...+
T Consensus        73 ~~~~Pfr~phhs~s~~~liGgg~~~~PGeislAh---~GVLflDE~~ef~~~vld~Lr~ple~g~v~i~R~~~~~~~Pa~  149 (206)
T PF01078_consen   73 IRQRPFRAPHHSASEAALIGGGRPPRPGEISLAH---RGVLFLDELNEFDRSVLDALRQPLEDGEVTISRAGGSVTYPAR  149 (206)
T ss_dssp             EE---EEEE-TT--HHHHHEEGGGEEE-CGGGGT---TSEEEECETTTS-HHHHHHHHHHHHHSBEEEEETTEEEEEB--
T ss_pred             ecCCCcccCCCCcCHHHHhCCCcCCCcCHHHHhc---CCEEEechhhhcCHHHHHHHHHHHHCCeEEEEECCceEEEecc
Confidence                 0001111222222111000      0111   23999999999988888888887754321          3567


Q ss_pred             EEEEEecC
Q psy200          332 LVLVGVAN  339 (490)
Q Consensus       332 vilI~~tn  339 (490)
                      +++|+++|
T Consensus       150 f~lv~a~N  157 (206)
T PF01078_consen  150 FLLVAAMN  157 (206)
T ss_dssp             EEEEEEE-
T ss_pred             cEEEEEec
Confidence            89999988

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.

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=98.86  E-value=1.7e-08  Score=86.70  Aligned_cols=118  Identities=23%  Similarity=0.216  Sum_probs=65.6

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcC-CCCCCcHHHHHHHHHHHHhcCC
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKL-KPGGKSERHQLGAILKYFDTKH  297 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~-~~~~~s~~~~~~~l~~~l~~~~  297 (490)
                      ...++|+||+|+|||++++.++..+.... ..++++++............ ...... .........+...+.. ... .
T Consensus         2 ~~~~~l~G~~G~GKTtl~~~l~~~~~~~~-~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~-~~~-~   77 (148)
T smart00382        2 GEVILIVGPPGSGKTTLARALARELGPPG-GGVIYIDGEDILEEVLDQLL-LIIVGGKKASGSGELRLRLALAL-ARK-L   77 (148)
T ss_pred             CCEEEEECCCCCcHHHHHHHHHhccCCCC-CCEEEECCEEccccCHHHHH-hhhhhccCCCCCHHHHHHHHHHH-HHh-c
Confidence            46899999999999999999999886222 25677776655322211110 000111 1111223333333332 222 2


Q ss_pred             CeEEEEEecCccccccCHHHHHHh-----HhCCCCCCCcEEEEEecCC
Q psy200          298 KSILLILDEIDALESRKQTILYTI-----FEWPSIPGSKLVLVGVANA  340 (490)
Q Consensus       298 ~~~vI~IDEid~l~~~~~~~L~~l-----~~~~~~~~~~vilI~~tn~  340 (490)
                      .+.+|||||++.+...........     ..........+.+|+++|.
T Consensus        78 ~~~viiiDei~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~  125 (148)
T smart00382       78 KPDVLILDEITSLLDAEQEALLLLLEELRLLLLLKSEKNLTVILTTND  125 (148)
T ss_pred             CCCEEEEECCcccCCHHHHHHHHhhhhhHHHHHHHhcCCCEEEEEeCC
Confidence            257999999999987754433221     0011123445677777773

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.

>PRK07132 DNA polymerase III subunit delta'; Validated

Probab=98.85  E-value=2.3e-07  Score=90.46  Aligned_cols=168  Identities=14%  Similarity=0.160  Sum_probs=109.0

Q ss_pred             HHHHHhhhccC-CCCeEEEECCCCCcHHHHHHHHHHHhhhcC---------CceEEEEeccCCCCHHHHHHHHHHHhcCC
Q psy200          207 RQFLLGHVNNE-TSGSMYISGPPGTGKSASLNLLVSRAEIKD---------AFKTIYINCNSVRNAASVYETIVNELKLK  276 (490)
Q Consensus       207 ~~~L~~~~~~~-~~~~ill~GppGtGKTtla~~l~~~l~~~~---------~~~~~~v~~~~~~~~~~l~~~i~~~l~~~  276 (490)
                      .+.|...+..+ -.+..+++|+.|.||+.++..+++.+-+..         ...+.+++..                   
T Consensus         5 ~~~l~~~i~~~~l~haYLf~G~eg~gk~~~a~~~a~~l~c~~~~~~~~~~~p~n~~~~d~~-------------------   65 (299)
T PRK07132          5 IKFLDNSATQNKISHSFLLKSNYNEDIDEKILYFLNKFNNLQITNLNEQELPANIILFDIF-------------------   65 (299)
T ss_pred             HHHHHHHHHhCCCCeEEEEeCCCCCCHHHHHHHHHHHHcCcCCCCCCCCCCCcceEEeccC-------------------
Confidence            34444444444 445566999999999999999999873210         1112222200                   


Q ss_pred             CCCCcHHHHHHHHHHHHhcC---CCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEEEecCCCChhHhhhHHhhh
Q psy200          277 PGGKSERHQLGAILKYFDTK---HKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVANALDLTDRMLPRLQA  353 (490)
Q Consensus       277 ~~~~s~~~~~~~l~~~l~~~---~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI~~tn~~~~~~~l~~~l~~  353 (490)
                      ....+.+++++.....-...   +...|+|||+++.+....++.|..+++.   ++...++|.+++.   ...+.+.+++
T Consensus        66 g~~i~vd~Ir~l~~~~~~~~~~~~~~KvvII~~~e~m~~~a~NaLLK~LEE---Pp~~t~~il~~~~---~~kll~TI~S  139 (299)
T PRK07132         66 DKDLSKSEFLSAINKLYFSSFVQSQKKILIIKNIEKTSNSLLNALLKTIEE---PPKDTYFLLTTKN---INKVLPTIVS  139 (299)
T ss_pred             CCcCCHHHHHHHHHHhccCCcccCCceEEEEecccccCHHHHHHHHHHhhC---CCCCeEEEEEeCC---hHhChHHHHh
Confidence            11134556665555442222   4677999999999988888888888774   3445555555542   4788899999


Q ss_pred             ccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHHHH
Q psy200          354 NVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDIT  415 (490)
Q Consensus       354 R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll  415 (490)
                      ||.    .+.|.+++.+++...|...        .++++....++.    ..|++..|+.++
T Consensus       140 Rc~----~~~f~~l~~~~l~~~l~~~--------~~~~~~a~~~a~----~~~~~~~a~~~~  185 (299)
T PRK07132        140 RCQ----VFNVKEPDQQKILAKLLSK--------NKEKEYNWFYAY----IFSNFEQAEKYI  185 (299)
T ss_pred             CeE----EEECCCCCHHHHHHHHHHc--------CCChhHHHHHHH----HcCCHHHHHHHH
Confidence            995    8999999999999888753        135555555543    566677776654

>PRK06921 hypothetical protein; Provisional

Probab=98.83  E-value=5.6e-08  Score=93.63  Aligned_cols=101  Identities=13%  Similarity=0.285  Sum_probs=60.9

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCC
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFDTKH  297 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~  297 (490)
                      ....++|+|++|+|||+|+.++++++....++.++|+..      .+++..+...+         ..+.+.+.. +   .
T Consensus       116 ~~~~l~l~G~~G~GKThLa~aia~~l~~~~g~~v~y~~~------~~l~~~l~~~~---------~~~~~~~~~-~---~  176 (266)
T PRK06921        116 RKNSIALLGQPGSGKTHLLTAAANELMRKKGVPVLYFPF------VEGFGDLKDDF---------DLLEAKLNR-M---K  176 (266)
T ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHHhhhcCceEEEEEH------HHHHHHHHHHH---------HHHHHHHHH-h---c
Confidence            467899999999999999999999986433577788853      33333332221         111122222 2   2


Q ss_pred             CeEEEEEecCcc-c------cccCHHHHHHhHhCCCCCCCcEEEEEecC
Q psy200          298 KSILLILDEIDA-L------ESRKQTILYTIFEWPSIPGSKLVLVGVAN  339 (490)
Q Consensus       298 ~~~vI~IDEid~-l------~~~~~~~L~~l~~~~~~~~~~vilI~~tn  339 (490)
                      ..-||||||++. +      ....++.|+.+++.....+..+  |.++|
T Consensus       177 ~~dlLiIDDl~~~~~g~e~~t~~~~~~lf~iin~R~~~~k~t--Iitsn  223 (266)
T PRK06921        177 KVEVLFIDDLFKPVNGKPRATEWQIEQMYSVLNYRYLNHKPI--LISSE  223 (266)
T ss_pred             CCCEEEEeccccccCCCccCCHHHHHHHHHHHHHHHHCCCCE--EEECC
Confidence            345999999954 1      1223456777776543333444  33455

>PRK04841 transcriptional regulator MalT; Provisional

Probab=98.80  E-value=3.1e-07  Score=104.40  Aligned_cols=194  Identities=12%  Similarity=0.205  Sum_probs=117.8

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCC-CCHHHHHHHHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSV-RNAASVYETIVNE  272 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~-~~~~~l~~~i~~~  272 (490)
                      ..++-|...++.|..       ....+.++|+||+|.||||++..+++..    + .++|+++... .++..|+..++..
T Consensus        14 ~~~~~R~rl~~~l~~-------~~~~~~~~v~apaG~GKTtl~~~~~~~~----~-~~~w~~l~~~d~~~~~f~~~l~~~   81 (903)
T PRK04841         14 HNTVVRERLLAKLSG-------ANNYRLVLVTSPAGYGKTTLISQWAAGK----N-NLGWYSLDESDNQPERFASYLIAA   81 (903)
T ss_pred             cccCcchHHHHHHhc-------ccCCCeEEEECCCCCCHHHHHHHHHHhC----C-CeEEEecCcccCCHHHHHHHHHHH
Confidence            567777766655432       2356789999999999999999988653    2 5778877544 4667788888888


Q ss_pred             hcCCCCC--------------CcHHHHHHHHHHHHhcCCCeEEEEEecCccccccC-HHHHHHhHhCCCCCCCcEEEEEe
Q psy200          273 LKLKPGG--------------KSERHQLGAILKYFDTKHKSILLILDEIDALESRK-QTILYTIFEWPSIPGSKLVLVGV  337 (490)
Q Consensus       273 l~~~~~~--------------~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~-~~~L~~l~~~~~~~~~~vilI~~  337 (490)
                      |.....+              .....+...+...+...+.+++|||||+|.+.... .+.+..++...   ...+.+|.+
T Consensus        82 l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~lvlDD~h~~~~~~~~~~l~~l~~~~---~~~~~lv~~  158 (903)
T PRK04841         82 LQQATNGHCSKSEALAQKRQYASLSSLFAQLFIELADWHQPLYLVIDDYHLITNPEIHEAMRFFLRHQ---PENLTLVVL  158 (903)
T ss_pred             HHHhcCcccchhhhhhccCCcCCHHHHHHHHHHHHhcCCCCEEEEEeCcCcCCChHHHHHHHHHHHhC---CCCeEEEEE
Confidence            7421110              11222333333344444679999999999997554 33555555432   223333333


Q ss_pred             cCC-CChhHhhhHHhhhccCCCCeeEEeC----CCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHH
Q psy200          338 ANA-LDLTDRMLPRLQANVTLQPTLMNFA----PYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAI  412 (490)
Q Consensus       338 tn~-~~~~~~l~~~l~~R~~~~~~~i~~~----pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai  412 (490)
                      +.. ..+  . ...++-+-    ..+.+.    +++.+|+..++...+..     .++++.++.|.+    .+++-+.++
T Consensus       159 sR~~~~~--~-~~~l~~~~----~~~~l~~~~l~f~~~e~~~ll~~~~~~-----~~~~~~~~~l~~----~t~Gwp~~l  222 (903)
T PRK04841        159 SRNLPPL--G-IANLRVRD----QLLEIGSQQLAFDHQEAQQFFDQRLSS-----PIEAAESSRLCD----DVEGWATAL  222 (903)
T ss_pred             eCCCCCC--c-hHhHHhcC----cceecCHHhCCCCHHHHHHHHHhccCC-----CCCHHHHHHHHH----HhCChHHHH
Confidence            432 111  1 11222111    134444    99999999999876543     368888888886    666666666


Q ss_pred             HHHHHH
Q psy200          413 DITNHL  418 (490)
Q Consensus       413 ~ll~~a  418 (490)
                      .++..+
T Consensus       223 ~l~~~~  228 (903)
T PRK04841        223 QLIALS  228 (903)
T ss_pred             HHHHHH
Confidence            654433

>PTZ00111 DNA replication licensing factor MCM4; Provisional

Probab=98.77  E-value=2.1e-07  Score=101.31  Aligned_cols=231  Identities=15%  Similarity=0.154  Sum_probs=132.6

Q ss_pred             CCCCChHHHHHHHHHHHHhhhcc-----------------CCCCeEEEECCCCCcHHHHHHHHHHHhhhc---CCceEEE
Q psy200          194 CELPGREVQLEGIRQFLLGHVNN-----------------ETSGSMYISGPPGTGKSASLNLLVSRAEIK---DAFKTIY  253 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~-----------------~~~~~ill~GppGtGKTtla~~l~~~l~~~---~~~~~~~  253 (490)
                      ..++|++..+..|.-.|-.....                 ....+|||+|+||||||.+|+++++.....   .+-.+..
T Consensus       450 P~I~G~e~vK~ailL~L~gG~~k~~~~~~~~dg~~~~~~iRgdihVLLvGDPGTGKSqLAr~Ih~lspR~~ytsG~~~s~  529 (915)
T PTZ00111        450 PSIKARNNVKIGLLCQLFSGNKNSSDFNKSPDACYKVDNFRGIINVLLCGDPGTAKSQLLHYTHLLSPRSIYTSGKSSSS  529 (915)
T ss_pred             CeEECCHHHHHHHHHHHhcCCccccccccccccccccccccCCceEEEeCCCCccHHHHHHHHHHhCCccccCCCCCCcc
Confidence            78999999888776655432210                 112389999999999999999997743210   0012222


Q ss_pred             EeccCCCCHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCHHHHHHhHhCCCC------
Q psy200          254 INCNSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPSI------  327 (490)
Q Consensus       254 v~~~~~~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~------  327 (490)
                      ++|...         . .. .....|.-   ..+  .-++.. ...-+++|||++.|....|..|..+|+-...      
T Consensus       530 vgLTa~---------~-~~-~d~~tG~~---~le--~GaLvl-AdgGtL~IDEidkms~~~Q~aLlEaMEqqtIsI~KaG  592 (915)
T PTZ00111        530 VGLTAS---------I-KF-NESDNGRA---MIQ--PGAVVL-ANGGVCCIDELDKCHNESRLSLYEVMEQQTVTIAKAG  592 (915)
T ss_pred             ccccch---------h-hh-cccccCcc---ccc--CCcEEE-cCCCeEEecchhhCCHHHHHHHHHHHhCCEEEEecCC
Confidence            222211         0 00 00000000   000  000110 0112999999999999889989888864321      


Q ss_pred             ----CCCcEEEEEecCCCCh----------hHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHh------------
Q psy200          328 ----PGSKLVLVGVANALDL----------TDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLK------------  381 (490)
Q Consensus       328 ----~~~~vilI~~tn~~~~----------~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~------------  381 (490)
                          .+.++.||+++|...-          .-.+.+.+.+||.+  ..+.++.++.+.=..|-.+.+.            
T Consensus       593 i~~tL~ar~rVIAAaNP~~gryd~~~s~~eni~Lp~~LLSRFDL--If~l~D~~d~~~D~~lA~hI~~~~~~~h~~~~~~  670 (915)
T PTZ00111        593 IVATLKAETAILASCNPINSRYNKNKAVIENINISPSLFTRFDL--IYLVLDHIDQDTDQLISLSIAKDFLLPHMTGSGN  670 (915)
T ss_pred             cceecCCCeEEEEEcCCcccccCcccCcccccCCChHHhhhhcE--EEEecCCCChHHHHHHHHHHHHhhcccccccccc
Confidence                2468899999995421          11234678889875  2445555554432222222111            


Q ss_pred             -------------------------------------cc--CCCCCCCHHHHHHHHHHHHHhh-----------------
Q psy200          382 -------------------------------------QT--DKFNMFNASALQLLAGKVAAVS-----------------  405 (490)
Q Consensus       382 -------------------------------------~~--~~~~~~~~~~i~~i~~~i~~~~-----------------  405 (490)
                                                           -.  .....+++++.+.|.+.+....                 
T Consensus       671 ~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~lLrkYI~YAR~~~~P~Ls~eA~~~i~~~Yv~mR~~~~~~~~~~~~~~~~~  750 (915)
T PTZ00111        671 DEDTYDRSNTMHVEDESLRSEKDYNKNDLDMLRMYIKFSKLHCFPKLSDEAKKVITREYVKMRQGNFQTSNLDELEHAQE  750 (915)
T ss_pred             cccchhccccccccccccccccccCCCCHHHHHHHHHHHhccCCCCCCHHHHHHHHHHHHHHhhhhcccccccccccccc
Confidence                                                 00  1235578888888766443221                 


Q ss_pred             -----------C------CHHHHHHHHHHHHHHHHhccccCCcccccCHHHHHHHHHHhc
Q psy200          406 -----------G------DIRKAIDITNHLIDLTYDNVKENGEVTGIGLKEVLGVISSVY  448 (490)
Q Consensus       406 -----------G------d~r~ai~ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~~~~~  448 (490)
                                 |      .+|++-.+++.+-..|..+-     ...|+.+|+..|+.-+.
T Consensus       751 ~~~~~~~~~~~~~~~i~iT~RqLEsLIRLsEA~AK~rL-----s~~Vt~~Dv~~Ai~L~~  805 (915)
T PTZ00111        751 DDDDDLYYQSSGTRMIYVSSRMISSIIRISVSLARMRL-----STVVTPADALQAVQIVK  805 (915)
T ss_pred             ccccccccccccCCcccccHHHHHHHHHHHHHHhhhcC-----cCcccHHHHHHHHHHHH
Confidence                       1      26677677777777787777     67899999999887643

>PRK08699 DNA polymerase III subunit delta'; Validated

Probab=98.77  E-value=2e-07  Score=92.28  Aligned_cols=151  Identities=15%  Similarity=0.191  Sum_probs=93.5

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHh---cCC----C-----CCCcHHH
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNEL---KLK----P-----GGKSERH  284 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l---~~~----~-----~~~s~~~  284 (490)
                      .-++.++|+||+|+|||++|+.+++.+.....-. -...|..+.+...+...-.-++   ...    .     ...+.++
T Consensus        19 r~~hA~Lf~G~~G~GK~~la~~~a~~llC~~~~~-~~~~Cg~C~~C~~~~~~~HpD~~~~~p~~~~~~~g~~~~~I~id~   97 (325)
T PRK08699         19 RRPNAWLFAGKKGIGKTAFARFAAQALLCETPAP-GHKPCGECMSCHLFGQGSHPDFYEITPLSDEPENGRKLLQIKIDA   97 (325)
T ss_pred             CcceEEEeECCCCCCHHHHHHHHHHHHcCCCCCC-CCCCCCcCHHHHHHhcCCCCCEEEEecccccccccccCCCcCHHH
Confidence            5567899999999999999999999875321100 0012222211111110000000   000    0     1134666


Q ss_pred             HHHHHHHHHhc--CCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEEEecCCCChhHhhhHHhhhccCCCCeeE
Q psy200          285 QLGAILKYFDT--KHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVANALDLTDRMLPRLQANVTLQPTLM  362 (490)
Q Consensus       285 ~~~~l~~~l~~--~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI~~tn~~~~~~~l~~~l~~R~~~~~~~i  362 (490)
                      +++........  .++..|+|||+++.|....++.|..+++... .  ...+|.+++.   ...+.+.+.+||.    .+
T Consensus        98 iR~l~~~~~~~p~~~~~kV~iiEp~~~Ld~~a~naLLk~LEep~-~--~~~~Ilvth~---~~~ll~ti~SRc~----~~  167 (325)
T PRK08699         98 VREIIDNVYLTSVRGGLRVILIHPAESMNLQAANSLLKVLEEPP-P--QVVFLLVSHA---ADKVLPTIKSRCR----KM  167 (325)
T ss_pred             HHHHHHHHhhCcccCCceEEEEechhhCCHHHHHHHHHHHHhCc-C--CCEEEEEeCC---hHhChHHHHHHhh----hh
Confidence            66655443322  2456688899999999998898988887553 2  2434445542   4567788999996    79


Q ss_pred             EeCCCCHHHHHHHHHH
Q psy200          363 NFAPYSREQILEIISQ  378 (490)
Q Consensus       363 ~~~pls~~e~~~il~~  378 (490)
                      .|.+++.+++...|..
T Consensus       168 ~~~~~~~~~~~~~L~~  183 (325)
T PRK08699        168 VLPAPSHEEALAYLRE  183 (325)
T ss_pred             cCCCCCHHHHHHHHHh
Confidence            9999999999988865

>PRK07276 DNA polymerase III subunit delta'; Validated

Probab=98.76  E-value=3e-07  Score=88.97  Aligned_cols=185  Identities=12%  Similarity=0.218  Sum_probs=109.9

Q ss_pred             HHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHh---cCCC
Q psy200          201 VQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNEL---KLKP  277 (490)
Q Consensus       201 ~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l---~~~~  277 (490)
                      ..++.+...+..   +.-++..+++|+  +||+++|..++..+-......  .-.|..+.+...+...-.-++   ....
T Consensus         9 ~~~~~L~~~~~~---~rl~hAyLf~G~--~G~~~~A~~~A~~llC~~~~~--~~~Cg~C~~C~~i~~~~HPD~~~i~p~~   81 (290)
T PRK07276          9 KVFQRFQTILEQ---DRLNHAYLFSGD--FASFEMALFLAQSLFCEQKEG--VLPCGHCRSCRLIEQGEFSDVTVIEPQG   81 (290)
T ss_pred             HHHHHHHHHHHc---CCcceeeeeeCC--ccHHHHHHHHHHHHcCCCCCC--CCCCCCCHHHHHHhcCCCCCeeeecCCC
Confidence            444445555442   345677889995  789999999999875332110  012333322222111000000   0011


Q ss_pred             CCCcHHHHHHHHHHHHhc--CCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEEEecCCCChhHhhhHHhhhcc
Q psy200          278 GGKSERHQLGAILKYFDT--KHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVANALDLTDRMLPRLQANV  355 (490)
Q Consensus       278 ~~~s~~~~~~~l~~~l~~--~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI~~tn~~~~~~~l~~~l~~R~  355 (490)
                      ...+.+++++........  .++..|+|||++|.|.....+.|...++.+   ..+.++|.+++   -.+.+++.++|||
T Consensus        82 ~~I~idqIR~l~~~~~~~p~~~~~kV~II~~ad~m~~~AaNaLLKtLEEP---p~~t~~iL~t~---~~~~lLpTI~SRc  155 (290)
T PRK07276         82 QVIKTDTIRELVKNFSQSGYEGKQQVFIIKDADKMHVNAANSLLKVIEEP---QSEIYIFLLTN---DENKVLPTIKSRT  155 (290)
T ss_pred             CcCCHHHHHHHHHHHhhCcccCCcEEEEeehhhhcCHHHHHHHHHHhcCC---CCCeEEEEEEC---ChhhCchHHHHcc
Confidence            123566676655544322  245679999999999998889898888744   34455555554   2677899999999


Q ss_pred             CCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHHHH
Q psy200          356 TLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDIT  415 (490)
Q Consensus       356 ~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll  415 (490)
                      .    .+.|.+ +.+++.+++..    .+    ++.+..+.++    ...|++..|+.++
T Consensus       156 q----~i~f~~-~~~~~~~~L~~----~g----~~~~~a~~la----~~~~s~~~A~~l~  198 (290)
T PRK07276        156 Q----IFHFPK-NEAYLIQLLEQ----KG----LLKTQAELLA----KLAQSTSEAEKLA  198 (290)
T ss_pred             e----eeeCCC-cHHHHHHHHHH----cC----CChHHHHHHH----HHCCCHHHHHHHh
Confidence            6    899977 77777776653    21    3444344444    3567888887765

>KOG1051|consensus

Probab=98.76  E-value=1.3e-07  Score=102.72  Aligned_cols=136  Identities=14%  Similarity=0.206  Sum_probs=98.3

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccC----CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNE----TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETI  269 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~----~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i  269 (490)
                      +.++|+++.+..|.+.+..+-.+.    +...+++.||.|+|||-||++++..+- ...-.++.++.+.+..        
T Consensus       562 ~~V~gQ~eAv~aIa~AI~~sr~gl~~~~~~awflflGpdgvGKt~lAkaLA~~~F-gse~~~IriDmse~~e--------  632 (898)
T KOG1051|consen  562 ERVIGQDEAVAAIAAAIRRSRAGLKDPNPDAWFLFLGPDGVGKTELAKALAEYVF-GSEENFIRLDMSEFQE--------  632 (898)
T ss_pred             hhccchHHHHHHHHHHHHhhhcccCCCCCCeEEEEECCCchhHHHHHHHHHHHHc-CCccceEEechhhhhh--------
Confidence            899999999999999998764322    355788999999999999999999883 3444678887665422        


Q ss_pred             HHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCHHHHHHhHhCCCC--------CCCcEEEEEecC
Q psy200          270 VNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPSI--------PGSKLVLVGVAN  339 (490)
Q Consensus       270 ~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~--------~~~~vilI~~tn  339 (490)
                      ...+.+...|.-..+....|.++++. ...+||+||||+.-...-+..|.++++....        .-.++|||+++|
T Consensus       633 vskligsp~gyvG~e~gg~Lteavrr-rP~sVVLfdeIEkAh~~v~n~llq~lD~GrltDs~Gr~Vd~kN~I~IMTsn  709 (898)
T KOG1051|consen  633 VSKLIGSPPGYVGKEEGGQLTEAVKR-RPYSVVLFEEIEKAHPDVLNILLQLLDRGRLTDSHGREVDFKNAIFIMTSN  709 (898)
T ss_pred             hhhccCCCcccccchhHHHHHHHHhc-CCceEEEEechhhcCHHHHHHHHHHHhcCccccCCCcEeeccceEEEEecc
Confidence            22333333333344455566777765 4578999999999888778888888875532        245778888877

>PTZ00202 tuzin; Provisional

Probab=98.75  E-value=4.1e-07  Score=90.88  Aligned_cols=169  Identities=16%  Similarity=0.228  Sum_probs=103.4

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHh
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNEL  273 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l  273 (490)
                      ..|+||+.++..|...|... ....+..+.|+|++|+|||++++.+...+.    +..+++|..   +..+++..|+.+|
T Consensus       262 ~~FVGReaEla~Lr~VL~~~-d~~~privvLtG~~G~GKTTLlR~~~~~l~----~~qL~vNpr---g~eElLr~LL~AL  333 (550)
T PTZ00202        262 RQFVSREAEESWVRQVLRRL-DTAHPRIVVFTGFRGCGKSSLCRSAVRKEG----MPAVFVDVR---GTEDTLRSVVKAL  333 (550)
T ss_pred             cCCCCcHHHHHHHHHHHhcc-CCCCceEEEEECCCCCCHHHHHHHHHhcCC----ceEEEECCC---CHHHHHHHHHHHc
Confidence            68999999999999999742 223456888999999999999999998764    444555544   6799999999999


Q ss_pred             cCCCCCCcHHHHHHHHHHHH----hcCCCeEEEEE--ecCccccccCHHHHHHhHhCCCCCCCcEEEEEecCCCChhHhh
Q psy200          274 KLKPGGKSERHQLGAILKYF----DTKHKSILLIL--DEIDALESRKQTILYTIFEWPSIPGSKLVLVGVANALDLTDRM  347 (490)
Q Consensus       274 ~~~~~~~s~~~~~~~l~~~l----~~~~~~~vI~I--DEid~l~~~~~~~L~~l~~~~~~~~~~vilI~~tn~~~~~~~l  347 (490)
                      +.... ....++.++|.+++    ...++..||||  -|-..|..--.+.+. +  -....-+.+++=..-....+..-.
T Consensus       334 GV~p~-~~k~dLLrqIqeaLl~~~~e~GrtPVLII~lreg~~l~rvyne~v~-l--a~drr~ch~v~evpleslt~~~~~  409 (550)
T PTZ00202        334 GVPNV-EACGDLLDFISEACRRAKKMNGETPLLVLKLREGSSLQRVYNEVVA-L--ACDRRLCHVVIEVPLESLTIANTL  409 (550)
T ss_pred             CCCCc-ccHHHHHHHHHHHHHHHHHhCCCCEEEEEEecCCCcHHHHHHHHHH-H--HccchhheeeeeehHhhcchhccc
Confidence            97433 33345555555544    33244444444  455554322112111 1  111222333332211111122222


Q ss_pred             hHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhc
Q psy200          348 LPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQ  382 (490)
Q Consensus       348 ~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~  382 (490)
                      +|    |++    .+.+++++.++...+.++.+.-
T Consensus       410 lp----rld----f~~vp~fsr~qaf~y~~h~~da  436 (550)
T PTZ00202        410 LP----RLD----FYLVPNFSRSQAFAYTQHAIDA  436 (550)
T ss_pred             Cc----cce----eEecCCCCHHHHHHHHhhccch
Confidence            33    343    6888999999999988876543

>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=98.74  E-value=5.7e-08  Score=93.82  Aligned_cols=166  Identities=20%  Similarity=0.321  Sum_probs=94.1

Q ss_pred             HHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCCCCC
Q psy200          200 EVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKPGG  279 (490)
Q Consensus       200 e~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~~  279 (490)
                      -.+..+...++..++.  ...+++|+||+|||||++++.+.+.+. ...+.+..++++...+...+...+-..+. ...+
T Consensus        16 T~dt~r~~~ll~~l~~--~~~pvLl~G~~GtGKT~li~~~l~~l~-~~~~~~~~~~~s~~Tts~~~q~~ie~~l~-k~~~   91 (272)
T PF12775_consen   16 TVDTVRYSYLLDLLLS--NGRPVLLVGPSGTGKTSLIQNFLSSLD-SDKYLVITINFSAQTTSNQLQKIIESKLE-KRRG   91 (272)
T ss_dssp             -HHHHHHHHHHHHHHH--CTEEEEEESSTTSSHHHHHHHHHHCST-TCCEEEEEEES-TTHHHHHHHHCCCTTEC-ECTT
T ss_pred             cHHHHHHHHHHHHHHH--cCCcEEEECCCCCchhHHHHhhhccCC-ccccceeEeeccCCCCHHHHHHHHhhcEE-cCCC
Confidence            3444455556655554  367999999999999999999887764 22344566777665433332211100000 0000


Q ss_pred             CcHHHHHHHHHHHHhcCCCeEEEEEecCccccccC------HHHHHHhHhCC---CCCC------CcEEEEEecCCCChh
Q psy200          280 KSERHQLGAILKYFDTKHKSILLILDEIDALESRK------QTILYTIFEWP---SIPG------SKLVLVGVANALDLT  344 (490)
Q Consensus       280 ~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~------~~~L~~l~~~~---~~~~------~~vilI~~tn~~~~~  344 (490)
                      ..          +--..++.+|+||||+..-....      .+.|+++++..   ....      ..+.+||+++...-.
T Consensus        92 ~~----------~gP~~~k~lv~fiDDlN~p~~d~ygtq~~iElLRQ~i~~~g~yd~~~~~~~~i~~i~~vaa~~p~~Gr  161 (272)
T PF12775_consen   92 RV----------YGPPGGKKLVLFIDDLNMPQPDKYGTQPPIELLRQLIDYGGFYDRKKLEWKSIEDIQFVAAMNPTGGR  161 (272)
T ss_dssp             EE----------EEEESSSEEEEEEETTT-S---TTS--HHHHHHHHHHHCSEEECTTTTEEEEECSEEEEEEESSTTT-
T ss_pred             CC----------CCCCCCcEEEEEecccCCCCCCCCCCcCHHHHHHHHHHhcCcccCCCcEEEEEeeeEEEEecCCCCCC
Confidence            00          00013678999999998765331      36777777543   1111      245677777643222


Q ss_pred             HhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhcc
Q psy200          345 DRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQT  383 (490)
Q Consensus       345 ~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~  383 (490)
                      ..+.+++.+.|.    .+.+..++.+.+..|+...+...
T Consensus       162 ~~is~R~~r~f~----i~~~~~p~~~sl~~If~~il~~~  196 (272)
T PF12775_consen  162 NPISPRFLRHFN----ILNIPYPSDESLNTIFSSILQSH  196 (272)
T ss_dssp             -SHHHHHHTTEE----EEE----TCCHHHHHHHHHHHHH
T ss_pred             CCCChHHhhheE----EEEecCCChHHHHHHHHHHHhhh
Confidence            346678888775    89999999999999988887654

>PRK05917 DNA polymerase III subunit delta'; Validated

Probab=98.73  E-value=7.7e-07  Score=85.83  Aligned_cols=138  Identities=12%  Similarity=0.094  Sum_probs=86.8

Q ss_pred             HHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHH----h---cCC
Q psy200          204 EGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNE----L---KLK  276 (490)
Q Consensus       204 ~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~----l---~~~  276 (490)
                      +.|...+.   .+.-++..+++||.|+||+++|..+++.+-+...-    -.|          ..+...    +   ...
T Consensus         7 ~~L~~~i~---~~rl~HAyLf~G~~G~Gk~~lA~~~A~~llC~~~~----~~c----------~~~~~~~HPD~~~i~p~   69 (290)
T PRK05917          7 EALIQRVR---DQKVPSAIILHGQDLSNLSARAYELASLILKETSP----EAA----------YKISQKIHPDIHEFSPQ   69 (290)
T ss_pred             HHHHHHHH---cCCcCeeEeeECCCCCcHHHHHHHHHHHHhCCCCc----cHH----------HHHhcCCCCCEEEEecC
Confidence            34444444   23456778899999999999999999987532100    000          000000    0   000


Q ss_pred             CC--CCcHHHHHHHHHHHHhc--CCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEEEecCCCChhHhhhHHhh
Q psy200          277 PG--GKSERHQLGAILKYFDT--KHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVANALDLTDRMLPRLQ  352 (490)
Q Consensus       277 ~~--~~s~~~~~~~l~~~l~~--~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI~~tn~~~~~~~l~~~l~  352 (490)
                      ..  ..+.+++++...+....  .+...|+|||++|.|....++.|..+++.+   ...+++|.+++   -.+.+++.++
T Consensus        70 ~~~~~I~idqiR~l~~~~~~~p~e~~~kv~ii~~ad~mt~~AaNaLLK~LEEP---p~~~~fiL~~~---~~~~ll~TI~  143 (290)
T PRK05917         70 GKGRLHSIETPRAIKKQIWIHPYESPYKIYIIHEADRMTLDAISAFLKVLEDP---PQHGVIILTSA---KPQRLPPTIR  143 (290)
T ss_pred             CCCCcCcHHHHHHHHHHHhhCccCCCceEEEEechhhcCHHHHHHHHHHhhcC---CCCeEEEEEeC---ChhhCcHHHH
Confidence            01  12455665544443322  255679999999999999999999988754   34555555554   2577889999


Q ss_pred             hccCCCCeeEEeCCCC
Q psy200          353 ANVTLQPTLMNFAPYS  368 (490)
Q Consensus       353 ~R~~~~~~~i~~~pls  368 (490)
                      |||.    .+.|.++.
T Consensus       144 SRcq----~~~~~~~~  155 (290)
T PRK05917        144 SRSL----SIHIPMEE  155 (290)
T ss_pred             hcce----EEEccchh
Confidence            9996    78998763

>PRK08181 transposase; Validated

Probab=98.73  E-value=9.5e-08  Score=91.79  Aligned_cols=91  Identities=19%  Similarity=0.327  Sum_probs=58.3

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCC
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFDTKH  297 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~  297 (490)
                      ...+++|+||+|+|||+|+.++++++.. .++.++|++      ..+++..+.....    ......   .+.. +   .
T Consensus       105 ~~~nlll~Gp~GtGKTHLa~Aia~~a~~-~g~~v~f~~------~~~L~~~l~~a~~----~~~~~~---~l~~-l---~  166 (269)
T PRK08181        105 KGANLLLFGPPGGGKSHLAAAIGLALIE-NGWRVLFTR------TTDLVQKLQVARR----ELQLES---AIAK-L---D  166 (269)
T ss_pred             cCceEEEEecCCCcHHHHHHHHHHHHHH-cCCceeeee------HHHHHHHHHHHHh----CCcHHH---HHHH-H---h
Confidence            3567999999999999999999988742 356677774      3445554433211    112222   2222 2   2


Q ss_pred             CeEEEEEecCccccccC--HHHHHHhHhCCC
Q psy200          298 KSILLILDEIDALESRK--QTILYTIFEWPS  326 (490)
Q Consensus       298 ~~~vI~IDEid~l~~~~--~~~L~~l~~~~~  326 (490)
                      +.-+|||||++.+....  +..|+++++..+
T Consensus       167 ~~dLLIIDDlg~~~~~~~~~~~Lf~lin~R~  197 (269)
T PRK08181        167 KFDLLILDDLAYVTKDQAETSVLFELISARY  197 (269)
T ss_pred             cCCEEEEeccccccCCHHHHHHHHHHHHHHH
Confidence            34599999999886543  457888887443

>KOG0741|consensus

Probab=98.73  E-value=3e-07  Score=92.58  Aligned_cols=165  Identities=19%  Similarity=0.300  Sum_probs=102.2

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCCCCCCcHHH----HHHHHHHHH
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKPGGKSERH----QLGAILKYF  293 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~~~s~~~----~~~~l~~~l  293 (490)
                      +-..++|.||||+|||+||-.++..    ++|+|+.+..+..                 -.|.++..    +...|.++.
T Consensus       537 ~lvSvLl~Gp~~sGKTaLAA~iA~~----S~FPFvKiiSpe~-----------------miG~sEsaKc~~i~k~F~DAY  595 (744)
T KOG0741|consen  537 PLVSVLLEGPPGSGKTALAAKIALS----SDFPFVKIISPED-----------------MIGLSESAKCAHIKKIFEDAY  595 (744)
T ss_pred             cceEEEEecCCCCChHHHHHHHHhh----cCCCeEEEeChHH-----------------ccCccHHHHHHHHHHHHHHhh
Confidence            4457999999999999999888876    6799998854432                 12233333    444555554


Q ss_pred             hcCCCeEEEEEecCccccccC-------H---HHHHHhHhCCCCCCCcEEEEEecCCCChhHhhhHHhhhccCCCCeeEE
Q psy200          294 DTKHKSILLILDEIDALESRK-------Q---TILYTIFEWPSIPGSKLVLVGVANALDLTDRMLPRLQANVTLQPTLMN  363 (490)
Q Consensus       294 ~~~~~~~vI~IDEid~l~~~~-------~---~~L~~l~~~~~~~~~~vilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~  363 (490)
                      +  ..-.+|+||+++.|....       .   .+|.-++....-.+.+++++|+|.+.++...+.  +..-|+   ..|.
T Consensus       596 k--S~lsiivvDdiErLiD~vpIGPRfSN~vlQaL~VllK~~ppkg~kLli~~TTS~~~vL~~m~--i~~~F~---~~i~  668 (744)
T KOG0741|consen  596 K--SPLSIIVVDDIERLLDYVPIGPRFSNLVLQALLVLLKKQPPKGRKLLIFGTTSRREVLQEMG--ILDCFS---STIH  668 (744)
T ss_pred             c--CcceEEEEcchhhhhcccccCchhhHHHHHHHHHHhccCCCCCceEEEEecccHHHHHHHcC--HHHhhh---heee
Confidence            4  346799999999986542       1   223333333333456888888887555544432  223344   3788


Q ss_pred             eCCCCH-HHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhC--CHHHHHHHHHH
Q psy200          364 FAPYSR-EQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSG--DIRKAIDITNH  417 (490)
Q Consensus       364 ~~pls~-~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~G--d~r~ai~ll~~  417 (490)
                      ++.++. +++.+++...       ..|.++.++.+++.....+-  ++.+++.+++.
T Consensus       669 Vpnl~~~~~~~~vl~~~-------n~fsd~~~~~~~~~~~~~~~~vgIKklL~lie~  718 (744)
T KOG0741|consen  669 VPNLTTGEQLLEVLEEL-------NIFSDDEVRAIAEQLLSKKVNVGIKKLLMLIEM  718 (744)
T ss_pred             cCccCchHHHHHHHHHc-------cCCCcchhHHHHHHHhccccchhHHHHHHHHHH
Confidence            888886 7777777652       34677777777774444332  24444444433

>COG3899 Predicted ATPase [General function prediction only]

Probab=98.73  E-value=5.3e-07  Score=100.21  Aligned_cols=263  Identities=14%  Similarity=0.197  Sum_probs=144.6

Q ss_pred             CCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCC---CHHH---HHHH
Q psy200          195 ELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVR---NAAS---VYET  268 (490)
Q Consensus       195 ~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~---~~~~---l~~~  268 (490)
                      .++||+.+++.|...+.... .+....+++.|.+|+|||.+++.|.+.+.... -.++.-.|..+.   ....   .+++
T Consensus         1 ~l~GRe~ev~~Ll~~f~~v~-~g~~~~~lv~G~sGIGKsalv~ev~~~i~~~~-~~~i~~~f~q~~~~ipl~~lvq~~r~   78 (849)
T COG3899           1 PLYGRETELAQLLAAFDRVS-KGRGEVVLVAGESGIGKSALVNEVHKPITQQR-GYFIKGKFDQFERNIPLSPLVQAFRD   78 (849)
T ss_pred             CCCchHhHHHHHHHHHHHHh-CCCeEEEEEeecCCCcHHHHHHHHHHHHhccc-eeeeHhhcccccCCCchHHHHHHHHH
Confidence            47999999999999998753 45667999999999999999999999886331 123333333221   1122   2333


Q ss_pred             HHHHh-------------------cCC-------------CCC----------CcHHHHH----HHHHHHHhcCCCeEEE
Q psy200          269 IVNEL-------------------KLK-------------PGG----------KSERHQL----GAILKYFDTKHKSILL  302 (490)
Q Consensus       269 i~~~l-------------------~~~-------------~~~----------~s~~~~~----~~l~~~l~~~~~~~vI  302 (490)
                      +..++                   +..             -.|          .......    ..+...+....+|.||
T Consensus        79 l~~~ll~~~~~~~~~~~~~il~~~g~~~~~~~~vip~L~~i~g~~~~~~el~~~~~~~r~n~~~~~~i~~~~~~~~plVi  158 (849)
T COG3899          79 LMGQLLSESDTRILSWRARLLAALGENGQVIIDVIPELELIIGKRPPALELSPTAAQNRFNLAFLRFIQVFTAEEHPLVI  158 (849)
T ss_pred             HHHHHhhccchHHHHHHHHHHHHhcccchhHHhhhHHHHhhcCCCcchhhcccchhHHHHHHHHHHHHHHHHhccCCeEE
Confidence            33332                   100             000          0011111    1111223334679999


Q ss_pred             EEecCccccccCHHHHHHhHhCCC--CCCCcEEEEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHH
Q psy200          303 ILDEIDALESRKQTILYTIFEWPS--IPGSKLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKL  380 (490)
Q Consensus       303 ~IDEid~l~~~~~~~L~~l~~~~~--~~~~~vilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l  380 (490)
                      |+||+|+.+....+.|..+++...  ...-+-+++..+..    ..+..-.++.  ...+.|.+.|++..+...++...+
T Consensus       159 ~leDlhWaD~~SL~lL~~lm~~~~~~~~~~n~v~~~h~~~----~~~~~~~~~~--~~i~~I~L~PL~~~d~~~lV~~~l  232 (849)
T COG3899         159 VLEDLHWADSASLKLLQLLMDRIAIGAYRDNEVLLLHPLR----PTLGEILKSA--TNITTITLAPLSRADTNQLVAATL  232 (849)
T ss_pred             EEecccccChhHHHHHHHHHHhcchhhhhccccccCCCcc----chhhHHhhcC--CceeEEecCcCchhhHHHHHHHHh
Confidence            999999999888888877776432  00001111111111    1111112221  122589999999999999999998


Q ss_pred             hccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHHHHHHHHHH-----HHhccccCCcccccCHHHHHHHHHHhccCccccc
Q psy200          381 KQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITNHLIDL-----TYDNVKENGEVTGIGLKEVLGVISSVYCTSQSLH  455 (490)
Q Consensus       381 ~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll~~a~~~-----a~~~~~~~~~~~~It~~~v~~a~~~~~~~~~~~~  455 (490)
                      ...   .....+.++.+.+   .+.|++=.+.++++.....     ....+.|+.....|..-....++-+..       
T Consensus       233 ~~~---~~~~~p~~~~i~~---kt~GnPfFi~e~lk~l~~~~~i~f~~~~~~w~~~~~~i~~~~~~~~vv~~l-------  299 (849)
T COG3899         233 GCT---KLLPAPLLELIFE---KTKGNPFFIEEFLKALYEEGLLVFNFDTGAWQCSIASLGILATTDAVVEFL-------  299 (849)
T ss_pred             CCc---ccccchHHHHHHH---HhcCCCccHHHHHHHHHhCCeeEecCCCcceeccHHhcCCchhhHHHHHHH-------
Confidence            874   3345666777776   4556433333344333321     111222211111222222222222222       


Q ss_pred             cccccCCCChHhHHHHHHHHHHhc
Q psy200          456 CSKDEDSFPLQQKLALASLLLLKS  479 (490)
Q Consensus       456 ~~~~l~~L~~~qk~vL~al~~~~~  479 (490)
                       ..+++.||-..+.||.+.+....
T Consensus       300 -~~rl~kL~~~t~~Vl~~AA~iG~  322 (849)
T COG3899         300 -AARLQKLPGTTREVLKAAACIGN  322 (849)
T ss_pred             -HHHHhcCCHHHHHHHHHHHHhCc
Confidence             35678898888889887776653

>PRK05818 DNA polymerase III subunit delta'; Validated

Probab=98.72  E-value=2.7e-07  Score=87.07  Aligned_cols=173  Identities=13%  Similarity=0.119  Sum_probs=108.9

Q ss_pred             cCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcC---CCCCCcHHHHHHHHHHH
Q psy200          216 NETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKL---KPGGKSERHQLGAILKY  292 (490)
Q Consensus       216 ~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~---~~~~~s~~~~~~~l~~~  292 (490)
                      ...++.++++|+.|+||..+|.+++..+-.....    -.|..+.+...+...-.-++..   .......+++++.....
T Consensus         4 ~~~~HA~Lf~G~~G~G~~~lA~~~A~~llC~~~~----~~Cg~C~sC~~i~~~~HPDl~~i~p~~~~I~id~ir~l~~~l   79 (261)
T PRK05818          4 KNKTHPLLLIERKGSFLKPFLYEYLTSIVCTKAN----GFCKTCESCLKILNGKYNDFYLIFDQKNPIKKEDALSIINKL   79 (261)
T ss_pred             CCCCcceeeeCCCCCcHHHHHHHHHHHHcCCCCC----CCCCCCHHHHHHhcCCCCCEEEecCCcccCCHHHHHHHHHHH
Confidence            3567889999999999999999999987533211    1244443332222111111110   11123456666555443


Q ss_pred             Hhc---CCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEEEecCCCChhHhhhHHhhhccCCCCeeEEeCCC--
Q psy200          293 FDT---KHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPY--  367 (490)
Q Consensus       293 l~~---~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pl--  367 (490)
                      ...   .++..|+|||++|.|.....+.|..+++.   +..+.++|.+++   -.+++++.++|||.    .+.|.++  
T Consensus        80 ~~~s~e~~~~KV~II~~ae~m~~~AaNaLLK~LEE---Pp~~t~fiLit~---~~~~lLpTI~SRCq----~~~~~~~~~  149 (261)
T PRK05818         80 NRPSVESNGKKIYIIYGIEKLNKQSANSLLKLIEE---PPKNTYGIFTTR---NENNILNTILSRCV----QYVVLSKEK  149 (261)
T ss_pred             ccCchhcCCCEEEEeccHhhhCHHHHHHHHHhhcC---CCCCeEEEEEEC---ChHhCchHhhhhee----eeecCChhh
Confidence            221   23467999999999998888888888774   445566666665   26788999999995    7888887  


Q ss_pred             --------CHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHHHHH
Q psy200          368 --------SREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITN  416 (490)
Q Consensus       368 --------s~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll~  416 (490)
                              +..++.+.+..+..       +++ .+..      ...|+...++.++.
T Consensus       150 ~~~~~~~~~~~~i~~~L~~~~~-------~d~-~i~~------~a~g~~~~a~~l~~  192 (261)
T PRK05818        150 KVPFKVESNDRYFQYILLSFYS-------VDE-QLQA------YNNGSFSKLKNIIE  192 (261)
T ss_pred             hcccccccChHHHHHHHHHccC-------ccH-HHHH------HcCCCHHHHHHHHH
Confidence                    55555555544321       233 2333      45799999988877

>PF07724 AAA_2: AAA domain (Cdc48 subfamily); InterPro: IPR013093 ATPases Associated to a variety of cellular Activities (AAA) are a family distinguished by a highly conserved module of 230 amino acids []

Probab=98.71  E-value=1.3e-08  Score=91.37  Aligned_cols=109  Identities=20%  Similarity=0.283  Sum_probs=70.2

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCC
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFDTKHK  298 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~  298 (490)
                      ...+++.||+|+|||.+++++++.+.......++.+++..+....+....+...++....         . ..+-.. + 
T Consensus         3 ~~~~ll~GpsGvGKT~la~~la~~l~~~~~~~~~~~d~s~~~~~~~~~~~~~~l~~~~~~---------~-v~~~~~-g-   70 (171)
T PF07724_consen    3 KSNFLLAGPSGVGKTELAKALAELLFVGSERPLIRIDMSEYSEGDDVESSVSKLLGSPPG---------Y-VGAEEG-G-   70 (171)
T ss_dssp             SEEEEEESSTTSSHHHHHHHHHHHHT-SSCCEEEEEEGGGHCSHHHCSCHCHHHHHHTTC---------H-HHHHHH-T-
T ss_pred             EEEEEEECCCCCCHHHHHHHHHHHhccCCccchHHHhhhcccccchHHhhhhhhhhcccc---------e-eeccch-h-
Confidence            457899999999999999999999852233488999999886522211111000000000         0 111111 2 


Q ss_pred             eEEEEEecCccccc-----------cCHHHHHHhHhCCC--------CCCCcEEEEEecCCC
Q psy200          299 SILLILDEIDALES-----------RKQTILYTIFEWPS--------IPGSKLVLVGVANAL  341 (490)
Q Consensus       299 ~~vI~IDEid~l~~-----------~~~~~L~~l~~~~~--------~~~~~vilI~~tn~~  341 (490)
                        ||+|||||....           .-|+.|+.+++-..        ..-.+++||+++|..
T Consensus        71 --VVllDEidKa~~~~~~~~~v~~~~V~~~LL~~le~g~~~d~~g~~vd~~n~ifI~Tsn~~  130 (171)
T PF07724_consen   71 --VVLLDEIDKAHPSNSGGADVSGEGVQNSLLQLLEGGTLTDSYGRTVDTSNIIFIMTSNFG  130 (171)
T ss_dssp             --EEEEETGGGCSHTTTTCSHHHHHHHHHHHHHHHHHSEEEETTCCEEEGTTEEEEEEESSS
T ss_pred             --hhhhHHHhhccccccccchhhHHHHHHHHHHHhcccceecccceEEEeCCceEEEecccc
Confidence              999999999998           66888888875431        123578999999844

The highly conserved nature of this module across taxa suggests that it has a key cellular role. Members of the family are involved in diverse cellular functions including gene expression, peroxisome assembly and vesicle mediated transport. Although the role of ATPase AAA-2 domain is not, as yet, clear, the AAA+ superfamily of proteins to which the AAA ATPases belong has a chaperone-like function in the assembly, operation or disassembly of proteins []. Some of these ATPases function as a chaperone subunit of a proteasome-like degradation complex. This ATPase family includes some proteins not detected by IPR003959 from INTERPRO.; GO: 0005524 ATP binding; PDB: 1R6B_X 1KSF_X 3PXI_C 1KYI_T 1G3I_S 1OFH_B 1OFI_A 1G41_A 1IM2_A 1HQY_E ....

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

Probab=98.71  E-value=1e-07  Score=91.21  Aligned_cols=106  Identities=21%  Similarity=0.359  Sum_probs=70.5

Q ss_pred             hHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCCCC
Q psy200          199 REVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKPG  278 (490)
Q Consensus       199 re~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~  278 (490)
                      +.+.+..+..+....   ....+++|+|++|+|||+|+.++++++. ..++.+.++      +..+++.+|......   
T Consensus        88 ~~~~l~~~~~~~~~~---~~~~nl~l~G~~G~GKThLa~Ai~~~l~-~~g~sv~f~------~~~el~~~Lk~~~~~---  154 (254)
T COG1484          88 DKKALEDLASLVEFF---ERGENLVLLGPPGVGKTHLAIAIGNELL-KAGISVLFI------TAPDLLSKLKAAFDE---  154 (254)
T ss_pred             hHHHHHHHHHHHHHh---ccCCcEEEECCCCCcHHHHHHHHHHHHH-HcCCeEEEE------EHHHHHHHHHHHHhc---
Confidence            455666666555432   2688999999999999999999999997 667788888      445566666555433   


Q ss_pred             CCcHHHHHHHHHHHHhcCCCeEEEEEecCcccccc--CHHHHHHhHhC
Q psy200          279 GKSERHQLGAILKYFDTKHKSILLILDEIDALESR--KQTILYTIFEW  324 (490)
Q Consensus       279 ~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~--~~~~L~~l~~~  324 (490)
                      +....    .|.+.+.   +.-||||||+......  ..+.+++++..
T Consensus       155 ~~~~~----~l~~~l~---~~dlLIiDDlG~~~~~~~~~~~~~q~I~~  195 (254)
T COG1484         155 GRLEE----KLLRELK---KVDLLIIDDIGYEPFSQEEADLLFQLISR  195 (254)
T ss_pred             CchHH----HHHHHhh---cCCEEEEecccCccCCHHHHHHHHHHHHH
Confidence            12222    2222222   2349999999997554  35666666543

>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=98.69  E-value=3.4e-09  Score=88.40  Aligned_cols=118  Identities=15%  Similarity=0.185  Sum_probs=61.3

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcC-CCe
Q psy200          221 SMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFDTK-HKS  299 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~-~~~  299 (490)
                      ++||.|+||+|||++++++++.++    ..+..|.|.....+.++...-   +-....+.        +.  +..+ --.
T Consensus         1 HvLleg~PG~GKT~la~~lA~~~~----~~f~RIq~tpdllPsDi~G~~---v~~~~~~~--------f~--~~~GPif~   63 (131)
T PF07726_consen    1 HVLLEGVPGVGKTTLAKALARSLG----LSFKRIQFTPDLLPSDILGFP---VYDQETGE--------FE--FRPGPIFT   63 (131)
T ss_dssp             -EEEES---HHHHHHHHHHHHHTT------EEEEE--TT--HHHHHEEE---EEETTTTE--------EE--EEE-TT-S
T ss_pred             CEeeECCCccHHHHHHHHHHHHcC----CceeEEEecCCCCcccceeee---eeccCCCe--------eE--eecChhhh
Confidence            589999999999999999999976    455667765544444443110   00000000        00  0000 001


Q ss_pred             EEEEEecCccccccCHHHHHHhHhCCCC--------CCCcEEEEEecCCCCh--hHhhhHHhhhcc
Q psy200          300 ILLILDEIDALESRKQTILYTIFEWPSI--------PGSKLVLVGVANALDL--TDRMLPRLQANV  355 (490)
Q Consensus       300 ~vI~IDEid~l~~~~~~~L~~l~~~~~~--------~~~~vilI~~tn~~~~--~~~l~~~l~~R~  355 (490)
                      -|+++|||.+...+.|.+|++.++..+.        -...++||++.|..+.  ...+-+.+.+||
T Consensus        64 ~ill~DEiNrappktQsAlLeam~Er~Vt~~g~~~~lp~pf~ViATqNp~e~~Gty~Lpea~~DRF  129 (131)
T PF07726_consen   64 NILLADEINRAPPKTQSALLEAMEERQVTIDGQTYPLPDPFFVIATQNPVEQEGTYPLPEAQLDRF  129 (131)
T ss_dssp             SEEEEETGGGS-HHHHHHHHHHHHHSEEEETTEEEE--SS-EEEEEE-TT--S------HHHHTTS
T ss_pred             ceeeecccccCCHHHHHHHHHHHHcCeEEeCCEEEECCCcEEEEEecCccccCceecCCHHHhccc
Confidence            2999999999999999999998764322        2456888999896543  334455666776

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.

>PRK06526 transposase; Provisional

Probab=98.65  E-value=1.2e-07  Score=90.50  Aligned_cols=90  Identities=20%  Similarity=0.294  Sum_probs=55.7

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCC
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFDTKH  297 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~  297 (490)
                      ...+++|+||+|+|||+|+.+++.++.. .++.++++      +..+++..+.....   . .   .....+.. +   .
T Consensus        97 ~~~nlll~Gp~GtGKThLa~al~~~a~~-~g~~v~f~------t~~~l~~~l~~~~~---~-~---~~~~~l~~-l---~  158 (254)
T PRK06526         97 GKENVVFLGPPGTGKTHLAIGLGIRACQ-AGHRVLFA------TAAQWVARLAAAHH---A-G---RLQAELVK-L---G  158 (254)
T ss_pred             cCceEEEEeCCCCchHHHHHHHHHHHHH-CCCchhhh------hHHHHHHHHHHHHh---c-C---cHHHHHHH-h---c
Confidence            3568999999999999999999988742 34455444      33445544433211   1 1   11122222 2   2


Q ss_pred             CeEEEEEecCcccccc--CHHHHHHhHhCC
Q psy200          298 KSILLILDEIDALESR--KQTILYTIFEWP  325 (490)
Q Consensus       298 ~~~vI~IDEid~l~~~--~~~~L~~l~~~~  325 (490)
                      +.-+|||||++.+...  .++.|+.+++..
T Consensus       159 ~~dlLIIDD~g~~~~~~~~~~~L~~li~~r  188 (254)
T PRK06526        159 RYPLLIVDEVGYIPFEPEAANLFFQLVSSR  188 (254)
T ss_pred             cCCEEEEcccccCCCCHHHHHHHHHHHHHH
Confidence            3459999999987533  356788877643

>PF10923 DUF2791: P-loop Domain of unknown function (DUF2791); InterPro: IPR021228 This is a family of proteins found in archaea and bacteria

Probab=98.64  E-value=7.1e-06  Score=82.94  Aligned_cols=79  Identities=25%  Similarity=0.380  Sum_probs=60.2

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCC-------HHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRN-------AASVY  266 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~-------~~~l~  266 (490)
                      .--|||+.+++.+...|.. +..+....-+|.|.-|+|||++++.+.+.. ...+|-+.+++++....       ...+|
T Consensus        25 ~~~VGr~~e~~~l~~~l~~-v~~G~s~~kfi~G~YGsGKTf~l~~i~~~A-~~~~fvvs~v~ls~e~~lh~~~g~~~~~Y  102 (416)
T PF10923_consen   25 HIAVGREREIEALDRDLDR-VADGGSSFKFIRGEYGSGKTFFLRLIRERA-LEKGFVVSEVDLSPERPLHGTGGQLEALY  102 (416)
T ss_pred             ceeechHHHHHHHHHHHHH-HhCCCCeEEEEEeCCCCcHHHHHHHHHHHH-HHcCCEEEEEecCCCcccccccccHHHHH
Confidence            3469999999999999875 456777788899999999999999886654 45677777877766432       23467


Q ss_pred             HHHHHHhc
Q psy200          267 ETIVNELK  274 (490)
Q Consensus       267 ~~i~~~l~  274 (490)
                      ++|+..|.
T Consensus       103 r~l~~nL~  110 (416)
T PF10923_consen  103 RELMRNLS  110 (416)
T ss_pred             HHHHHhcC
Confidence            77777664

Some of the proteins in this family are annotated as being methyl-accepting chemotaxis proteins and ATP/GTP binding proteins.

>smart00763 AAA_PrkA PrkA AAA domain

Probab=98.61  E-value=2.7e-06  Score=84.17  Aligned_cols=52  Identities=25%  Similarity=0.385  Sum_probs=45.4

Q ss_pred             CCCCChHHHHHHHHHHHHhhhcc--CCCCeEEEECCCCCcHHHHHHHHHHHhhh
Q psy200          194 CELPGREVQLEGIRQFLLGHVNN--ETSGSMYISGPPGTGKSASLNLLVSRAEI  245 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~--~~~~~ill~GppGtGKTtla~~l~~~l~~  245 (490)
                      ++++|.++.++++.+++..+..+  ...+.++|+||||+||||+|++|++.+..
T Consensus        51 ~~~~G~~~~i~~lv~~l~~~a~g~~~~r~il~L~GPPGsGKStla~~La~~l~~  104 (361)
T smart00763       51 HDFFGMEEAIERFVNYFKSAAQGLEERKQILYLLGPVGGGKSSLVECLKRGLEE  104 (361)
T ss_pred             hhccCcHHHHHHHHHHHHHHHhcCCCCCcEEEEECCCCCCHHHHHHHHHHHHhh
Confidence            58999999999999999887652  24578899999999999999999999863

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

>PRK08939 primosomal protein DnaI; Reviewed

Probab=98.61  E-value=3.9e-07  Score=89.49  Aligned_cols=122  Identities=20%  Similarity=0.246  Sum_probs=72.0

Q ss_pred             ChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCCC
Q psy200          198 GREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKP  277 (490)
Q Consensus       198 gre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~  277 (490)
                      ++...+.....|+.........++++|+|++|+|||+|+.++++++. ..++.+.++..      ..++..+...+..  
T Consensus       135 ~~~~~~~~~~~fi~~~~~~~~~~gl~L~G~~G~GKThLa~Aia~~l~-~~g~~v~~~~~------~~l~~~lk~~~~~--  205 (306)
T PRK08939        135 DRLDALMAALDFLEAYPPGEKVKGLYLYGDFGVGKSYLLAAIANELA-KKGVSSTLLHF------PEFIRELKNSISD--  205 (306)
T ss_pred             HHHHHHHHHHHHHHHhhccCCCCeEEEECCCCCCHHHHHHHHHHHHH-HcCCCEEEEEH------HHHHHHHHHHHhc--
Confidence            45555666666776543333567999999999999999999999986 34566677743      3455555444421  


Q ss_pred             CCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccC--H-HHHHHhHhCCCCCCCcEEEEEecC
Q psy200          278 GGKSERHQLGAILKYFDTKHKSILLILDEIDALESRK--Q-TILYTIFEWPSIPGSKLVLVGVAN  339 (490)
Q Consensus       278 ~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~--~-~~L~~l~~~~~~~~~~vilI~~tn  339 (490)
                        .+..   +.+.. +   .+.-||||||+..-....  . +.|..+++.-...  +..+|.++|
T Consensus       206 --~~~~---~~l~~-l---~~~dlLiIDDiG~e~~s~~~~~~ll~~Il~~R~~~--~~~ti~TSN  259 (306)
T PRK08939        206 --GSVK---EKIDA-V---KEAPVLMLDDIGAEQMSSWVRDEVLGVILQYRMQE--ELPTFFTSN  259 (306)
T ss_pred             --CcHH---HHHHH-h---cCCCEEEEecCCCccccHHHHHHHHHHHHHHHHHC--CCeEEEECC
Confidence              1222   22222 2   234599999998764332  2 3444454422112  233444566

>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]

Probab=98.57  E-value=1.1e-05  Score=86.27  Aligned_cols=244  Identities=17%  Similarity=0.190  Sum_probs=145.1

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCC-CHHHHHHHHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVR-NAASVYETIVNE  272 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~-~~~~l~~~i~~~  272 (490)
                      ...+-|...++    .|..   +...+.++|.-|.|.||||++-.++....  ++..+.|+++.+.. ++..|++.++..
T Consensus        19 ~~~v~R~rL~~----~L~~---~~~~RL~li~APAGfGKttl~aq~~~~~~--~~~~v~Wlslde~dndp~rF~~yLi~a   89 (894)
T COG2909          19 DNYVVRPRLLD----RLRR---ANDYRLILISAPAGFGKTTLLAQWRELAA--DGAAVAWLSLDESDNDPARFLSYLIAA   89 (894)
T ss_pred             ccccccHHHHH----HHhc---CCCceEEEEeCCCCCcHHHHHHHHHHhcC--cccceeEeecCCccCCHHHHHHHHHHH
Confidence            34455554443    3432   34678999999999999999999987433  55677888887764 678899999888


Q ss_pred             hcC--CCCC------------CcHHHHHHHHHHHHhcCCCeEEEEEecCccccccC-HHHHHHhHhCCCCCCCcEEEEEe
Q psy200          273 LKL--KPGG------------KSERHQLGAILKYFDTKHKSILLILDEIDALESRK-QTILYTIFEWPSIPGSKLVLVGV  337 (490)
Q Consensus       273 l~~--~~~~------------~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~-~~~L~~l~~~~~~~~~~vilI~~  337 (490)
                      ++.  +..+            .+...+++.+..-+....+|+.+||||.|.+.... ...+..+++.   ...++.+|.+
T Consensus        90 l~~~~p~~~~~a~~l~q~~~~~~l~~l~~~L~~Ela~~~~pl~LVlDDyHli~~~~l~~~l~fLl~~---~P~~l~lvv~  166 (894)
T COG2909          90 LQQATPTLGDEAQTLLQKHQYVSLESLLSSLLNELASYEGPLYLVLDDYHLISDPALHEALRFLLKH---APENLTLVVT  166 (894)
T ss_pred             HHHhCccccHHHHHHHHhcccccHHHHHHHHHHHHHhhcCceEEEeccccccCcccHHHHHHHHHHh---CCCCeEEEEE
Confidence            863  2222            23344455555545556779999999999998765 4555556552   3456766666


Q ss_pred             cCC-CCh-hHhhhHHhhhcc-CCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHHH
Q psy200          338 ANA-LDL-TDRMLPRLQANV-TLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDI  414 (490)
Q Consensus       338 tn~-~~~-~~~l~~~l~~R~-~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~l  414 (490)
                      |.. ..+ ..+  -+++.-+ .++   -.--.++.+|..++|.....     ..++...++.+.+.+.+|.+.++.+.  
T Consensus       167 SR~rP~l~la~--lRlr~~llEi~---~~~Lrf~~eE~~~fl~~~~~-----l~Ld~~~~~~L~~~teGW~~al~L~a--  234 (894)
T COG2909         167 SRSRPQLGLAR--LRLRDELLEIG---SEELRFDTEEAAAFLNDRGS-----LPLDAADLKALYDRTEGWAAALQLIA--  234 (894)
T ss_pred             eccCCCCcccc--eeehhhHHhcC---hHhhcCChHHHHHHHHHcCC-----CCCChHHHHHHHhhcccHHHHHHHHH--
Confidence            641 111 011  0111100 010   11124568899999987653     34788889999986666665555332  


Q ss_pred             HHHHHHHHHhccccCCcccccCHHHHHHHHHHhccCccccccccccCCCChHhHHHHHHHH
Q psy200          415 TNHLIDLTYDNVKENGEVTGIGLKEVLGVISSVYCTSQSLHCSKDEDSFPLQQKLALASLL  475 (490)
Q Consensus       415 l~~a~~~a~~~~~~~~~~~~It~~~v~~a~~~~~~~~~~~~~~~~l~~L~~~qk~vL~al~  475 (490)
                        .+    .+++... +...-......+.+.++...       +.+..||..-+.+|....
T Consensus       235 --La----~~~~~~~-~q~~~~LsG~~~~l~dYL~e-------eVld~Lp~~l~~FLl~~s  281 (894)
T COG2909         235 --LA----LRNNTSA-EQSLRGLSGAASHLSDYLVE-------EVLDRLPPELRDFLLQTS  281 (894)
T ss_pred             --HH----ccCCCcH-HHHhhhccchHHHHHHHHHH-------HHHhcCCHHHHHHHHHHH
Confidence              22    2211000 00011122234556665533       447889888888886544

>COG1241 MCM2 Predicted ATPase involved in replication control, Cdc46/Mcm family [DNA replication, recombination, and repair]

Probab=98.52  E-value=1.4e-06  Score=92.63  Aligned_cols=239  Identities=15%  Similarity=0.165  Sum_probs=141.8

Q ss_pred             CCcchHHHhhcCCCCCCChHHHHHHHHHHHHhhhccC--------CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEE
Q psy200          181 EDKPKVEEKAKDSCELPGREVQLEGIRQFLLGHVNNE--------TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTI  252 (490)
Q Consensus       181 ~~~~~~~~~~l~~~~lvgre~~~~~l~~~L~~~~~~~--------~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~  252 (490)
                      .+.|......+. ..+.|++...+.|.-.|-......        ..-++||+|.||+|||.|++.+++-+.     ..+
T Consensus       274 ~~i~~~l~~Sia-PsIyG~e~VKkAilLqLfgGv~k~~~~g~~iRGDInILLvGDPgtaKSqlLk~v~~~aP-----r~v  347 (682)
T COG1241         274 PDIYDILIKSIA-PSIYGHEDVKKAILLQLFGGVKKNLPDGTRIRGDIHILLVGDPGTAKSQLLKYVAKLAP-----RGV  347 (682)
T ss_pred             CcHHHHHHHHhc-ccccCcHHHHHHHHHHhcCCCcccCCCCcccccceeEEEcCCCchhHHHHHHHHHhhCC-----ceE
Confidence            344554443333 789999998877766654433221        124899999999999999999987753     345


Q ss_pred             EEeccCCCCHHHHHHHHHHHhcCCCCCCcHHHHHHHH-HHH-HhcC----CCeEEEEEecCccccccCHHHHHHhHhCCC
Q psy200          253 YINCNSVRNAASVYETIVNELKLKPGGKSERHQLGAI-LKY-FDTK----HKSILLILDEIDALESRKQTILYTIFEWPS  326 (490)
Q Consensus       253 ~v~~~~~~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l-~~~-l~~~----~~~~vI~IDEid~l~~~~~~~L~~l~~~~~  326 (490)
                      |.++.....                .|.+..-..+.. .++ +..+    ...-|..|||+|.|......++...|+-..
T Consensus       348 ytsgkgss~----------------~GLTAav~rd~~tge~~LeaGALVlAD~Gv~cIDEfdKm~~~dr~aihEaMEQQt  411 (682)
T COG1241         348 YTSGKGSSA----------------AGLTAAVVRDKVTGEWVLEAGALVLADGGVCCIDEFDKMNEEDRVAIHEAMEQQT  411 (682)
T ss_pred             EEccccccc----------------cCceeEEEEccCCCeEEEeCCEEEEecCCEEEEEeccCCChHHHHHHHHHHHhcE
Confidence            554332210                000000000000 000 1110    012288999999999988888888776432


Q ss_pred             C----------CCCcEEEEEecCCCC--------hhHh--hhHHhhhccCCCCeeEEeCCCCHHH---H-HHHHHHH---
Q psy200          327 I----------PGSKLVLVGVANALD--------LTDR--MLPRLQANVTLQPTLMNFAPYSREQ---I-LEIISQK---  379 (490)
Q Consensus       327 ~----------~~~~vilI~~tn~~~--------~~~~--l~~~l~~R~~~~~~~i~~~pls~~e---~-~~il~~~---  379 (490)
                      .          -+.++-+++++|+.-        +.++  +.+.|.+||.+  ..+..+.++.+.   + ..++..+   
T Consensus       412 IsIaKAGI~atLnARcsvLAAaNP~~Gryd~~~~~~enI~l~~~lLSRFDL--ifvl~D~~d~~~D~~ia~hil~~h~~~  489 (682)
T COG1241         412 ISIAKAGITATLNARCSVLAAANPKFGRYDPKKTVAENINLPAPLLSRFDL--IFVLKDDPDEEKDEEIAEHILDKHRGE  489 (682)
T ss_pred             eeecccceeeecchhhhhhhhhCCCCCcCCCCCCHHHhcCCChhHHhhCCe--eEEecCCCCccchHHHHHHHHHHHhcc
Confidence            1          235566778888331        1222  34678999985  233334444321   1 1222222   


Q ss_pred             -------------------------Hhcc--CCCCCCCHHHHHHHHHHHHHhhCC-------------HHHHHHHHHHHH
Q psy200          380 -------------------------LKQT--DKFNMFNASALQLLAGKVAAVSGD-------------IRKAIDITNHLI  419 (490)
Q Consensus       380 -------------------------l~~~--~~~~~~~~~~i~~i~~~i~~~~Gd-------------~r~ai~ll~~a~  419 (490)
                                               +.-.  .....+++++.+.|.+.......+             .|++-.+++.+-
T Consensus       490 ~~~~~~~~~~~~~~~~~~~~~lrkYI~YAR~~v~P~lt~ea~e~l~~~Yv~~Rk~~~~~~~~~~~piT~RqLEsiiRLae  569 (682)
T COG1241         490 EPEETISLDGVDEVEERDFELLRKYISYARKNVTPVLTEEAREELEDYYVEMRKKSALVEEKRTIPITARQLESIIRLAE  569 (682)
T ss_pred             ccccccccccccccccCcHHHHHHHHHHHhccCCcccCHHHHHHHHHHHHHhhhccccccccCcccccHHHHHHHHHHHH
Confidence                                     1111  123578899999888866544432             566777888888


Q ss_pred             HHHHhccccCCcccccCHHHHHHHHHHhc
Q psy200          420 DLTYDNVKENGEVTGIGLKEVLGVISSVY  448 (490)
Q Consensus       420 ~~a~~~~~~~~~~~~It~~~v~~a~~~~~  448 (490)
                      ..|..+-     ...|+.+|+..|+.-+.
T Consensus       570 A~Ak~rL-----S~~V~~eD~~eAi~lv~  593 (682)
T COG1241         570 AHAKMRL-----SDVVEEEDVDEAIRLVD  593 (682)
T ss_pred             HHHhhhc-----cCCCCHHHHHHHHHHHH
Confidence            8888887     67999999999988764

>COG4650 RtcR Sigma54-dependent transcription regulator containing an AAA-type ATPase domain and a DNA-binding domain [Transcription / Signal transduction mechanisms]

Probab=98.52  E-value=8.2e-07  Score=83.40  Aligned_cols=232  Identities=20%  Similarity=0.251  Sum_probs=132.5

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCc--eEEEEeccCCCCHHHHHHHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAF--KTIYINCNSVRNAASVYETIVN  271 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~--~~~~v~~~~~~~~~~l~~~i~~  271 (490)
                      ..+.-|...++++.+.++... ...-..++|.||.|.||+.|++.|+..-....++  .|+.+||..... ...++.++.
T Consensus       184 sgiatrnp~fnrmieqierva-~rsr~p~ll~gptgagksflarriyelk~arhq~sg~fvevncatlrg-d~amsalfg  261 (531)
T COG4650         184 SGIATRNPHFNRMIEQIERVA-IRSRAPILLNGPTGAGKSFLARRIYELKQARHQFSGAFVEVNCATLRG-DTAMSALFG  261 (531)
T ss_pred             hcccccChHHHHHHHHHHHHH-hhccCCeEeecCCCcchhHHHHHHHHHHHHHHhcCCceEEEeeeeecC-chHHHHHHh
Confidence            556666666666666665432 2345678999999999999999998654333333  789999998853 334556666


Q ss_pred             HhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCHHHHHHhHhCC--------CCCCCcEEEEEecCCCCh
Q psy200          272 ELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWP--------SIPGSKLVLVGVANALDL  343 (490)
Q Consensus       272 ~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~--------~~~~~~vilI~~tn~~~~  343 (490)
                      .+.+.+.|..  +-.+-+.....  +  -++|+|||..|....|..|...++..        ..-.+.+-+|+-|.+ |+
T Consensus       262 hvkgaftga~--~~r~gllrsad--g--gmlfldeigelgadeqamllkaieekrf~pfgsdr~v~sdfqliagtvr-dl  334 (531)
T COG4650         262 HVKGAFTGAR--ESREGLLRSAD--G--GMLFLDEIGELGADEQAMLLKAIEEKRFYPFGSDRQVSSDFQLIAGTVR-DL  334 (531)
T ss_pred             hhccccccch--hhhhhhhccCC--C--ceEehHhhhhcCccHHHHHHHHHHhhccCCCCCccccccchHHhhhhHH-HH
Confidence            6665555432  22222222122  2  29999999999988888888766532        112344545543321 12


Q ss_pred             hHh-----hhHHhhhccCCCCeeEEeCCCC----HHHHHHH----HHHHHhccCCCCCCCHHHHHHHHHHH----HHhhC
Q psy200          344 TDR-----MLPRLQANVTLQPTLMNFAPYS----REQILEI----ISQKLKQTDKFNMFNASALQLLAGKV----AAVSG  406 (490)
Q Consensus       344 ~~~-----l~~~l~~R~~~~~~~i~~~pls----~~e~~~i----l~~~l~~~~~~~~~~~~~i~~i~~~i----~~~~G  406 (490)
                      ...     +.+.+..|+.    ...|.-+.    .+++..-    +..+....+....|.-++-.......    +.|.|
T Consensus       335 rq~vaeg~fredl~arin----lwtf~lpgl~qr~ediepnldyelerha~~~g~~vrfntearra~l~fa~spqa~w~g  410 (531)
T COG4650         335 RQLVAEGKFREDLYARIN----LWTFTLPGLRQRQEDIEPNLDYELERHASLTGDSVRFNTEARRAWLAFATSPQATWRG  410 (531)
T ss_pred             HHHHhccchHHHHHHhhh----eeeeeccccccCccccCCCccHHHHHHHHhhCceeeeehHHHHHHHHhccCcchhhcc
Confidence            221     1234445554    23333332    2222211    22233333445556666555443322    56889


Q ss_pred             CHHHHHHHHHHHHHHHHhccccCCcccccCHHHHHHHHHH
Q psy200          407 DIRKAIDITNHLIDLTYDNVKENGEVTGIGLKEVLGVISS  446 (490)
Q Consensus       407 d~r~ai~ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~~~  446 (490)
                      |.|.+-..+.++..+|..        ..|+.+.|..-+..
T Consensus       411 nfrelsasvtrmatlad~--------grit~~~ve~ei~r  442 (531)
T COG4650         411 NFRELSASVTRMATLADS--------GRITLDVVEDEINR  442 (531)
T ss_pred             cHHHHhHHHHHHHHHhcC--------CceeHHHHHHHHHH
Confidence            999988777776666653        34666666654443

>PHA00729 NTP-binding motif containing protein

Probab=98.49  E-value=2.2e-06  Score=79.48  Aligned_cols=125  Identities=16%  Similarity=0.148  Sum_probs=68.7

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcC
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFDTK  296 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~  296 (490)
                      .....++|+|+||+||||+|.++++.+.    +.+..+.     .....+.    . +....-.+..++.+.+..++...
T Consensus        15 ~~f~nIlItG~pGvGKT~LA~aLa~~l~----~~l~~l~-----~~~~~~d----~-~~~~~fid~~~Ll~~L~~a~~~~   80 (226)
T PHA00729         15 NGFVSAVIFGKQGSGKTTYALKVARDVF----WKLNNLS-----TKDDAWQ----Y-VQNSYFFELPDALEKIQDAIDND   80 (226)
T ss_pred             CCeEEEEEECCCCCCHHHHHHHHHHHHH----hhccccc-----chhhHHh----c-CCcEEEEEHHHHHHHHHHHHhcC
Confidence            3446899999999999999999999864    0000000     0000000    0 00000123455555555544432


Q ss_pred             CCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHH
Q psy200          297 HKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEII  376 (490)
Q Consensus       297 ~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il  376 (490)
                      .+.-+|||||+.--....   .     |...   ..     .    ....+.+.+++|+.    .+.|.+++++++.+.|
T Consensus        81 ~~~dlLIIDd~G~~~~~~---~-----wh~~---~~-----~----~yf~L~~aLrSR~~----l~il~~ls~edL~~~L  136 (226)
T PHA00729         81 YRIPLIIFDDAGIWLSKY---V-----WYED---YM-----K----TFYKIYALIRTRVS----AVIFTTPSPEDLAFYL  136 (226)
T ss_pred             CCCCEEEEeCCchhhccc---c-----hhhh---cc-----c----hHHHHHHHHHhhCc----EEEEecCCHHHHHHHH
Confidence            233489999975422110   0     1100   00     1    12345566777775    7899999999999888


Q ss_pred             HHH
Q psy200          377 SQK  379 (490)
Q Consensus       377 ~~~  379 (490)
                      +.+
T Consensus       137 r~R  139 (226)
T PHA00729        137 REK  139 (226)
T ss_pred             HhC
Confidence            764

>PF10443 RNA12: RNA12 protein; InterPro: IPR018850 Mitochondrial escape protein 2 (also known as RNA12) plays a role in maintaining the mitochondrial genome and in controlling mtDNA escape [, ]

Probab=98.48  E-value=9e-06  Score=81.49  Aligned_cols=170  Identities=13%  Similarity=0.317  Sum_probs=106.2

Q ss_pred             hHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHH-HHHHHHhhhcCCceEEEEeccCCC---CHHHHHHHHHHHhc
Q psy200          199 REVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASL-NLLVSRAEIKDAFKTIYINCNSVR---NAASVYETIVNELK  274 (490)
Q Consensus       199 re~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla-~~l~~~l~~~~~~~~~~v~~~~~~---~~~~l~~~i~~~l~  274 (490)
                      |.+.+++|..||..    .....|+|.||.|+||+.|+ ..+.+.-     -.+++++|..+.   +...++..+..++|
T Consensus         1 R~e~~~~L~~wL~e----~~~TFIvV~GPrGSGK~elV~d~~L~~r-----~~vL~IDC~~i~~ar~D~~~I~~lA~qvG   71 (431)
T PF10443_consen    1 RKEAIEQLKSWLNE----NPNTFIVVQGPRGSGKRELVMDHVLKDR-----KNVLVIDCDQIVKARGDAAFIKNLASQVG   71 (431)
T ss_pred             CchHHHHHHHHHhc----CCCeEEEEECCCCCCccHHHHHHHHhCC-----CCEEEEEChHhhhccChHHHHHHHHHhcC
Confidence            45677888888864    56678999999999999999 6665542     248999998774   45667777777664


Q ss_pred             C-----------------------CCCC--C-cHHHHHHHHH---HHHhc------------------------CCCeEE
Q psy200          275 L-----------------------KPGG--K-SERHQLGAIL---KYFDT------------------------KHKSIL  301 (490)
Q Consensus       275 ~-----------------------~~~~--~-s~~~~~~~l~---~~l~~------------------------~~~~~v  301 (490)
                      -                       ...|  . ...++.+.|.   .+++.                        ....-|
T Consensus        72 Y~PvFsw~nSiss~IDLa~qGltGqKaGfSes~e~Ql~~IL~~t~~ALr~ial~~~~~~~~~~~l~e~~yl~~hPe~~PV  151 (431)
T PF10443_consen   72 YFPVFSWMNSISSFIDLAVQGLTGQKAGFSESLETQLKKILQTTATALRDIALSNRKKDDKDANLKEEDYLEAHPERRPV  151 (431)
T ss_pred             CCcchHHHHHHHHHHHHHHhhccccccCCCCChHHHHHHHHHHHHHHHHHHHHHhhhccccccccCchhhhhhCCccCCE
Confidence            1                       1111  1 1222222222   12211                        012459


Q ss_pred             EEEecCccccccCHHHHHH-hHhCC----CCCCCcEEEEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHH
Q psy200          302 LILDEIDALESRKQTILYT-IFEWP----SIPGSKLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEII  376 (490)
Q Consensus       302 I~IDEid~l~~~~~~~L~~-l~~~~----~~~~~~vilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il  376 (490)
                      ||||.|.+-... .+.++. +.+|.    ...-.+|||+  |+.......+...+-.|.-   ..|.+...+++..+.++
T Consensus       152 VVIdnF~~k~~~-~~~iy~~laeWAa~Lv~~nIAHVIFl--T~dv~~~k~LskaLPn~vf---~tI~L~Das~~~Ak~yV  225 (431)
T PF10443_consen  152 VVIDNFLHKAEE-NDFIYDKLAEWAASLVQNNIAHVIFL--TDDVSYSKPLSKALPNRVF---KTISLSDASPESAKQYV  225 (431)
T ss_pred             EEEcchhccCcc-cchHHHHHHHHHHHHHhcCccEEEEE--CCCCchhhhHHHhCCCCce---eEEeecCCCHHHHHHHH
Confidence            999999887655 344443 55664    2233445554  5544455555555444321   47999999999999999


Q ss_pred             HHHHhcc
Q psy200          377 SQKLKQT  383 (490)
Q Consensus       377 ~~~l~~~  383 (490)
                      ..+|...
T Consensus       226 ~~~L~~~  232 (431)
T PF10443_consen  226 LSQLDED  232 (431)
T ss_pred             HHHhccc
Confidence            9999764

It is also involved in the regulation of mtDNA nucleotide structure and number []. Additionally, this protein have a dispensable role in the early maturation of pre-rRNA [].

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

Probab=98.48  E-value=3e-07  Score=83.18  Aligned_cols=101  Identities=20%  Similarity=0.331  Sum_probs=57.3

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCC
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFDTKH  297 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~  297 (490)
                      .+.+++|+|++|+|||+||.++++++-. .++.+.|++      ..+++..+    ...........   .+.. +..  
T Consensus        46 ~~~~l~l~G~~G~GKThLa~ai~~~~~~-~g~~v~f~~------~~~L~~~l----~~~~~~~~~~~---~~~~-l~~--  108 (178)
T PF01695_consen   46 NGENLILYGPPGTGKTHLAVAIANEAIR-KGYSVLFIT------ASDLLDEL----KQSRSDGSYEE---LLKR-LKR--  108 (178)
T ss_dssp             C--EEEEEESTTSSHHHHHHHHHHHHHH-TT--EEEEE------HHHHHHHH----HCCHCCTTHCH---HHHH-HHT--
T ss_pred             cCeEEEEEhhHhHHHHHHHHHHHHHhcc-CCcceeEee------cCceeccc----cccccccchhh---hcCc-ccc--
Confidence            4678999999999999999999998753 566778884      34444444    32222222222   2332 322  


Q ss_pred             CeEEEEEecCcccccc--CHHHHHHhHhCCCCCCCcEEEEEecC
Q psy200          298 KSILLILDEIDALESR--KQTILYTIFEWPSIPGSKLVLVGVAN  339 (490)
Q Consensus       298 ~~~vI~IDEid~l~~~--~~~~L~~l~~~~~~~~~~vilI~~tn  339 (490)
                       .-+|||||+......  ..+.|+.+++.-+. +..  .|.+||
T Consensus       109 -~dlLilDDlG~~~~~~~~~~~l~~ii~~R~~-~~~--tIiTSN  148 (178)
T PF01695_consen  109 -VDLLILDDLGYEPLSEWEAELLFEIIDERYE-RKP--TIITSN  148 (178)
T ss_dssp             -SSCEEEETCTSS---HHHHHCTHHHHHHHHH-T-E--EEEEES
T ss_pred             -ccEecccccceeeecccccccchhhhhHhhc-ccC--eEeeCC
Confidence             339999999876432  34556666654332 223  334677

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.

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

Probab=98.45  E-value=1.2e-05  Score=82.05  Aligned_cols=123  Identities=21%  Similarity=0.322  Sum_probs=74.9

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeE
Q psy200          221 SMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFDTKHKSI  300 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~  300 (490)
                      .++|+||.+|||||+++.+...+...    +++++-.+.....                ....+....+.+....  +..
T Consensus        39 i~~i~GpR~~GKTtll~~l~~~~~~~----~iy~~~~d~~~~~----------------~~l~d~~~~~~~~~~~--~~~   96 (398)
T COG1373          39 IILILGPRQVGKTTLLKLLIKGLLEE----IIYINFDDLRLDR----------------IELLDLLRAYIELKER--EKS   96 (398)
T ss_pred             EEEEECCccccHHHHHHHHHhhCCcc----eEEEEecchhcch----------------hhHHHHHHHHHHhhcc--CCc
Confidence            89999999999999998887766411    5666533331100                1111222222222221  457


Q ss_pred             EEEEecCccccccCHHHHHHhHhCCCCCCCcEEEEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHH
Q psy200          301 LLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILE  374 (490)
Q Consensus       301 vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~  374 (490)
                      .|||||||.+.. .+..+..+.+....   .+++.|.+. .-+.....+.+..|.    ..+.+.|++-.|...
T Consensus        97 yifLDEIq~v~~-W~~~lk~l~d~~~~---~v~itgsss-~ll~~~~~~~L~GR~----~~~~l~PlSF~Efl~  161 (398)
T COG1373          97 YIFLDEIQNVPD-WERALKYLYDRGNL---DVLITGSSS-SLLSKEISESLAGRG----KDLELYPLSFREFLK  161 (398)
T ss_pred             eEEEecccCchh-HHHHHHHHHccccc---eEEEECCch-hhhccchhhhcCCCc----eeEEECCCCHHHHHh
Confidence            999999999854 45566666654332   556655443 223344455666664    489999999988865

>PRK09183 transposase/IS protein; Provisional

Probab=98.42  E-value=1.9e-06  Score=82.88  Aligned_cols=102  Identities=17%  Similarity=0.244  Sum_probs=59.2

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCC
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFDTKH  297 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~  297 (490)
                      .+.+++|+||+|+|||+|+.+++..+. ..++.+.++++.      ++...+......    .   .+...+...+   .
T Consensus       101 ~~~~v~l~Gp~GtGKThLa~al~~~a~-~~G~~v~~~~~~------~l~~~l~~a~~~----~---~~~~~~~~~~---~  163 (259)
T PRK09183        101 RNENIVLLGPSGVGKTHLAIALGYEAV-RAGIKVRFTTAA------DLLLQLSTAQRQ----G---RYKTTLQRGV---M  163 (259)
T ss_pred             cCCeEEEEeCCCCCHHHHHHHHHHHHH-HcCCeEEEEeHH------HHHHHHHHHHHC----C---cHHHHHHHHh---c
Confidence            466899999999999999999987753 244566666432      333332211110    0   1112222222   3


Q ss_pred             CeEEEEEecCcccccc--CHHHHHHhHhCCCCCCCcEEEEEecC
Q psy200          298 KSILLILDEIDALESR--KQTILYTIFEWPSIPGSKLVLVGVAN  339 (490)
Q Consensus       298 ~~~vI~IDEid~l~~~--~~~~L~~l~~~~~~~~~~vilI~~tn  339 (490)
                      .+.+++|||++.+...  ..+.|+.+++..+..+ .  +|.++|
T Consensus       164 ~~dlLiiDdlg~~~~~~~~~~~lf~li~~r~~~~-s--~iiTsn  204 (259)
T PRK09183        164 APRLLIIDEIGYLPFSQEEANLFFQVIAKRYEKG-S--MILTSN  204 (259)
T ss_pred             CCCEEEEcccccCCCChHHHHHHHHHHHHHHhcC-c--EEEecC
Confidence            3569999999986443  3346777776433232 3  344565

>PRK14700 recombination factor protein RarA; Provisional

Probab=98.41  E-value=2.2e-06  Score=82.04  Aligned_cols=110  Identities=13%  Similarity=0.173  Sum_probs=86.2

Q ss_pred             CCCCCCcEEEEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhcc---C-CCCCCCHHHHHHHHHH
Q psy200          325 PSIPGSKLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQT---D-KFNMFNASALQLLAGK  400 (490)
Q Consensus       325 ~~~~~~~vilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~---~-~~~~~~~~~i~~i~~~  400 (490)
                      +....+.+++||+|+..- .-.+.+.|.+||.    ++.|.+++.+++..++++-+...   + ....+++++++.|++ 
T Consensus         2 p~vE~G~i~LIGATTENP-~f~vn~ALlSR~~----v~~l~~L~~~di~~il~ral~~~~~~~~~~~~i~~~al~~ia~-   75 (300)
T PRK14700          2 PYVESGKIILIGATTENP-TYYLNDALVSRLF----ILRLKRLSLVATQKLIEKALSQDEVLAKHKFKIDDGLYNAMHN-   75 (300)
T ss_pred             CCccCCcEEEEeecCCCc-cceecHhhhhhhh----eeeecCCCHHHHHHHHHHHHHhhhccCCcCCCcCHHHHHHHHH-
Confidence            345678899999997543 2345789999996    89999999999999999988642   1 235799999999998 


Q ss_pred             HHHhhCCHHHHHHHHHHHHHHHHhccccCCcccccCHHHHHHHHHHh
Q psy200          401 VAAVSGDIRKAIDITNHLIDLTYDNVKENGEVTGIGLKEVLGVISSV  447 (490)
Q Consensus       401 i~~~~Gd~r~ai~ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~~~~  447 (490)
                        ...||.|.++|+|+.|+..+...+     ...||.+++.+++..-
T Consensus        76 --~a~GDaR~aLN~LE~a~~~~~~~~-----~~~it~~~~~~~~~~~  115 (300)
T PRK14700         76 --YNEGDCRKILNLLERMFLISTRGD-----EIYLNKELFDQAVGET  115 (300)
T ss_pred             --hcCCHHHHHHHHHHHHHhhccccC-----CCccCHHHHHHHHhHH
Confidence              888999999999999875432222     2259999999988653

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

Probab=98.39  E-value=6.4e-05  Score=74.18  Aligned_cols=55  Identities=22%  Similarity=0.321  Sum_probs=37.6

Q ss_pred             ChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEE
Q psy200          198 GREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYI  254 (490)
Q Consensus       198 gre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v  254 (490)
                      .|+..+ +|.+.|...........++|+|++|+|||+++..+..... ..++-++++
T Consensus         3 vR~~t~-el~~~l~~~~~~~~~~r~vL~G~~GsGKS~~L~q~~~~A~-~~~wiVl~v   57 (309)
T PF10236_consen    3 VRKPTL-ELINKLKEADKSSKNNRYVLTGERGSGKSVLLAQAVHYAR-ENGWIVLYV   57 (309)
T ss_pred             cchHHH-HHHHHHHHhcccCCceEEEEECCCCCCHHHHHHHHHHHHH-hCCEEEEEc
Confidence            344444 4555565555566788999999999999999888877653 234444444

The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This entry represents a family of conserved proteins which were originally described as death-associated-protein-3 (DAP-3). The proteins carry a P-loop DNA-binding motif, and induce apoptosis []. DAP3 has been shown to be a pro-apoptotic factor in the mitochondrial matrix [] and to be crucial for mitochondrial biogenesis and so has also been designated as MRP-S29 (mitochondrial ribosomal protein subunit 29).

>PRK00771 signal recognition particle protein Srp54; Provisional

Probab=98.39  E-value=3e-05  Score=79.61  Aligned_cols=243  Identities=12%  Similarity=0.158  Sum_probs=120.6

Q ss_pred             CCChHHHHHHHHHHHHhhhcc--------CCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCC-HHHHH
Q psy200          196 LPGREVQLEGIRQFLLGHVNN--------ETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRN-AASVY  266 (490)
Q Consensus       196 lvgre~~~~~l~~~L~~~~~~--------~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~-~~~l~  266 (490)
                      +..++..++.|.+.|...+..        ..+..++|+|++|+||||++..++..+.. .++.+..++|...+. ..+.+
T Consensus        64 ~~~~~~~~~~v~~~L~~~l~~~~~~~~~~~~p~vI~lvG~~GsGKTTtaakLA~~L~~-~g~kV~lV~~D~~R~aa~eQL  142 (437)
T PRK00771         64 LTPREHVIKIVYEELVKLLGEETEPLVLPLKPQTIMLVGLQGSGKTTTAAKLARYFKK-KGLKVGLVAADTYRPAAYDQL  142 (437)
T ss_pred             CCcHHHHHHHHHHHHHHHhCCCccccccCCCCeEEEEECCCCCcHHHHHHHHHHHHHH-cCCeEEEecCCCCCHHHHHHH
Confidence            334455556666655554332        24678999999999999999999998863 346777777765543 34456


Q ss_pred             HHHHHHhcCCCCCC-cHHHHHHHHHHHHhcCCCeEEEEEecCccccccCHHH---HHHhHhCCCCCCCcEEEEEecCCCC
Q psy200          267 ETIVNELKLKPGGK-SERHQLGAILKYFDTKHKSILLILDEIDALESRKQTI---LYTIFEWPSIPGSKLVLVGVANALD  342 (490)
Q Consensus       267 ~~i~~~l~~~~~~~-s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~---L~~l~~~~~~~~~~vilI~~tn~~~  342 (490)
                      ..+...++.+..+. ...+....+.+++......-+||||....+... .+.   |..+.... .....++++-++...+
T Consensus       143 ~~la~~~gvp~~~~~~~~d~~~i~~~al~~~~~~DvVIIDTAGr~~~d-~~lm~El~~l~~~~-~pdevlLVvda~~gq~  220 (437)
T PRK00771        143 KQLAEKIGVPFYGDPDNKDAVEIAKEGLEKFKKADVIIVDTAGRHALE-EDLIEEMKEIKEAV-KPDEVLLVIDATIGQQ  220 (437)
T ss_pred             HHHHHHcCCcEEecCCccCHHHHHHHHHHHhhcCCEEEEECCCcccch-HHHHHHHHHHHHHh-cccceeEEEeccccHH
Confidence            66777776543321 112222223333322112359999999876532 222   22222211 1222334443333222


Q ss_pred             hhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhcc---------CC----CCCCCHHHHHHHHHHHHHhhCCHH
Q psy200          343 LTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQT---------DK----FNMFNASALQLLAGKVAAVSGDIR  409 (490)
Q Consensus       343 ~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~---------~~----~~~~~~~~i~~i~~~i~~~~Gd~r  409 (490)
                      ..+. ...+...+++  ..+-|..++.....-.+.......         |.    -..+++   +.++..+ -.-||+-
T Consensus       221 av~~-a~~F~~~l~i--~gvIlTKlD~~a~~G~~ls~~~~~~~Pi~fig~Ge~v~Dle~f~~---~~~~~~i-lgmgd~~  293 (437)
T PRK00771        221 AKNQ-AKAFHEAVGI--GGIIITKLDGTAKGGGALSAVAETGAPIKFIGTGEKIDDLERFDP---DRFISRL-LGMGDLE  293 (437)
T ss_pred             HHHH-HHHHHhcCCC--CEEEEecccCCCcccHHHHHHHHHCcCEEEEecCCCcccCCcCCH---HHHHHHH-hCCCChH
Confidence            2221 2233332322  356677776443222211111111         11    112333   3333322 2358888


Q ss_pred             HHHHHHHHHHHHHHhcc-ccCCcccccCHHHHHHHHHHhc
Q psy200          410 KAIDITNHLIDLTYDNV-KENGEVTGIGLKEVLGVISSVY  448 (490)
Q Consensus       410 ~ai~ll~~a~~~a~~~~-~~~~~~~~It~~~v~~a~~~~~  448 (490)
                      .++.-.+.++....... .+.......+++|+..-+..+.
T Consensus       294 ~l~e~~~~~~~~~~~~~~~~~~~~~~f~l~d~~~q~~~~~  333 (437)
T PRK00771        294 SLLEKVEEALDEEEEEKDVEKMMKGKFTLKDMYKQLEAMN  333 (437)
T ss_pred             HHHHHHHHhhhHHHHHHHHHHHHcCCcCHHHHHHHHHHHH
Confidence            77765555533211100 0000134788999998877764

>PF03969 AFG1_ATPase: AFG1-like ATPase; InterPro: IPR005654 ATPase family gene 1 (AFG1) ATPase is a 377 amino acid putative protein with an ATPase motif typical of the protein family including SEC18p PAS1, CDC48-VCP and TBP

Probab=98.37  E-value=1.5e-06  Score=87.05  Aligned_cols=107  Identities=21%  Similarity=0.276  Sum_probs=68.2

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCCC-CCCcHHHHHHHHHHHHhc
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKP-GGKSERHQLGAILKYFDT  295 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~-~~~s~~~~~~~l~~~l~~  295 (490)
                      ..+++++|+|++|+|||+|+..+++.+....+.++         -...|+..+...|.... .......+    .+.+. 
T Consensus        60 ~~~~GlYl~G~vG~GKT~Lmd~f~~~lp~~~k~R~---------HFh~Fm~~vh~~l~~~~~~~~~l~~v----a~~l~-  125 (362)
T PF03969_consen   60 PPPKGLYLWGPVGRGKTMLMDLFYDSLPIKRKRRV---------HFHEFMLDVHSRLHQLRGQDDPLPQV----ADELA-  125 (362)
T ss_pred             CCCceEEEECCCCCchhHHHHHHHHhCCccccccc---------cccHHHHHHHHHHHHHhCCCccHHHH----HHHHH-
Confidence            46899999999999999999999998753222111         23466666666654322 11222222    22232 


Q ss_pred             CCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEEEecCC
Q psy200          296 KHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVANA  340 (490)
Q Consensus       296 ~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI~~tn~  340 (490)
                       +...||.+||++--.-.+.-.|..+++...  ...+++|+++|.
T Consensus       126 -~~~~lLcfDEF~V~DiaDAmil~rLf~~l~--~~gvvlVaTSN~  167 (362)
T PF03969_consen  126 -KESRLLCFDEFQVTDIADAMILKRLFEALF--KRGVVLVATSNR  167 (362)
T ss_pred             -hcCCEEEEeeeeccchhHHHHHHHHHHHHH--HCCCEEEecCCC
Confidence             223499999999876655555666665432  346889999994

AFG1 also has substantial homology to these proteins outside the ATPase domain []. This family of proteins contains a P-loop motif.; GO: 0005524 ATP binding

>KOG1051|consensus

Probab=98.37  E-value=3.6e-06  Score=91.71  Aligned_cols=167  Identities=20%  Similarity=0.216  Sum_probs=102.8

Q ss_pred             CCCCCh-HHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcC------CceEEEEeccCCCCHHHHH
Q psy200          194 CELPGR-EVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKD------AFKTIYINCNSVRNAASVY  266 (490)
Q Consensus       194 ~~lvgr-e~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~------~~~~~~v~~~~~~~~~~l~  266 (490)
                      +.++|| ++++.++.+.|..    ...++-+|+|.+|+|||.++..+++.+....      ...++.++......     
T Consensus       186 dPvigr~deeirRvi~iL~R----rtk~NPvLVG~~gvgktaiv~gla~ri~~G~vp~~l~~~~l~~l~~g~l~a-----  256 (898)
T KOG1051|consen  186 DPVIGRHDEEIRRVIEILSR----KTKNNPVLVGEPGVGKTAIVEGLAQRIATGDVPETLKDKKLIALDFGSLVA-----  256 (898)
T ss_pred             CCccCCchHHHHHHHHHHhc----cCCCCceEEecCCCCchhHHHHHHHHhhcCCCCccccccceEEEEhhhccc-----
Confidence            778898 9999999999964    4447788899999999999999999885221      12334443222100     


Q ss_pred             HHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCHH----HHHHhHhCCCCCCCcEEEEEecCCCC
Q psy200          267 ETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQT----ILYTIFEWPSIPGSKLVLVGVANALD  342 (490)
Q Consensus       267 ~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~~----~L~~l~~~~~~~~~~vilI~~tn~~~  342 (490)
                             +..+.+.-...+... .+.....+..+||||||++++......    ....++.. ......+.+||+|+...
T Consensus       257 -------Ga~~rge~E~rlk~l-~k~v~~~~~gvILfigelh~lvg~g~~~~~~d~~nlLkp-~L~rg~l~~IGatT~e~  327 (898)
T KOG1051|consen  257 -------GAKRRGEFEERLKEL-LKEVESGGGGVILFLGELHWLVGSGSNYGAIDAANLLKP-LLARGGLWCIGATTLET  327 (898)
T ss_pred             -------CcccchHHHHHHHHH-HHHHhcCCCcEEEEecceeeeecCCCcchHHHHHHhhHH-HHhcCCeEEEecccHHH
Confidence                   112222222222222 222333567899999999999876422    11122211 12233499999987443


Q ss_pred             hhHhh--hHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhc
Q psy200          343 LTDRM--LPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQ  382 (490)
Q Consensus       343 ~~~~l--~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~  382 (490)
                      +...+  +|.+.+||.    .+.+.-++.++...+|...-..
T Consensus       328 Y~k~iekdPalErrw~----l~~v~~pS~~~~~~iL~~l~~~  365 (898)
T KOG1051|consen  328 YRKCIEKDPALERRWQ----LVLVPIPSVENLSLILPGLSER  365 (898)
T ss_pred             HHHHHhhCcchhhCcc----eeEeccCcccchhhhhhhhhhh
Confidence            43333  578999886    6778888877766665544333

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

Probab=98.35  E-value=1.6e-06  Score=82.40  Aligned_cols=96  Identities=14%  Similarity=0.167  Sum_probs=59.1

Q ss_pred             cCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCce-EEEEeccC--CCCHHHHHHHHHHHhcCCCCCCcHH-------HH
Q psy200          216 NETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFK-TIYINCNS--VRNAASVYETIVNELKLKPGGKSER-------HQ  285 (490)
Q Consensus       216 ~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~-~~~v~~~~--~~~~~~l~~~i~~~l~~~~~~~s~~-------~~  285 (490)
                      -+.+..++|+|++|+||||+++.+++.+... .+. ++|+....  ..+..+++..+...+-....+....       .+
T Consensus        13 i~~Gqr~~I~G~~G~GKTTLlr~I~n~l~~~-~fdv~~~v~vI~er~~ev~el~~~I~~~~v~~~~~~~~~~~~~~~~~~   91 (249)
T cd01128          13 IGKGQRGLIVAPPKAGKTTLLQSIANAITKN-HPEVYLIVLLIDERPEEVTDMQRSVKGEVIASTFDEPPERHVQVAEMV   91 (249)
T ss_pred             cCCCCEEEEECCCCCCHHHHHHHHHhccccc-cCCeEEEEEEccCCCccHHHHHHHhccEEEEecCCCCHHHHHHHHHHH
Confidence            3567899999999999999999999987633 332 22333222  2477888888733322211111111       11


Q ss_pred             HHHHHHHHhcCCCeEEEEEecCcccccc
Q psy200          286 LGAILKYFDTKHKSILLILDEIDALESR  313 (490)
Q Consensus       286 ~~~l~~~l~~~~~~~vI~IDEid~l~~~  313 (490)
                      ...... +...++.++|||||++++...
T Consensus        92 ~~~a~~-~~~~G~~vll~iDei~r~a~a  118 (249)
T cd01128          92 LEKAKR-LVEHGKDVVILLDSITRLARA  118 (249)
T ss_pred             HHHHHH-HHHCCCCEEEEEECHHHhhhh
Confidence            222222 223478999999999998644

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.

>COG1618 Predicted nucleotide kinase [Nucleotide transport and metabolism]

Probab=98.33  E-value=1.9e-05  Score=68.12  Aligned_cols=27  Identities=22%  Similarity=0.489  Sum_probs=24.1

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHhhh
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRAEI  245 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l~~  245 (490)
                      ...++|+|+||+||||++..+++.+..
T Consensus         5 ~mki~ITG~PGvGKtTl~~ki~e~L~~   31 (179)
T COG1618           5 AMKIFITGRPGVGKTTLVLKIAEKLRE   31 (179)
T ss_pred             ceEEEEeCCCCccHHHHHHHHHHHHHh
Confidence            457899999999999999999998863

>PRK10536 hypothetical protein; Provisional

Probab=98.33  E-value=5e-06  Score=78.39  Aligned_cols=137  Identities=14%  Similarity=0.192  Sum_probs=75.0

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCH-----------
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNA-----------  262 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~-----------  262 (490)
                      ..+.++......+..+|..      ...++++|++|||||+|+.+++.+.-....+..+++.-+.....           
T Consensus        55 ~~i~p~n~~Q~~~l~al~~------~~lV~i~G~aGTGKT~La~a~a~~~l~~~~~~kIiI~RP~v~~ge~LGfLPG~~~  128 (262)
T PRK10536         55 SPILARNEAQAHYLKAIES------KQLIFATGEAGCGKTWISAAKAAEALIHKDVDRIIVTRPVLQADEDLGFLPGDIA  128 (262)
T ss_pred             ccccCCCHHHHHHHHHHhc------CCeEEEECCCCCCHHHHHHHHHHHHHhcCCeeEEEEeCCCCCchhhhCcCCCCHH
Confidence            3456666666666666643      35899999999999999999998643234566666654443211           


Q ss_pred             ---HHHHHHHHHHhcCCCCCCcHHHHHHHHH-----------HHHhc-CCCeEEEEEecCccccccCHHHHHHhHhCCCC
Q psy200          263 ---ASVYETIVNELKLKPGGKSERHQLGAIL-----------KYFDT-KHKSILLILDEIDALESRKQTILYTIFEWPSI  327 (490)
Q Consensus       263 ---~~l~~~i~~~l~~~~~~~s~~~~~~~l~-----------~~l~~-~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~  327 (490)
                         ..++.-+.+.|..-..   ...+...+.           .++.+ .-...+|||||++++......   .++.- ..
T Consensus       129 eK~~p~~~pi~D~L~~~~~---~~~~~~~~~~~~~~Iei~~l~ymRGrtl~~~~vIvDEaqn~~~~~~k---~~ltR-~g  201 (262)
T PRK10536        129 EKFAPYFRPVYDVLVRRLG---ASFMQYCLRPEIGKVEIAPFAYMRGRTFENAVVILDEAQNVTAAQMK---MFLTR-LG  201 (262)
T ss_pred             HHHHHHHHHHHHHHHHHhC---hHHHHHHHHhccCcEEEecHHHhcCCcccCCEEEEechhcCCHHHHH---HHHhh-cC
Confidence               1123333333322111   011111110           01111 012359999999999764322   22221 23


Q ss_pred             CCCcEEEEEecCCCCh
Q psy200          328 PGSKLVLVGVANALDL  343 (490)
Q Consensus       328 ~~~~vilI~~tn~~~~  343 (490)
                      .+++++++|-.+-.|+
T Consensus       202 ~~sk~v~~GD~~QiD~  217 (262)
T PRK10536        202 ENVTVIVNGDITQCDL  217 (262)
T ss_pred             CCCEEEEeCChhhccC
Confidence            6788899887654443

>cd01120 RecA-like_NTPases RecA-like NTPases

Probab=98.29  E-value=9.1e-06  Score=71.88  Aligned_cols=38  Identities=21%  Similarity=0.364  Sum_probs=30.4

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCC
Q psy200          221 SMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSV  259 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~  259 (490)
                      .++|+|++|+|||+++..++..+.. .+..++++++...
T Consensus         1 ~~~i~G~~G~GKT~l~~~i~~~~~~-~~~~v~~~~~e~~   38 (165)
T cd01120           1 LILVFGPTGSGKTTLALQLALNIAT-KGGKVVYVDIEEE   38 (165)
T ss_pred             CeeEeCCCCCCHHHHHHHHHHHHHh-cCCEEEEEECCcc
Confidence            3689999999999999999998753 3457788877654

This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.

>PRK12723 flagellar biosynthesis regulator FlhF; Provisional

Probab=98.28  E-value=1.2e-05  Score=81.20  Aligned_cols=149  Identities=11%  Similarity=0.123  Sum_probs=80.0

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhc---CCceEEEEeccCCCCH-HHHHHHHHHHhcCCCC-CCcHHHHHHHHHHH
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIK---DAFKTIYINCNSVRNA-ASVYETIVNELKLKPG-GKSERHQLGAILKY  292 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~---~~~~~~~v~~~~~~~~-~~l~~~i~~~l~~~~~-~~s~~~~~~~l~~~  292 (490)
                      .++.++++||.|+||||++..++..+...   .+..+..+++-.++.. ...+..+++.++.+.. .....++...+.+ 
T Consensus       173 ~~~vi~lvGptGvGKTTT~aKLA~~~~~~~~~~g~~V~lit~Dt~R~aa~eQL~~~a~~lgvpv~~~~~~~~l~~~L~~-  251 (388)
T PRK12723        173 KKRVFILVGPTGVGKTTTIAKLAAIYGINSDDKSLNIKIITIDNYRIGAKKQIQTYGDIMGIPVKAIESFKDLKEEITQ-  251 (388)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHhhhccCCCeEEEEeccCccHHHHHHHHHHhhcCCcceEeeCcHHHHHHHHHH-
Confidence            35789999999999999999999887532   2334444444444322 2335666666665422 2233444444433 


Q ss_pred             HhcCCCeEEEEEecCccccccCH--HHHHHhHhCCCCCCCcEEEEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHH
Q psy200          293 FDTKHKSILLILDEIDALESRKQ--TILYTIFEWPSIPGSKLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSRE  370 (490)
Q Consensus       293 l~~~~~~~vI~IDEid~l~~~~~--~~L~~l~~~~~~~~~~vilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~  370 (490)
                         ....-+||||++..+.....  ..+..+++........++|+.++...+....+...+.   .++...+-|..++..
T Consensus       252 ---~~~~DlVLIDTaGr~~~~~~~l~el~~~l~~~~~~~e~~LVlsat~~~~~~~~~~~~~~---~~~~~~~I~TKlDet  325 (388)
T PRK12723        252 ---SKDFDLVLVDTIGKSPKDFMKLAEMKELLNACGRDAEFHLAVSSTTKTSDVKEIFHQFS---PFSYKTVIFTKLDET  325 (388)
T ss_pred             ---hCCCCEEEEcCCCCCccCHHHHHHHHHHHHhcCCCCeEEEEEcCCCCHHHHHHHHHHhc---CCCCCEEEEEeccCC
Confidence               23456999999999864321  2333343322212134455554442211222222221   223356778888765


Q ss_pred             HHH
Q psy200          371 QIL  373 (490)
Q Consensus       371 e~~  373 (490)
                      ...
T Consensus       326 ~~~  328 (388)
T PRK12723        326 TCV  328 (388)
T ss_pred             Ccc
Confidence            433

>KOG0480|consensus

Probab=98.27  E-value=4.7e-06  Score=85.93  Aligned_cols=232  Identities=17%  Similarity=0.229  Sum_probs=130.9

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccC--------CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNE--------TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASV  265 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~--------~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l  265 (490)
                      ..+.|++..+.-|.-.|-..+...        ..-+|+|+|.||+||+-++++++.-+.     +-+|+++... +...+
T Consensus       345 PsIyGhe~VK~GilL~LfGGv~K~a~eg~~lRGDinv~iVGDPgt~KSQfLk~v~~fsP-----R~vYtsGkaS-SaAGL  418 (764)
T KOG0480|consen  345 PSIYGHELVKAGILLSLFGGVHKSAGEGTSLRGDINVCIVGDPGTGKSQFLKAVCAFSP-----RSVYTSGKAS-SAAGL  418 (764)
T ss_pred             ccccchHHHHhhHHHHHhCCccccCCCCccccCCceEEEeCCCCccHHHHHHHHhccCC-----cceEecCccc-ccccc
Confidence            789999988877665554322211        234899999999999999999977553     4566654332 11111


Q ss_pred             HHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCHHHHHHhHhCCCC--C--------CCcEEEE
Q psy200          266 YETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPSI--P--------GSKLVLV  335 (490)
Q Consensus       266 ~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~--~--------~~~vilI  335 (490)
                      .-.+      .....+.+-..+.=.-.+...|   |=-|||||.|...+|.++...|+-..+  .        +.+--+|
T Consensus       419 TaaV------vkD~esgdf~iEAGALmLADnG---ICCIDEFDKMd~~dqvAihEAMEQQtISIaKAGv~aTLnARtSIl  489 (764)
T KOG0480|consen  419 TAAV------VKDEESGDFTIEAGALMLADNG---ICCIDEFDKMDVKDQVAIHEAMEQQTISIAKAGVVATLNARTSIL  489 (764)
T ss_pred             eEEE------EecCCCCceeeecCcEEEccCc---eEEechhcccChHhHHHHHHHHHhheehheecceEEeecchhhhh
Confidence            0000      0000111101110000122222   777899999999888888888764422  1        2334466


Q ss_pred             EecCCCC--------hhH--hhhHHhhhccCCCCeeEEeCCCC-----------------------------HHHHHHHH
Q psy200          336 GVANALD--------LTD--RMLPRLQANVTLQPTLMNFAPYS-----------------------------REQILEII  376 (490)
Q Consensus       336 ~~tn~~~--------~~~--~l~~~l~~R~~~~~~~i~~~pls-----------------------------~~e~~~il  376 (490)
                      +++|+..        +.+  ++...+.+||.+.  .|-++..+                             .+++..+|
T Consensus       490 AAANPv~GhYdR~ktl~eNi~msApimSRFDL~--FiLlD~~nE~~D~~ia~hIld~h~~i~~~~~~~~~~~~e~vrkYi  567 (764)
T KOG0480|consen  490 AAANPVGGHYDRKKTLRENINMSAPIMSRFDLF--FILLDDCNEVVDYAIARHILDLHRGIDDATERVCVYTLEQVRKYI  567 (764)
T ss_pred             hhcCCcCCccccccchhhhcCCCchhhhhhcEE--EEEecCCchHHHHHHHHHHHHHhccccccccccccccHHHHHHHH
Confidence            7777331        111  2356778888752  34444444                             44444443


Q ss_pred             HHHHhccCCCCCCCHHHHHHHHHHHHHhh-------------CCHHHHHHHHHHHHHHHHhccccCCcccccCHHHHHHH
Q psy200          377 SQKLKQTDKFNMFNASALQLLAGKVAAVS-------------GDIRKAIDITNHLIDLTYDNVKENGEVTGIGLKEVLGV  443 (490)
Q Consensus       377 ~~~l~~~~~~~~~~~~~i~~i~~~i~~~~-------------Gd~r~ai~ll~~a~~~a~~~~~~~~~~~~It~~~v~~a  443 (490)
                      ... +  ...+.++.++-+.|.+++....             --.|++-.+++.+-.+|..+-     ...|+.+|+.+|
T Consensus       568 ~yA-R--~~~P~ls~ea~~~lve~Y~~lR~~~~~~~~~~s~~ITvRqLESlIRLsEA~Ar~~~-----~devt~~~v~ea  639 (764)
T KOG0480|consen  568 RYA-R--NFKPKLSKEASEMLVEKYKGLRQRDAQGNNRSSYRITVRQLESLIRLSEARARVEC-----RDEVTKEDVEEA  639 (764)
T ss_pred             HHH-H--hcCccccHHHHHHHHHHHHHHHHhhccccCcccccccHHHHHHHHHHHHHHHhhhh-----hhhccHHHHHHH
Confidence            321 1  2345667777777766552221             125666666666666666665     568999999999


Q ss_pred             HHHhccC
Q psy200          444 ISSVYCT  450 (490)
Q Consensus       444 ~~~~~~~  450 (490)
                      +.-+..+
T Consensus       640 ~eLlk~S  646 (764)
T KOG0480|consen  640 VELLKKS  646 (764)
T ss_pred             HHHHHhh
Confidence            8866543

>PF12780 AAA_8: P-loop containing dynein motor region D4; InterPro: IPR024317 The 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases

Probab=98.24  E-value=7.3e-05  Score=71.91  Aligned_cols=159  Identities=18%  Similarity=0.228  Sum_probs=87.5

Q ss_pred             CCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhc
Q psy200          195 ELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELK  274 (490)
Q Consensus       195 ~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~  274 (490)
                      ++|--++.++.+....+-  ...+.++++|.|.+|+||.++++..+.-.    ++.++.+.....               
T Consensus         9 ~lVlf~~ai~hi~ri~Rv--L~~~~Gh~LLvG~~GsGr~sl~rLaa~i~----~~~~~~i~~~~~---------------   67 (268)
T PF12780_consen    9 NLVLFDEAIEHIARISRV--LSQPRGHALLVGVGGSGRQSLARLAAFIC----GYEVFQIEITKG---------------   67 (268)
T ss_dssp             -----HHHHHHHHHHHHH--HCSTTEEEEEECTTTSCHHHHHHHHHHHT----TEEEE-TTTSTT---------------
T ss_pred             ceeeHHHHHHHHHHHHHH--HcCCCCCeEEecCCCccHHHHHHHHHHHh----ccceEEEEeeCC---------------
Confidence            466667777777766543  23567899999999999999999776653    366666654332               


Q ss_pred             CCCCCCcHHHHHHHHHHHHh---cCCCeEEEEEecCccccccCHH-----------------------------------
Q psy200          275 LKPGGKSERHQLGAILKYFD---TKHKSILLILDEIDALESRKQT-----------------------------------  316 (490)
Q Consensus       275 ~~~~~~s~~~~~~~l~~~l~---~~~~~~vI~IDEid~l~~~~~~-----------------------------------  316 (490)
                           .+..++.+.+..++.   -.+++++++|+|-|-....-.+                                   
T Consensus        68 -----y~~~~f~~dLk~~~~~ag~~~~~~vfll~d~qi~~~~fLe~in~LL~sGeip~LF~~eE~~~i~~~l~~~~~~~~  142 (268)
T PF12780_consen   68 -----YSIKDFKEDLKKALQKAGIKGKPTVFLLTDSQIVDESFLEDINSLLSSGEIPNLFTKEELDNIISSLREEAKAEG  142 (268)
T ss_dssp             -----THHHHHHHHHHHHHHHHHCS-S-EEEEEECCCSSSCHHHHHHHHHHHCSS-TTTS-TCHHHHHHHHHHHHHHHCT
T ss_pred             -----cCHHHHHHHHHHHHHHHhccCCCeEEEecCcccchHhHHHHHHHHHhCCCCCCCccHHHHHHHHHHhHHHHHHcC
Confidence                 223334333433332   1356677777766544322111                                   


Q ss_pred             ------HHHHhHhCCCCCCCcEEEEEecCCCChhH--hhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhcc
Q psy200          317 ------ILYTIFEWPSIPGSKLVLVGVANALDLTD--RMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQT  383 (490)
Q Consensus       317 ------~L~~l~~~~~~~~~~vilI~~tn~~~~~~--~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~  383 (490)
                            .++.+|-..-..+-+|+++..+....+..  +..|.+..+|.    +..|.+++.+.+..+-...+...
T Consensus       143 ~~~~~~~~~~~F~~rvr~nLHivl~~sp~~~~~r~~~~~fPaL~~~ct----IdW~~~W~~eaL~~Va~~~l~~~  213 (268)
T PF12780_consen  143 ISDSRESLYEFFIERVRKNLHIVLCMSPVGPNFRDRCRSFPALVNCCT----IDWFDPWPEEALLSVANKFLSDI  213 (268)
T ss_dssp             --SSHHHHHHHHHHHHCCCEEEEEEESTTTTCCCHHHHHHCCHHHHSE----EEEEES--HHHHHHHHHHHCCHH
T ss_pred             CCCchHHHHHHHHHHHHhheeEEEEECCCCchHHHHHHhCcchhcccE----EEeCCcCCHHHHHHHHHHHHHhh
Confidence                  11111110011344556555444333333  34678888775    78999999999999888777654

The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four (D1 - D4) correspond to the ATP binding sites with P-loop signatures described previously, and two (D5, D6) are modules in which the P loop has been lost in evolution. This particular entry represents the D4 ATP-binding domain of the motor [].; PDB: 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A 3VKH_A 3VKG_A.

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

Probab=98.24  E-value=1.3e-05  Score=73.83  Aligned_cols=120  Identities=24%  Similarity=0.347  Sum_probs=62.6

Q ss_pred             HHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCCCCCC
Q psy200          201 VQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKPGGK  280 (490)
Q Consensus       201 ~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~~~  280 (490)
                      ++.+.+..++.     ...+.++|.|++|||||++++.+...+... ++.++.+. +.    ......+...++...  .
T Consensus         5 ~Q~~a~~~~l~-----~~~~~~~l~G~aGtGKT~~l~~~~~~~~~~-g~~v~~~a-pT----~~Aa~~L~~~~~~~a--~   71 (196)
T PF13604_consen    5 EQREAVRAILT-----SGDRVSVLQGPAGTGKTTLLKALAEALEAA-GKRVIGLA-PT----NKAAKELREKTGIEA--Q   71 (196)
T ss_dssp             HHHHHHHHHHH-----CTCSEEEEEESTTSTHHHHHHHHHHHHHHT-T--EEEEE-SS----HHHHHHHHHHHTS-E--E
T ss_pred             HHHHHHHHHHh-----cCCeEEEEEECCCCCHHHHHHHHHHHHHhC-CCeEEEEC-Cc----HHHHHHHHHhhCcch--h
Confidence            34445555553     445788899999999999999998877643 35555542 21    112222333322110  0


Q ss_pred             cHHHHHHHHHHHHhc-------CCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEEEecC
Q psy200          281 SERHQLGAILKYFDT-------KHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVAN  339 (490)
Q Consensus       281 s~~~~~~~l~~~l~~-------~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI~~tn  339 (490)
                      +..   .++......       ..+..+|||||+..+...   .+..++......+.+++++|-.+
T Consensus        72 Ti~---~~l~~~~~~~~~~~~~~~~~~vliVDEasmv~~~---~~~~ll~~~~~~~~klilvGD~~  131 (196)
T PF13604_consen   72 TIH---SFLYRIPNGDDEGRPELPKKDVLIVDEASMVDSR---QLARLLRLAKKSGAKLILVGDPN  131 (196)
T ss_dssp             EHH---HHTTEECCEECCSSCC-TSTSEEEESSGGG-BHH---HHHHHHHHS-T-T-EEEEEE-TT
T ss_pred             hHH---HHHhcCCcccccccccCCcccEEEEecccccCHH---HHHHHHHHHHhcCCEEEEECCcc
Confidence            111   111100000       123459999999999754   34444444444577899998765

>KOG0478|consensus

Probab=98.24  E-value=1.4e-05  Score=83.26  Aligned_cols=160  Identities=15%  Similarity=0.235  Sum_probs=87.5

Q ss_pred             CCCCChHHHHHHHHHHHHhhhcc--------CCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVNN--------ETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASV  265 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~--------~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l  265 (490)
                      ..+.|+++.++.|.-.|-..-..        ...-+|||+|.||||||.+++.+++-+.     +-+|.++-.- +...+
T Consensus       429 PsIye~edvKkglLLqLfGGt~k~~~~~~~~R~~INILL~GDPGtsKSqlLqyv~~l~p-----Rg~yTSGkGs-SavGL  502 (804)
T KOG0478|consen  429 PSIYELEDVKKGLLLQLFGGTRKEDEKSGRFRGDINILLVGDPGTSKSQLLQYCHRLLP-----RGVYTSGKGS-SAVGL  502 (804)
T ss_pred             hhhhcccchhhhHHHHHhcCCcccccccccccccceEEEecCCCcCHHHHHHHHHHhCC-----cceeecCCcc-chhcc
Confidence            67888887776655444321110        0125899999999999999999987653     2344433221 00000


Q ss_pred             HHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCHHHHHHhHhCCCC----------CCCcEEEE
Q psy200          266 YETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPSI----------PGSKLVLV  335 (490)
Q Consensus       266 ~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~----------~~~~vilI  335 (490)
                      .      ........+.+-+.+. ....-..+.  +=-|||||.|....+..|.+.|+-...          -+.+.-|+
T Consensus       503 T------ayVtrd~dtkqlVLes-GALVLSD~G--iCCIDEFDKM~dStrSvLhEvMEQQTvSIAKAGII~sLNAR~SVL  573 (804)
T KOG0478|consen  503 T------AYVTKDPDTRQLVLES-GALVLSDNG--ICCIDEFDKMSDSTRSVLHEVMEQQTLSIAKAGIIASLNARCSVL  573 (804)
T ss_pred             e------eeEEecCccceeeeec-CcEEEcCCc--eEEchhhhhhhHHHHHHHHHHHHHhhhhHhhcceeeeccccceee
Confidence            0      0000000000000000 000011122  566899999988888888888764321          24566678


Q ss_pred             EecCCCC--------hhHhh--hHHhhhccCCCCeeEEeCCCCHH
Q psy200          336 GVANALD--------LTDRM--LPRLQANVTLQPTLMNFAPYSRE  370 (490)
Q Consensus       336 ~~tn~~~--------~~~~l--~~~l~~R~~~~~~~i~~~pls~~  370 (490)
                      +++|..+        +.+.+  -+.|.+||++  ..+-|++.++.
T Consensus       574 AaANP~~skynp~k~i~eNI~LpptLLSRFDL--IylllD~~DE~  616 (804)
T KOG0478|consen  574 AAANPIRSKYNPNKSIIENINLPPTLLSRFDL--IFLLLDKPDER  616 (804)
T ss_pred             eeeccccccCCCCCchhhccCCChhhhhhhcE--EEEEecCcchh
Confidence            8888321        23333  3788999986  35666766654

>PRK12608 transcription termination factor Rho; Provisional

Probab=98.23  E-value=1e-05  Score=80.43  Aligned_cols=98  Identities=12%  Similarity=0.182  Sum_probs=65.2

Q ss_pred             cCCCCeEEEECCCCCcHHHHHHHHHHHhhhc-CCceEEEEeccC-CCCHHHHHHHHHHHhcCCCCCCcHHH------HHH
Q psy200          216 NETSGSMYISGPPGTGKSASLNLLVSRAEIK-DAFKTIYINCNS-VRNAASVYETIVNELKLKPGGKSERH------QLG  287 (490)
Q Consensus       216 ~~~~~~ill~GppGtGKTtla~~l~~~l~~~-~~~~~~~v~~~~-~~~~~~l~~~i~~~l~~~~~~~s~~~------~~~  287 (490)
                      -+.+..++|+|++|+||||+++.+++.+... ++..++++-+.+ ..+..+|+..+...+...........      ...
T Consensus       130 iGkGQR~LIvG~pGtGKTTLl~~la~~i~~~~~dv~~vv~lIgER~~EV~df~~~i~~~Vvast~de~~~~~~~v~~~~~  209 (380)
T PRK12608        130 IGKGQRGLIVAPPRAGKTVLLQQIAAAVAANHPEVHLMVLLIDERPEEVTDMRRSVKGEVYASTFDRPPDEHIRVAELVL  209 (380)
T ss_pred             cCCCceEEEECCCCCCHHHHHHHHHHHHHhcCCCceEEEEEecCCCCCHHHHHHHHhhhEEeecCCCCHHHHHHHHHHHH
Confidence            3677889999999999999999999988632 234333433332 34778899988887765432222111      122


Q ss_pred             HHHHHHhcCCCeEEEEEecCcccccc
Q psy200          288 AILKYFDTKHKSILLILDEIDALESR  313 (490)
Q Consensus       288 ~l~~~l~~~~~~~vI~IDEid~l~~~  313 (490)
                      .+.+.+...++.+|||+||+..+...
T Consensus       210 ~~Ae~f~~~GkdVVLvlDsltr~A~A  235 (380)
T PRK12608        210 ERAKRLVEQGKDVVILLDSLTRLARA  235 (380)
T ss_pred             HHHHHHHHcCCCEEEEEeCcHHHHHH
Confidence            33344445688999999999988643

>TIGR00767 rho transcription termination factor Rho

Probab=98.16  E-value=9e-06  Score=81.35  Aligned_cols=96  Identities=13%  Similarity=0.168  Sum_probs=60.7

Q ss_pred             cCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCc-eEEEEeccCC--CCHHHHHHHHHHHhcCCCCCCcHHH-------H
Q psy200          216 NETSGSMYISGPPGTGKSASLNLLVSRAEIKDAF-KTIYINCNSV--RNAASVYETIVNELKLKPGGKSERH-------Q  285 (490)
Q Consensus       216 ~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~-~~~~v~~~~~--~~~~~l~~~i~~~l~~~~~~~s~~~-------~  285 (490)
                      -+.+..++|+||+|+|||++++.+++.+... ++ ..+++.....  .+..+++..+...+-....+.....       +
T Consensus       165 ig~Gq~~~IvG~~g~GKTtL~~~i~~~I~~n-hfdv~v~VlLIgER~~EVtDLqrsIlg~Vvast~d~p~~~~~~va~~v  243 (415)
T TIGR00767       165 IGKGQRGLIVAPPKAGKTVLLQKIAQAITRN-HPEVELIVLLIDERPEEVTDMQRSVKGEVVASTFDEPASRHVQVAEMV  243 (415)
T ss_pred             eCCCCEEEEECCCCCChhHHHHHHHHhhccc-CCceEEEEEEcCCCCccHHHHHHHhhceEEEecCCCChHHHHHHHHHH
Confidence            3578899999999999999999999987633 22 1223333322  4777888888544432222222211       1


Q ss_pred             HHHHHHHHhcCCCeEEEEEecCcccccc
Q psy200          286 LGAILKYFDTKHKSILLILDEIDALESR  313 (490)
Q Consensus       286 ~~~l~~~l~~~~~~~vI~IDEid~l~~~  313 (490)
                      .+.... +...|+.+||||||++++...
T Consensus       244 ~e~Ae~-~~~~GkdVVLlIDEitR~arA  270 (415)
T TIGR00767       244 IEKAKR-LVEHKKDVVILLDSITRLARA  270 (415)
T ss_pred             HHHHHH-HHHcCCCeEEEEEChhHHHHH
Confidence            122222 234578999999999998654

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

>PF00493 MCM: MCM2/3/5 family This family extends the MCM domain of Prosite

Probab=98.16  E-value=3e-07  Score=91.59  Aligned_cols=233  Identities=17%  Similarity=0.189  Sum_probs=114.0

Q ss_pred             CCCCChHHHHHHHHHHHHhhhcc--------CCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVNN--------ETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASV  265 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~--------~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l  265 (490)
                      ..++|++..+..|.-.|-.....        ...-++||+|.||+|||.|++.+++-.     .+.+++++...... .+
T Consensus        24 P~i~g~~~iK~aill~L~~~~~~~~~~~~~~r~~ihiLlvGdpg~gKS~ll~~~~~~~-----pr~v~~~g~~~s~~-gL   97 (331)
T PF00493_consen   24 PSIYGHEDIKKAILLQLFGGVEKNDPDGTRIRGNIHILLVGDPGTGKSQLLKYVAKLA-----PRSVYTSGKGSSAA-GL   97 (331)
T ss_dssp             STTTT-HHHHHHHCCCCTT--SCCCCT-TEE--S--EEEECSCHHCHHHHHHCCCCT------SSEEEEECCGSTCC-CC
T ss_pred             CcCcCcHHHHHHHHHHHHhccccccccccccccccceeeccchhhhHHHHHHHHHhhC-----CceEEECCCCcccC-Cc
Confidence            77889887765554433322211        123489999999999999999885443     24456654443110 00


Q ss_pred             HHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCHHHHHHhHhCCCC----------CCCcEEEE
Q psy200          266 YETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPSI----------PGSKLVLV  335 (490)
Q Consensus       266 ~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~----------~~~~vilI  335 (490)
                      ...+.   ..+..+.-.-+. ..+.  +..+|   |++|||++.+.......|...|+-...          -+.+.-|+
T Consensus        98 ta~~~---~d~~~~~~~lea-Galv--lad~G---iccIDe~dk~~~~~~~~l~eaMEqq~isi~kagi~~~l~ar~svl  168 (331)
T PF00493_consen   98 TASVS---RDPVTGEWVLEA-GALV--LADGG---ICCIDEFDKMKEDDRDALHEAMEQQTISIAKAGIVTTLNARCSVL  168 (331)
T ss_dssp             CEEEC---CCGGTSSECEEE--HHH--HCTTS---EEEECTTTT--CHHHHHHHHHHHCSCEEECTSSSEEEEE---EEE
T ss_pred             cceec---cccccceeEEeC-Cchh--cccCc---eeeecccccccchHHHHHHHHHHcCeeccchhhhcccccchhhhH
Confidence            00000   000000000000 0111  22223   999999999998888889888875421          14566788


Q ss_pred             EecCCCCh--------hH--hhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhcc----------------------
Q psy200          336 GVANALDL--------TD--RMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQT----------------------  383 (490)
Q Consensus       336 ~~tn~~~~--------~~--~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~----------------------  383 (490)
                      +++|...-        .+  .+.+.+.+||++  ..+-++..+.+.-..+..+.+...                      
T Consensus       169 aa~NP~~g~~~~~~~~~~ni~l~~~LLSRFDL--if~l~D~~d~~~D~~la~~il~~~~~~~~~~~~~~~~~~~~~~~~~  246 (331)
T PF00493_consen  169 AAANPKFGRYDPNKSLSENINLPPPLLSRFDL--IFLLRDKPDEEEDERLAEHILDSHRNGKKSKEKKIKKNDKPISEDL  246 (331)
T ss_dssp             EEE--TT--S-TTS-CGCCT-S-CCCHCC-SE--EECC--TTT-HHHHHHHHHHHTTT---S--------SSS-TT-HCC
T ss_pred             HHHhhhhhhcchhhhhHHhcccchhhHhhcCE--EEEeccccccccccccceEEEeccccccccccccccccCCccCHHH
Confidence            88884421        11  234578889984  112245666443333333332221                      


Q ss_pred             ----------CCCCCCCHHHHHHHHHHHHHhh-----------CCHHHHHHHHHHHHHHHHhccccCCcccccCHHHHHH
Q psy200          384 ----------DKFNMFNASALQLLAGKVAAVS-----------GDIRKAIDITNHLIDLTYDNVKENGEVTGIGLKEVLG  442 (490)
Q Consensus       384 ----------~~~~~~~~~~i~~i~~~i~~~~-----------Gd~r~ai~ll~~a~~~a~~~~~~~~~~~~It~~~v~~  442 (490)
                                ...+.+++++.+.|.+.+....           -.+|.+..+++.+-..|..+.     ...|+.+|+..
T Consensus       247 lr~yI~yar~~~~P~ls~ea~~~I~~~Yv~lR~~~~~~~~~~~iT~R~LeSLIRLseA~AKl~l-----r~~V~~~Dv~~  321 (331)
T PF00493_consen  247 LRKYIAYARQNIHPVLSEEAKELIINYYVELRKESKSNNKSIPITIRQLESLIRLSEAHAKLRL-----RDEVTEEDVEE  321 (331)
T ss_dssp             CHHHHHHHHHHC--EE-HHCHHHHHHHHCCCCHCHHCHSS-B-SSCCCCCHHHHHHHHHHHCTT-----SSECSHHHHHH
T ss_pred             HHHHHHHHHhhcccccCHHHHHHHHHHHHHhcccccccccccccchhhHHHHHHHHHHHHHHhc-----cCceeHHHHHH
Confidence                      1234466666666665331111           013333456777777777777     67899999999


Q ss_pred             HHHHhc
Q psy200          443 VISSVY  448 (490)
Q Consensus       443 a~~~~~  448 (490)
                      |+.-+.
T Consensus       322 Ai~L~~  327 (331)
T PF00493_consen  322 AIRLFE  327 (331)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            886543

; InterPro: IPR001208 MCM proteins are DNA-dependent ATPases required for the initiation of eukaryotic DNA replication [, , ]. In eukaryotes there is a family of six proteins, MCM2 to MCM7. They were first identified in yeast where most of them have a direct role in the initiation of chromosomal DNA replication by interacting directly with autonomously replicating sequences (ARS). They were thus called minichromosome maintenance proteins, MCM proteins []. This family is also present in the archebacteria in 1 to 4 copies. Methanocaldococcus jannaschii (Methanococcus jannaschii) has four members, MJ0363, MJ0961, MJ1489 and MJECL13. The "MCM motif" contains Walker-A and Walker-B type nucleotide binding motifs. The diagnostic sequence defining the MCMs is IDEFDKM. Only Mcm2 (aka Cdc19 or Nda1) has been subjected to mutational analysis in this region, and most mutations abolish its activity []. The presence of a putative ATP-binding domain implies that these proteins may be involved in an ATP-consuming step in the initiation of DNA replication in eukaryotes. The MCM proteins bind together in a large complex []. Within this complex, individual subunits associate with different affinities, and there is a tightly associated core of Mcm4 (Cdc21), Mcm6 (Mis5) and Mcm7 []. This core complex in human MCMs has been associated with helicase activity in vitro [], leading to the suggestion that the MCM proteins are the eukaryotic replicative helicase. Schizosaccharomyces pombe (Fission yeast) MCMs, like those in metazoans, are found in the nucleus throughout the cell cycle. This is in contrast to the Saccharomyces cerevisiae (Baker's yeast) in which MCM proteins move in and out of the nucleus during each cell cycle. The assembly of the MCM complex in S. pombe is required for MCM localisation, ensuring that only intact MCM complexes remain in the nucleus [].; GO: 0003677 DNA binding, 0005524 ATP binding, 0006260 DNA replication; PDB: 3F8T_A 3F9V_A.

>PRK09376 rho transcription termination factor Rho; Provisional

Probab=98.15  E-value=6.9e-06  Score=81.77  Aligned_cols=97  Identities=19%  Similarity=0.230  Sum_probs=58.2

Q ss_pred             cCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceE-EEEeccCCC--CHHHHHHHHHHHhcCC-CCCCcHHHHH---HH
Q psy200          216 NETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKT-IYINCNSVR--NAASVYETIVNELKLK-PGGKSERHQL---GA  288 (490)
Q Consensus       216 ~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~-~~v~~~~~~--~~~~l~~~i~~~l~~~-~~~~s~~~~~---~~  288 (490)
                      -+.+.-.+|+||+|+|||||++.|++.+... ++.+ +|+......  ...+++..+...+-.. +.......+.   ..
T Consensus       166 IGkGQR~lIvgppGvGKTTLaK~Ian~I~~n-hFDv~~~VvLIgER~~EVtdiqrsIlg~vv~st~d~~~~~~~~~a~~~  244 (416)
T PRK09376        166 IGKGQRGLIVAPPKAGKTVLLQNIANSITTN-HPEVHLIVLLIDERPEEVTDMQRSVKGEVVASTFDEPAERHVQVAEMV  244 (416)
T ss_pred             cccCceEEEeCCCCCChhHHHHHHHHHHHhh-cCCeEEEEEEeCCchhHHHHHHHHhcCcEEEECCCCCHHHHHHHHHHH
Confidence            3578889999999999999999999988643 3322 233333333  4456666665332211 2211111111   11


Q ss_pred             H--HHHHhcCCCeEEEEEecCcccccc
Q psy200          289 I--LKYFDTKHKSILLILDEIDALESR  313 (490)
Q Consensus       289 l--~~~l~~~~~~~vI~IDEid~l~~~  313 (490)
                      +  .+.+...++.++|||||++++...
T Consensus       245 ie~Ae~~~e~G~dVlL~iDsItR~arA  271 (416)
T PRK09376        245 IEKAKRLVEHGKDVVILLDSITRLARA  271 (416)
T ss_pred             HHHHHHHHHcCCCEEEEEEChHHHHHH
Confidence            1  122234578999999999998754

>KOG0482|consensus

Probab=98.14  E-value=6.7e-05  Score=75.65  Aligned_cols=241  Identities=15%  Similarity=0.190  Sum_probs=137.4

Q ss_pred             CcchHHHhhcCCCCCCChHHHHHHHHHHHHhhhccC--------CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEE
Q psy200          182 DKPKVEEKAKDSCELPGREVQLEGIRQFLLGHVNNE--------TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIY  253 (490)
Q Consensus       182 ~~~~~~~~~l~~~~lvgre~~~~~l~~~L~~~~~~~--------~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~  253 (490)
                      +.|......+. .+++|+++.++.|.-.|-......        ..-+|+|.|.||+-|+-|++++.+-..     +-+|
T Consensus       331 d~yekLa~SiA-PEIyGheDVKKaLLLlLVGgvd~~~~dGMKIRGdINicLmGDPGVAKSQLLkyi~rlap-----RgvY  404 (721)
T KOG0482|consen  331 DFYEKLAASIA-PEIYGHEDVKKALLLLLVGGVDKSPGDGMKIRGDINICLMGDPGVAKSQLLKYISRLAP-----RGVY  404 (721)
T ss_pred             cHHHHHHHhhc-hhhccchHHHHHHHHHhhCCCCCCCCCCceeecceeEEecCCCchhHHHHHHHHHhcCc-----ccce
Confidence            34544433333 889999999988888776543322        234789999999999999999966432     2233


Q ss_pred             EeccCCCCHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHH--HhcC----CCeEEEEEecCccccccCHHHHHHhHhCCCC
Q psy200          254 INCNSVRNAASVYETIVNELKLKPGGKSERHQLGAILKY--FDTK----HKSILLILDEIDALESRKQTILYTIFEWPSI  327 (490)
Q Consensus       254 v~~~~~~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~--l~~~----~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~  327 (490)
                      ..+-.-                ...|.+..-+.+-+...  ++++    ...-|-.|||||.|...+..++...++-..+
T Consensus       405 TTGrGS----------------SGVGLTAAVmkDpvTgEM~LEGGALVLAD~GICCIDEfDKM~e~DRtAIHEVMEQQTI  468 (721)
T KOG0482|consen  405 TTGRGS----------------SGVGLTAAVMKDPVTGEMVLEGGALVLADGGICCIDEFDKMDESDRTAIHEVMEQQTI  468 (721)
T ss_pred             ecCCCC----------------CccccchhhhcCCCCCeeEeccceEEEccCceEeehhhhhhhhhhhHHHHHHHHhhhh
Confidence            322111                01111111111111000  1110    0011667899999998887777776653321


Q ss_pred             ----------CCCcEEEEEecCCC--------ChhHh--hhHHhhhccCCC---------------------------Ce
Q psy200          328 ----------PGSKLVLVGVANAL--------DLTDR--MLPRLQANVTLQ---------------------------PT  360 (490)
Q Consensus       328 ----------~~~~vilI~~tn~~--------~~~~~--l~~~l~~R~~~~---------------------------~~  360 (490)
                                -+.+..+++++|..        ...+.  +-.+|.+||.+-                           .-
T Consensus       469 SIaKAGI~TtLNAR~sILaAANPayGRYnprrs~e~NI~LPaALLSRFDll~Li~D~pdrd~D~~LA~HiTyVH~H~~qp  548 (721)
T KOG0482|consen  469 SIAKAGINTTLNARTSILAAANPAYGRYNPRRSPEQNINLPAALLSRFDLLWLIQDRPDRDNDLRLAQHITYVHQHEEQP  548 (721)
T ss_pred             hhhhhccccchhhhHHhhhhcCccccccCcccChhHhcCCcHHHHHhhhhhhhhccCCcccchHHHHHHhHhhhccCCCC
Confidence                      24566677777722        11111  224666777531                           01


Q ss_pred             eEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHh-----------hCCHHHHHHHHHHHHHHHHhccccC
Q psy200          361 LMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAV-----------SGDIRKAIDITNHLIDLTYDNVKEN  429 (490)
Q Consensus       361 ~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~-----------~Gd~r~ai~ll~~a~~~a~~~~~~~  429 (490)
                      ...|.|++.+-++.+|.. ++..  ...++++.-+.|.......           .-..|.++.+++.+..+|..+-   
T Consensus       549 ~~~fepl~~~~mR~yI~~-ak~~--~P~vp~~l~dyi~~AYv~~Rrea~~~~~~t~ttpRtLL~IlRls~AlarLRl---  622 (721)
T KOG0482|consen  549 PLDFEPLDPNLMRRYISL-AKRK--NPVVPEALADYITGAYVELRREARSSKDFTYTTPRTLLGILRLSTALARLRL---  622 (721)
T ss_pred             CccCCCCCHHHHHHHHHH-Hhhc--CCCCCHHHHHHHHHHHHHHHHHhhccCCCcccCHHHHHHHHHHHHHHHHhhh---
Confidence            244555666555555543 2222  3445665555555433111           1247888889999988998887   


Q ss_pred             CcccccCHHHHHHHHHHhccCcc
Q psy200          430 GEVTGIGLKEVLGVISSVYCTSQ  452 (490)
Q Consensus       430 ~~~~~It~~~v~~a~~~~~~~~~  452 (490)
                        ...|..+||.+|+.-+.-+..
T Consensus       623 --s~~V~~~DV~EALRLme~sK~  643 (721)
T KOG0482|consen  623 --SDSVEEDDVNEALRLMEMSKD  643 (721)
T ss_pred             --ccccchhhHHHHHHHHHhhhc
Confidence              678999999999987654433

>PRK04296 thymidine kinase; Provisional

Probab=98.13  E-value=3.9e-06  Score=76.84  Aligned_cols=111  Identities=17%  Similarity=0.191  Sum_probs=60.2

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCCCCC---CcHHHHHHHHHHHHhc
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKPGG---KSERHQLGAILKYFDT  295 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~~---~s~~~~~~~l~~~l~~  295 (490)
                      +...+++|++|+||||++..++..+... +..++.+.. .+.+ ......+...++.....   ....++...+.+   .
T Consensus         2 g~i~litG~~GsGKTT~~l~~~~~~~~~-g~~v~i~k~-~~d~-~~~~~~i~~~lg~~~~~~~~~~~~~~~~~~~~---~   75 (190)
T PRK04296          2 AKLEFIYGAMNSGKSTELLQRAYNYEER-GMKVLVFKP-AIDD-RYGEGKVVSRIGLSREAIPVSSDTDIFELIEE---E   75 (190)
T ss_pred             cEEEEEECCCCCHHHHHHHHHHHHHHHc-CCeEEEEec-cccc-cccCCcEecCCCCcccceEeCChHHHHHHHHh---h
Confidence            3468899999999999999998887532 344454432 1111 11122344444432111   223444444443   2


Q ss_pred             CCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEEEec
Q psy200          296 KHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVA  338 (490)
Q Consensus       296 ~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI~~t  338 (490)
                      .++.-+|+|||++.+...   .+..+++.....+..+++.+..
T Consensus        76 ~~~~dvviIDEaq~l~~~---~v~~l~~~l~~~g~~vi~tgl~  115 (190)
T PRK04296         76 GEKIDCVLIDEAQFLDKE---QVVQLAEVLDDLGIPVICYGLD  115 (190)
T ss_pred             CCCCCEEEEEccccCCHH---HHHHHHHHHHHcCCeEEEEecC
Confidence            345669999999987542   2333333322244556665544

>COG2842 Uncharacterized ATPase, putative transposase [General function prediction only]

Probab=98.12  E-value=8.1e-05  Score=70.88  Aligned_cols=209  Identities=18%  Similarity=0.175  Sum_probs=121.5

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHh
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNEL  273 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l  273 (490)
                      .+|++-... .++..++...  ...+....+||.+|.|||+.++.+++.-.     ..+.+......+...++..++...
T Consensus        72 ~~~l~tkt~-r~~~~~~~~A--~k~g~l~~vyg~~g~gKt~a~~~y~~s~p-----~~~l~~~~p~~~a~~~i~~i~~~~  143 (297)
T COG2842          72 PDFLETKTV-RRIFFRTRPA--SKTGSLVVVYGYAGLGKTQAAKNYAPSNP-----NALLIEADPSYTALVLILIICAAA  143 (297)
T ss_pred             ccccccchh-HhHhhhhhhh--hhcCceEEEeccccchhHHHHHhhcccCc-----cceeecCChhhHHHHHHHHHHHHH
Confidence            344443322 2344444432  23455888999999999999998877532     334455555545556666666555


Q ss_pred             cCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEEEecCCCCh---hHhhhHH
Q psy200          274 KLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVANALDL---TDRMLPR  350 (490)
Q Consensus       274 ~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI~~tn~~~~---~~~l~~~  350 (490)
                      ..... .........+...+.  +...+|++||.++|.-...+.|..+.+   ..+..++++|.......   ...-..+
T Consensus       144 ~~~~~-~~~~d~~~~~~~~l~--~~~~~iivDEA~~L~~~ale~lr~i~d---~~Gi~~vLvG~prL~~~l~~~~~~~~r  217 (297)
T COG2842         144 FGATD-GTINDLTERLMIRLR--DTVRLIIVDEADRLPYRALEELRRIHD---KTGIGVVLVGMPRLFKVLRRPEDELSR  217 (297)
T ss_pred             hcccc-hhHHHHHHHHHHHHc--cCcceeeeehhhccChHHHHHHHHHHH---hhCceEEEecChHHHhccccchHHHHH
Confidence            44333 233334443333343  446699999999999877777776655   34566777776641111   1111233


Q ss_pred             hhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHhcc
Q psy200          351 LQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITNHLIDLTYDNV  426 (490)
Q Consensus       351 l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll~~a~~~a~~~~  426 (490)
                      +.+|...+ ..+...-.+.++.+.+....+..      +.++.+..+..   ...|+++.+-.++..+...+..++
T Consensus       218 l~srv~v~-~~~~~~~~d~d~~~~~~~~~l~~------~~~~~v~~~~~---~~~g~~~~L~~~l~~~~~~a~~~~  283 (297)
T COG2842         218 LYSRVRVG-KLLGEKFPDADELAEIAALVLPT------EDELVLMQVIK---ETEGNIRRLDKILAGAVGTARSNG  283 (297)
T ss_pred             HHHHhhhH-hhhhhhhhhhHHHHHHHHhhCcc------chHHHHHHHHH---hcchhHhHHHHHHhhhhhhhhhcc
Confidence            44443221 12222333346666666655432      34455544443   688999999999999988888877

>PRK08485 DNA polymerase III subunit delta'; Validated

Probab=98.04  E-value=0.00012  Score=66.07  Aligned_cols=128  Identities=13%  Similarity=0.245  Sum_probs=88.6

Q ss_pred             CcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEEEecCCCChhHhhhHHhhhccCCC-
Q psy200          280 KSERHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVANALDLTDRMLPRLQANVTLQ-  358 (490)
Q Consensus       280 ~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI~~tn~~~~~~~l~~~l~~R~~~~-  358 (490)
                      ...+++++.+..+.-...... ++||++|.|....+++|...++.   +..++++|.+++   -...+++.+++||... 
T Consensus        37 i~Vd~iReii~~~~~~~~~~k-~iI~~a~~l~~~A~NaLLK~LEE---Pp~~~~fiL~t~---~~~~llpTI~SRc~~~~  109 (206)
T PRK08485         37 FKIEDAKEVIAEAYIAESEEK-IIVIAAPSYGIEAQNALLKILEE---PPKNICFIIVAK---SKNLLLPTIRSRLIIEK  109 (206)
T ss_pred             CCHHHHHHHHHHHhhCCCCcE-EEEEchHhhCHHHHHHHHHHhcC---CCCCeEEEEEeC---ChHhCchHHHhhheecc
Confidence            456777776666543322222 45789999998888888888774   444565555554   2577889999999521 


Q ss_pred             --------CeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHHHHHHHHH
Q psy200          359 --------PTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITNHLID  420 (490)
Q Consensus       359 --------~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll~~a~~  420 (490)
                              ...+.|.+++.+++.+++.+ +..+  .....+++.+.|+.   ...|.+|.++.+.++++.
T Consensus       110 ~~~~~~~~~l~l~l~~l~~~~i~~~L~~-~~ke--~~~~~~ea~~lIa~---la~~s~r~~l~l~~q~l~  173 (206)
T PRK08485        110 RKQKKPVKPLDLDLKKLDLKDIYEFLKE-LEKE--NKLSKEELKELIES---LLKECVKYKIPLNEEELE  173 (206)
T ss_pred             ccccccccccccccCCCCHHHHHHHHHH-HHHc--ccccHHHHHHHHHH---HHHHHHHHHcCccHHHHH
Confidence                    12488999999999999998 5554  34567888888887   566777877666555543

>PRK06581 DNA polymerase III subunit delta'; Validated

Probab=98.00  E-value=0.00091  Score=62.23  Aligned_cols=174  Identities=10%  Similarity=0.027  Sum_probs=112.2

Q ss_pred             CCCCeEEEECCCC-CcHHHHHHHHHHHhhhc-----CCceEEEEeccCCCCHHHHHHHHHHHhcCCCCCCcHHHHHHHHH
Q psy200          217 ETSGSMYISGPPG-TGKSASLNLLVSRAEIK-----DAFKTIYINCNSVRNAASVYETIVNELKLKPGGKSERHQLGAIL  290 (490)
Q Consensus       217 ~~~~~ill~GppG-tGKTtla~~l~~~l~~~-----~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~  290 (490)
                      .-.+..++.|..+ .||..++..++..+...     .+-.+..+.-... .            .......+.+++++...
T Consensus        13 kLshAYLfeG~n~~~~~~~~~~f~~~~l~~~~i~~~~HPD~~~I~pe~~-~------------~~~~~~I~IdqIReL~~   79 (263)
T PRK06581         13 KLYNSWLIEAENIEQALKDLEKFIYIKLFKNSIPLENNPDYHFIARETS-A------------TSNAKNISIEQIRKLQD   79 (263)
T ss_pred             cchheeeEeCCChhhHHHHHHHHHHHHHhccCcccCCCCCEEEEecccc-c------------cccCCcccHHHHHHHHH
Confidence            4567788999998 99999999888876421     1112222211000 0            00011235666666444


Q ss_pred             HHHhc--CCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCC
Q psy200          291 KYFDT--KHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYS  368 (490)
Q Consensus       291 ~~l~~--~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls  368 (490)
                      .....  .++..|++||++|.|.....+.|+.+++.+   ....++|..+.   -..++++.+++||.    .+.|..+.
T Consensus        80 ~l~~~p~~g~~KViII~~ae~mt~~AANALLKtLEEP---P~~t~fILit~---~~~~LLpTIrSRCq----~i~~~~p~  149 (263)
T PRK06581         80 FLSKTSAISGYKVAIIYSAELMNLNAANSCLKILEDA---PKNSYIFLITS---RAASIISTIRSRCF----KINVRSSI  149 (263)
T ss_pred             HHhhCcccCCcEEEEEechHHhCHHHHHHHHHhhcCC---CCCeEEEEEeC---ChhhCchhHhhceE----EEeCCCCC
Confidence            33322  356779999999999998888888888753   44555554443   25778999999995    89999999


Q ss_pred             HHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHHHHHHHHHH
Q psy200          369 REQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITNHLIDL  421 (490)
Q Consensus       369 ~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll~~a~~~  421 (490)
                      .....++....+.-     ..+..-++.|.+   ....|...++...+.++.+
T Consensus       150 ~~~~~e~~~~~~~p-----~~~~~~l~~i~~---~~~~d~~~w~~~~~~~~~~  194 (263)
T PRK06581        150 LHAYNELYSQFIQP-----IADNKTLDFINR---FTTKDRELWLDFIDNLLLL  194 (263)
T ss_pred             HHHHHHHHHHhccc-----ccccHHHHHHHH---HhhhhHHHHHHHHHHHHHH
Confidence            98888887776543     345566788877   4556666666655555443

>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=97.98  E-value=0.0001  Score=73.93  Aligned_cols=91  Identities=19%  Similarity=0.281  Sum_probs=55.0

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhc-CCceEEEEeccCCC-CHHHHHHHHHHHhcCCCCC-CcHHHHHHHHHHHHh
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIK-DAFKTIYINCNSVR-NAASVYETIVNELKLKPGG-KSERHQLGAILKYFD  294 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~-~~~~~~~v~~~~~~-~~~~l~~~i~~~l~~~~~~-~s~~~~~~~l~~~l~  294 (490)
                      .++.++|+||+|+||||++..++..+... ....+..+.+..+. ...+.+..+...++.+... ....++...+.+.  
T Consensus       136 ~g~ii~lvGptGvGKTTtiakLA~~~~~~~G~~~V~lit~D~~R~ga~EqL~~~a~~~gv~~~~~~~~~~l~~~l~~l--  213 (374)
T PRK14722        136 RGGVFALMGPTGVGKTTTTAKLAARCVMRFGASKVALLTTDSYRIGGHEQLRIFGKILGVPVHAVKDGGDLQLALAEL--  213 (374)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHHHhcCCCeEEEEecccccccHHHHHHHHHHHcCCceEecCCcccHHHHHHHh--
Confidence            46789999999999999999999876422 22345555544443 3344555555556553321 1222333333322  


Q ss_pred             cCCCeEEEEEecCccccc
Q psy200          295 TKHKSILLILDEIDALES  312 (490)
Q Consensus       295 ~~~~~~vI~IDEid~l~~  312 (490)
                        .+.-+|+||.+.....
T Consensus       214 --~~~DlVLIDTaG~~~~  229 (374)
T PRK14722        214 --RNKHMVLIDTIGMSQR  229 (374)
T ss_pred             --cCCCEEEEcCCCCCcc
Confidence              2345899999987643

>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=97.94  E-value=0.00026  Score=72.89  Aligned_cols=145  Identities=14%  Similarity=0.191  Sum_probs=77.5

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHhh-hcCCceEEEEeccCCCCH-HHHHHHHHHHhcCCCC-CCcHHHHHHHHHHHHhc
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRAE-IKDAFKTIYINCNSVRNA-ASVYETIVNELKLKPG-GKSERHQLGAILKYFDT  295 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l~-~~~~~~~~~v~~~~~~~~-~~l~~~i~~~l~~~~~-~~s~~~~~~~l~~~l~~  295 (490)
                      ++.++|+||+|+||||++..++..+. ...+..+..+++...... .+.+..+...++.+.. .....++...+...   
T Consensus       221 ~~~i~~vGptGvGKTTt~~kLA~~~~~~~~g~~V~li~~D~~r~~a~eqL~~~a~~~~vp~~~~~~~~~l~~~l~~~---  297 (424)
T PRK05703        221 GGVVALVGPTGVGKTTTLAKLAARYALLYGKKKVALITLDTYRIGAVEQLKTYAKIMGIPVEVVYDPKELAKALEQL---  297 (424)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHhcCCCeEEEEECCccHHHHHHHHHHHHHHhCCceEccCCHHhHHHHHHHh---
Confidence            46889999999999999999988875 345567778877654321 2223344444444321 12344444444432   


Q ss_pred             CCCeEEEEEecCcccccc--CHHHHHHhHhCCCCCCCcEEEEEecC-CCChhHhhhHHhhhccCCCCeeEEeCCCCHHH
Q psy200          296 KHKSILLILDEIDALESR--KQTILYTIFEWPSIPGSKLVLVGVAN-ALDLTDRMLPRLQANVTLQPTLMNFAPYSREQ  371 (490)
Q Consensus       296 ~~~~~vI~IDEid~l~~~--~~~~L~~l~~~~~~~~~~vilI~~tn-~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e  371 (490)
                       ...-+||||........  ..+.|..+++... ....+.++..++ .......+...+. .++  ...+-|..++...
T Consensus       298 -~~~DlVlIDt~G~~~~d~~~~~~L~~ll~~~~-~~~~~~LVl~a~~~~~~l~~~~~~f~-~~~--~~~vI~TKlDet~  371 (424)
T PRK05703        298 -RDCDVILIDTAGRSQRDKRLIEELKALIEFSG-EPIDVYLVLSATTKYEDLKDIYKHFS-RLP--LDGLIFTKLDETS  371 (424)
T ss_pred             -CCCCEEEEeCCCCCCCCHHHHHHHHHHHhccC-CCCeEEEEEECCCCHHHHHHHHHHhC-CCC--CCEEEEecccccc
Confidence             23459999998775433  1234555555211 223434443333 2112222222222 222  2356677776543

>cd00046 DEXDc DEAD-like helicases superfamily

Probab=97.93  E-value=5.3e-05  Score=64.59  Aligned_cols=26  Identities=19%  Similarity=0.304  Sum_probs=22.5

Q ss_pred             CeEEEECCCCCcHHHHHHHHHHHhhh
Q psy200          220 GSMYISGPPGTGKSASLNLLVSRAEI  245 (490)
Q Consensus       220 ~~ill~GppGtGKTtla~~l~~~l~~  245 (490)
                      ++++|+|++|+|||+++-.++..+..
T Consensus         1 ~~~~i~~~~G~GKT~~~~~~~~~~~~   26 (144)
T cd00046           1 RDVLLAAPTGSGKTLAALLPILELLD   26 (144)
T ss_pred             CCEEEECCCCCchhHHHHHHHHHHHh
Confidence            36899999999999999999888763

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

>PRK14974 cell division protein FtsY; Provisional

Probab=97.92  E-value=0.00068  Score=67.34  Aligned_cols=92  Identities=18%  Similarity=0.231  Sum_probs=58.9

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCC-HHHHHHHHHHHhcCCCC----CCcHHH-HHHHHHH
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRN-AASVYETIVNELKLKPG----GKSERH-QLGAILK  291 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~-~~~l~~~i~~~l~~~~~----~~s~~~-~~~~l~~  291 (490)
                      .+..++|+|++|+||||++..++..+. ..++.++.+++..++. ....+..+...++.+..    +..... +.+.+..
T Consensus       139 ~~~vi~~~G~~GvGKTTtiakLA~~l~-~~g~~V~li~~Dt~R~~a~eqL~~~a~~lgv~v~~~~~g~dp~~v~~~ai~~  217 (336)
T PRK14974        139 KPVVIVFVGVNGTGKTTTIAKLAYYLK-KNGFSVVIAAGDTFRAGAIEQLEEHAERLGVKVIKHKYGADPAAVAYDAIEH  217 (336)
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHHH-HcCCeEEEecCCcCcHHHHHHHHHHHHHcCCceecccCCCCHHHHHHHHHHH
Confidence            356889999999999999999998875 3345666777665542 23456666777765321    222222 3344443


Q ss_pred             HHhcCCCeEEEEEecCccccc
Q psy200          292 YFDTKHKSILLILDEIDALES  312 (490)
Q Consensus       292 ~l~~~~~~~vI~IDEid~l~~  312 (490)
                      +...  ..-+|+||....+..
T Consensus       218 ~~~~--~~DvVLIDTaGr~~~  236 (336)
T PRK14974        218 AKAR--GIDVVLIDTAGRMHT  236 (336)
T ss_pred             HHhC--CCCEEEEECCCccCC
Confidence            3322  234999999999864

>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=97.91  E-value=0.00024  Score=66.70  Aligned_cols=147  Identities=19%  Similarity=0.283  Sum_probs=76.0

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHH-hcCCCCCCcHH----HHHHHHHHHH
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNE-LKLKPGGKSER----HQLGAILKYF  293 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~-l~~~~~~~s~~----~~~~~l~~~l  293 (490)
                      +-.++|.|++|+|||+++..+...+.  ..+..+++-+....  ..+..-++.. +.........+    ...+.+.+..
T Consensus        13 ~fr~viIG~sGSGKT~li~~lL~~~~--~~f~~I~l~t~~~n--~~~~~~i~p~~i~~~~~~e~le~~l~~~k~~I~k~~   88 (241)
T PF04665_consen   13 PFRMVIIGKSGSGKTTLIKSLLYYLR--HKFDHIFLITPEYN--NEYYKYIWPDHIFKVFDKEELEYILIRQKEKIEKYI   88 (241)
T ss_pred             CceEEEECCCCCCHHHHHHHHHHhhc--ccCCEEEEEecCCc--hhhhhhcchhhccccccHHHHHHHHHHHHHHHHHHh
Confidence            44788999999999999999998875  45655665544322  2222222211 11111101111    1122233333


Q ss_pred             hc-----CCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCC
Q psy200          294 DT-----KHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYS  368 (490)
Q Consensus       294 ~~-----~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls  368 (490)
                      .+     ...+++||+||+..-. .....+.+++.....-+..+++++-+-     ..+.+.++.-+.   ..+.| ..+
T Consensus        89 ~k~~~~k~~~~~LiIlDD~~~~~-~k~~~l~~~~~~gRH~~is~i~l~Q~~-----~~lp~~iR~n~~---y~i~~-~~s  158 (241)
T PF04665_consen   89 KKSPQKKNNPRFLIILDDLGDKK-LKSKILRQFFNNGRHYNISIIFLSQSY-----FHLPPNIRSNID---YFIIF-NNS  158 (241)
T ss_pred             hhhcccCCCCCeEEEEeCCCCch-hhhHHHHHHHhcccccceEEEEEeeec-----ccCCHHHhhcce---EEEEe-cCc
Confidence            21     1338899999986521 234556777764443444444443331     223344544333   23445 467


Q ss_pred             HHHHHHHHHHH
Q psy200          369 REQILEIISQK  379 (490)
Q Consensus       369 ~~e~~~il~~~  379 (490)
                      ..++..+++..
T Consensus       159 ~~dl~~i~~~~  169 (241)
T PF04665_consen  159 KRDLENIYRNM  169 (241)
T ss_pred             HHHHHHHHHhc
Confidence            77776666654

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

>KOG2170|consensus

Probab=97.91  E-value=0.00077  Score=64.21  Aligned_cols=132  Identities=17%  Similarity=0.191  Sum_probs=77.6

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccC---CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNE---TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIV  270 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~---~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~  270 (490)
                      ..+.|+--..+.+...+...+...   ++-.+-++|.+||||..+++.|++.+-...             ....++..+.
T Consensus        82 ~~lfGQHla~~~Vv~alk~~~~n~~p~KPLvLSfHG~tGTGKN~Va~iiA~n~~~~G-------------l~S~~V~~fv  148 (344)
T KOG2170|consen   82 RALFGQHLAKQLVVNALKSHWANPNPRKPLVLSFHGWTGTGKNYVAEIIAENLYRGG-------------LRSPFVHHFV  148 (344)
T ss_pred             HHhhchHHHHHHHHHHHHHHhcCCCCCCCeEEEecCCCCCchhHHHHHHHHHHHhcc-------------ccchhHHHhh
Confidence            567777666666666666555443   233455899999999999999999874111             0111222222


Q ss_pred             HHhcCCCCCCcHHHHHHHHHHH----HhcCCCeEEEEEecCccccccCHHHHHHhHhCC----CCCCCcEEEEEecCC
Q psy200          271 NELKLKPGGKSERHQLGAILKY----FDTKHKSILLILDEIDALESRKQTILYTIFEWP----SIPGSKLVLVGVANA  340 (490)
Q Consensus       271 ~~l~~~~~~~s~~~~~~~l~~~----l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~----~~~~~~vilI~~tn~  340 (490)
                      ..+..+.. ...+...+.|...    +.. .++.+.|+||+|.|...-.+.|.-+++..    .....+-|+|..+|.
T Consensus       149 at~hFP~~-~~ie~Yk~eL~~~v~~~v~~-C~rslFIFDE~DKmp~gLld~lkpfLdyyp~v~gv~frkaIFIfLSN~  224 (344)
T KOG2170|consen  149 ATLHFPHA-SKIEDYKEELKNRVRGTVQA-CQRSLFIFDEVDKLPPGLLDVLKPFLDYYPQVSGVDFRKAIFIFLSNA  224 (344)
T ss_pred             hhccCCCh-HHHHHHHHHHHHHHHHHHHh-cCCceEEechhhhcCHhHHHHHhhhhccccccccccccceEEEEEcCC
Confidence            22222211 1233333333333    333 45679999999999887777777776632    123345677777773

>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=97.90  E-value=0.00029  Score=64.67  Aligned_cols=144  Identities=16%  Similarity=0.165  Sum_probs=81.7

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCC-HHHHHHHHHHHhcCCCC----CCcHHH-HHHHHHHH
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRN-AASVYETIVNELKLKPG----GKSERH-QLGAILKY  292 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~-~~~l~~~i~~~l~~~~~----~~s~~~-~~~~l~~~  292 (490)
                      ++.++|+||.|+||||++-.++..+... +..+..+++...+- ..+-+..+.+.++.+..    .....+ +.+.+.+.
T Consensus         1 p~vi~lvGptGvGKTTt~aKLAa~~~~~-~~~v~lis~D~~R~ga~eQL~~~a~~l~vp~~~~~~~~~~~~~~~~~l~~~   79 (196)
T PF00448_consen    1 PKVIALVGPTGVGKTTTIAKLAARLKLK-GKKVALISADTYRIGAVEQLKTYAEILGVPFYVARTESDPAEIAREALEKF   79 (196)
T ss_dssp             SEEEEEEESTTSSHHHHHHHHHHHHHHT-T--EEEEEESTSSTHHHHHHHHHHHHHTEEEEESSTTSCHHHHHHHHHHHH
T ss_pred             CEEEEEECCCCCchHhHHHHHHHHHhhc-cccceeecCCCCCccHHHHHHHHHHHhccccchhhcchhhHHHHHHHHHHH
Confidence            3578999999999999999999998765 66777777666653 34557777888876421    122333 33444443


Q ss_pred             HhcCCCeEEEEEecCccccccC--HHHHHHhHhCCCCCCCcEEEEEecC-CCChhHhhhHHhhhccCCCCeeEEeCCCCH
Q psy200          293 FDTKHKSILLILDEIDALESRK--QTILYTIFEWPSIPGSKLVLVGVAN-ALDLTDRMLPRLQANVTLQPTLMNFAPYSR  369 (490)
Q Consensus       293 l~~~~~~~vI~IDEid~l~~~~--~~~L~~l~~~~~~~~~~vilI~~tn-~~~~~~~l~~~l~~R~~~~~~~i~~~pls~  369 (490)
                      ..  .+.-+||||=........  ...|..+++..  ....++++..++ ..+.... ...+...+++  ..+-|..++.
T Consensus        80 ~~--~~~D~vlIDT~Gr~~~d~~~~~el~~~~~~~--~~~~~~LVlsa~~~~~~~~~-~~~~~~~~~~--~~lIlTKlDe  152 (196)
T PF00448_consen   80 RK--KGYDLVLIDTAGRSPRDEELLEELKKLLEAL--NPDEVHLVLSATMGQEDLEQ-ALAFYEAFGI--DGLILTKLDE  152 (196)
T ss_dssp             HH--TTSSEEEEEE-SSSSTHHHHHHHHHHHHHHH--SSSEEEEEEEGGGGGHHHHH-HHHHHHHSST--CEEEEESTTS
T ss_pred             hh--cCCCEEEEecCCcchhhHHHHHHHHHHhhhc--CCccceEEEecccChHHHHH-HHHHhhcccC--ceEEEEeecC
Confidence            33  223499999987764332  23344444322  334555554444 2221221 2233333433  4677887775


Q ss_pred             H
Q psy200          370 E  370 (490)
Q Consensus       370 ~  370 (490)
                      .
T Consensus       153 t  153 (196)
T PF00448_consen  153 T  153 (196)
T ss_dssp             S
T ss_pred             C
Confidence            4

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 ....

>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]

Probab=97.89  E-value=0.00013  Score=72.22  Aligned_cols=91  Identities=23%  Similarity=0.389  Sum_probs=57.0

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCCCCC--CcHHHHHHHHHHHHhc
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKPGG--KSERHQLGAILKYFDT  295 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~~--~s~~~~~~~l~~~l~~  295 (490)
                      ++..+||-|.||+|||||+-.++..+....  +++|+..-+  +..++ .--.+.|+.....  .-.+.-.+.+...+..
T Consensus        92 ~Gs~iLIgGdPGIGKSTLLLQva~~lA~~~--~vLYVsGEE--S~~Qi-klRA~RL~~~~~~l~l~aEt~~e~I~~~l~~  166 (456)
T COG1066          92 PGSVILIGGDPGIGKSTLLLQVAARLAKRG--KVLYVSGEE--SLQQI-KLRADRLGLPTNNLYLLAETNLEDIIAELEQ  166 (456)
T ss_pred             cccEEEEccCCCCCHHHHHHHHHHHHHhcC--cEEEEeCCc--CHHHH-HHHHHHhCCCccceEEehhcCHHHHHHHHHh
Confidence            567899999999999999999999987333  889997654  33332 2223344432111  1111112222233333


Q ss_pred             CCCeEEEEEecCccccccC
Q psy200          296 KHKSILLILDEIDALESRK  314 (490)
Q Consensus       296 ~~~~~vI~IDEid~l~~~~  314 (490)
                       .+|.++|||-||.+....
T Consensus       167 -~~p~lvVIDSIQT~~s~~  184 (456)
T COG1066         167 -EKPDLVVIDSIQTLYSEE  184 (456)
T ss_pred             -cCCCEEEEeccceeeccc
Confidence             568899999999997653

>PF02562 PhoH: PhoH-like protein; InterPro: IPR003714 PhoH is a cytoplasmic protein and predicted ATPase that is induced by phosphate starvation and belongings to the phosphate regulon (pho) in Escherichia coli []

Probab=97.87  E-value=5.7e-05  Score=69.31  Aligned_cols=114  Identities=18%  Similarity=0.239  Sum_probs=51.0

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHhhhcCCc-eEEEEeccCC--CC----HHH-------HHHHHHHHhcCCCCCCcHHH
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRAEIKDAF-KTIYINCNSV--RN----AAS-------VYETIVNELKLKPGGKSERH  284 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l~~~~~~-~~~~v~~~~~--~~----~~~-------l~~~i~~~l~~~~~~~s~~~  284 (490)
                      ...+++.||+|||||+||-+.+-++-....+ +++++...-.  .+    +.+       ++.-+.+.|..-......+.
T Consensus        19 ~~~v~~~G~AGTGKT~LA~a~Al~~v~~g~~~kiii~Rp~v~~~~~lGflpG~~~eK~~p~~~p~~d~l~~~~~~~~~~~   98 (205)
T PF02562_consen   19 NDLVIVNGPAGTGKTFLALAAALELVKEGEYDKIIITRPPVEAGEDLGFLPGDLEEKMEPYLRPIYDALEELFGKEKLEE   98 (205)
T ss_dssp             -SEEEEE--TTSSTTHHHHHHHHHHHHTTS-SEEEEEE-S--TT----SS---------TTTHHHHHHHTTTS-TTCHHH
T ss_pred             CCeEEEECCCCCcHHHHHHHHHHHHHHhCCCcEEEEEecCCCCccccccCCCCHHHHHHHHHHHHHHHHHHHhChHhHHH
Confidence            5689999999999999999998776545555 3444322110  00    011       22233333332211111222


Q ss_pred             HHHHHHHH---------Hhc-CCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEEEecC
Q psy200          285 QLGAILKY---------FDT-KHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVAN  339 (490)
Q Consensus       285 ~~~~l~~~---------l~~-~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI~~tn  339 (490)
                      +.   .+.         +++ .=...+|||||+|++....   +..++.. -..+++++++|-..
T Consensus        99 ~~---~~~~Ie~~~~~~iRGrt~~~~~iIvDEaQN~t~~~---~k~ilTR-~g~~skii~~GD~~  156 (205)
T PF02562_consen   99 LI---QNGKIEIEPLAFIRGRTFDNAFIIVDEAQNLTPEE---LKMILTR-IGEGSKIIITGDPS  156 (205)
T ss_dssp             HH---HTTSEEEEEGGGGTT--B-SEEEEE-SGGG--HHH---HHHHHTT-B-TT-EEEEEE---
T ss_pred             Hh---hcCeEEEEehhhhcCccccceEEEEecccCCCHHH---HHHHHcc-cCCCcEEEEecCce
Confidence            11   110         010 0125799999999997643   3333322 23678999988665

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

>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=97.86  E-value=3e-05  Score=69.37  Aligned_cols=24  Identities=33%  Similarity=0.823  Sum_probs=21.3

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHhh
Q psy200          221 SMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      +++|+|+||+||||+++.+++.+.
T Consensus         1 ~i~iTG~pG~GKTTll~k~i~~l~   24 (168)
T PF03266_consen    1 HIFITGPPGVGKTTLLKKVIEELK   24 (168)
T ss_dssp             EEEEES-TTSSHHHHHHHHHHHHH
T ss_pred             CEEEECcCCCCHHHHHHHHHHHhh
Confidence            489999999999999999999984

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.

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

Probab=97.86  E-value=0.00019  Score=59.96  Aligned_cols=51  Identities=24%  Similarity=0.300  Sum_probs=41.6

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccC---CCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNE---TSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~---~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      ..|+|+.-..+.|...|...+...   ++-.+.++|++|||||.+++.|++.+-
T Consensus        25 ~~l~GQhla~~~v~~ai~~~l~~~~p~KpLVlSfHG~tGtGKn~v~~liA~~ly   78 (127)
T PF06309_consen   25 RNLFGQHLAVEVVVNAIKGHLANPNPRKPLVLSFHGWTGTGKNFVSRLIAEHLY   78 (127)
T ss_pred             HHccCcHHHHHHHHHHHHHHHcCCCCCCCEEEEeecCCCCcHHHHHHHHHHHHH
Confidence            789999988888888888777543   333455999999999999999999974

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

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

Probab=97.84  E-value=7.3e-05  Score=75.43  Aligned_cols=93  Identities=23%  Similarity=0.278  Sum_probs=48.2

Q ss_pred             CeEEEECCCCCcHHHHHHHHHHHhh-hcCCceEEEEeccCCCCHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHH---hc
Q psy200          220 GSMYISGPPGTGKSASLNLLVSRAE-IKDAFKTIYINCNSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYF---DT  295 (490)
Q Consensus       220 ~~ill~GppGtGKTtla~~l~~~l~-~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l---~~  295 (490)
                      ..++|.|.||||||.|+-.++..+. .......+++... ..-...+...+..................++...-   ..
T Consensus         2 ~v~~I~G~aGTGKTvla~~l~~~l~~~~~~~~~~~l~~n-~~l~~~l~~~l~~~~~~~~~~~~~~~~~~~i~~~~~~~~~   80 (352)
T PF09848_consen    2 QVILITGGAGTGKTVLALNLAKELQNSEEGKKVLYLCGN-HPLRNKLREQLAKKYNPKLKKSDFRKPTSFINNYSESDKE   80 (352)
T ss_pred             eEEEEEecCCcCHHHHHHHHHHHhhccccCCceEEEEec-chHHHHHHHHHhhhcccchhhhhhhhhHHHHhhccccccc
Confidence            3688999999999999999999981 1122233333221 11112222222222211111112222222332221   11


Q ss_pred             CCCeEEEEEecCcccccc
Q psy200          296 KHKSILLILDEIDALESR  313 (490)
Q Consensus       296 ~~~~~vI~IDEid~l~~~  313 (490)
                      ....-+|||||+|.|...
T Consensus        81 ~~~~DviivDEAqrl~~~   98 (352)
T PF09848_consen   81 KNKYDVIIVDEAQRLRTK   98 (352)
T ss_pred             CCcCCEEEEehhHhhhhc
Confidence            234559999999999873

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

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

Probab=97.83  E-value=5.7e-05  Score=76.50  Aligned_cols=30  Identities=30%  Similarity=0.598  Sum_probs=26.8

Q ss_pred             ccCCCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          215 NNETSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       215 ~~~~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      ....+..++|.|++|||||++++++.+.+.
T Consensus        18 ~~~~~~~~fv~G~~GtGKs~l~~~i~~~~~   47 (364)
T PF05970_consen   18 ENEEGLNFFVTGPAGTGKSFLIKAIIDYLR   47 (364)
T ss_pred             HccCCcEEEEEcCCCCChhHHHHHHHHHhc
Confidence            346788999999999999999999999875

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

>COG5271 MDN1 AAA ATPase containing von Willebrand factor type A (vWA) domain [General function prediction only]

Probab=97.81  E-value=0.00032  Score=79.40  Aligned_cols=164  Identities=15%  Similarity=0.225  Sum_probs=99.9

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcC
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFDTK  296 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~  296 (490)
                      +-.++++|-|-||+|||+|+.++|+..+    -..+.+|.+...+.-+++..   ++-....|.-.-. -.-|..+++.+
T Consensus      1541 qv~kpilLEGsPGVGKTSlItaLAr~tG----~kliRINLSeQTdL~DLfGs---d~Pve~~Gef~w~-dapfL~amr~G 1612 (4600)
T COG5271        1541 QVGKPILLEGSPGVGKTSLITALARKTG----KKLIRINLSEQTDLCDLFGS---DLPVEEGGEFRWM-DAPFLHAMRDG 1612 (4600)
T ss_pred             hcCCceeecCCCCccHHHHHHHHHHHhc----CceEEeeccccchHHHHhCC---CCCcccCceeEec-ccHHHHHhhcC
Confidence            4578999999999999999999999865    56788988876554444321   1111111111101 11233344443


Q ss_pred             CCeEEEEEecCccccccCHHHHHHhHhCC-----------CCCCCcEEEEEecCCCCh---hHhhhHHhhhccCCCCeeE
Q psy200          297 HKSILLILDEIDALESRKQTILYTIFEWP-----------SIPGSKLVLVGVANALDL---TDRMLPRLQANVTLQPTLM  362 (490)
Q Consensus       297 ~~~~vI~IDEid~l~~~~~~~L~~l~~~~-----------~~~~~~vilI~~tn~~~~---~~~l~~~l~~R~~~~~~~i  362 (490)
                      +   -+++||+.-....-.+.|...++.-           ...+.++.|.++-|+.+-   ..-+-..+..||.    ++
T Consensus      1613 ~---WVlLDEiNLaSQSVlEGLNacLDhR~eayIPEld~~f~~HpnfrVFAaqNPq~qggGRKgLPkSF~nRFs----vV 1685 (4600)
T COG5271        1613 G---WVLLDEINLASQSVLEGLNACLDHRREAYIPELDKTFDVHPNFRVFAAQNPQDQGGGRKGLPKSFLNRFS----VV 1685 (4600)
T ss_pred             C---EEEeehhhhhHHHHHHHHHHHHhhccccccccccceeeccCCeeeeeecCchhcCCCcccCCHHHhhhhh----eE
Confidence            3   7889999876655445554444321           123567778777774321   1112345677886    89


Q ss_pred             EeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHH
Q psy200          363 NFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKV  401 (490)
Q Consensus       363 ~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i  401 (490)
                      .++.++.+++..|..+....      +.++.+..|.+.+
T Consensus      1686 ~~d~lt~dDi~~Ia~~~yp~------v~~d~~~kiik~m 1718 (4600)
T COG5271        1686 KMDGLTTDDITHIANKMYPQ------VNEDWRLKIIKFM 1718 (4600)
T ss_pred             EecccccchHHHHHHhhCCc------cChHHHHHHHHHH
Confidence            99999999999998876443      4555554444433

>PRK10867 signal recognition particle protein; Provisional

Probab=97.81  E-value=0.003  Score=64.90  Aligned_cols=221  Identities=15%  Similarity=0.149  Sum_probs=110.7

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCH-HHHHHHHHHHhcCCC----CCCcHHHHHHHHHHH
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNA-ASVYETIVNELKLKP----GGKSERHQLGAILKY  292 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~-~~l~~~i~~~l~~~~----~~~s~~~~~~~l~~~  292 (490)
                      .+..++++|++|+||||++..++..+....+..+..++|-..+.. .+-+..+...++.+.    .+.+...+.....+.
T Consensus        99 ~p~vI~~vG~~GsGKTTtaakLA~~l~~~~G~kV~lV~~D~~R~aa~eQL~~~a~~~gv~v~~~~~~~dp~~i~~~a~~~  178 (433)
T PRK10867         99 PPTVIMMVGLQGAGKTTTAGKLAKYLKKKKKKKVLLVAADVYRPAAIEQLKTLGEQIGVPVFPSGDGQDPVDIAKAALEE  178 (433)
T ss_pred             CCEEEEEECCCCCcHHHHHHHHHHHHHHhcCCcEEEEEccccchHHHHHHHHHHhhcCCeEEecCCCCCHHHHHHHHHHH
Confidence            356889999999999999999998876443567778887766543 334555666665432    223344444322222


Q ss_pred             HhcCCCeEEEEEecCccccccC--HHHHHHhHhCCCCCCCcEEEEEecC-CCChhHhhhHHhhhccCCCCeeEEeCCCCH
Q psy200          293 FDTKHKSILLILDEIDALESRK--QTILYTIFEWPSIPGSKLVLVGVAN-ALDLTDRMLPRLQANVTLQPTLMNFAPYSR  369 (490)
Q Consensus       293 l~~~~~~~vI~IDEid~l~~~~--~~~L~~l~~~~~~~~~~vilI~~tn-~~~~~~~l~~~l~~R~~~~~~~i~~~pls~  369 (490)
                      ... ...-+||||=...+....  ...|..+.+..  ....++++..+. ..+..+ ....+..++++  ..+-+..++.
T Consensus       179 a~~-~~~DvVIIDTaGrl~~d~~lm~eL~~i~~~v--~p~evllVlda~~gq~av~-~a~~F~~~~~i--~giIlTKlD~  252 (433)
T PRK10867        179 AKE-NGYDVVIVDTAGRLHIDEELMDELKAIKAAV--NPDEILLVVDAMTGQDAVN-TAKAFNEALGL--TGVILTKLDG  252 (433)
T ss_pred             HHh-cCCCEEEEeCCCCcccCHHHHHHHHHHHHhh--CCCeEEEEEecccHHHHHH-HHHHHHhhCCC--CEEEEeCccC
Confidence            221 234599999998875321  12233333322  222344443332 111111 12333333333  3566777764


Q ss_pred             HHHHHHHHHHHhcc---------CC----CCCCCHHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHhcc-ccCCccccc
Q psy200          370 EQILEIISQKLKQT---------DK----FNMFNASALQLLAGKVAAVSGDIRKAIDITNHLIDLTYDNV-KENGEVTGI  435 (490)
Q Consensus       370 ~e~~~il~~~l~~~---------~~----~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll~~a~~~a~~~~-~~~~~~~~I  435 (490)
                      +...-.+.......         +.    -..|++   +.+++.+. .-||+-.++.-.+.++....... .+.......
T Consensus       253 ~~rgG~alsi~~~~~~PI~fig~Ge~v~DLe~f~p---~~~~~~il-gmgD~~~l~e~~~~~~~~~~~~~~~~~~~~g~f  328 (433)
T PRK10867        253 DARGGAALSIRAVTGKPIKFIGTGEKLDDLEPFHP---DRMASRIL-GMGDVLSLIEKAQEVVDEEKAEKLAKKLKKGKF  328 (433)
T ss_pred             cccccHHHHHHHHHCcCEEEEeCCCccccCccCCH---HHHHHHHh-CCCChHHHHHHHHHhhCHHHHHHHHHHHHhCCC
Confidence            33222221111111         11    122333   33333222 46888777765555433211100 000002468


Q ss_pred             CHHHHHHHHHHhc
Q psy200          436 GLKEVLGVISSVY  448 (490)
Q Consensus       436 t~~~v~~a~~~~~  448 (490)
                      +++|+..-+..+.
T Consensus       329 ~l~d~~~q~~~~~  341 (433)
T PRK10867        329 DLEDFLEQLQQMK  341 (433)
T ss_pred             CHHHHHHHHHHHH
Confidence            8999988887764

>PRK13695 putative NTPase; Provisional

Probab=97.81  E-value=0.00015  Score=65.47  Aligned_cols=75  Identities=13%  Similarity=0.260  Sum_probs=44.0

Q ss_pred             CeEEEEEecCccccccC---HHHHHHhHhCCCCCCCcEEEEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHH
Q psy200          298 KSILLILDEIDALESRK---QTILYTIFEWPSIPGSKLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILE  374 (490)
Q Consensus       298 ~~~vI~IDEid~l~~~~---~~~L~~l~~~~~~~~~~vilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~  374 (490)
                      ++-+|+|||++.+....   .+.+..+++    .+.  .+|++.+.. ....+..++..+.+.  ..+.+.+-+.+++..
T Consensus        96 ~~~~lllDE~~~~e~~~~~~~~~l~~~~~----~~~--~~i~v~h~~-~~~~~~~~i~~~~~~--~i~~~~~~~r~~~~~  166 (174)
T PRK13695         96 EADVIIIDEIGKMELKSPKFVKAVEEVLD----SEK--PVIATLHRR-SVHPFVQEIKSRPGG--RVYELTPENRDSLPF  166 (174)
T ss_pred             CCCEEEEECCCcchhhhHHHHHHHHHHHh----CCC--eEEEEECch-hhHHHHHHHhccCCc--EEEEEcchhhhhHHH
Confidence            46689999987764433   233333332    233  333345432 233445566666554  578899989888887


Q ss_pred             HHHHHHh
Q psy200          375 IISQKLK  381 (490)
Q Consensus       375 il~~~l~  381 (490)
                      .+..+++
T Consensus       167 ~~~~~~~  173 (174)
T PRK13695        167 EILNRLK  173 (174)
T ss_pred             HHHHHHh
Confidence            7766543

>TIGR00959 ffh signal recognition particle protein

Probab=97.80  E-value=0.0053  Score=63.06  Aligned_cols=219  Identities=16%  Similarity=0.165  Sum_probs=108.6

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCH-HHHHHHHHHHhcCCCC----CCcHHHHH-HHHHHH
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNA-ASVYETIVNELKLKPG----GKSERHQL-GAILKY  292 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~-~~l~~~i~~~l~~~~~----~~s~~~~~-~~l~~~  292 (490)
                      +..++++|++|+||||++..++..+....+..+..++|-..+.. .+-+..+...++.+..    +....++. +.+..+
T Consensus        99 p~vi~~vG~~GsGKTTtaakLA~~l~~~~g~kV~lV~~D~~R~~a~~QL~~~a~~~gvp~~~~~~~~~P~~i~~~al~~~  178 (428)
T TIGR00959        99 PTVILMVGLQGSGKTTTCGKLAYYLKKKQGKKVLLVACDLYRPAAIEQLKVLGQQVGVPVFALGKGQSPVEIARRALEYA  178 (428)
T ss_pred             CEEEEEECCCCCcHHHHHHHHHHHHHHhCCCeEEEEeccccchHHHHHHHHHHHhcCCceEecCCCCCHHHHHHHHHHHH
Confidence            56789999999999999999998875334567888888776543 3335555565554322    12333332 233332


Q ss_pred             HhcCCCeEEEEEecCccccccC--HHHHHHhHhCCCCCCCcEEEEEe-cCCCChhHhhhHHhhhccCCCCeeEEeCCCCH
Q psy200          293 FDTKHKSILLILDEIDALESRK--QTILYTIFEWPSIPGSKLVLVGV-ANALDLTDRMLPRLQANVTLQPTLMNFAPYSR  369 (490)
Q Consensus       293 l~~~~~~~vI~IDEid~l~~~~--~~~L~~l~~~~~~~~~~vilI~~-tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~  369 (490)
                      ..  ...-+||||=...+....  ...+..+.+..  ....+++|.- +...+... ....+..++++  .-+-+..++.
T Consensus       179 ~~--~~~DvVIIDTaGr~~~d~~l~~eL~~i~~~~--~p~e~lLVvda~tgq~~~~-~a~~f~~~v~i--~giIlTKlD~  251 (428)
T TIGR00959       179 KE--NGFDVVIVDTAGRLQIDEELMEELAAIKEIL--NPDEILLVVDAMTGQDAVN-TAKTFNERLGL--TGVVLTKLDG  251 (428)
T ss_pred             Hh--cCCCEEEEeCCCccccCHHHHHHHHHHHHhh--CCceEEEEEeccchHHHHH-HHHHHHhhCCC--CEEEEeCccC
Confidence            22  234599999998875321  12222222221  1223344333 22111111 12333334443  3566777764


Q ss_pred             HHHHHHHHHHHhcc---------CC----CCCCCHHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHhcc-ccCCccccc
Q psy200          370 EQILEIISQKLKQT---------DK----FNMFNASALQLLAGKVAAVSGDIRKAIDITNHLIDLTYDNV-KENGEVTGI  435 (490)
Q Consensus       370 ~e~~~il~~~l~~~---------~~----~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll~~a~~~a~~~~-~~~~~~~~I  435 (490)
                      +...-.+.......         +.    -..+++   +.++..+. .-||+-.++.-.+.++....... .+.......
T Consensus       252 ~~~~G~~lsi~~~~~~PI~fi~~Ge~i~dl~~f~p---~~~~~~iL-g~gD~~~l~e~~~~~~~~~~~~~~~~~~~~~~f  327 (428)
T TIGR00959       252 DARGGAALSVRSVTGKPIKFIGVGEKIDDLEPFHP---ERMASRIL-GMGDILSLVEKAQEVVDEEEAKKLAEKMKKGQF  327 (428)
T ss_pred             cccccHHHHHHHHHCcCEEEEeCCCChhhCccCCH---HHHHHHHh-CCCChHHHHHHHHHhhCHHHHHHHHHHHHhCCC
Confidence            33222222221111         11    112333   23333222 46788777765555443211100 000002468


Q ss_pred             CHHHHHHHHHHhc
Q psy200          436 GLKEVLGVISSVY  448 (490)
Q Consensus       436 t~~~v~~a~~~~~  448 (490)
                      +++|+..-+..+.
T Consensus       328 ~l~d~~~q~~~~~  340 (428)
T TIGR00959       328 DLEDFLEQLRQIK  340 (428)
T ss_pred             CHHHHHHHHHHHH
Confidence            8899888777664

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.

>cd01124 KaiC KaiC is a circadian clock protein primarily found in cyanobacteria KaiC is a RecA-like ATPase, having both Walker A and Walker B motifs

Probab=97.80  E-value=0.00017  Score=65.67  Aligned_cols=87  Identities=16%  Similarity=0.244  Sum_probs=50.1

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCC--------------C--CCCcHH-
Q psy200          221 SMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLK--------------P--GGKSER-  283 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~--------------~--~~~s~~-  283 (490)
                      .++|+|+||+|||+++..++.... ..+..++|++...  +...+...+ ..++..              .  ...+.. 
T Consensus         1 ~~li~G~~G~GKT~l~~~~~~~~~-~~g~~v~~~s~e~--~~~~~~~~~-~~~g~~~~~l~~~g~l~~~d~~~~~~s~~~   76 (187)
T cd01124           1 STLLSGGPGTGKTTFALQFLYAGL-ARGEPGLYVTLEE--SPEELIENA-ESLGWDLERLEDEGLLAIVDADPDEIGPAE   76 (187)
T ss_pred             CEEEEcCCCCCHHHHHHHHHHHHH-HCCCcEEEEECCC--CHHHHHHHH-HHcCCChHHHHhcCCeEEEecCccccchhh
Confidence            378999999999999999887754 2345677775433  444443332 222211              0  000111 


Q ss_pred             -----HHHHHHHHHHhcCCCeEEEEEecCccccc
Q psy200          284 -----HQLGAILKYFDTKHKSILLILDEIDALES  312 (490)
Q Consensus       284 -----~~~~~l~~~l~~~~~~~vI~IDEid~l~~  312 (490)
                           ++...+...... .++.+||||++..+..
T Consensus        77 ~~~~~~~~~~i~~~~~~-~~~~~lviD~~~~~~~  109 (187)
T cd01124          77 SSLRLELIQRLKDAIEE-FKAKRVVIDSVSGLLL  109 (187)
T ss_pred             hhhhHHHHHHHHHHHHH-hCCCEEEEeCcHHHhh
Confidence                 223334433332 3467999999998764

A related protein is found in archaea.

>COG5271 MDN1 AAA ATPase containing von Willebrand factor type A (vWA) domain [General function prediction only]

Probab=97.79  E-value=0.00075  Score=76.67  Aligned_cols=149  Identities=17%  Similarity=0.253  Sum_probs=105.7

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCCCCC-CcHHHHHHHHHHHHhc
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKPGG-KSERHQLGAILKYFDT  295 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~~-~s~~~~~~~l~~~l~~  295 (490)
                      ...-.++|.||..+|||+++..+++..+    .+|+.+|.....+..+.+.....    ...| .+.+  ...+.+++++
T Consensus       886 ~~~fP~LiQGpTSSGKTSMI~yla~~tg----hkfVRINNHEHTdlqeYiGTyvT----dd~G~lsFk--EGvLVeAlR~  955 (4600)
T COG5271         886 LSNFPLLIQGPTSSGKTSMILYLARETG----HKFVRINNHEHTDLQEYIGTYVT----DDDGSLSFK--EGVLVEALRR  955 (4600)
T ss_pred             hcCCcEEEecCCCCCcchHHHHHHHHhC----ccEEEecCcccchHHHHhhceee----cCCCceeee--hhHHHHHHhc
Confidence            4566899999999999999999999865    68899998887665554433221    1111 1111  1245566654


Q ss_pred             CCCeEEEEEecCccccccCHHHHHHhHhCC-----------CCCCCcEEEEEecCCCCh---hHhhhHHhhhccCCCCee
Q psy200          296 KHKSILLILDEIDALESRKQTILYTIFEWP-----------SIPGSKLVLVGVANALDL---TDRMLPRLQANVTLQPTL  361 (490)
Q Consensus       296 ~~~~~vI~IDEid~l~~~~~~~L~~l~~~~-----------~~~~~~vilI~~tn~~~~---~~~l~~~l~~R~~~~~~~  361 (490)
                      +   .-|++||+.-....-.++|.++++-.           -.++..+.+.++-|+...   ...+.++++.||-    .
T Consensus       956 G---yWIVLDELNLApTDVLEaLNRLLDDNRelfIPETqevV~PHp~F~lFATQNppg~YgGRK~LSrAFRNRFl----E 1028 (4600)
T COG5271         956 G---YWIVLDELNLAPTDVLEALNRLLDDNRELFIPETQEVVVPHPNFRLFATQNPPGGYGGRKGLSRAFRNRFL----E 1028 (4600)
T ss_pred             C---cEEEeeccccCcHHHHHHHHHhhccccceecCCcceeeccCCCeeEEeecCCCccccchHHHHHHHHhhhH----h
Confidence            3   48999999988877778888876532           124667777777774432   2345678999995    7


Q ss_pred             EEeCCCCHHHHHHHHHHHHhc
Q psy200          362 MNFAPYSREQILEIISQKLKQ  382 (490)
Q Consensus       362 i~~~pls~~e~~~il~~~l~~  382 (490)
                      ++|.....+|+..||..+|.-
T Consensus      1029 ~hFddipedEle~ILh~rc~i 1049 (4600)
T COG5271        1029 MHFDDIPEDELEEILHGRCEI 1049 (4600)
T ss_pred             hhcccCcHHHHHHHHhccCcc
Confidence            999999999999999987654

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

Probab=97.78  E-value=0.001  Score=66.47  Aligned_cols=144  Identities=14%  Similarity=0.181  Sum_probs=81.8

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhh-h--cCCceEEEEeccCCCCHHHHHHHHHHHhcCCCC-CCcHHHHHHHHHHHH
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAE-I--KDAFKTIYINCNSVRNAASVYETIVNELKLKPG-GKSERHQLGAILKYF  293 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~-~--~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~-~~s~~~~~~~l~~~l  293 (490)
                      ..+.+.|+||.|+||||++-.+|..+. .  ..++.++..++..+ ...+-+...++-|+.+.. -.+..++...+....
T Consensus       202 ~~~vi~LVGPTGVGKTTTlAKLAar~~~~~~~~kVaiITtDtYRI-GA~EQLk~Ya~im~vp~~vv~~~~el~~ai~~l~  280 (407)
T COG1419         202 QKRVIALVGPTGVGKTTTLAKLAARYVMLKKKKKVAIITTDTYRI-GAVEQLKTYADIMGVPLEVVYSPKELAEAIEALR  280 (407)
T ss_pred             cCcEEEEECCCCCcHHHHHHHHHHHHHhhccCcceEEEEeccchh-hHHHHHHHHHHHhCCceEEecCHHHHHHHHHHhh
Confidence            478999999999999999988888775 2  23445666666555 233334555555665432 135666666665543


Q ss_pred             hcCCCeEEEEEecCccccccC--HHHHHHhHhCCCCCCCcEEEEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHH
Q psy200          294 DTKHKSILLILDEIDALESRK--QTILYTIFEWPSIPGSKLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSRE  370 (490)
Q Consensus       294 ~~~~~~~vI~IDEid~l~~~~--~~~L~~l~~~~~~~~~~vilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~  370 (490)
                      ..    -+|+||=+.+=....  ...|..+++... .-...+++.+|...+....+..++. .|.+  ..+-|..+++.
T Consensus       281 ~~----d~ILVDTaGrs~~D~~~i~el~~~~~~~~-~i~~~Lvlsat~K~~dlkei~~~f~-~~~i--~~~I~TKlDET  351 (407)
T COG1419         281 DC----DVILVDTAGRSQYDKEKIEELKELIDVSH-SIEVYLVLSATTKYEDLKEIIKQFS-LFPI--DGLIFTKLDET  351 (407)
T ss_pred             cC----CEEEEeCCCCCccCHHHHHHHHHHHhccc-cceEEEEEecCcchHHHHHHHHHhc-cCCc--ceeEEEccccc
Confidence            32    499999888754332  234555555442 2223344444432222333344432 3333  35666666654

>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=97.77  E-value=0.0026  Score=62.72  Aligned_cols=51  Identities=25%  Similarity=0.345  Sum_probs=44.7

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccC--CCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNE--TSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~--~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      ++++|-++.++++..++.....+.  ..+.++|.||.|+|||++++.+.+.+.
T Consensus        61 ~~~~G~~~~i~~lV~~fk~AA~g~~~~krIl~L~GPvg~GKSsl~~~Lk~~le  113 (358)
T PF08298_consen   61 DEFYGMEETIERLVNYFKSAAQGLEERKRILLLLGPVGGGKSSLAELLKRGLE  113 (358)
T ss_pred             ccccCcHHHHHHHHHHHHHHHhccCccceEEEEECCCCCCHHHHHHHHHHHhh
Confidence            689999999999999998765433  567899999999999999999988875

PrkA possesses the A-motif of nucleotide-binding proteins and exhibits distant homology to eukaryotic protein kinases []. Note that many of these are hypothetical.

>PF00910 RNA_helicase: RNA helicase; InterPro: IPR000605 Helicases have been classified in 5 superfamilies (SF1-SF5)

Probab=97.73  E-value=9.1e-05  Score=61.03  Aligned_cols=23  Identities=39%  Similarity=0.634  Sum_probs=21.2

Q ss_pred             EEEECCCCCcHHHHHHHHHHHhh
Q psy200          222 MYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       222 ill~GppGtGKTtla~~l~~~l~  244 (490)
                      |+|+|++|+|||++++.++..+.
T Consensus         1 I~i~G~~G~GKS~l~~~l~~~l~   23 (107)
T PF00910_consen    1 IWIYGPPGIGKSTLAKELAKDLL   23 (107)
T ss_pred             CEEECCCCCCHHHHHHHHHHHHH
Confidence            57999999999999999998876

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

>TIGR01448 recD_rel helicase, putative, RecD/TraA family

Probab=97.72  E-value=0.00022  Score=78.42  Aligned_cols=111  Identities=20%  Similarity=0.268  Sum_probs=59.4

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCCCCCCcHHHHHHHH-----HHHH
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKPGGKSERHQLGAI-----LKYF  293 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l-----~~~l  293 (490)
                      .+.++|+|+|||||||+++++.+.+........+.+.++...-..    .+.+..+..  ..+...+....     ....
T Consensus       338 ~~~~iitGgpGTGKTt~l~~i~~~~~~~~~~~~v~l~ApTg~AA~----~L~e~~g~~--a~Tih~lL~~~~~~~~~~~~  411 (720)
T TIGR01448       338 HKVVILTGGPGTGKTTITRAIIELAEELGGLLPVGLAAPTGRAAK----RLGEVTGLT--ASTIHRLLGYGPDTFRHNHL  411 (720)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHHHcCCCceEEEEeCchHHHH----HHHHhcCCc--cccHHHHhhccCCccchhhh
Confidence            458999999999999999999888763322223444333321112    222222211  01111111110     0001


Q ss_pred             hcCCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEEEecC
Q psy200          294 DTKHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVAN  339 (490)
Q Consensus       294 ~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI~~tn  339 (490)
                      .......+|||||+..+...   .+..++... ..+.+++++|-.+
T Consensus       412 ~~~~~~~llIvDEaSMvd~~---~~~~Ll~~~-~~~~rlilvGD~~  453 (720)
T TIGR01448       412 EDPIDCDLLIVDESSMMDTW---LALSLLAAL-PDHARLLLVGDTD  453 (720)
T ss_pred             hccccCCEEEEeccccCCHH---HHHHHHHhC-CCCCEEEEECccc
Confidence            11123459999999999653   344444422 2567899987665

This model describes a family similar to RecD, the exodeoxyribonuclease V alpha chain of TIGR01447. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD.

>TIGR03877 thermo_KaiC_1 KaiC domain protein, Ph0284 family

Probab=97.71  E-value=0.00056  Score=64.98  Aligned_cols=113  Identities=17%  Similarity=0.224  Sum_probs=65.3

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCCC--------------------
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKP--------------------  277 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~--------------------  277 (490)
                      .+..++|+|+||+|||+++..++.+.. ..+..++|+....  ++.++.+.+. .++...                    
T Consensus        20 ~gs~~lI~G~pGsGKT~la~~~l~~~~-~~ge~~lyvs~ee--~~~~i~~~~~-~~g~~~~~~~~~g~l~~~d~~~~~~~   95 (237)
T TIGR03877        20 ERNVVLLSGGPGTGKSIFSQQFLWNGL-QMGEPGIYVALEE--HPVQVRRNMA-QFGWDVRKYEEEGKFAIVDAFTGGIG   95 (237)
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHHH-HcCCcEEEEEeeC--CHHHHHHHHH-HhCCCHHHHhhcCCEEEEeccccccc
Confidence            567899999999999999988766542 2345677776543  4555544322 221100                    


Q ss_pred             -----------CCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCH----HHHHHhHhCCCCCCCcEEEE
Q psy200          278 -----------GGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQ----TILYTIFEWPSIPGSKLVLV  335 (490)
Q Consensus       278 -----------~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~----~~L~~l~~~~~~~~~~vilI  335 (490)
                                 ...+..++...+.+.+... +.-+|+||-+..+.....    ..++.+..+....+..++++
T Consensus        96 ~~~~~~~~~~~~~~~~~~~~~~i~~~i~~~-~~~~vVIDSls~l~~~~~~~~r~~l~~l~~~lk~~~~t~llt  167 (237)
T TIGR03877        96 EAAEREKYVVKDPTDVRELIDVLRQAIRDI-NAKRVVIDSVTTLYITKPAMARSIVMQLKRVLSGLGCTSIFV  167 (237)
T ss_pred             cccccccccccCcccHHHHHHHHHHHHHHh-CCCEEEEcChhHhhcCChHHHHHHHHHHHHHHHhCCCEEEEE
Confidence                       0123455556666655442 355899999998754431    23344444333344444554

Members of this family contain a single copy of the KaiC domain (pfam06745) that occurs in two copies of the circadian clock protein kinase KaiC itself. Members occur primarily in thermophilic archaea and in Thermotoga.

>COG0464 SpoVK ATPases of the AAA+ class [Posttranslational modification, protein turnover, chaperones]

Probab=97.71  E-value=0.0028  Score=67.10  Aligned_cols=201  Identities=19%  Similarity=0.221  Sum_probs=119.4

Q ss_pred             cCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHhc
Q psy200          216 NETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFDT  295 (490)
Q Consensus       216 ~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~  295 (490)
                      .....+++++||+|+|||.+++.+++. .  ..+  ..+++.....              .+.+.+.......+..+...
T Consensus        15 ~~~~~~v~~~g~~~~~~t~~~~~~a~~-~--~~~--~~~~~~~~~~--------------~~~~~~~~~~~~~~~~a~~~   75 (494)
T COG0464          15 IEPPKGVLLHGPPGTGKTLLARALANE-G--AEF--LSINGPEILS--------------KYVGESELRLRELFEEAEKL   75 (494)
T ss_pred             CCCCCCceeeCCCCCchhHHHHHHHhc-c--Ccc--cccCcchhhh--------------hhhhHHHHHHHHHHHHHHHh
Confidence            357889999999999999999999987 2  222  3343333211              33445566677777666553


Q ss_pred             CCCeEEEEEecCccccccCHH-----------HHHHhHhCCCCCCCcEEEEEecCCCChhHhhhHHhhhccCCCCeeEEe
Q psy200          296 KHKSILLILDEIDALESRKQT-----------ILYTIFEWPSIPGSKLVLVGVANALDLTDRMLPRLQANVTLQPTLMNF  364 (490)
Q Consensus       296 ~~~~~vI~IDEid~l~~~~~~-----------~L~~l~~~~~~~~~~vilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~  364 (490)
                        .+.++++||++.+......           .+..+++-.. ... +++++.++..+..+....+. .||.   ..+.+
T Consensus        76 --~~~ii~~d~~~~~~~~~~~~~~~~~~~v~~~l~~~~d~~~-~~~-v~~~~~~~~~~~~~~a~~~~-~~~~---~~~~~  147 (494)
T COG0464          76 --APSIIFIDEIDALAPKRSSDQGEVERRVVAQLLALMDGLK-RGQ-VIVIGATNRPDGLDPAKRRP-GRFD---REIEV  147 (494)
T ss_pred             --CCCeEeechhhhcccCccccccchhhHHHHHHHHhccccc-CCc-eEEEeecCCccccChhHhCc-cccc---eeeec
Confidence              3479999999999766322           2333333223 444 88888887655444322221 2333   46777


Q ss_pred             CCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHH-HHHHHHHHHHHHHHhcc-ccCCcccccCHHHHHH
Q psy200          365 APYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIR-KAIDITNHLIDLTYDNV-KENGEVTGIGLKEVLG  442 (490)
Q Consensus       365 ~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r-~ai~ll~~a~~~a~~~~-~~~~~~~~It~~~v~~  442 (490)
                      ..+......+++........   .-.+..++.++.   ...|... .+-.++..+...+..+. ........++.+++..
T Consensus       148 ~~~~~~~~~ei~~~~~~~~~---~~~~~~~~~~a~---~~~~~~~~~~~~l~~~~~~~~~~r~~~~~~~~~~~~~~~~~~  221 (494)
T COG0464         148 NLPDEAGRLEILQIHTRLMF---LGPPGTGKTLAA---RTVGKSGADLGALAKEAALRELRRAIDLVGEYIGVTEDDFEE  221 (494)
T ss_pred             CCCCHHHHHHHHHHHHhcCC---CcccccHHHHHH---hcCCccHHHHHHHHHHHHHHHHHhhhccCcccccccHHHHHH
Confidence            77777666666665544331   112445566665   3444333 33345656655555443 1112245788999999


Q ss_pred             HHHHhcc
Q psy200          443 VISSVYC  449 (490)
Q Consensus       443 a~~~~~~  449 (490)
                      ++..+.+
T Consensus       222 ~l~~~~~  228 (494)
T COG0464         222 ALKKVLP  228 (494)
T ss_pred             HHHhcCc
Confidence            9999765

>TIGR03499 FlhF flagellar biosynthetic protein FlhF

Probab=97.70  E-value=0.00054  Score=66.80  Aligned_cols=104  Identities=20%  Similarity=0.277  Sum_probs=60.0

Q ss_pred             HHHHHHHHHHHHhhhcc--------CCCCeEEEECCCCCcHHHHHHHHHHHhhhc-CCceEEEEeccCCCCH-HHHHHHH
Q psy200          200 EVQLEGIRQFLLGHVNN--------ETSGSMYISGPPGTGKSASLNLLVSRAEIK-DAFKTIYINCNSVRNA-ASVYETI  269 (490)
Q Consensus       200 e~~~~~l~~~L~~~~~~--------~~~~~ill~GppGtGKTtla~~l~~~l~~~-~~~~~~~v~~~~~~~~-~~l~~~i  269 (490)
                      +...+.+.+.|...+..        ..++.++|+||.|+||||++..++..+... ....+..+++...... ...+..+
T Consensus       167 ~~~~~~~~~~l~~~l~~~~~~~~~~~~~~vi~~vGptGvGKTTt~~kLa~~~~~~~g~~~V~li~~D~~r~~a~eql~~~  246 (282)
T TIGR03499       167 EDAWRWLREALEKMLPVKPEEDEILEQGGVIALVGPTGVGKTTTLAKLAARFVLEHGNKKVALITTDTYRIGAVEQLKTY  246 (282)
T ss_pred             HHHHHHHHHHHHHHhccCCccccccCCCeEEEEECCCCCCHHHHHHHHHHHHHHHcCCCeEEEEECCccchhHHHHHHHH
Confidence            34445555666554421        135688899999999999999999988644 3467777776654322 2223333


Q ss_pred             HHHhcCCCC-CCcHHHHHHHHHHHHhcCCCeEEEEEecC
Q psy200          270 VNELKLKPG-GKSERHQLGAILKYFDTKHKSILLILDEI  307 (490)
Q Consensus       270 ~~~l~~~~~-~~s~~~~~~~l~~~l~~~~~~~vI~IDEi  307 (490)
                      ...++.+.. .....++.+.+..+    ...-+||||..
T Consensus       247 ~~~~~~p~~~~~~~~~l~~~l~~~----~~~d~vliDt~  281 (282)
T TIGR03499       247 AKILGVPVKVARDPKELRKALDRL----RDKDLILIDTA  281 (282)
T ss_pred             HHHhCCceeccCCHHHHHHHHHHc----cCCCEEEEeCC
Confidence            344443322 12334444444332    22458888864

>PRK09361 radB DNA repair and recombination protein RadB; Provisional

Probab=97.70  E-value=0.00025  Score=66.74  Aligned_cols=88  Identities=25%  Similarity=0.268  Sum_probs=52.7

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHH--------hcCCCCCCcHHHHH---
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNE--------LKLKPGGKSERHQL---  286 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~--------l~~~~~~~s~~~~~---  286 (490)
                      .+..++|+|+||+|||+++..++.+... .+..++|+++. ..+...+ .++...        +.... ..+..+..   
T Consensus        22 ~g~i~~i~G~~GsGKT~l~~~la~~~~~-~~~~v~yi~~e-~~~~~r~-~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~i   97 (225)
T PRK09361         22 RGTITQIYGPPGSGKTNICLQLAVEAAK-NGKKVIYIDTE-GLSPERF-KQIAGEDFEELLSNIIIFE-PSSFEEQSEAI   97 (225)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHH-CCCeEEEEECC-CCCHHHH-HHHHhhChHhHhhCeEEEe-CCCHHHHHHHH
Confidence            4568899999999999999999887642 35678888876 2233322 222221        11100 11222322   


Q ss_pred             HHHHHHHhcCCCeEEEEEecCcccc
Q psy200          287 GAILKYFDTKHKSILLILDEIDALE  311 (490)
Q Consensus       287 ~~l~~~l~~~~~~~vI~IDEid~l~  311 (490)
                      +.+...+.  .+..+||||.+..+.
T Consensus        98 ~~~~~~~~--~~~~lvVIDsi~al~  120 (225)
T PRK09361         98 RKAEKLAK--ENVGLIVLDSATSLY  120 (225)
T ss_pred             HHHHHHHH--hcccEEEEeCcHHHh
Confidence            22333332  456799999998765

>KOG3347|consensus

Probab=97.70  E-value=5.5e-05  Score=64.32  Aligned_cols=72  Identities=22%  Similarity=0.300  Sum_probs=49.2

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCC
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFDTKH  297 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~  297 (490)
                      ...+|||+|-||+||||++..++...      .+.|++++.......++...-......  -...+.+.+.|..++.+++
T Consensus         6 ~~PNILvtGTPG~GKstl~~~lae~~------~~~~i~isd~vkEn~l~~gyDE~y~c~--i~DEdkv~D~Le~~m~~Gg   77 (176)
T KOG3347|consen    6 ERPNILVTGTPGTGKSTLAERLAEKT------GLEYIEISDLVKENNLYEGYDEEYKCH--ILDEDKVLDELEPLMIEGG   77 (176)
T ss_pred             cCCCEEEeCCCCCCchhHHHHHHHHh------CCceEehhhHHhhhcchhcccccccCc--cccHHHHHHHHHHHHhcCC
Confidence            35689999999999999999999764      456677776655555555443333222  2356777788877776643

>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=97.69  E-value=0.0019  Score=64.82  Aligned_cols=167  Identities=11%  Similarity=0.147  Sum_probs=88.1

Q ss_pred             HHHHHHHHHHHHhhhc-----cCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCC-CHHHHHHHHHHHh
Q psy200          200 EVQLEGIRQFLLGHVN-----NETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVR-NAASVYETIVNEL  273 (490)
Q Consensus       200 e~~~~~l~~~L~~~~~-----~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~-~~~~l~~~i~~~l  273 (490)
                      +..++.+.+.+...+.     ...++.++|+||+|+||||++..++..+. ..+..+..+++...+ ...+-+......+
T Consensus       217 ~~~~~~l~~~l~~~l~~~~~~~~~~~vI~LVGptGvGKTTTiaKLA~~L~-~~GkkVglI~aDt~RiaAvEQLk~yae~l  295 (436)
T PRK11889        217 EEVIEYILEDMRSHFNTENVFEKEVQTIALIGPTGVGKTTTLAKMAWQFH-GKKKTVGFITTDHSRIGTVQQLQDYVKTI  295 (436)
T ss_pred             HHHHHHHHHHHHHHhccccccccCCcEEEEECCCCCcHHHHHHHHHHHHH-HcCCcEEEEecCCcchHHHHHHHHHhhhc
Confidence            3444555554433332     12347889999999999999999998875 334566667665554 1222344444455


Q ss_pred             cCCCC-CCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccC--HHHHHHhHhCCCCCCCcEEEEEecCCCChhHhhhHH
Q psy200          274 KLKPG-GKSERHQLGAILKYFDTKHKSILLILDEIDALESRK--QTILYTIFEWPSIPGSKLVLVGVANALDLTDRMLPR  350 (490)
Q Consensus       274 ~~~~~-~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~--~~~L~~l~~~~~~~~~~vilI~~tn~~~~~~~l~~~  350 (490)
                      +.+.. ..+...+.+.+..+... .+.-+||||-..+.....  ...|..++.... ....++++.++........+...
T Consensus       296 gipv~v~~d~~~L~~aL~~lk~~-~~~DvVLIDTaGRs~kd~~lm~EL~~~lk~~~-PdevlLVLsATtk~~d~~~i~~~  373 (436)
T PRK11889        296 GFEVIAVRDEAAMTRALTYFKEE-ARVDYILIDTAGKNYRASETVEEMIETMGQVE-PDYICLTLSASMKSKDMIEIITN  373 (436)
T ss_pred             CCcEEecCCHHHHHHHHHHHHhc-cCCCEEEEeCccccCcCHHHHHHHHHHHhhcC-CCeEEEEECCccChHHHHHHHHH
Confidence            54432 23456666655544321 124599999998865432  223334443221 22223334333221111222333


Q ss_pred             hhhccCCCCeeEEeCCCCHHHH
Q psy200          351 LQANVTLQPTLMNFAPYSREQI  372 (490)
Q Consensus       351 l~~R~~~~~~~i~~~pls~~e~  372 (490)
                      +.. +  +...+-|..++....
T Consensus       374 F~~-~--~idglI~TKLDET~k  392 (436)
T PRK11889        374 FKD-I--HIDGIVFTKFDETAS  392 (436)
T ss_pred             hcC-C--CCCEEEEEcccCCCC
Confidence            332 2  335677887776543

>TIGR02768 TraA_Ti Ti-type conjugative transfer relaxase TraA

Probab=97.69  E-value=0.00025  Score=78.19  Aligned_cols=110  Identities=25%  Similarity=0.240  Sum_probs=58.9

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCC
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFDTKHK  298 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~  298 (490)
                      .+.++|.|++||||||+++.+...+.. .++.++.+ ++.. ...   ..+....+..  ..+...+...+.........
T Consensus       368 ~~~~il~G~aGTGKTtll~~i~~~~~~-~g~~V~~~-ApTg-~Aa---~~L~~~~g~~--a~Ti~~~~~~~~~~~~~~~~  439 (744)
T TIGR02768       368 GDIAVVVGRAGTGKSTMLKAAREAWEA-AGYRVIGA-ALSG-KAA---EGLQAESGIE--SRTLASLEYAWANGRDLLSD  439 (744)
T ss_pred             CCEEEEEecCCCCHHHHHHHHHHHHHh-CCCeEEEE-eCcH-HHH---HHHHhccCCc--eeeHHHHHhhhccCcccCCC
Confidence            468899999999999999999877652 24444443 2211 111   1111111211  11222221111110011134


Q ss_pred             eEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEEEecC
Q psy200          299 SILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVAN  339 (490)
Q Consensus       299 ~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI~~tn  339 (490)
                      ..+|||||+-.+...   .+..++......+++++++|-.+
T Consensus       440 ~~llIvDEasMv~~~---~~~~Ll~~~~~~~~kliLVGD~~  477 (744)
T TIGR02768       440 KDVLVIDEAGMVGSR---QMARVLKEAEEAGAKVVLVGDPE  477 (744)
T ss_pred             CcEEEEECcccCCHH---HHHHHHHHHHhcCCEEEEECChH
Confidence            569999999998654   33444443333578899987443

This protein contains domains distinctive of a single strand exonuclease (N-terminus, MobA/MobL, pfam03389) as well as a helicase domain (central region, homologous to the corresponding region of the F-type relaxase TraI, TIGR02760). This protein likely fills the same role as TraI(F), nicking (at the oriT site) and unwinding the coiled plasmid prior to conjugative transfer.

>PLN02674 adenylate kinase

Probab=97.69  E-value=0.00064  Score=64.32  Aligned_cols=27  Identities=22%  Similarity=0.493  Sum_probs=23.6

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      ....++|.|+||+||+|+++.+++.++
T Consensus        30 ~~~~i~l~G~PGsGKgT~a~~La~~~~   56 (244)
T PLN02674         30 PDKRLILIGPPGSGKGTQSPIIKDEYC   56 (244)
T ss_pred             cCceEEEECCCCCCHHHHHHHHHHHcC
Confidence            356789999999999999999998853

>TIGR01425 SRP54_euk signal recognition particle protein SRP54

Probab=97.68  E-value=0.0086  Score=61.27  Aligned_cols=219  Identities=13%  Similarity=0.170  Sum_probs=108.9

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCC-HHHHHHHHHHHhcCCCCC----CcHHH-HHHHHHH
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRN-AASVYETIVNELKLKPGG----KSERH-QLGAILK  291 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~-~~~l~~~i~~~l~~~~~~----~s~~~-~~~~l~~  291 (490)
                      .+..++|+|++|+||||++..++..+. ..++.+..++|-..+. ..+.+..+...++.+...    ..... ..+.+..
T Consensus        99 ~~~vi~lvG~~GvGKTTtaaKLA~~l~-~~G~kV~lV~~D~~R~aA~eQLk~~a~~~~vp~~~~~~~~dp~~i~~~~l~~  177 (429)
T TIGR01425        99 KQNVIMFVGLQGSGKTTTCTKLAYYYQ-RKGFKPCLVCADTFRAGAFDQLKQNATKARIPFYGSYTESDPVKIASEGVEK  177 (429)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHH-HCCCCEEEEcCcccchhHHHHHHHHhhccCCeEEeecCCCCHHHHHHHHHHH
Confidence            356889999999999999999998875 3356777787766653 223334455555543221    12222 2233443


Q ss_pred             HHhcCCCeEEEEEecCccccccCHHHHHHhHhCC-CCCCCcEEEEEec-CCCChhHhhhHHhhhccCCCCeeEEeCCCCH
Q psy200          292 YFDTKHKSILLILDEIDALESRKQTILYTIFEWP-SIPGSKLVLVGVA-NALDLTDRMLPRLQANVTLQPTLMNFAPYSR  369 (490)
Q Consensus       292 ~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~-~~~~~~vilI~~t-n~~~~~~~l~~~l~~R~~~~~~~i~~~pls~  369 (490)
                      +..  ...-+||||=...+... ...+..+.... ......++++..+ .-.+..+ ....+...+++  ..+-|..++.
T Consensus       178 ~~~--~~~DvViIDTaGr~~~d-~~lm~El~~i~~~~~p~e~lLVlda~~Gq~a~~-~a~~F~~~~~~--~g~IlTKlD~  251 (429)
T TIGR01425       178 FKK--ENFDIIIVDTSGRHKQE-DSLFEEMLQVAEAIQPDNIIFVMDGSIGQAAEA-QAKAFKDSVDV--GSVIITKLDG  251 (429)
T ss_pred             HHh--CCCCEEEEECCCCCcch-HHHHHHHHHHhhhcCCcEEEEEeccccChhHHH-HHHHHHhccCC--cEEEEECccC
Confidence            332  23459999998876432 22333332221 1122234444332 2212211 23444443333  4677888876


Q ss_pred             HHHHH-HHHHHHhc-c-------CC----CCCCCHH-HHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHhcc-ccCCcccc
Q psy200          370 EQILE-IISQKLKQ-T-------DK----FNMFNAS-ALQLLAGKVAAVSGDIRKAIDITNHLIDLTYDNV-KENGEVTG  434 (490)
Q Consensus       370 ~e~~~-il~~~l~~-~-------~~----~~~~~~~-~i~~i~~~i~~~~Gd~r~ai~ll~~a~~~a~~~~-~~~~~~~~  434 (490)
                      +...- +|.-.... .       +.    -..|+++ .+..|     ..-||+..++.-.+.++....... .+......
T Consensus       252 ~argG~aLs~~~~t~~PI~fig~Ge~v~Dle~f~p~~~~~ri-----lgmgDi~~L~ek~~~~~~~~~~~~~~~k~~~~~  326 (429)
T TIGR01425       252 HAKGGGALSAVAATKSPIIFIGTGEHIDDFEIFKTQPFISKL-----LGMGDIEGLIDKVQDLKLDDNEKALIEKLKEGT  326 (429)
T ss_pred             CCCccHHhhhHHHHCCCeEEEcCCCChhhcCcCChHHHHHHH-----hcCCCcHHHHHHHHHhhhHHHHHHHHHHHHhCC
Confidence            53321 11111100 0       11    1123332 22222     246888877775555543321100 00001347


Q ss_pred             cCHHHHHHHHHHhc
Q psy200          435 IGLKEVLGVISSVY  448 (490)
Q Consensus       435 It~~~v~~a~~~~~  448 (490)
                      .+++|+..-+..+.
T Consensus       327 f~l~D~~~q~~~i~  340 (429)
T TIGR01425       327 FTLRDMYEQFQNLL  340 (429)
T ss_pred             CCHHHHHHHHHHHH
Confidence            88999988777764

This model represents examples from the eukaryotic cytosol of the signal recognition particle protein component, SRP54. This GTP-binding protein is a component of the eukaryotic signal recognition particle, along with several other protein subunits and a 7S RNA. Some species, including Arabidopsis, have several closely related forms. The extreme C-terminal region is glycine-rich and lower in complexity, poorly conserved between species, and excluded from this model.

>TIGR01618 phage_P_loop phage nucleotide-binding protein

Probab=97.67  E-value=8.1e-05  Score=69.22  Aligned_cols=23  Identities=35%  Similarity=0.625  Sum_probs=20.4

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHH
Q psy200          218 TSGSMYISGPPGTGKSASLNLLV  240 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~  240 (490)
                      .+..++|||+||+||||+|+.+.
T Consensus        11 ~~~~~liyG~~G~GKtt~a~~~~   33 (220)
T TIGR01618        11 IPNMYLIYGKPGTGKTSTIKYLP   33 (220)
T ss_pred             CCcEEEEECCCCCCHHHHHHhcC
Confidence            35679999999999999999885

This model represents an uncharacterized family of proteins from a number of phage of Gram-positive bacteria. This protein contains a P-loop motif, G/A-X-X-G-X-G-K-T near its amino end. The function of this protein is unknown.

>PRK11823 DNA repair protein RadA; Provisional

Probab=97.67  E-value=0.00038  Score=72.19  Aligned_cols=86  Identities=23%  Similarity=0.350  Sum_probs=53.8

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCCCC------CCcHHHHHHHHHH
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKPG------GKSERHQLGAILK  291 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~------~~s~~~~~~~l~~  291 (490)
                      .+..++|+|+||+|||+++..++..+. ..+..++|++...  +..++... +..++....      ......+.+    
T Consensus        79 ~Gs~~lI~G~pG~GKTtL~lq~a~~~a-~~g~~vlYvs~Ee--s~~qi~~r-a~rlg~~~~~l~~~~e~~l~~i~~----  150 (446)
T PRK11823         79 PGSVVLIGGDPGIGKSTLLLQVAARLA-AAGGKVLYVSGEE--SASQIKLR-AERLGLPSDNLYLLAETNLEAILA----  150 (446)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHHH-hcCCeEEEEEccc--cHHHHHHH-HHHcCCChhcEEEeCCCCHHHHHH----
Confidence            456889999999999999999998775 2345788887543  34444322 344443111      112333332    


Q ss_pred             HHhcCCCeEEEEEecCccccc
Q psy200          292 YFDTKHKSILLILDEIDALES  312 (490)
Q Consensus       292 ~l~~~~~~~vI~IDEid~l~~  312 (490)
                      .+.. .++.+||||+++.+..
T Consensus       151 ~i~~-~~~~lVVIDSIq~l~~  170 (446)
T PRK11823        151 TIEE-EKPDLVVIDSIQTMYS  170 (446)
T ss_pred             HHHh-hCCCEEEEechhhhcc
Confidence            2322 3567999999998864

>cd01121 Sms Sms (bacterial radA) DNA repair protein

Probab=97.66  E-value=0.00015  Score=73.14  Aligned_cols=112  Identities=19%  Similarity=0.290  Sum_probs=64.3

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCCCC------CCcHHHHHHHHHH
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKPG------GKSERHQLGAILK  291 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~------~~s~~~~~~~l~~  291 (490)
                      .+..++|+|+||+|||+++..++..+.. .+..++|++...  +..++.. -...++....      ....+.+.+    
T Consensus        81 ~GslvLI~G~pG~GKStLllq~a~~~a~-~g~~VlYvs~EE--s~~qi~~-Ra~rlg~~~~~l~l~~e~~le~I~~----  152 (372)
T cd01121          81 PGSVILIGGDPGIGKSTLLLQVAARLAK-RGGKVLYVSGEE--SPEQIKL-RADRLGISTENLYLLAETNLEDILA----  152 (372)
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHHHHh-cCCeEEEEECCc--CHHHHHH-HHHHcCCCcccEEEEccCcHHHHHH----
Confidence            4568999999999999999999987753 234778887543  3333322 2334443211      112233333    


Q ss_pred             HHhcCCCeEEEEEecCccccccC-----------HHHHHHhHhCCCCCCCcEEEEEec
Q psy200          292 YFDTKHKSILLILDEIDALESRK-----------QTILYTIFEWPSIPGSKLVLVGVA  338 (490)
Q Consensus       292 ~l~~~~~~~vI~IDEid~l~~~~-----------~~~L~~l~~~~~~~~~~vilI~~t  338 (490)
                      .+.. .++.+||||+++.+....           .+.+..+.++....+..+++++-.
T Consensus       153 ~i~~-~~~~lVVIDSIq~l~~~~~~~~~g~~~qvr~~~~~L~~lak~~~itvilvghv  209 (372)
T cd01121         153 SIEE-LKPDLVIIDSIQTVYSSELTSAPGSVSQVRECTAELMRFAKERNIPIFIVGHV  209 (372)
T ss_pred             HHHh-cCCcEEEEcchHHhhccccccCCCCHHHHHHHHHHHHHHHHHcCCeEEEEeec
Confidence            3322 357799999999885321           122333444433345566666543

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.

>PF07034 ORC3_N: Origin recognition complex (ORC) subunit 3 N-terminus; InterPro: IPR020795 The Origin Recognition Complex (ORC) is a six-subunit ATP-dependent DNA-binding complex encoded in yeast by ORC1-6 []

Probab=97.65  E-value=0.0062  Score=60.75  Aligned_cols=220  Identities=13%  Similarity=0.158  Sum_probs=140.9

Q ss_pred             HHHHHHHHHHHHhhhccC---------------CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHH
Q psy200          200 EVQLEGIRQFLLGHVNNE---------------TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAAS  264 (490)
Q Consensus       200 e~~~~~l~~~L~~~~~~~---------------~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~  264 (490)
                      .+.+++|.+|++......               -+..+++.|..=..=..+...+...+....+..++.++...+.+.+.
T Consensus        55 ~~~f~~l~~Fi~~~~~~~~~~~~~~~~~~~~~~IPtA~lltGvN~~dh~~~F~~L~~~L~~~~~~~vv~L~S~dc~~lk~  134 (330)
T PF07034_consen   55 SKLFDDLVDFIRNSHSSDESSARDWASQMNSREIPTALLLTGVNIPDHDLLFEQLSERLQSSVGPYVVRLNSKDCSNLKS  134 (330)
T ss_pred             HHHHHHHHHHHHhhcCccccccccccccccccccchHHHHhCCCCccHHHHHHHHHHHHHhCCCcEEEEEecccchHHHH
Confidence            566677777777654321               22356778988888888999999988765566788888888888899


Q ss_pred             HHHHHHHHhcCCCCCC----------------cHHHHHHHHHHH------------Hh---cCCCeEEEEEecCcccccc
Q psy200          265 VYETIVNELKLKPGGK----------------SERHQLGAILKY------------FD---TKHKSILLILDEIDALESR  313 (490)
Q Consensus       265 l~~~i~~~l~~~~~~~----------------s~~~~~~~l~~~------------l~---~~~~~~vI~IDEid~l~~~  313 (490)
                      .+..|+.++.....+.                +...+.......            ..   ....++||+|+|++.+...
T Consensus       135 ~lk~iv~ql~~~~~~~~~~~~~~~~~~~~~~yd~~~L~~wy~~~~~~~~~~~~~~~~~~~~~~~~~lVIi~eD~EsF~~~  214 (330)
T PF07034_consen  135 ALKSIVRQLMSDKSDVDEDEEEEEKGQRRLNYDMDILAAWYQNNTKKNDSPSKQKNFSSSRDKSPPLVIIFEDFESFDSQ  214 (330)
T ss_pred             HHHHHHHHHHhcccccccccchhhcccCcCCCCHHHHHHHHHhhhccccchhhhcccccccccCCCEEEEEcccccCCHH
Confidence            9999998885322111                233333333310            00   1135899999999999764


Q ss_pred             CHHHHHHhHhCCCCCCCcE-EEEEecCCCChhHhhhH-HhhhccCCCCeeEEeCCCCHH-HHHHHHHHHHhccCCCCCCC
Q psy200          314 KQTILYTIFEWPSIPGSKL-VLVGVANALDLTDRMLP-RLQANVTLQPTLMNFAPYSRE-QILEIISQKLKQTDKFNMFN  390 (490)
Q Consensus       314 ~~~~L~~l~~~~~~~~~~v-ilI~~tn~~~~~~~l~~-~l~~R~~~~~~~i~~~pls~~-e~~~il~~~l~~~~~~~~~~  390 (490)
                      -..-|..++.. .....++ +++|+++..+.....++ ...+++.    .-.|.-.+.. -+..++...+-.......+.
T Consensus       215 VL~dlI~ils~-~~~~lP~vli~GiaTs~~~~~~~Lp~~~~~~L~----~~~F~~~~~~~~l~~v~~~~l~~~~~~~~l~  289 (330)
T PF07034_consen  215 VLQDLILILSS-YLDRLPFVLIFGIATSVEAFHSRLPRSTLSLLR----IKKFQLQSSSEILERVLEKVLLSPDFPFKLG  289 (330)
T ss_pred             HHHHHHHHHHh-ccCCcCEEEEEecCCChHHHHhhCCHHHHhhcC----ceEEEeCChHHHHHHHHHHHhcCCCCCceEC
Confidence            33323333321 2234445 45566666555555443 5555554    3345555544 45556666655544456788


Q ss_pred             HHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHh
Q psy200          391 ASALQLLAGKVAAVSGDIRKAIDITNHLIDLTYD  424 (490)
Q Consensus       391 ~~~i~~i~~~i~~~~Gd~r~ai~ll~~a~~~a~~  424 (490)
                      +..++.|..........+...+..++.|++....
T Consensus       290 ~~~~~~L~~~f~~~~~Sv~~fi~~lk~~~m~HF~  323 (330)
T PF07034_consen  290 PRVLQFLLDRFLDHDFSVDSFISGLKYAYMEHFY  323 (330)
T ss_pred             HHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHhc
Confidence            9999999998888888999999888888765543

ORC is a central component for eukaryotic DNA replication, and binds chromatin at replication origins throughout the cell cycle []. ORC directs DNA replication throughout the genome and is required for its initiation [, , ]. ORC bound at replication origins serves as the foundation for assembly of the pre-replicative complex (pre-RC), which includes Cdc6, Tah11 (aka Cdt1), and the Mcm2-7 complex [, , ]. Pre-RC assembly during G1 is required for replication licensing of chromosomes prior to DNA synthesis during S phase [, , ]. Cell cycle-regulated phosphorylation of Orc2, Orc6, Cdc6, and MCM by the cyclin-dependent protein kinase Cdc28 regulates initiation of DNA replication, including blocking reinitiation in G2/M phase [, , , ]. In yeast, ORC also plays a role in the establishment of silencing at the mating-type loci Hidden MAT Left (HML) and Hidden MAT Right (HMR) [, , ]. ORC participates in the assembly of transcriptionally silent chromatin at HML and HMR by recruiting the Sir1 silencing protein to the HML and HMR silencers [, , ]. Both Orc1 and Orc5 bind ATP, though only Orc1 has ATPase activity []. The binding of ATP by Orc1 is required for ORC binding to DNA and is essential for cell viability []. The ATPase activity of Orc1 is involved in formation of the pre-RC [, , ]. ATP binding by Orc5 is crucial for the stability of ORC as a whole. Only the Orc1-5 subunits are required for origin binding; Orc6 is essential for maintenance of pre-RCs once formed []. Interactions within ORC suggest that Orc2-3-6 may form a core complex []. ORC homologues have been found in various eukaryotes, including fission yeast, insects, amphibians, and humans []. ; GO: 0003677 DNA binding, 0006260 DNA replication, 0005664 nuclear origin of replication recognition complex

>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=97.65  E-value=0.0024  Score=57.41  Aligned_cols=88  Identities=18%  Similarity=0.223  Sum_probs=52.4

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCC-HHHHHHHHHHHhcCC----CCCCcHHHHH-HHHHHHHh
Q psy200          221 SMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRN-AASVYETIVNELKLK----PGGKSERHQL-GAILKYFD  294 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~-~~~l~~~i~~~l~~~----~~~~s~~~~~-~~l~~~l~  294 (490)
                      .++++|++|+|||+++..++..+... +..++.++|..... ....+..+...++.+    .......++. +.+.....
T Consensus         2 ~~~~~G~~G~GKTt~~~~la~~~~~~-g~~v~~i~~D~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   80 (173)
T cd03115           2 VILLVGLQGVGKTTTAAKLALYLKKK-GKKVLLVAADTYRPAAIEQLRVLGEQVGVPVFEEGEGKDPVSIAKRAIEHARE   80 (173)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHC-CCcEEEEEcCCCChHHHHHHHHhcccCCeEEEecCCCCCHHHHHHHHHHHHHh
Confidence            47899999999999999999887533 45778888776542 233344444444321    1112233322 33333232


Q ss_pred             cCCCeEEEEEecCcccc
Q psy200          295 TKHKSILLILDEIDALE  311 (490)
Q Consensus       295 ~~~~~~vI~IDEid~l~  311 (490)
                        ....+||||......
T Consensus        81 --~~~d~viiDt~g~~~   95 (173)
T cd03115          81 --ENFDVVIVDTAGRLQ   95 (173)
T ss_pred             --CCCCEEEEECcccch
Confidence              234477799988764

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.

>KOG0477|consensus

Probab=97.64  E-value=0.00064  Score=70.37  Aligned_cols=50  Identities=24%  Similarity=0.284  Sum_probs=38.2

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccC--------CCCeEEEECCCCCcHHHHHHHHHHHh
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNE--------TSGSMYISGPPGTGKSASLNLLVSRA  243 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~--------~~~~ill~GppGtGKTtla~~l~~~l  243 (490)
                      ..++|++..+..+.-.|-..+...        ..-++||.|.|||||+-+++++.+-.
T Consensus       449 PsIyGh~~VK~AvAlaLfGGv~kn~~~khkvRGDinvLL~GDPGTaKSQFLKY~eK~s  506 (854)
T KOG0477|consen  449 PSIYGHEDVKRAVALALFGGVPKNPGGKHKVRGDINVLLLGDPGTAKSQFLKYAEKTS  506 (854)
T ss_pred             chhhchHHHHHHHHHHHhcCCccCCCCCceeccceeEEEecCCCccHHHHHHHHHhcC
Confidence            779999998888877775433222        22379999999999999999987653

>cd03281 ABC_MSH5_euk MutS5 homolog in eukaryotes

Probab=97.64  E-value=7e-05  Score=69.85  Aligned_cols=23  Identities=35%  Similarity=0.524  Sum_probs=20.9

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHH
Q psy200          219 SGSMYISGPPGTGKSASLNLLVS  241 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~  241 (490)
                      .+.++|+||.|+||||+++.++.
T Consensus        29 ~~~~~itGpNg~GKStlLk~i~~   51 (213)
T cd03281          29 PSIMVITGPNSSGKSVYLKQVAL   51 (213)
T ss_pred             ceEEEEECCCCCChHHHHHHHHH
Confidence            37899999999999999999984

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

>cd01131 PilT Pilus retraction ATPase PilT

Probab=97.63  E-value=0.00012  Score=67.44  Aligned_cols=83  Identities=16%  Similarity=0.257  Sum_probs=45.6

Q ss_pred             CeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCe
Q psy200          220 GSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFDTKHKS  299 (490)
Q Consensus       220 ~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~  299 (490)
                      +.++|+||+|+||||++++++..+.......++.+.......... ...+   +.....+.....+.+.+..++..  .+
T Consensus         2 GlilI~GptGSGKTTll~~ll~~~~~~~~~~i~t~e~~~E~~~~~-~~~~---i~q~~vg~~~~~~~~~i~~aLr~--~p   75 (198)
T cd01131           2 GLVLVTGPTGSGKSTTLAAMIDYINKNKTHHILTIEDPIEFVHES-KRSL---INQREVGLDTLSFENALKAALRQ--DP   75 (198)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHhhhcCCcEEEEEcCCccccccC-ccce---eeecccCCCccCHHHHHHHHhcC--Cc
Confidence            578999999999999999999887533223333332211000000 0000   00011122223455556666653  46


Q ss_pred             EEEEEecCc
Q psy200          300 ILLILDEID  308 (490)
Q Consensus       300 ~vI~IDEid  308 (490)
                      -+|++||+-
T Consensus        76 d~ii~gEir   84 (198)
T cd01131          76 DVILVGEMR   84 (198)
T ss_pred             CEEEEcCCC
Confidence            799999984

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.

>KOG2383|consensus

Probab=97.62  E-value=8.2e-05  Score=73.22  Aligned_cols=113  Identities=19%  Similarity=0.291  Sum_probs=65.8

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHH-------hcCCCCCCcHH---HHH
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNE-------LKLKPGGKSER---HQL  286 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~-------l~~~~~~~s~~---~~~  286 (490)
                      +.+++++|||..|||||+|...++..+..  ..+--.+      -..+++..+...       .+....+.+..   +..
T Consensus       112 ~~PkGlYlYG~VGcGKTmLMDlFy~~~~~--i~rkqRv------HFh~fM~~VH~r~H~~k~~~~~~~~~~a~~~~~Dpl  183 (467)
T KOG2383|consen  112 GPPKGLYLYGSVGCGKTMLMDLFYDALPP--IWRKQRV------HFHGFMLSVHKRMHELKQEQGAEKPGYAKSWEIDPL  183 (467)
T ss_pred             CCCceEEEecccCcchhHHHHHHhhcCCc--hhhhhhh------hHHHHHHHHHHHHHHHHHhccccCccccccccCCcc
Confidence            35789999999999999999999876531  0000011      234454444333       22211221111   223


Q ss_pred             HHHHHHHhcCCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEEEecCCC
Q psy200          287 GAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVANAL  341 (490)
Q Consensus       287 ~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI~~tn~~  341 (490)
                      ..+...+..  ..+||-+||++--.-.+.-+|..+|....  .-.+++++++|+.
T Consensus       184 ~~vA~eIa~--ea~lLCFDEfQVTDVADAmiL~rLf~~Lf--~~GvVlvATSNR~  234 (467)
T KOG2383|consen  184 PVVADEIAE--EAILLCFDEFQVTDVADAMILKRLFEHLF--KNGVVLVATSNRA  234 (467)
T ss_pred             HHHHHHHhh--hceeeeechhhhhhHHHHHHHHHHHHHHH--hCCeEEEEeCCCC
Confidence            333333332  25699999999876655556677766432  2268888888853

>PRK12724 flagellar biosynthesis regulator FlhF; Provisional

Probab=97.62  E-value=0.0024  Score=64.77  Aligned_cols=146  Identities=11%  Similarity=0.138  Sum_probs=76.6

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHH-HHHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCC
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAA-SVYETIVNELKLKPGGKSERHQLGAILKYFDTKH  297 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~-~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~  297 (490)
                      +..++|+||+|+||||++..++..+....+..+..+++...+... ..+...+..++.+..  ....+... ...+.. .
T Consensus       223 ~~vi~lvGptGvGKTTtaaKLA~~~~~~~G~~V~Lit~Dt~R~aA~eQLk~yAe~lgvp~~--~~~~~~~l-~~~l~~-~  298 (432)
T PRK12724        223 RKVVFFVGPTGSGKTTSIAKLAAKYFLHMGKSVSLYTTDNYRIAAIEQLKRYADTMGMPFY--PVKDIKKF-KETLAR-D  298 (432)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHhcCCeEEEecccchhhhHHHHHHHHHHhcCCCee--ehHHHHHH-HHHHHh-C
Confidence            356889999999999999999986643345566777766554432 334444455554332  12223222 222322 2


Q ss_pred             CeEEEEEecCcccccc--CHHHHHHhHhCCCC--CCCcEEEEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHH
Q psy200          298 KSILLILDEIDALESR--KQTILYTIFEWPSI--PGSKLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQ  371 (490)
Q Consensus       298 ~~~vI~IDEid~l~~~--~~~~L~~l~~~~~~--~~~~vilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e  371 (490)
                      ..-+||||=.......  ..+.|..++.....  ....++|+.++...+....+...+ +.++  ...+-|..++...
T Consensus       299 ~~D~VLIDTaGr~~rd~~~l~eL~~~~~~~~~~~~~e~~LVLsAt~~~~~~~~~~~~f-~~~~--~~glIlTKLDEt~  373 (432)
T PRK12724        299 GSELILIDTAGYSHRNLEQLERMQSFYSCFGEKDSVENLLVLSSTSSYHHTLTVLKAY-ESLN--YRRILLTKLDEAD  373 (432)
T ss_pred             CCCEEEEeCCCCCccCHHHHHHHHHHHHhhcCCCCCeEEEEEeCCCCHHHHHHHHHHh-cCCC--CCEEEEEcccCCC
Confidence            3458999976654322  22334444432211  122344444444322222222332 3333  3578888887654

>TIGR02237 recomb_radB DNA repair and recombination protein RadB

Probab=97.61  E-value=0.00033  Score=65.15  Aligned_cols=90  Identities=22%  Similarity=0.295  Sum_probs=54.1

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHh----cCC---CCCCcHHHH---HH
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNEL----KLK---PGGKSERHQ---LG  287 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l----~~~---~~~~s~~~~---~~  287 (490)
                      .+..+.|+|+||+|||+++..++..... .+..++|+++.. .+...+.. +....    ...   ..-.+..+.   ..
T Consensus        11 ~g~i~~i~G~~GsGKT~l~~~~~~~~~~-~g~~v~yi~~e~-~~~~rl~~-~~~~~~~~~~~~i~~~~~~~~~~~~~~~~   87 (209)
T TIGR02237        11 RGTITQIYGPPGSGKTNICMILAVNAAR-QGKKVVYIDTEG-LSPERFKQ-IAEDRPERALSNFIVFEVFDFDEQGVAIQ   87 (209)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHh-CCCeEEEEECCC-CCHHHHHH-HHHhChHHHhcCEEEEECCCHHHHHHHHH
Confidence            4678889999999999999999877642 346789998865 34443332 22211    000   000122222   33


Q ss_pred             HHHHHHhcCCCeEEEEEecCcccc
Q psy200          288 AILKYFDTKHKSILLILDEIDALE  311 (490)
Q Consensus       288 ~l~~~l~~~~~~~vI~IDEid~l~  311 (490)
                      .+.+.+.. .++.+||||-+..+.
T Consensus        88 ~l~~~~~~-~~~~lvVIDSis~l~  110 (209)
T TIGR02237        88 KTSKFIDR-DSASLVVVDSFTALY  110 (209)
T ss_pred             HHHHHHhh-cCccEEEEeCcHHHh
Confidence            33333333 357799999999874

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

>smart00487 DEXDc DEAD-like helicases superfamily

Probab=97.60  E-value=0.00036  Score=63.29  Aligned_cols=53  Identities=13%  Similarity=0.154  Sum_probs=29.9

Q ss_pred             CeEEEECCCCCcHHH-HHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHh
Q psy200          220 GSMYISGPPGTGKSA-SLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNEL  273 (490)
Q Consensus       220 ~~ill~GppGtGKTt-la~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l  273 (490)
                      +.++|.|++|+|||+ ++..+...+.......++++ ++......+++..+...+
T Consensus        25 ~~~~i~~~~GsGKT~~~~~~~~~~~~~~~~~~~l~~-~p~~~~~~~~~~~~~~~~   78 (201)
T smart00487       25 RDVILAAPTGSGKTLAALLPALEALKRGKGKRVLVL-VPTRELAEQWAEELKKLG   78 (201)
T ss_pred             CcEEEECCCCCchhHHHHHHHHHHhcccCCCcEEEE-eCCHHHHHHHHHHHHHHh
Confidence            789999999999999 55555554432222344554 332222334444444433

>PRK12727 flagellar biosynthesis regulator FlhF; Provisional

Probab=97.60  E-value=0.0019  Score=67.20  Aligned_cols=90  Identities=16%  Similarity=0.266  Sum_probs=52.8

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcC-CceEEEEeccCCCC-HHHHHHHHHHHhcCCCCC-CcHHHHHHHHHHHHh
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKD-AFKTIYINCNSVRN-AASVYETIVNELKLKPGG-KSERHQLGAILKYFD  294 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~-~~~~~~v~~~~~~~-~~~l~~~i~~~l~~~~~~-~s~~~~~~~l~~~l~  294 (490)
                      .++.+.|+|+.|+||||++..++..+.... ...+..+++..... ..+.+......++..... .....+...+.+.  
T Consensus       349 ~G~vIaLVGPtGvGKTTtaakLAa~la~~~~gkkVaLIdtDtyRigA~EQLk~ya~iLgv~v~~a~d~~~L~~aL~~l--  426 (559)
T PRK12727        349 RGGVIALVGPTGAGKTTTIAKLAQRFAAQHAPRDVALVTTDTQRVGGREQLHSYGRQLGIAVHEADSAESLLDLLERL--  426 (559)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHHHHhcCCCceEEEecccccccHHHHHHHhhcccCceeEecCcHHHHHHHHHHh--
Confidence            467889999999999999999998764322 23455555543332 223344444444432221 2233444444332  


Q ss_pred             cCCCeEEEEEecCcccc
Q psy200          295 TKHKSILLILDEIDALE  311 (490)
Q Consensus       295 ~~~~~~vI~IDEid~l~  311 (490)
                        ...-+||||......
T Consensus       427 --~~~DLVLIDTaG~s~  441 (559)
T PRK12727        427 --RDYKLVLIDTAGMGQ  441 (559)
T ss_pred             --ccCCEEEecCCCcch
Confidence              234599999998764

>COG4088 Predicted nucleotide kinase [Nucleotide transport and metabolism]

Probab=97.59  E-value=0.00079  Score=60.68  Aligned_cols=25  Identities=24%  Similarity=0.418  Sum_probs=23.1

Q ss_pred             CeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          220 GSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       220 ~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      ..++++|.||+||||+++.+++.+.
T Consensus         2 pLiIlTGyPgsGKTtfakeLak~L~   26 (261)
T COG4088           2 PLIILTGYPGSGKTTFAKELAKELR   26 (261)
T ss_pred             ceEEEecCCCCCchHHHHHHHHHHH
Confidence            4688999999999999999999986

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

Probab=97.59  E-value=0.00081  Score=65.21  Aligned_cols=50  Identities=10%  Similarity=0.111  Sum_probs=35.7

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHH
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETI  269 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i  269 (490)
                      .+..++|.|++|+|||+++..++..+....+..++|++.-.  +..++...+
T Consensus        29 ~g~~~~i~g~~G~GKT~l~~~~~~~~~~~~g~~vl~iS~E~--~~~~~~~r~   78 (271)
T cd01122          29 KGELIILTAGTGVGKTTFLREYALDLITQHGVRVGTISLEE--PVVRTARRL   78 (271)
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHHHHHhcCceEEEEEccc--CHHHHHHHH
Confidence            56688999999999999999998876433356778876543  334444433

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

>cd00984 DnaB_C DnaB helicase C terminal domain

Probab=97.57  E-value=0.00084  Score=63.87  Aligned_cols=50  Identities=12%  Similarity=0.214  Sum_probs=36.5

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHH
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETI  269 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i  269 (490)
                      .+..++|.|+||+|||+++..++.......+..++|+++-.  +...+...+
T Consensus        12 ~G~l~lI~G~~G~GKT~~~~~~~~~~~~~~g~~vly~s~E~--~~~~~~~r~   61 (242)
T cd00984          12 PGDLIIIAARPSMGKTAFALNIAENIAKKQGKPVLFFSLEM--SKEQLLQRL   61 (242)
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHHHHHhCCCceEEEeCCC--CHHHHHHHH
Confidence            45688999999999999999998877544466778887544  344444443

The hexameric helicase DnaB unwinds the DNA duplex at the chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis.

>PHA02774 E1; Provisional

Probab=97.54  E-value=0.00071  Score=70.69  Aligned_cols=35  Identities=29%  Similarity=0.389  Sum_probs=28.0

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEec
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINC  256 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~  256 (490)
                      .++++|+||||||||+++.++++.+.   +..+.++|.
T Consensus       434 knciv~~GPP~TGKS~fa~sL~~~L~---G~vi~fvN~  468 (613)
T PHA02774        434 KNCLVIYGPPDTGKSMFCMSLIKFLK---GKVISFVNS  468 (613)
T ss_pred             ccEEEEECCCCCCHHHHHHHHHHHhC---CCEEEEEEC
Confidence            46899999999999999999999874   223455664

>PF12774 AAA_6: Hydrolytic ATP binding site of dynein motor region D1; PDB: 3VKH_A 3VKG_A 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A

Probab=97.54  E-value=0.0016  Score=61.27  Aligned_cols=69  Identities=20%  Similarity=0.265  Sum_probs=47.6

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCC
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFDTKHK  298 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~  298 (490)
                      ..+-.++||.|||||.+++.+++.++    ..++.+||....+                    ...+.+.+.-....+  
T Consensus        32 ~~~~~~~GpagtGKtetik~La~~lG----~~~~vfnc~~~~~--------------------~~~l~ril~G~~~~G--   85 (231)
T PF12774_consen   32 NLGGALSGPAGTGKTETIKDLARALG----RFVVVFNCSEQMD--------------------YQSLSRILKGLAQSG--   85 (231)
T ss_dssp             TTEEEEESSTTSSHHHHHHHHHHCTT------EEEEETTSSS---------------------HHHHHHHHHHHHHHT--
T ss_pred             CCCCCCcCCCCCCchhHHHHHHHHhC----CeEEEeccccccc--------------------HHHHHHHHHHHhhcC--
Confidence            45566899999999999999999886    5677789987633                    333444444444332  


Q ss_pred             eEEEEEecCccccccC
Q psy200          299 SILLILDEIDALESRK  314 (490)
Q Consensus       299 ~~vI~IDEid~l~~~~  314 (490)
                       .-+.+||+++|....
T Consensus        86 -aW~cfdefnrl~~~v  100 (231)
T PF12774_consen   86 -AWLCFDEFNRLSEEV  100 (231)
T ss_dssp             --EEEEETCCCSSHHH
T ss_pred             -chhhhhhhhhhhHHH
Confidence             378889999987654

>cd01123 Rad51_DMC1_radA Rad51_DMC1_radA,B

Probab=97.54  E-value=0.00047  Score=65.28  Aligned_cols=93  Identities=22%  Similarity=0.273  Sum_probs=55.7

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcC-----CceEEEEeccCCCCHHHHHHHHHHHhcCCC----------CCCcH
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKD-----AFKTIYINCNSVRNAASVYETIVNELKLKP----------GGKSE  282 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~-----~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~----------~~~s~  282 (490)
                      .+..+.|+|++|+|||+++..++.......     +..++|++.....+...+ .++...++...          ...+.
T Consensus        18 ~g~i~~i~G~~GsGKT~l~~~l~~~~~~~~~~~g~~~~viyi~~e~~~~~~rl-~~~~~~~~~~~~~~~~~i~~~~~~~~   96 (235)
T cd01123          18 TGSITEIFGEFGSGKTQLCHQLAVTVQLPIELGGLEGKAVYIDTEGTFRPERL-VQIAERFGLDPEEVLDNIYVARAYNS   96 (235)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHeeCccccCCCCccEEEEeCCCCcCHHHH-HHHHHHhccChHhHhcCEEEEecCCH
Confidence            567888999999999999999986543222     357888887664343333 22333222110          00122


Q ss_pred             HH---HHHHHHHHHhcCCCeEEEEEecCcccc
Q psy200          283 RH---QLGAILKYFDTKHKSILLILDEIDALE  311 (490)
Q Consensus       283 ~~---~~~~l~~~l~~~~~~~vI~IDEid~l~  311 (490)
                      .+   +...+...+...++..+||||-+..+.
T Consensus        97 ~~l~~~l~~l~~~l~~~~~~~liVIDSis~~~  128 (235)
T cd01123          97 DHQLQLLEELEAILIESSRIKLVIVDSVTALF  128 (235)
T ss_pred             HHHHHHHHHHHHHHhhcCCeeEEEEeCcHHHH
Confidence            23   333444445444478899999998763

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 .

>COG1485 Predicted ATPase [General function prediction only]

Probab=97.52  E-value=0.00028  Score=68.83  Aligned_cols=108  Identities=19%  Similarity=0.249  Sum_probs=66.5

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcC
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFDTK  296 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~  296 (490)
                      ...++++++|+-|.|||.|+..+++.+....+.+         .-...|+..+.+.+.... |.+  +....+...+.  
T Consensus        63 ~~~~GlYl~GgVGrGKT~LMD~Fy~~lp~~~k~R---------~HFh~FM~~vH~~l~~l~-g~~--dpl~~iA~~~~--  128 (367)
T COG1485          63 GPVRGLYLWGGVGRGKTMLMDLFYESLPGERKRR---------LHFHRFMARVHQRLHTLQ-GQT--DPLPPIADELA--  128 (367)
T ss_pred             CCCceEEEECCCCccHHHHHHHHHhhCCcccccc---------ccHHHHHHHHHHHHHHHc-CCC--CccHHHHHHHH--
Confidence            4668999999999999999999999875222111         134566766666654322 222  33333333333  


Q ss_pred             CCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEEEecCC
Q psy200          297 HKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVANA  340 (490)
Q Consensus       297 ~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI~~tn~  340 (490)
                      +...||.+||++--.-.+.-+|..|++..  -...|++++++|.
T Consensus       129 ~~~~vLCfDEF~VtDI~DAMiL~rL~~~L--f~~GV~lvaTSN~  170 (367)
T COG1485         129 AETRVLCFDEFEVTDIADAMILGRLLEAL--FARGVVLVATSNT  170 (367)
T ss_pred             hcCCEEEeeeeeecChHHHHHHHHHHHHH--HHCCcEEEEeCCC
Confidence            22449999999875544444455555432  1236888888883

>PRK15455 PrkA family serine protein kinase; Provisional

Probab=97.51  E-value=0.00013  Score=75.93  Aligned_cols=52  Identities=31%  Similarity=0.379  Sum_probs=44.3

Q ss_pred             CCCCChHHHHHHHHHHHHhhhcc--CCCCeEEEECCCCCcHHHHHHHHHHHhhh
Q psy200          194 CELPGREVQLEGIRQFLLGHVNN--ETSGSMYISGPPGTGKSASLNLLVSRAEI  245 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~--~~~~~ill~GppGtGKTtla~~l~~~l~~  245 (490)
                      ++++|.++.++++.++|...+.+  .....++|.||||+|||+|++.|++.+..
T Consensus        76 ~d~yGlee~ieriv~~l~~Aa~gl~~~~~IL~LvGPpG~GKSsLa~~la~~le~  129 (644)
T PRK15455         76 EEFYGMEEAIEQIVSYFRHAAQGLEEKKQILYLLGPVGGGKSSLAERLKSLMER  129 (644)
T ss_pred             hcccCcHHHHHHHHHHHHHHHHhcCCCCceEEEecCCCCCchHHHHHHHHHHHh
Confidence            67999999999999999655432  35678999999999999999999998863

>PRK05574 holA DNA polymerase III subunit delta; Reviewed

Probab=97.51  E-value=0.012  Score=58.94  Aligned_cols=135  Identities=22%  Similarity=0.239  Sum_probs=90.5

Q ss_pred             CeEEEEEecCcccccc-CHHHHHHhHhCCC-CCCCcEEEEEecCCCChhHhh---hHHhhhccCCCCeeEEeCCCCHHHH
Q psy200          298 KSILLILDEIDALESR-KQTILYTIFEWPS-IPGSKLVLVGVANALDLTDRM---LPRLQANVTLQPTLMNFAPYSREQI  372 (490)
Q Consensus       298 ~~~vI~IDEid~l~~~-~~~~L~~l~~~~~-~~~~~vilI~~tn~~~~~~~l---~~~l~~R~~~~~~~i~~~pls~~e~  372 (490)
                      ...+|+|++++.+... ..+.+..+.+... .....++++...+..+-...+   ...+..++    ..+.+.+++..++
T Consensus        76 ~~klvii~~~~~l~~~~~~~~l~~l~~~l~~~~~~~~~li~~~~~~~~~~k~~k~~k~~~~~~----~~~~~~~~~~~~~  151 (340)
T PRK05574         76 DRKLVELRLPEFLTGAKGEKALKRLEAYLNPLPHPDLLLIVRLPKLDKAKKKSAWFKALKKKA----VVVEAQPPKEAEL  151 (340)
T ss_pred             cCeEEEEECCCCCCchhHHHHHHHHHHhccCCCCCcEEEEEECCcCCHHHHhhHHHHHHHhCc----eEEEcCCCCHHHH
Confidence            3458889999988654 2334444544321 122345555555543333333   34454444    3789999999999


Q ss_pred             HHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHhccccCCcccccCHHHHHHHHHHhcc
Q psy200          373 LEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITNHLIDLTYDNVKENGEVTGIGLKEVLGVISSVYC  449 (490)
Q Consensus       373 ~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~~~~~~  449 (490)
                      ..++...+...  ...+++++++.+++   ..+||+..+.+-++.....+. ++       .||.++|...+.....
T Consensus       152 ~~~i~~~~~~~--g~~i~~~a~~~L~~---~~~~d~~~l~~El~KL~l~~~-~~-------~It~~~I~~~i~~~~~  215 (340)
T PRK05574        152 PQWIQQRLKQQ--GLQIDAAALQLLAE---RVEGNLLALAQELEKLALLYP-DG-------KITLEDVEEAVPDSAR  215 (340)
T ss_pred             HHHHHHHHHHc--CCCCCHHHHHHHHH---HhCchHHHHHHHHHHHHhhcC-CC-------CCCHHHHHHHHhhhhc
Confidence            99999999887  46689999999987   667889888887777665542 12       3889998888776543

>TIGR02012 tigrfam_recA protein RecA

Probab=97.49  E-value=0.00078  Score=66.29  Aligned_cols=88  Identities=14%  Similarity=0.211  Sum_probs=56.0

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCC------CCCCcHHHHHHHHHH
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLK------PGGKSERHQLGAILK  291 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~------~~~~s~~~~~~~l~~  291 (490)
                      .+..+.|+||+|+|||+|+..++.+... .+-.++|+++....+..     .+..++..      ......++....+..
T Consensus        54 ~G~iteI~G~~GsGKTtLaL~~~~~~~~-~g~~v~yId~E~~~~~~-----~a~~lGvd~~~l~v~~p~~~eq~l~~~~~  127 (321)
T TIGR02012        54 RGRIIEIYGPESSGKTTLALHAIAEAQK-AGGTAAFIDAEHALDPV-----YARKLGVDIDNLLVSQPDTGEQALEIAET  127 (321)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHH-cCCcEEEEcccchhHHH-----HHHHcCCCHHHeEEecCCCHHHHHHHHHH
Confidence            5568889999999999999888777643 34567788765543321     23333321      111234455555554


Q ss_pred             HHhcCCCeEEEEEecCccccc
Q psy200          292 YFDTKHKSILLILDEIDALES  312 (490)
Q Consensus       292 ~l~~~~~~~vI~IDEid~l~~  312 (490)
                      .+.. +...+||||-+..+..
T Consensus       128 li~~-~~~~lIVIDSv~al~~  147 (321)
T TIGR02012       128 LVRS-GAVDIIVVDSVAALVP  147 (321)
T ss_pred             Hhhc-cCCcEEEEcchhhhcc
Confidence            4433 5577999999998864

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.

>TIGR01447 recD exodeoxyribonuclease V, alpha subunit

Probab=97.49  E-value=0.0005  Score=73.57  Aligned_cols=26  Identities=35%  Similarity=0.492  Sum_probs=23.1

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      .+.++|+|+|||||||++..+...+.
T Consensus       160 ~~~~vitGgpGTGKTt~v~~ll~~l~  185 (586)
T TIGR01447       160 SNFSLITGGPGTGKTTTVARLLLALV  185 (586)
T ss_pred             CCeEEEEcCCCCCHHHHHHHHHHHHH
Confidence            46899999999999999999988764

This family describes the exodeoxyribonuclease V alpha subunit, RecD. RecD is part of a RecBCD complex. A related family in the Gram-positive bacteria separates in a phylogenetic tree, has an additional N-terminal extension of about 200 residues, and is not supported as a member of a RecBCD complex by neighboring genes. The related family is consequently described by a different model.

>TIGR03881 KaiC_arch_4 KaiC domain protein, PAE1156 family

Probab=97.49  E-value=0.002  Score=60.82  Aligned_cols=92  Identities=16%  Similarity=0.173  Sum_probs=56.4

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCC---------------------
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLK---------------------  276 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~---------------------  276 (490)
                      .+..++|+|+||+|||+++..++.+... .+..++|++...  +...+... ...++..                     
T Consensus        19 ~G~~~~i~G~~G~GKT~l~~~~~~~~~~-~g~~~~~is~e~--~~~~i~~~-~~~~g~~~~~~~~~~~l~i~d~~~~~~~   94 (229)
T TIGR03881        19 RGFFVAVTGEPGTGKTIFCLHFAYKGLR-DGDPVIYVTTEE--SRESIIRQ-AAQFGMDFEKAIEEGKLVIIDALMKEKE   94 (229)
T ss_pred             CCeEEEEECCCCCChHHHHHHHHHHHHh-cCCeEEEEEccC--CHHHHHHH-HHHhCCCHHHHhhcCCEEEEEccccccc
Confidence            5678999999999999999987765432 344677776532  33333222 1111110                     


Q ss_pred             --C--CCCcHHHHHHHHHHHHhcCC-CeEEEEEecCcccccc
Q psy200          277 --P--GGKSERHQLGAILKYFDTKH-KSILLILDEIDALESR  313 (490)
Q Consensus       277 --~--~~~s~~~~~~~l~~~l~~~~-~~~vI~IDEid~l~~~  313 (490)
                        +  .+.+..++...+.+.....+ ++.+++||.+..+...
T Consensus        95 ~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~vvIDsl~~l~~~  136 (229)
T TIGR03881        95 DEWSLRELSIEELLNKVIEAKKYLGYGHARLVIDSMSAFWLD  136 (229)
T ss_pred             cccccccCCHHHHHHHHHHHHHhhccCceEEEecCchhhhcc
Confidence              0  12345666666666655432 4568999999988543

Members of this protein family are archaeal single-domain KaiC_related proteins, homologous to the Cyanobacterial circadian clock cycle protein KaiC, an autokinase/autophosphorylase that has two copies of the domain.

>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=97.49  E-value=0.00012  Score=61.52  Aligned_cols=31  Identities=42%  Similarity=0.693  Sum_probs=25.6

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEe
Q psy200          221 SMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYIN  255 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~  255 (490)
                      .++|+|++|+||||+++.+++.++    +.++.++
T Consensus         1 vI~I~G~~gsGKST~a~~La~~~~----~~~i~~d   31 (121)
T PF13207_consen    1 VIIISGPPGSGKSTLAKELAERLG----FPVISMD   31 (121)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHT----CEEEEEH
T ss_pred             CEEEECCCCCCHHHHHHHHHHHHC----CeEEEec
Confidence            478999999999999999999875    5555543

...

>TIGR01359 UMP_CMP_kin_fam UMP-CMP kinase family

Probab=97.49  E-value=0.001  Score=60.28  Aligned_cols=24  Identities=25%  Similarity=0.530  Sum_probs=21.5

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHhh
Q psy200          221 SMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      .++|+|+||+||||+++.+++.++
T Consensus         1 ~i~i~G~pGsGKst~a~~la~~~~   24 (183)
T TIGR01359         1 VVFVLGGPGSGKGTQCAKIVENFG   24 (183)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHcC
Confidence            378999999999999999999864

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.

>PRK10875 recD exonuclease V subunit alpha; Provisional

Probab=97.49  E-value=0.00075  Score=72.44  Aligned_cols=117  Identities=17%  Similarity=0.219  Sum_probs=62.7

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHhhhcC--CceEEEEeccCCCCHHHHHHHHHHHhcCCCC--------CCcHHHHHHH
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRAEIKD--AFKTIYINCNSVRNAASVYETIVNELKLKPG--------GKSERHQLGA  288 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l~~~~--~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~--------~~s~~~~~~~  288 (490)
                      .+.++|+|+|||||||++..+...+....  ....+.+..+...-...+.+.+...+.....        ......+-.+
T Consensus       167 ~~~~vItGgpGTGKTt~v~~ll~~l~~~~~~~~~~i~l~APTgkAA~rL~e~~~~~~~~~~~~~~~~~~~~~~a~TiHrl  246 (615)
T PRK10875        167 RRISVISGGPGTGKTTTVAKLLAALIQLADGERCRIRLAAPTGKAAARLTESLGKALRQLPLTDEQKKRIPEEASTLHRL  246 (615)
T ss_pred             CCeEEEEeCCCCCHHHHHHHHHHHHHHhcCCCCcEEEEECCcHHHHHHHHHHHHhhhhccccchhhhhcCCCchHHHHHH
Confidence            56899999999999999999988764211  2234555555443344444443322211000        0011111111


Q ss_pred             HHHH-----Hhc-CCC---eEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEEEecC
Q psy200          289 ILKY-----FDT-KHK---SILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVAN  339 (490)
Q Consensus       289 l~~~-----l~~-~~~---~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI~~tn  339 (490)
                      +...     +.. ...   .-+|||||+-.+.-   ..+..+++.. ..+.++|++|-.+
T Consensus       247 Lg~~~~~~~~~~~~~~~l~~dvlIvDEaSMvd~---~lm~~ll~al-~~~~rlIlvGD~~  302 (615)
T PRK10875        247 LGAQPGSQRLRYHAGNPLHLDVLVVDEASMVDL---PMMARLIDAL-PPHARVIFLGDRD  302 (615)
T ss_pred             hCcCCCccchhhccccCCCCCeEEEChHhcccH---HHHHHHHHhc-ccCCEEEEecchh
Confidence            1110     000 111   24999999998853   4445555432 3568999998665

>PRK13889 conjugal transfer relaxase TraA; Provisional

Probab=97.48  E-value=0.00082  Score=75.49  Aligned_cols=107  Identities=24%  Similarity=0.226  Sum_probs=57.7

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHh---c
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFD---T  295 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~---~  295 (490)
                      ...++|+|.+||||||+++.+...+. ..++.++.+ ++.. ...   ..|-...     |.....+..++.....   .
T Consensus       362 ~~v~vv~G~AGTGKTT~l~~~~~~~e-~~G~~V~~~-ApTG-kAA---~~L~e~t-----Gi~a~TI~sll~~~~~~~~~  430 (988)
T PRK13889        362 RDLGVVVGYAGTGKSAMLGVAREAWE-AAGYEVRGA-ALSG-IAA---ENLEGGS-----GIASRTIASLEHGWGQGRDL  430 (988)
T ss_pred             CCeEEEEeCCCCCHHHHHHHHHHHHH-HcCCeEEEe-cCcH-HHH---HHHhhcc-----CcchhhHHHHHhhhcccccc
Confidence            34778999999999999998876654 223444433 2211 111   1111111     1111222222211111   1


Q ss_pred             CCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEEEecC
Q psy200          296 KHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVAN  339 (490)
Q Consensus       296 ~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI~~tn  339 (490)
                      .....||||||+-.+...   .+..++......+.++++||-+.
T Consensus       431 l~~~~vlIVDEASMv~~~---~m~~LL~~a~~~garvVLVGD~~  471 (988)
T PRK13889        431 LTSRDVLVIDEAGMVGTR---QLERVLSHAADAGAKVVLVGDPQ  471 (988)
T ss_pred             cccCcEEEEECcccCCHH---HHHHHHHhhhhCCCEEEEECCHH
Confidence            123469999999988654   34455544334678999998664

>PRK05800 cobU adenosylcobinamide kinase/adenosylcobinamide-phosphate guanylyltransferase; Validated

Probab=97.48  E-value=0.00045  Score=61.92  Aligned_cols=108  Identities=12%  Similarity=0.147  Sum_probs=59.0

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCCCCCC----cHHHHHHHHHHHHhcC
Q psy200          221 SMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKPGGK----SERHQLGAILKYFDTK  296 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~~~----s~~~~~~~l~~~l~~~  296 (490)
                      .++|+|++|+|||+++..++..++    ..++|+..... ...++...+..+......+.    ...++.+.+....   
T Consensus         3 ~ili~G~~~sGKS~~a~~l~~~~~----~~~~~iat~~~-~~~e~~~ri~~h~~~R~~~w~t~E~~~~l~~~i~~~~---   74 (170)
T PRK05800          3 LILVTGGARSGKSRFAERLAAQSG----LQVLYIATAQP-FDDEMAARIAHHRQRRPAHWQTVEEPLDLAELLRADA---   74 (170)
T ss_pred             EEEEECCCCccHHHHHHHHHHHcC----CCcEeCcCCCC-ChHHHHHHHHHHHhcCCCCCeEecccccHHHHHHhhc---
Confidence            689999999999999999988753    24566654443 34455555544433211111    1112333332222   


Q ss_pred             CCeEEEEEecCcccccc----C-----HHHHHHhHhCCCCCCCcEEEEE
Q psy200          297 HKSILLILDEIDALESR----K-----QTILYTIFEWPSIPGSKLVLVG  336 (490)
Q Consensus       297 ~~~~vI~IDEid~l~~~----~-----~~~L~~l~~~~~~~~~~vilI~  336 (490)
                      .+.-+|+||-+..+...    .     ...+..++++....+..+++++
T Consensus        75 ~~~~~VlID~Lt~~~~n~l~~~~~~~~~~~l~~li~~L~~~~~tvVlVs  123 (170)
T PRK05800         75 APGRCVLVDCLTTWVTNLLFEEGEEAIAAEIDALLAALQQLPAKIILVT  123 (170)
T ss_pred             CCCCEEEehhHHHHHHHHhcccchHHHHHHHHHHHHHHHcCCCCEEEEE
Confidence            22348999998877421    1     1233344444333455666663

>COG0541 Ffh Signal recognition particle GTPase [Intracellular trafficking and secretion]

Probab=97.48  E-value=0.011  Score=59.45  Aligned_cols=92  Identities=15%  Similarity=0.191  Sum_probs=64.5

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCC-CHHHHHHHHHHHhcCCCCCC----cHHHH-HHHHHH
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVR-NAASVYETIVNELKLKPGGK----SERHQ-LGAILK  291 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~-~~~~l~~~i~~~l~~~~~~~----s~~~~-~~~l~~  291 (490)
                      ++..|+++|--|+||||++-.++..+.. .+..+..+.|..++ -..+-+..+..+++.++.+.    +..++ .+.+..
T Consensus        99 ~P~vImmvGLQGsGKTTt~~KLA~~lkk-~~~kvllVaaD~~RpAA~eQL~~La~q~~v~~f~~~~~~~Pv~Iak~al~~  177 (451)
T COG0541          99 PPTVILMVGLQGSGKTTTAGKLAKYLKK-KGKKVLLVAADTYRPAAIEQLKQLAEQVGVPFFGSGTEKDPVEIAKAALEK  177 (451)
T ss_pred             CCeEEEEEeccCCChHhHHHHHHHHHHH-cCCceEEEecccCChHHHHHHHHHHHHcCCceecCCCCCCHHHHHHHHHHH
Confidence            4677999999999999999999999975 66677777777664 34556788888887765433    23333 334443


Q ss_pred             HHhcCCCeEEEEEecCccccc
Q psy200          292 YFDTKHKSILLILDEIDALES  312 (490)
Q Consensus       292 ~l~~~~~~~vI~IDEid~l~~  312 (490)
                      +...  ..-+||||=+.++.-
T Consensus       178 ak~~--~~DvvIvDTAGRl~i  196 (451)
T COG0541         178 AKEE--GYDVVIVDTAGRLHI  196 (451)
T ss_pred             HHHc--CCCEEEEeCCCcccc
Confidence            3332  245899998887753

>PRK06067 flagellar accessory protein FlaH; Validated

Probab=97.45  E-value=0.0016  Score=61.71  Aligned_cols=89  Identities=20%  Similarity=0.306  Sum_probs=56.1

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCC---------------------
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLK---------------------  276 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~---------------------  276 (490)
                      .+..++|+|++|+|||+++..++.... ..+..++|+....  +..+++..+ ..++..                     
T Consensus        24 ~g~~~~i~G~~GsGKt~l~~~~~~~~~-~~g~~~~y~~~e~--~~~~~~~~~-~~~g~~~~~~~~~g~l~i~~~~~~~~~   99 (234)
T PRK06067         24 FPSLILIEGDHGTGKSVLSQQFVYGAL-KQGKKVYVITTEN--TSKSYLKQM-ESVKIDISDFFLWGYLRIFPLNTEGFE   99 (234)
T ss_pred             CCcEEEEECCCCCChHHHHHHHHHHHH-hCCCEEEEEEcCC--CHHHHHHHH-HHCCCChhHHHhCCCceEEeccccccc
Confidence            567889999999999999999976542 2355778887643  445554432 222211                     


Q ss_pred             CCCCcHHHHHHHHHHHHhcCCCeEEEEEecCcccc
Q psy200          277 PGGKSERHQLGAILKYFDTKHKSILLILDEIDALE  311 (490)
Q Consensus       277 ~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~  311 (490)
                      +.....+.+...+.+.+.. .++.+|+||++-.+.
T Consensus       100 ~~~~~~~~ll~~l~~~i~~-~~~~~iviDs~t~~~  133 (234)
T PRK06067        100 WNSTLANKLLELIIEFIKS-KREDVIIIDSLTIFA  133 (234)
T ss_pred             cCcchHHHHHHHHHHHHHh-cCCCEEEEecHHHHH
Confidence            0112234555555555554 356699999998653

>TIGR02688 conserved hypothetical protein TIGR02688

Probab=97.45  E-value=0.00085  Score=67.69  Aligned_cols=69  Identities=22%  Similarity=0.250  Sum_probs=43.7

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCC
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFDTKH  297 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~  297 (490)
                      ...++++.||+|||||+++.++........+         ...+...++..+..                   ..+..-+
T Consensus       208 ~~~Nli~lGp~GTGKThla~~l~~~~a~~sG---------~f~T~a~Lf~~L~~-------------------~~lg~v~  259 (449)
T TIGR02688       208 PNYNLIELGPKGTGKSYIYNNLSPYVILISG---------GTITVAKLFYNIST-------------------RQIGLVG  259 (449)
T ss_pred             cCCcEEEECCCCCCHHHHHHHHhHHHHHHcC---------CcCcHHHHHHHHHH-------------------HHHhhhc
Confidence            4678999999999999999998776211111         23344555444322                   1122224


Q ss_pred             CeEEEEEecCccccccC
Q psy200          298 KSILLILDEIDALESRK  314 (490)
Q Consensus       298 ~~~vI~IDEid~l~~~~  314 (490)
                      +.-+|+|||+..+.-..
T Consensus       260 ~~DlLI~DEvgylp~~~  276 (449)
T TIGR02688       260 RWDVVAFDEVATLKFAK  276 (449)
T ss_pred             cCCEEEEEcCCCCcCCc
Confidence            45699999999975443

Members of this family are uncharacterized proteins sporadically distributed in bacteria and archaea, about 470 amino acids in length. Several members of this family appear in public databases with annotation as ATP-dependent protease La, despite the lack of similarity to families TIGR00763 (ATP-dependent protease La) or pfam02190 (ATP-dependent protease La (LON) domain). This protein is repeatedly found downstream of another uncharacterized protein of about 880 amino acids in length, described by model TIGR02687.

>PRK05973 replicative DNA helicase; Provisional

Probab=97.44  E-value=0.0015  Score=61.45  Aligned_cols=114  Identities=13%  Similarity=0.211  Sum_probs=62.5

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCCC------------CCCcHHHH
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKP------------GGKSERHQ  285 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~------------~~~s~~~~  285 (490)
                      ++..++|.|+||+|||+++..++.+... .+..++|++...  +..++...+. .++...            .......+
T Consensus        63 ~Gsl~LIaG~PG~GKT~lalqfa~~~a~-~Ge~vlyfSlEe--s~~~i~~R~~-s~g~d~~~~~~~~~~d~~d~~~~~~i  138 (237)
T PRK05973         63 PGDLVLLGARPGHGKTLLGLELAVEAMK-SGRTGVFFTLEY--TEQDVRDRLR-ALGADRAQFADLFEFDTSDAICADYI  138 (237)
T ss_pred             CCCEEEEEeCCCCCHHHHHHHHHHHHHh-cCCeEEEEEEeC--CHHHHHHHHH-HcCCChHHhccceEeecCCCCCHHHH
Confidence            5668899999999999999998876642 355677775543  4455544432 222210            01122222


Q ss_pred             HHHHHHHHhcCCCeEEEEEecCcccccc--CHH---HHHHhHhCCCCCCCcEEEEEecC
Q psy200          286 LGAILKYFDTKHKSILLILDEIDALESR--KQT---ILYTIFEWPSIPGSKLVLVGVAN  339 (490)
Q Consensus       286 ~~~l~~~l~~~~~~~vI~IDEid~l~~~--~~~---~L~~l~~~~~~~~~~vilI~~tn  339 (490)
                      ...+.   .. .+.-+||||-++.+...  ..+   .+..+..+....+..+++++-.+
T Consensus       139 i~~l~---~~-~~~~lVVIDsLq~l~~~~~~~el~~~~~~Lk~~Ak~~gitvIl~sQl~  193 (237)
T PRK05973        139 IARLA---SA-PRGTLVVIDYLQLLDQRREKPDLSVQVRALKSFARERGLIIVFISQID  193 (237)
T ss_pred             HHHHH---Hh-hCCCEEEEEcHHHHhhcccchhHHHHHHHHHHHHHhCCCeEEEEecCc
Confidence            22222   21 23459999999988533  111   22223333333455666655444

>PRK14532 adenylate kinase; Provisional

Probab=97.44  E-value=0.0017  Score=59.15  Aligned_cols=24  Identities=29%  Similarity=0.569  Sum_probs=21.6

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHhh
Q psy200          221 SMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      .++|.|+||+||||+++.+++.++
T Consensus         2 ~i~~~G~pGsGKsT~a~~la~~~g   25 (188)
T PRK14532          2 NLILFGPPAAGKGTQAKRLVEERG   25 (188)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHcC
Confidence            488999999999999999998864

>TIGR03878 thermo_KaiC_2 KaiC domain protein, AF_0795 family

Probab=97.43  E-value=0.0015  Score=62.91  Aligned_cols=39  Identities=15%  Similarity=0.265  Sum_probs=29.7

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEecc
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCN  257 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~  257 (490)
                      .+..++|+|+||+|||+++..++.+... .+..++|+..-
T Consensus        35 ~gs~~lI~G~pGtGKT~l~~qf~~~~a~-~Ge~vlyis~E   73 (259)
T TIGR03878        35 AYSVINITGVSDTGKSLMVEQFAVTQAS-RGNPVLFVTVE   73 (259)
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHHHHh-CCCcEEEEEec
Confidence            5678899999999999999998776432 34566777654

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

>PTZ00494 tuzin-like protein; Provisional

Probab=97.41  E-value=0.005  Score=62.04  Aligned_cols=169  Identities=14%  Similarity=0.163  Sum_probs=100.3

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHh
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNEL  273 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l  273 (490)
                      ..++.|+.+-..+.+.|.+. ....+++++|+|..|+||+++.+......    +...++++.-..   ++-++.+...|
T Consensus       371 ~~~V~R~~eE~~vRqvL~ql-d~aHPRIvV~TG~~GcGKSslcRsAvrkE----~~paV~VDVRg~---EDtLrsVVKAL  442 (664)
T PTZ00494        371 AFEVRREDEEALVRSVLTQM-APSHPRIVALAGGSGGGRCVPCRRAVRVE----GVALVHVDVGGT---EDTLRSVVRAL  442 (664)
T ss_pred             ccccchhhHHHHHHHHHhhc-cCCCCcEEEEecCCCCCchHHHHHHHHHc----CCCeEEEEecCC---cchHHHHHHHh
Confidence            45899999888888888764 44578899999999999999999887764    366677765443   44567777778


Q ss_pred             cCCCCCCcHHHHHHHHHHHHhc-----CCC-e-EEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEEEecCCCChhHh
Q psy200          274 KLKPGGKSERHQLGAILKYFDT-----KHK-S-ILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVANALDLTDR  346 (490)
Q Consensus       274 ~~~~~~~s~~~~~~~l~~~l~~-----~~~-~-~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI~~tn~~~~~~~  346 (490)
                      +.+.. +.-.++.+++.++..+     .++ | +|+-|-|-..|..--.+.+.-.   ....-+.+++-..-..+.+..-
T Consensus       443 gV~nv-e~CGDlLdFI~ea~~~A~~~~~g~~P~lVlkLREGssL~RVYnE~vaLa---cDrRlCHvv~EVplESLT~~n~  518 (664)
T PTZ00494        443 GVSNV-EVCGDLLGFVEEAMRGATVKASDGVPFLVMRLREGSDLGRVYGEVVSLV---SDCQACHIVLAVPMKALTPLNV  518 (664)
T ss_pred             CCCCh-hhhccHHHHHHHHHHHHHHhcCCCCCEEEEEeccCCcHHHHHHHHHHHH---ccchhheeeeechHhhhchhhc
Confidence            77554 2233455555554422     233 2 3444556665543222222111   1112233333211111111222


Q ss_pred             hhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhc
Q psy200          347 MLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQ  382 (490)
Q Consensus       347 l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~  382 (490)
                      .+|    |++    .+.+++++..+.+++.++.+.-
T Consensus       519 ~LP----RLD----Fy~VPnFSr~QAf~YtqH~lDa  546 (664)
T PTZ00494        519 SSR----RLD----FYCIPPFSRRQAFAYAEHTLDA  546 (664)
T ss_pred             cCc----cce----eEecCCcCHHHHHHHHhcccch
Confidence            233    443    6888999999999998877644

>PF04851 ResIII: Type III restriction enzyme, res subunit; InterPro: IPR006935 This entry represents a domain found in the N terminus of several proteins, including helicases, the R subunit (HsdR) of type I restriction endonucleases (3

Probab=97.41  E-value=0.0025  Score=57.30  Aligned_cols=47  Identities=17%  Similarity=0.263  Sum_probs=32.8

Q ss_pred             HHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEE
Q psy200          201 VQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYI  254 (490)
Q Consensus       201 ~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v  254 (490)
                      +.++.+...+..   ....+.++|.+|+|+|||.++-.++.++..    .++++
T Consensus        10 ~ai~~i~~~~~~---~~~~~~~ll~~~tGsGKT~~~~~~~~~l~~----~~l~~   56 (184)
T PF04851_consen   10 EAIARIINSLEN---KKEERRVLLNAPTGSGKTIIALALILELAR----KVLIV   56 (184)
T ss_dssp             HHHHHHHHHHHT---TSGCSEEEEEESTTSSHHHHHHHHHHHHHC----EEEEE
T ss_pred             HHHHHHHHHHHh---cCCCCCEEEEECCCCCcChhhhhhhhcccc----ceeEe
Confidence            444444444432   124789999999999999999988887752    55555

1.21.3 from EC), the Res subunit of type III endonucleases (3.1.21.5 from EC), and the B subunit of excinuclease ABC (uvrB) [, , ].; GO: 0003677 DNA binding, 0005524 ATP binding, 0016787 hydrolase activity; PDB: 2Y3T_B 2W74_B 2FWR_A 2FZ4_A 3UWX_B 3H1T_A 3B6E_A 2FDC_A 1D9Z_A 1T5L_B ....

>PRK14723 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=97.40  E-value=0.0048  Score=67.24  Aligned_cols=91  Identities=19%  Similarity=0.227  Sum_probs=58.5

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHhhhcC-CceEEEEeccCCC-CHHHHHHHHHHHhcCCCC-CCcHHHHHHHHHHHHhc
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRAEIKD-AFKTIYINCNSVR-NAASVYETIVNELKLKPG-GKSERHQLGAILKYFDT  295 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l~~~~-~~~~~~v~~~~~~-~~~~l~~~i~~~l~~~~~-~~s~~~~~~~l~~~l~~  295 (490)
                      +..++|+||.|+||||++..++..+.... ...+..+.+.... ...+-+..+.+.++.+.. ..+..++.+.+.+..  
T Consensus       185 g~Vi~lVGpnGvGKTTTiaKLA~~~~~~~G~kkV~lit~Dt~RigA~eQL~~~a~~~gvpv~~~~~~~~l~~al~~~~--  262 (767)
T PRK14723        185 GGVLALVGPTGVGKTTTTAKLAARCVAREGADQLALLTTDSFRIGALEQLRIYGRILGVPVHAVKDAADLRFALAALG--  262 (767)
T ss_pred             CeEEEEECCCCCcHHHHHHHHHhhHHHHcCCCeEEEecCcccchHHHHHHHHHHHhCCCCccccCCHHHHHHHHHHhc--
Confidence            56889999999999999999998774222 2355555555443 233445666666665432 235566665555432  


Q ss_pred             CCCeEEEEEecCcccccc
Q psy200          296 KHKSILLILDEIDALESR  313 (490)
Q Consensus       296 ~~~~~vI~IDEid~l~~~  313 (490)
                        ..-+||||=.......
T Consensus       263 --~~D~VLIDTAGRs~~d  278 (767)
T PRK14723        263 --DKHLVLIDTVGMSQRD  278 (767)
T ss_pred             --CCCEEEEeCCCCCccC
Confidence              2349999999876543

>PRK00279 adk adenylate kinase; Reviewed

Probab=97.39  E-value=0.00055  Score=63.96  Aligned_cols=24  Identities=25%  Similarity=0.653  Sum_probs=21.7

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHhh
Q psy200          221 SMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      .|+|+|+||+||||+++.+++.++
T Consensus         2 ~I~v~G~pGsGKsT~a~~la~~~~   25 (215)
T PRK00279          2 RLILLGPPGAGKGTQAKFIAEKYG   25 (215)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhC
Confidence            488999999999999999998864

>cd00983 recA RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response

Probab=97.38  E-value=0.0013  Score=64.92  Aligned_cols=88  Identities=15%  Similarity=0.197  Sum_probs=56.8

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCC------CCCCcHHHHHHHHHH
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLK------PGGKSERHQLGAILK  291 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~------~~~~s~~~~~~~l~~  291 (490)
                      .+..+.|+||+|+|||+|+-.++.+... .+-.++|+++....++     ..+..++..      ....+.++....+..
T Consensus        54 ~G~iteI~Gp~GsGKTtLal~~~~~~~~-~g~~~vyId~E~~~~~-----~~a~~lGvd~~~l~v~~p~~~eq~l~i~~~  127 (325)
T cd00983          54 KGRIIEIYGPESSGKTTLALHAIAEAQK-LGGTVAFIDAEHALDP-----VYAKKLGVDLDNLLISQPDTGEQALEIADS  127 (325)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHH-cCCCEEEECccccHHH-----HHHHHcCCCHHHheecCCCCHHHHHHHHHH
Confidence            4568889999999999999998877643 2346778876554333     223333321      111245555665555


Q ss_pred             HHhcCCCeEEEEEecCccccc
Q psy200          292 YFDTKHKSILLILDEIDALES  312 (490)
Q Consensus       292 ~l~~~~~~~vI~IDEid~l~~  312 (490)
                      .+.. +...+||||-+-.+..
T Consensus       128 li~s-~~~~lIVIDSvaal~~  147 (325)
T cd00983         128 LVRS-GAVDLIVVDSVAALVP  147 (325)
T ss_pred             HHhc-cCCCEEEEcchHhhcc
Confidence            4443 5677999999998864

RecA couples ATP hydrolysis to DNA strand exchange.

>KOG0481|consensus

Probab=97.36  E-value=0.0036  Score=63.66  Aligned_cols=156  Identities=18%  Similarity=0.254  Sum_probs=86.4

Q ss_pred             CcchHHHhhcCCCCCCChHHHHHHHHHHHHhhhc--------cCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEE
Q psy200          182 DKPKVEEKAKDSCELPGREVQLEGIRQFLLGHVN--------NETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIY  253 (490)
Q Consensus       182 ~~~~~~~~~l~~~~lvgre~~~~~l~~~L~~~~~--------~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~  253 (490)
                      +.|........ ..++|+++..+.+...|-..-.        -...-++||.|.|||-|+-|++.+-+-..     .-+|
T Consensus       320 d~Ye~is~sIA-PSIfG~~DiKkAiaClLFgGsrK~LpDg~~lRGDINVLLLGDPgtAKSQlLKFvEkvsP-----IaVY  393 (729)
T KOG0481|consen  320 DVYERISKSIA-PSIFGHEDIKKAIACLLFGGSRKRLPDGVTLRGDINVLLLGDPGTAKSQLLKFVEKVSP-----IAVY  393 (729)
T ss_pred             cHHHHHhhccC-chhcCchhHHHHHHHHhhcCccccCCCcceeccceeEEEecCCchhHHHHHHHHHhcCc-----eEEE
Confidence            45665554444 7899999999888887753211        11334799999999999999998844321     2234


Q ss_pred             EeccCCCCHHHHHHHHHHHhcCCCCCCcHHHHHHHHHH----HHhcCCCeEEEEEecCccccccCHHHHHHhHhCCC---
Q psy200          254 INCNSVRNAASVYETIVNELKLKPGGKSERHQLGAILK----YFDTKHKSILLILDEIDALESRKQTILYTIFEWPS---  326 (490)
Q Consensus       254 v~~~~~~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~----~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~---  326 (490)
                      .++-.- +...+...+.++   +    .   -++++.+    .+..+|   |+.|||||.|...+.-++...|+-..   
T Consensus       394 TSGKGS-SAAGLTASV~RD---~----~---tReFylEGGAMVLADgG---VvCIDEFDKMre~DRVAIHEAMEQQTISI  459 (729)
T KOG0481|consen  394 TSGKGS-SAAGLTASVIRD---P----S---TREFYLEGGAMVLADGG---VVCIDEFDKMREDDRVAIHEAMEQQTISI  459 (729)
T ss_pred             ecCCCc-ccccceeeEEec---C----C---cceEEEecceEEEecCC---EEEeehhhccCchhhhHHHHHHHhhhHHH
Confidence            332211 111110000000   0    0   0011100    011122   89999999998887666655554221   


Q ss_pred             -------CCCCcEEEEEecCCC----Ch------hHhhhHHhhhccCC
Q psy200          327 -------IPGSKLVLVGVANAL----DL------TDRMLPRLQANVTL  357 (490)
Q Consensus       327 -------~~~~~vilI~~tn~~----~~------~~~l~~~l~~R~~~  357 (490)
                             .-+++.-|++++|..    |.      .-.+.+.+.+||.+
T Consensus       460 AKAGITT~LNSRtSVLAAANpvfGRyDd~Kt~~dNIDf~~TILSRFDm  507 (729)
T KOG0481|consen  460 AKAGITTTLNSRTSVLAAANPVFGRYDDTKTGEDNIDFMPTILSRFDM  507 (729)
T ss_pred             hhhcceeeecchhhhhhhcCCccccccccCCcccccchhhhHhhhccE
Confidence                   235667777777722    11      11246788899985

>COG4608 AppF ABC-type oligopeptide transport system, ATPase component [Amino acid transport and metabolism]

Probab=97.35  E-value=0.0013  Score=62.30  Aligned_cols=115  Identities=15%  Similarity=0.175  Sum_probs=65.8

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCC-----HHHHHHHHHHHhcCCC-------CCCcHHH
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRN-----AASVYETIVNELKLKP-------GGKSERH  284 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~-----~~~l~~~i~~~l~~~~-------~~~s~~~  284 (490)
                      ..+..+.|+|+.||||||+++.+..-..  +...-+++.......     ....+.+++..++...       +..+..+
T Consensus        37 ~~ge~~glVGESG~GKSTlgr~i~~L~~--pt~G~i~f~g~~i~~~~~~~~~~~v~elL~~Vgl~~~~~~ryPhelSGGQ  114 (268)
T COG4608          37 KEGETLGLVGESGCGKSTLGRLILGLEE--PTSGEILFEGKDITKLSKEERRERVLELLEKVGLPEEFLYRYPHELSGGQ  114 (268)
T ss_pred             cCCCEEEEEecCCCCHHHHHHHHHcCcC--CCCceEEEcCcchhhcchhHHHHHHHHHHHHhCCCHHHhhcCCcccCchh
Confidence            4677899999999999999999988764  333445555443321     2234556666655321       0111111


Q ss_pred             -HHHHHHHHHhcCCCeEEEEEecCcccccc-CHHHHHHhH-hCCCCCCCcEEEE
Q psy200          285 -QLGAILKYFDTKHKSILLILDEIDALESR-KQTILYTIF-EWPSIPGSKLVLV  335 (490)
Q Consensus       285 -~~~~l~~~l~~~~~~~vI~IDEid~l~~~-~~~~L~~l~-~~~~~~~~~vilI  335 (490)
                       -+-.+.+++.  -+|.+|+.||.-..... .|....+++ ++....+...++|
T Consensus       115 rQRi~IARALa--l~P~liV~DEpvSaLDvSiqaqIlnLL~dlq~~~~lt~lFI  166 (268)
T COG4608         115 RQRIGIARALA--LNPKLIVADEPVSALDVSVQAQILNLLKDLQEELGLTYLFI  166 (268)
T ss_pred             hhhHHHHHHHh--hCCcEEEecCchhhcchhHHHHHHHHHHHHHHHhCCeEEEE
Confidence             2223444444  45889999999988765 333334433 2222334444554

>PRK08533 flagellar accessory protein FlaH; Reviewed

Probab=97.35  E-value=0.0018  Score=61.09  Aligned_cols=49  Identities=16%  Similarity=0.263  Sum_probs=33.5

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHH
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETI  269 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i  269 (490)
                      .+..++|+|++|+|||+++..++..+. ..+..++|+....  +..+++..+
T Consensus        23 ~g~~~~i~G~~G~GKTtl~~~~~~~~~-~~g~~~~yi~~e~--~~~~~~~~~   71 (230)
T PRK08533         23 AGSLILIEGDESTGKSILSQRLAYGFL-QNGYSVSYVSTQL--TTTEFIKQM   71 (230)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHH-hCCCcEEEEeCCC--CHHHHHHHH
Confidence            456899999999999999766655542 2346677877333  455555554

>PRK04328 hypothetical protein; Provisional

Probab=97.34  E-value=0.0033  Score=60.13  Aligned_cols=91  Identities=14%  Similarity=0.213  Sum_probs=54.4

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCC---------------C-----
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLK---------------P-----  277 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~---------------~-----  277 (490)
                      .+..++|+|+||+|||+++..++.+.. ..+...+|++...  ++..+... +..++..               .     
T Consensus        22 ~gs~ili~G~pGsGKT~l~~~fl~~~~-~~ge~~lyis~ee--~~~~i~~~-~~~~g~d~~~~~~~~~l~iid~~~~~~~   97 (249)
T PRK04328         22 ERNVVLLSGGPGTGKSIFSQQFLWNGL-QMGEPGVYVALEE--HPVQVRRN-MRQFGWDVRKYEEEGKFAIVDAFTGGIG   97 (249)
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHHHH-hcCCcEEEEEeeC--CHHHHHHH-HHHcCCCHHHHhhcCCEEEEeccccccc
Confidence            567899999999999999998776532 2345677776544  34443332 2222210               0     


Q ss_pred             -----------CCCcHHHHHHHHHHHHhcCCCeEEEEEecCcccccc
Q psy200          278 -----------GGKSERHQLGAILKYFDTKHKSILLILDEIDALESR  313 (490)
Q Consensus       278 -----------~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~  313 (490)
                                 ......++.+.+.+.++.. +..+|+||-+-.+...
T Consensus        98 ~~~~~~~~~~~~~~~~~~~~~~i~~~i~~~-~~~~vVIDSlt~l~~~  143 (249)
T PRK04328         98 SAAKREKYVVKDPDDVRELIDVLRQAIKDI-GAKRVVIDSVSTLYLT  143 (249)
T ss_pred             cccccccccccCcccHHHHHHHHHHHHHhh-CCCEEEEeChhHhhcC
Confidence                       0123344555555555442 3568999999876433

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

Probab=97.34  E-value=0.0018  Score=60.82  Aligned_cols=93  Identities=19%  Similarity=0.209  Sum_probs=57.5

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcC-----CceEEEEeccCCCCHHHHHHHHHHHhcCC----------CCCCcH
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKD-----AFKTIYINCNSVRNAASVYETIVNELKLK----------PGGKSE  282 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~-----~~~~~~v~~~~~~~~~~l~~~i~~~l~~~----------~~~~s~  282 (490)
                      .+..+.|+|++|+|||+++..++.......     +..++|++......... +..+...+...          ....+.
T Consensus        18 ~g~v~~I~G~~GsGKT~l~~~ia~~~~~~~~~~g~~~~v~yi~~e~~~~~~r-l~~~~~~~~~~~~~~~~~i~~~~~~~~   96 (226)
T cd01393          18 TGRITEIFGEFGSGKTQLCLQLAVEAQLPGELGGLEGKVVYIDTEGAFRPER-LVQLAVRFGLDPEEVLDNIYVARPYNG   96 (226)
T ss_pred             CCcEEEEeCCCCCChhHHHHHHHHHhhcccccCCCcceEEEEecCCCCCHHH-HHHHHHHhccchhhhhccEEEEeCCCH
Confidence            466888999999999999999987753222     26788888765433333 33333332211          011234


Q ss_pred             HHHHHHHHHHHh--cCCCeEEEEEecCcccc
Q psy200          283 RHQLGAILKYFD--TKHKSILLILDEIDALE  311 (490)
Q Consensus       283 ~~~~~~l~~~l~--~~~~~~vI~IDEid~l~  311 (490)
                      .++...+.....  ...+..+||||-+..+.
T Consensus        97 ~~~~~~l~~~~~~~~~~~~~lvVIDsis~l~  127 (226)
T cd01393          97 EQQLEIVEELERIMSSGRVDLVVVDSVAALF  127 (226)
T ss_pred             HHHHHHHHHHHHHhhcCCeeEEEEcCcchhh
Confidence            555555554433  13567799999998874

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.

>PRK09354 recA recombinase A; Provisional

Probab=97.33  E-value=0.002  Score=64.00  Aligned_cols=88  Identities=15%  Similarity=0.209  Sum_probs=57.6

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCC------CCCCcHHHHHHHHHH
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLK------PGGKSERHQLGAILK  291 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~------~~~~s~~~~~~~l~~  291 (490)
                      .+..+.|+||+|+|||+|+-.++..... .+-.++|++.....+.     ..+..++..      ....+.++....+..
T Consensus        59 ~G~IteI~G~~GsGKTtLal~~~~~~~~-~G~~~~yId~E~s~~~-----~~a~~lGvdld~lli~qp~~~Eq~l~i~~~  132 (349)
T PRK09354         59 RGRIVEIYGPESSGKTTLALHAIAEAQK-AGGTAAFIDAEHALDP-----VYAKKLGVDIDNLLVSQPDTGEQALEIADT  132 (349)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHH-cCCcEEEECCccchHH-----HHHHHcCCCHHHeEEecCCCHHHHHHHHHH
Confidence            4568889999999999999998877642 3456788876654443     233333321      111234555555555


Q ss_pred             HHhcCCCeEEEEEecCccccc
Q psy200          292 YFDTKHKSILLILDEIDALES  312 (490)
Q Consensus       292 ~l~~~~~~~vI~IDEid~l~~  312 (490)
                      .++. +...+||||-+-.+..
T Consensus       133 li~s-~~~~lIVIDSvaaL~~  152 (349)
T PRK09354        133 LVRS-GAVDLIVVDSVAALVP  152 (349)
T ss_pred             Hhhc-CCCCEEEEeChhhhcc
Confidence            4443 5677999999998864

>PRK08118 topology modulation protein; Reviewed

Probab=97.33  E-value=0.00074  Score=60.40  Aligned_cols=25  Identities=24%  Similarity=0.356  Sum_probs=22.7

Q ss_pred             CeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          220 GSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       220 ~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      ..|+|+|++|+||||+++.|++.++
T Consensus         2 ~rI~I~G~~GsGKSTlak~L~~~l~   26 (167)
T PRK08118          2 KKIILIGSGGSGKSTLARQLGEKLN   26 (167)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHhC
Confidence            3589999999999999999999875

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

Probab=97.33  E-value=0.0018  Score=59.25  Aligned_cols=94  Identities=18%  Similarity=0.274  Sum_probs=51.3

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhc---------CCceEEEEeccCCCCHHHHHHHHHHHhcCC------------
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIK---------DAFKTIYINCNSVRNAASVYETIVNELKLK------------  276 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~---------~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~------------  276 (490)
                      .+..++|+|++|+|||+++..++..+...         ....++|++.-..  ...+...+...+...            
T Consensus        31 ~g~l~~i~g~~g~GKT~~~~~l~~~~~~g~~~~g~~~~~~~~Vl~i~~E~~--~~~~~~rl~~~~~~~~~~~~~~~~~~~  108 (193)
T PF13481_consen   31 RGELTLIAGPPGSGKTTLALQLAAALATGRPFLGELPPRPGRVLYISLEDS--ESQIARRLRALLQDYDDDANLFFVDLS  108 (193)
T ss_dssp             TTSEEEEEECSTSSHHHHHHHHHHHHHT---TT---------EEEEESSS---HHHHHHHHHHHHTTS-HHHHHHHHHH-
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHHHHhCCccCCcccccCceEEEEeccCC--HHHHHHHHHHHhcccCCccceEEeecc
Confidence            45689999999999999999999987632         3457888876553  333333332221110            


Q ss_pred             -----------CCCCcHHHHHHHHHHHHhcCCCeEEEEEecCcccccc
Q psy200          277 -----------PGGKSERHQLGAILKYFDTKHKSILLILDEIDALESR  313 (490)
Q Consensus       277 -----------~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~  313 (490)
                                 ..+.......+.+.+.+....++.+||||-+..+...
T Consensus       109 ~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~lvviD~l~~~~~~  156 (193)
T PF13481_consen  109 NWGCIRLFEPDSGGPLLDEDLEELEAALKELYGPDLVVIDPLQSLHDG  156 (193)
T ss_dssp             -E-EE---TTS---TTSHHHHHHHHHHHTT----SEEEEE-GGGG--S
T ss_pred             ccccceeeecccccccchHHHHHHHHHHhhcCCCcEEEEcCHHHHhcC
Confidence                       0111123344455555555344779999999888764

>PRK06762 hypothetical protein; Provisional

Probab=97.33  E-value=0.0042  Score=55.37  Aligned_cols=26  Identities=27%  Similarity=0.406  Sum_probs=23.1

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      +..++|+|++|+||||+++.+++.++
T Consensus         2 ~~li~i~G~~GsGKST~A~~L~~~l~   27 (166)
T PRK06762          2 TTLIIIRGNSGSGKTTIAKQLQERLG   27 (166)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhC
Confidence            45788999999999999999998873

>PRK12726 flagellar biosynthesis regulator FlhF; Provisional

Probab=97.32  E-value=0.014  Score=58.49  Aligned_cols=92  Identities=15%  Similarity=0.153  Sum_probs=62.5

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCC-HHHHHHHHHHHhcCCC-CCCcHHHHHHHHHHHHhc
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRN-AASVYETIVNELKLKP-GGKSERHQLGAILKYFDT  295 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~-~~~l~~~i~~~l~~~~-~~~s~~~~~~~l~~~l~~  295 (490)
                      .+..++|+||.|+||||++..++..+. ..+..+..+++...+. ....|......++.+. ...+..++.+.+..+...
T Consensus       205 ~~~ii~lvGptGvGKTTt~akLA~~l~-~~g~~V~lItaDtyR~gAveQLk~yae~lgvpv~~~~dp~dL~~al~~l~~~  283 (407)
T PRK12726        205 NHRIISLIGQTGVGKTTTLVKLGWQLL-KQNRTVGFITTDTFRSGAVEQFQGYADKLDVELIVATSPAELEEAVQYMTYV  283 (407)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHH-HcCCeEEEEeCCccCccHHHHHHHHhhcCCCCEEecCCHHHHHHHHHHHHhc
Confidence            467889999999999999999998764 2345677777766654 3445666666666543 234566666666544311


Q ss_pred             CCCeEEEEEecCcccc
Q psy200          296 KHKSILLILDEIDALE  311 (490)
Q Consensus       296 ~~~~~vI~IDEid~l~  311 (490)
                       ...-+||||=.....
T Consensus       284 -~~~D~VLIDTAGr~~  298 (407)
T PRK12726        284 -NCVDHILIDTVGRNY  298 (407)
T ss_pred             -CCCCEEEEECCCCCc
Confidence             224599999998865

>TIGR01128 holA DNA polymerase III, delta subunit

Probab=97.32  E-value=0.0031  Score=62.08  Aligned_cols=131  Identities=20%  Similarity=0.180  Sum_probs=89.1

Q ss_pred             CeEEEEEecCcccccc-CHHHHHHhHhCCCCCCCcEEEEEecCCCChhHhhhHHhhh--ccCCCCeeEEeCCCCHHHHHH
Q psy200          298 KSILLILDEIDALESR-KQTILYTIFEWPSIPGSKLVLVGVANALDLTDRMLPRLQA--NVTLQPTLMNFAPYSREQILE  374 (490)
Q Consensus       298 ~~~vI~IDEid~l~~~-~~~~L~~l~~~~~~~~~~vilI~~tn~~~~~~~l~~~l~~--R~~~~~~~i~~~pls~~e~~~  374 (490)
                      ...+|+|++++.+... ..+.|..++..   .....++|..++..+....+...+..  ++    ..+.|.+++..++..
T Consensus        46 ~~kliii~~~~~~~~~~~~~~L~~~l~~---~~~~~~~i~~~~~~~~~~~~~k~~~~~~~~----~~i~~~~~~~~~~~~  118 (302)
T TIGR01128        46 ERRLVELRNPEGKPGAKGLKALEEYLAN---PPPDTLLLIEAPKLDKRKKLTKWLKALKNA----QIVECKTPKEQELPR  118 (302)
T ss_pred             CCeEEEEECCCCCCCHHHHHHHHHHHhc---CCCCEEEEEecCCCCHhHHHHHHHHHhcCe----eEEEecCCCHHHHHH
Confidence            3458999999998643 34555555543   22334444444433332332222322  54    379999999999999


Q ss_pred             HHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHhccccCCcccccCHHHHHHHHHHhc
Q psy200          375 IISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITNHLIDLTYDNVKENGEVTGIGLKEVLGVISSVY  448 (490)
Q Consensus       375 il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~~~~~  448 (490)
                      ++...+...  ...+++++++.++.   ...||++.+.+.++.....+.  +      ..|+.++|...+....
T Consensus       119 ~i~~~~~~~--g~~i~~~a~~~l~~---~~~~d~~~l~~el~KL~~~~~--~------~~It~e~I~~~~~~~~  179 (302)
T TIGR01128       119 WIQARLKKL--GLRIDPDAVQLLAE---LVEGNLLAIAQELEKLALYAP--D------GKITLEDVEEAVSDSA  179 (302)
T ss_pred             HHHHHHHHc--CCCCCHHHHHHHHH---HhCcHHHHHHHHHHHHHhhCC--C------CCCCHHHHHHHHhhhh
Confidence            999999987  46689999999987   667899999998887765532  2      2588888888776543

subunit around DNA forming a DNA sliding clamp.

>PRK06995 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=97.31  E-value=0.0058  Score=63.51  Aligned_cols=90  Identities=19%  Similarity=0.286  Sum_probs=51.3

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcC-CceEEEEeccCCC-CHHHHHHHHHHHhcCCCCC-CcHHHHHHHHHHHHh
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKD-AFKTIYINCNSVR-NAASVYETIVNELKLKPGG-KSERHQLGAILKYFD  294 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~-~~~~~~v~~~~~~-~~~~l~~~i~~~l~~~~~~-~s~~~~~~~l~~~l~  294 (490)
                      .++.++|+||.|+||||++..++..+.... ...+..+.+.... ...+-+..+...++..... ....+....+.+ + 
T Consensus       255 ~g~Vi~LvGpnGvGKTTTiaKLA~~~~~~~G~~kV~LI~~Dt~RigA~EQLr~~AeilGVpv~~~~~~~Dl~~aL~~-L-  332 (484)
T PRK06995        255 RGGVFALMGPTGVGKTTTTAKLAARCVMRHGASKVALLTTDSYRIGGHEQLRIYGKILGVPVHAVKDAADLRLALSE-L-  332 (484)
T ss_pred             CCcEEEEECCCCccHHHHHHHHHHHHHHhcCCCeEEEEeCCccchhHHHHHHHHHHHhCCCeeccCCchhHHHHHHh-c-
Confidence            356889999999999999999998874332 2355566655443 2223344444444443211 122222222221 1 


Q ss_pred             cCCCeEEEEEecCcccc
Q psy200          295 TKHKSILLILDEIDALE  311 (490)
Q Consensus       295 ~~~~~~vI~IDEid~l~  311 (490)
                        ...-+++||......
T Consensus       333 --~d~d~VLIDTaGr~~  347 (484)
T PRK06995        333 --RNKHIVLIDTIGMSQ  347 (484)
T ss_pred             --cCCCeEEeCCCCcCh
Confidence              223499999977654

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

Probab=97.30  E-value=0.00093  Score=63.72  Aligned_cols=89  Identities=18%  Similarity=0.321  Sum_probs=61.4

Q ss_pred             cCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHh-cCCCCCCcHHHHHHHHHHHHh
Q psy200          216 NETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNEL-KLKPGGKSERHQLGAILKYFD  294 (490)
Q Consensus       216 ~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l-~~~~~~~s~~~~~~~l~~~l~  294 (490)
                      ..+.+.||++||.|+||||++.++.+++.......++.+.     ++-+++..=-..| .....|.....+...|..++.
T Consensus       122 ~~~~GLILVTGpTGSGKSTTlAamId~iN~~~~~HIlTIE-----DPIE~vh~skkslI~QREvG~dT~sF~~aLraALR  196 (353)
T COG2805         122 ESPRGLILVTGPTGSGKSTTLAAMIDYINKHKAKHILTIE-----DPIEYVHESKKSLINQREVGRDTLSFANALRAALR  196 (353)
T ss_pred             hCCCceEEEeCCCCCcHHHHHHHHHHHHhccCCcceEEec-----CchHhhhcchHhhhhHHHhcccHHHHHHHHHHHhh
Confidence            3567899999999999999999999999755555666553     3433332211111 113345566777888888887


Q ss_pred             cCCCeEEEEEecCcccc
Q psy200          295 TKHKSILLILDEIDALE  311 (490)
Q Consensus       295 ~~~~~~vI~IDEid~l~  311 (490)
                      +.  |-||+|-|+-.+.
T Consensus       197 eD--PDVIlvGEmRD~E  211 (353)
T COG2805         197 ED--PDVILVGEMRDLE  211 (353)
T ss_pred             cC--CCEEEEeccccHH
Confidence            54  7799999998764

>TIGR01420 pilT_fam pilus retraction protein PilT

Probab=97.28  E-value=0.00052  Score=68.88  Aligned_cols=84  Identities=17%  Similarity=0.247  Sum_probs=47.7

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHH-HHHHHhcCCCCCCcHHHHHHHHHHHHhcC
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYE-TIVNELKLKPGGKSERHQLGAILKYFDTK  296 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~-~i~~~l~~~~~~~s~~~~~~~l~~~l~~~  296 (490)
                      ..+.++|+||+|+||||++++++..+.......++.+.-     +.++.. .....+.....+.....+.+.+..++.  
T Consensus       121 ~~g~ili~G~tGSGKTT~l~al~~~i~~~~~~~i~tiEd-----p~E~~~~~~~~~i~q~evg~~~~~~~~~l~~~lr--  193 (343)
T TIGR01420       121 PRGLILVTGPTGSGKSTTLASMIDYINKNAAGHIITIED-----PIEYVHRNKRSLINQREVGLDTLSFANALRAALR--  193 (343)
T ss_pred             cCcEEEEECCCCCCHHHHHHHHHHhhCcCCCCEEEEEcC-----ChhhhccCccceEEccccCCCCcCHHHHHHHhhc--
Confidence            467899999999999999999998875322334444421     111110 000000111112222335555555565  


Q ss_pred             CCeEEEEEecCc
Q psy200          297 HKSILLILDEID  308 (490)
Q Consensus       297 ~~~~vI~IDEid  308 (490)
                      ..|-+|++||+-
T Consensus       194 ~~pd~i~vgEir  205 (343)
T TIGR01420       194 EDPDVILIGEMR  205 (343)
T ss_pred             cCCCEEEEeCCC
Confidence            357799999995

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.

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

Probab=97.26  E-value=0.0016  Score=61.39  Aligned_cols=89  Identities=20%  Similarity=0.310  Sum_probs=55.4

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCC----------------C--C-
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLK----------------P--G-  278 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~----------------~--~-  278 (490)
                      .+..++|+|+||+|||+++..++.+.....+-.++|+....  +...+.+.+- .++..                .  . 
T Consensus        18 ~gs~~li~G~~GsGKT~l~~q~l~~~~~~~ge~vlyvs~ee--~~~~l~~~~~-s~g~d~~~~~~~g~l~~~d~~~~~~~   94 (226)
T PF06745_consen   18 KGSVVLISGPPGSGKTTLALQFLYNGLKNFGEKVLYVSFEE--PPEELIENMK-SFGWDLEEYEDSGKLKIIDAFPERIG   94 (226)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHHHHHHT--EEEEESSS---HHHHHHHHH-TTTS-HHHHHHTTSEEEEESSGGGST
T ss_pred             CCcEEEEEeCCCCCcHHHHHHHHHHhhhhcCCcEEEEEecC--CHHHHHHHHH-HcCCcHHHHhhcCCEEEEeccccccc
Confidence            66789999999999999998877554322145667776533  4444444322 22210                0  0 


Q ss_pred             --CCcHHHHHHHHHHHHhcCCCeEEEEEecCccc
Q psy200          279 --GKSERHQLGAILKYFDTKHKSILLILDEIDAL  310 (490)
Q Consensus       279 --~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l  310 (490)
                        ......+...+.+.++.. ++.+++||-+..+
T Consensus        95 ~~~~~~~~l~~~i~~~i~~~-~~~~vVIDsls~l  127 (226)
T PF06745_consen   95 WSPNDLEELLSKIREAIEEL-KPDRVVIDSLSAL  127 (226)
T ss_dssp             -TSCCHHHHHHHHHHHHHHH-TSSEEEEETHHHH
T ss_pred             ccccCHHHHHHHHHHHHHhc-CCCEEEEECHHHH
Confidence              235666777777766552 2469999999988

More than one copy is sometimes found in each protein in this entry. These include KaiC, which is one of the Kai proteins among which direct protein-protein association may be a critical process in the generation of circadian rhythms in cyanobacteria []. The circadian clock protein KaiC, is encoded in the kaiABC operon that controls circadian rhythms and may be universal in Cyanobacteria. Each member contains two copies of this domain, which is also found in other proteins. KaiC performs autophosphorylation and acts as its own transcriptional repressor. RadA/Sms is a highly conserved eubacterial protein that shares sequence similarity with both RecA strand transferase and lon protease. The RadA/Sms family are probable ATP-dependent proteases involved in both DNA repair and degradation of proteins, peptides, glycopeptides. They are classified in as non-peptidase homologues and unassigned peptidases in MEROPS peptidase family S16 (lon protease family, clan SJ). RadA/Sms is involved in recombination and recombinational repair, most likely involving the stabilisation or processing of branched DNA molecules or blocked replication forks because of its genetic redundancy with RecG and RuvABC [].; PDB: 2W0M_A 2ZTS_C 4DUG_B 3K0E_B 3K09_B 3S1A_E 3JZM_E 2GBL_B 3DVL_A 1TF7_C ....

>TIGR00416 sms DNA repair protein RadA

Probab=97.26  E-value=0.0034  Score=65.31  Aligned_cols=86  Identities=20%  Similarity=0.288  Sum_probs=52.4

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCCC------CCCcHHHHHHHHHH
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKP------GGKSERHQLGAILK  291 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~------~~~s~~~~~~~l~~  291 (490)
                      .+..++|+|+||+||||++..++..+... +..++|++...  +..++... +..++...      ......    .+..
T Consensus        93 ~GsvilI~G~pGsGKTTL~lq~a~~~a~~-g~kvlYvs~EE--s~~qi~~r-a~rlg~~~~~l~~~~e~~~~----~I~~  164 (454)
T TIGR00416        93 PGSLILIGGDPGIGKSTLLLQVACQLAKN-QMKVLYVSGEE--SLQQIKMR-AIRLGLPEPNLYVLSETNWE----QICA  164 (454)
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHHHhc-CCcEEEEECcC--CHHHHHHH-HHHcCCChHHeEEcCCCCHH----HHHH
Confidence            56788999999999999999998877532 24678886543  34443322 22333211      111222    2333


Q ss_pred             HHhcCCCeEEEEEecCccccc
Q psy200          292 YFDTKHKSILLILDEIDALES  312 (490)
Q Consensus       292 ~l~~~~~~~vI~IDEid~l~~  312 (490)
                      .+.. .++.+||||.++.+..
T Consensus       165 ~i~~-~~~~~vVIDSIq~l~~  184 (454)
T TIGR00416       165 NIEE-ENPQACVIDSIQTLYS  184 (454)
T ss_pred             HHHh-cCCcEEEEecchhhcc
Confidence            3332 3467999999998853

The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).

>PRK14528 adenylate kinase; Provisional

Probab=97.24  E-value=0.0038  Score=56.90  Aligned_cols=25  Identities=32%  Similarity=0.687  Sum_probs=22.3

Q ss_pred             CeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          220 GSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       220 ~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      ..++|.|+||+||||+++.+++.++
T Consensus         2 ~~i~i~G~pGsGKtt~a~~la~~~~   26 (186)
T PRK14528          2 KNIIFMGPPGAGKGTQAKILCERLS   26 (186)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHhC
Confidence            4689999999999999999998864

>COG0194 Gmk Guanylate kinase [Nucleotide transport and metabolism]

Probab=97.24  E-value=0.0057  Score=54.62  Aligned_cols=26  Identities=31%  Similarity=0.500  Sum_probs=23.1

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHh
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRA  243 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l  243 (490)
                      .+..++|+||+|+||+|+++++.+..
T Consensus         3 ~G~l~vlsgPSG~GKsTl~k~L~~~~   28 (191)
T COG0194           3 KGLLIVLSGPSGVGKSTLVKALLEDD   28 (191)
T ss_pred             CceEEEEECCCCCCHHHHHHHHHhhc
Confidence            46688899999999999999998875

>PRK13808 adenylate kinase; Provisional

Probab=97.24  E-value=0.0028  Score=62.54  Aligned_cols=24  Identities=33%  Similarity=0.639  Sum_probs=21.6

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHhh
Q psy200          221 SMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      .|+|+||||+||||+++.|++.++
T Consensus         2 rIiv~GpPGSGK~T~a~~LA~~yg   25 (333)
T PRK13808          2 RLILLGPPGAGKGTQAQRLVQQYG   25 (333)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhC
Confidence            488999999999999999998864

>PRK10416 signal recognition particle-docking protein FtsY; Provisional

Probab=97.23  E-value=0.04  Score=54.60  Aligned_cols=93  Identities=16%  Similarity=0.209  Sum_probs=53.7

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCH-HHHHHHHHHHhcCCC----CCCcH-HHHHHHHHH
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNA-ASVYETIVNELKLKP----GGKSE-RHQLGAILK  291 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~-~~l~~~i~~~l~~~~----~~~s~-~~~~~~l~~  291 (490)
                      .+..++|+||+|+||||++..++..+.. .+..+..+++...... .+-+.......+...    .+... ....+.+..
T Consensus       113 ~~~vi~lvGpnGsGKTTt~~kLA~~l~~-~g~~V~Li~~D~~r~~a~eql~~~a~~~~i~~~~~~~~~dpa~~v~~~l~~  191 (318)
T PRK10416        113 KPFVILVVGVNGVGKTTTIGKLAHKYKA-QGKKVLLAAGDTFRAAAIEQLQVWGERVGVPVIAQKEGADPASVAFDAIQA  191 (318)
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHHHHh-cCCeEEEEecCccchhhHHHHHHHHHHcCceEEEeCCCCCHHHHHHHHHHH
Confidence            4568889999999999999999998863 3446666665544321 111222233333221    11122 223344443


Q ss_pred             HHhcCCCeEEEEEecCcccccc
Q psy200          292 YFDTKHKSILLILDEIDALESR  313 (490)
Q Consensus       292 ~l~~~~~~~vI~IDEid~l~~~  313 (490)
                      +..  ...-+||||=...+...
T Consensus       192 ~~~--~~~D~ViIDTaGr~~~~  211 (318)
T PRK10416        192 AKA--RGIDVLIIDTAGRLHNK  211 (318)
T ss_pred             HHh--CCCCEEEEeCCCCCcCC
Confidence            333  23459999999887644

>PF08433 KTI12: Chromatin associated protein KTI12 ; InterPro: IPR013641 This is a family of chromatin associated proteins which interact with the Elongator complex, a component of the elongating form of RNA polymerase II []

Probab=97.23  E-value=0.0017  Score=62.58  Aligned_cols=81  Identities=19%  Similarity=0.266  Sum_probs=40.5

Q ss_pred             CeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcC-CC-CCCcHHHHHHHHHHHHhcC-
Q psy200          220 GSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKL-KP-GGKSERHQLGAILKYFDTK-  296 (490)
Q Consensus       220 ~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~-~~-~~~s~~~~~~~l~~~l~~~-  296 (490)
                      ..|+|+|-||+||||+++.+.+.+.. .+..++.++-.      .+.      +.. .+ ....++..+..+...+... 
T Consensus         2 pLiil~G~P~SGKTt~a~~L~~~~~~-~~~~v~~i~~~------~~~------~~~~~y~~~~~Ek~~R~~l~s~v~r~l   68 (270)
T PF08433_consen    2 PLIILCGLPCSGKTTRAKELKKYLEE-KGKEVVIISDD------SLG------IDRNDYADSKKEKEARGSLKSAVERAL   68 (270)
T ss_dssp             -EEEEE--TTSSHHHHHHHHHHHHHH-TT--EEEE-TH------HHH-------TTSSS--GGGHHHHHHHHHHHHHHHH
T ss_pred             EEEEEEcCCCCcHHHHHHHHHHHHHh-cCCEEEEEccc------ccc------cchhhhhchhhhHHHHHHHHHHHHHhh
Confidence            36889999999999999999998764 44556666411      111      000 11 1233444444444433221 


Q ss_pred             CCeEEEEEecCcccccc
Q psy200          297 HKSILLILDEIDALESR  313 (490)
Q Consensus       297 ~~~~vI~IDEid~l~~~  313 (490)
                      .+..|||+|+...+-+-
T Consensus        69 s~~~iVI~Dd~nYiKg~   85 (270)
T PF08433_consen   69 SKDTIVILDDNNYIKGM   85 (270)
T ss_dssp             TT-SEEEE-S---SHHH
T ss_pred             ccCeEEEEeCCchHHHH
Confidence            23469999999987543

The Elongator complex has histone acetyltransferase activity. ; PDB: 3ADB_B 3ADC_B 3A4M_B 3A4N_B 3AM1_A 3A4L_B 3ADD_A.

>PRK07261 topology modulation protein; Provisional

Probab=97.21  E-value=0.00097  Score=59.90  Aligned_cols=24  Identities=29%  Similarity=0.343  Sum_probs=21.5

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHhh
Q psy200          221 SMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      .++|+|++|+||||+++.++..++
T Consensus         2 ri~i~G~~GsGKSTla~~l~~~~~   25 (171)
T PRK07261          2 KIAIIGYSGSGKSTLARKLSQHYN   25 (171)
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHhC
Confidence            478999999999999999988764

>COG3854 SpoIIIAA ncharacterized protein conserved in bacteria [Function unknown]

Probab=97.20  E-value=0.0015  Score=60.04  Aligned_cols=29  Identities=24%  Similarity=0.245  Sum_probs=24.5

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHhhh
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRAEI  245 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l~~  245 (490)
                      ...-+.+|.||||+||||+++-++..+..
T Consensus       135 ~g~lntLiigpP~~GKTTlLRdiaR~~s~  163 (308)
T COG3854         135 NGWLNTLIIGPPQVGKTTLLRDIARLLSD  163 (308)
T ss_pred             cCceeeEEecCCCCChHHHHHHHHHHhhc
Confidence            34456899999999999999999998863

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

Probab=97.20  E-value=0.0022  Score=57.32  Aligned_cols=85  Identities=14%  Similarity=0.155  Sum_probs=47.6

Q ss_pred             EEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEE
Q psy200          222 MYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFDTKHKSIL  301 (490)
Q Consensus       222 ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~v  301 (490)
                      ++|+|++|+|||+++..++....    -+++|+...... ..++...|.........+....+....+.+.+....+.-+
T Consensus         2 ~li~G~~~sGKS~~a~~~~~~~~----~~~~y~at~~~~-d~em~~rI~~H~~~R~~~w~t~E~~~~l~~~l~~~~~~~~   76 (169)
T cd00544           2 ILVTGGARSGKSRFAERLAAELG----GPVTYIATAEAF-DDEMAERIARHRKRRPAHWRTIETPRDLVSALKELDPGDV   76 (169)
T ss_pred             EEEECCCCCCHHHHHHHHHHhcC----CCeEEEEccCcC-CHHHHHHHHHHHHhCCCCceEeecHHHHHHHHHhcCCCCE
Confidence            68999999999999999987622    356666544432 2344444333222112222222333333444433223448


Q ss_pred             EEEecCcccc
Q psy200          302 LILDEIDALE  311 (490)
Q Consensus       302 I~IDEid~l~  311 (490)
                      |+||-+..+.
T Consensus        77 VLIDclt~~~   86 (169)
T cd00544          77 VLIDCLTLWV   86 (169)
T ss_pred             EEEEcHhHHH
Confidence            9999987653

CobU is bifunctional cobalbumin biosynthesis enzymes which display adenosylcobinamide kinase and adenosylcobinamide phosphate guanyltransferase activity. This enzyme is a homotrimer with a propeller-like shape.

>PRK13826 Dtr system oriT relaxase; Provisional

Probab=97.20  E-value=0.0017  Score=73.40  Aligned_cols=108  Identities=20%  Similarity=0.270  Sum_probs=60.2

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHH---h
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYF---D  294 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l---~  294 (490)
                      ..+.++|.|.+||||||+++.+...+. ..++.++-+ ++..    .....|-...+...  .+...   ++...-   .
T Consensus       396 ~~r~~~v~G~AGTGKTt~l~~~~~~~e-~~G~~V~g~-ApTg----kAA~~L~e~~Gi~a--~TIas---~ll~~~~~~~  464 (1102)
T PRK13826        396 PARIAAVVGRAGAGKTTMMKAAREAWE-AAGYRVVGG-ALAG----KAAEGLEKEAGIQS--RTLSS---WELRWNQGRD  464 (1102)
T ss_pred             cCCeEEEEeCCCCCHHHHHHHHHHHHH-HcCCeEEEE-cCcH----HHHHHHHHhhCCCe--eeHHH---HHhhhccCcc
Confidence            467899999999999999999987664 234444433 1111    11122222222211  12222   211110   1


Q ss_pred             cCCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEEEecC
Q psy200          295 TKHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVAN  339 (490)
Q Consensus       295 ~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI~~tn  339 (490)
                      ......||||||+-.+......   .++......+.++++||-..
T Consensus       465 ~l~~~~vlVIDEAsMv~~~~m~---~Ll~~~~~~garvVLVGD~~  506 (1102)
T PRK13826        465 QLDNKTVFVLDEAGMVASRQMA---LFVEAVTRAGAKLVLVGDPE  506 (1102)
T ss_pred             CCCCCcEEEEECcccCCHHHHH---HHHHHHHhcCCEEEEECCHH
Confidence            1133569999999998654433   44443334578899998664

>COG1124 DppF ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]

Probab=97.20  E-value=0.0021  Score=59.66  Aligned_cols=28  Identities=32%  Similarity=0.453  Sum_probs=24.1

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      ..+..+-|+|+.|+|||||++.++-...
T Consensus        31 ~~Ge~lgivGeSGsGKSTL~r~l~Gl~~   58 (252)
T COG1124          31 ERGETLGIVGESGSGKSTLARLLAGLEK   58 (252)
T ss_pred             cCCCEEEEEcCCCCCHHHHHHHHhcccC
Confidence            4677888999999999999999987653

>PRK14531 adenylate kinase; Provisional

Probab=97.19  E-value=0.0034  Score=57.02  Aligned_cols=25  Identities=28%  Similarity=0.530  Sum_probs=22.5

Q ss_pred             CeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          220 GSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       220 ~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      ..++|+|+||+||||+++.+++.++
T Consensus         3 ~~i~i~G~pGsGKsT~~~~la~~~g   27 (183)
T PRK14531          3 QRLLFLGPPGAGKGTQAARLCAAHG   27 (183)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHhC
Confidence            3689999999999999999999864

>PRK14527 adenylate kinase; Provisional

Probab=97.19  E-value=0.0073  Score=55.23  Aligned_cols=28  Identities=25%  Similarity=0.463  Sum_probs=24.7

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      ..+..++|+|+||+||||+++.+++.++
T Consensus         4 ~~~~~i~i~G~pGsGKsT~a~~La~~~~   31 (191)
T PRK14527          4 TKNKVVIFLGPPGAGKGTQAERLAQELG   31 (191)
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHHhC
Confidence            4567899999999999999999998864

>TIGR00064 ftsY signal recognition particle-docking protein FtsY

Probab=97.18  E-value=0.026  Score=54.64  Aligned_cols=92  Identities=17%  Similarity=0.263  Sum_probs=56.0

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCH-HHHHHHHHHHhcCCC----CCCcH-HHHHHHHHH
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNA-ASVYETIVNELKLKP----GGKSE-RHQLGAILK  291 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~-~~l~~~i~~~l~~~~----~~~s~-~~~~~~l~~  291 (490)
                      .++.++++|++|+||||++..++..+. ..+..+..+++-.++.. ..-+..+....+...    .+... ....+.+..
T Consensus        71 ~~~vi~l~G~~G~GKTTt~akLA~~l~-~~g~~V~li~~D~~r~~a~~ql~~~~~~~~i~~~~~~~~~dp~~~~~~~l~~  149 (272)
T TIGR00064        71 KPNVILFVGVNGVGKTTTIAKLANKLK-KQGKSVLLAAGDTFRAAAIEQLEEWAKRLGVDVIKQKEGADPAAVAFDAIQK  149 (272)
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHHHH-hcCCEEEEEeCCCCCHHHHHHHHHHHHhCCeEEEeCCCCCCHHHHHHHHHHH
Confidence            457888999999999999999998875 33457777776655432 222333444444321    11122 222344443


Q ss_pred             HHhcCCCeEEEEEecCccccc
Q psy200          292 YFDTKHKSILLILDEIDALES  312 (490)
Q Consensus       292 ~l~~~~~~~vI~IDEid~l~~  312 (490)
                      +..  ...-+||||=...+..
T Consensus       150 ~~~--~~~D~ViIDT~G~~~~  168 (272)
T TIGR00064       150 AKA--RNIDVVLIDTAGRLQN  168 (272)
T ss_pred             HHH--CCCCEEEEeCCCCCcc
Confidence            333  2345999999988764

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.

>COG4619 ABC-type uncharacterized transport system, ATPase component [General function prediction only]

Probab=97.17  E-value=0.0055  Score=53.64  Aligned_cols=41  Identities=27%  Similarity=0.405  Sum_probs=30.3

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCC
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSV  259 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~  259 (490)
                      ..+..++|+||.|+||+|+.+.++.-..  +....+++.+-..
T Consensus        27 ~~Ge~iaitGPSG~GKStllk~va~Lis--p~~G~l~f~Ge~v   67 (223)
T COG4619          27 RAGEFIAITGPSGCGKSTLLKIVASLIS--PTSGTLLFEGEDV   67 (223)
T ss_pred             cCCceEEEeCCCCccHHHHHHHHHhccC--CCCceEEEcCccc
Confidence            3567899999999999999999998765  3334455544444

>PRK14721 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=97.17  E-value=0.018  Score=58.90  Aligned_cols=88  Identities=16%  Similarity=0.223  Sum_probs=49.2

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhc---CCceEEEEeccCCCCHHHHHHHHHHHhcCCCC-CCcHHHHHHHHHHHH
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIK---DAFKTIYINCNSVRNAASVYETIVNELKLKPG-GKSERHQLGAILKYF  293 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~---~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~-~~s~~~~~~~l~~~l  293 (490)
                      .+..+.|+|+.|+||||++..++..+...   ....++..+.... ...+.+..+..-++.+.. .....++...+.. +
T Consensus       190 ~g~vi~lvGpnG~GKTTtlakLA~~~~~~~~~~~v~~i~~d~~ri-galEQL~~~a~ilGvp~~~v~~~~dl~~al~~-l  267 (420)
T PRK14721        190 QGGVYALIGPTGVGKTTTTAKLAARAVIRHGADKVALLTTDSYRI-GGHEQLRIYGKLLGVSVRSIKDIADLQLMLHE-L  267 (420)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHHHhcCCCeEEEEecCCcch-hHHHHHHHHHHHcCCceecCCCHHHHHHHHHH-h
Confidence            45689999999999999999998764211   1223333333332 222334444555554332 1233444433333 2


Q ss_pred             hcCCCeEEEEEecCccc
Q psy200          294 DTKHKSILLILDEIDAL  310 (490)
Q Consensus       294 ~~~~~~~vI~IDEid~l  310 (490)
                         ...-+++||.....
T Consensus       268 ---~~~d~VLIDTaGrs  281 (420)
T PRK14721        268 ---RGKHMVLIDTVGMS  281 (420)
T ss_pred             ---cCCCEEEecCCCCC
Confidence               22349999997544

>PF03796 DnaB_C: DnaB-like helicase C terminal domain; InterPro: IPR007694 The hexameric helicase DnaB unwinds the DNA duplex at the Escherichia coli chromosome replication fork

Probab=97.16  E-value=0.0061  Score=58.68  Aligned_cols=93  Identities=15%  Similarity=0.206  Sum_probs=59.4

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcC----------------------
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKL----------------------  275 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~----------------------  275 (490)
                      ++..++|-|.||+|||+++..++..+....+..++|++.-.  +..+++..++..+..                      
T Consensus        18 ~g~L~vi~a~pg~GKT~~~l~ia~~~a~~~~~~vly~SlEm--~~~~l~~R~la~~s~v~~~~i~~g~l~~~e~~~~~~~   95 (259)
T PF03796_consen   18 PGELTVIAARPGVGKTAFALQIALNAALNGGYPVLYFSLEM--SEEELAARLLARLSGVPYNKIRSGDLSDEEFERLQAA   95 (259)
T ss_dssp             TT-EEEEEESTTSSHHHHHHHHHHHHHHTTSSEEEEEESSS---HHHHHHHHHHHHHTSTHHHHHCCGCHHHHHHHHHHH
T ss_pred             cCcEEEEEecccCCchHHHHHHHHHHHHhcCCeEEEEcCCC--CHHHHHHHHHHHhhcchhhhhhccccCHHHHHHHHHH
Confidence            45688899999999999999999988765557888886432  455666555544421                      


Q ss_pred             ------------CCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccc
Q psy200          276 ------------KPGGKSERHQLGAILKYFDTKHKSILLILDEIDALES  312 (490)
Q Consensus       276 ------------~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~  312 (490)
                                  .....+..++...+........+.-+||||-++.+..
T Consensus        96 ~~~l~~~~l~i~~~~~~~~~~i~~~i~~~~~~~~~~~~v~IDyl~ll~~  144 (259)
T PF03796_consen   96 AEKLSDLPLYIEDTPSLTIDDIESKIRRLKREGKKVDVVFIDYLQLLKS  144 (259)
T ss_dssp             HHHHHTSEEEEEESSS-BHHHHHHHHHHHHHHSTTEEEEEEEEGGGSBT
T ss_pred             HHHHhhCcEEEECCCCCCHHHHHHHHHHHHhhccCCCEEEechHHHhcC
Confidence                        1112344555555544333324556888888887765

Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis. ; GO: 0003678 DNA helicase activity, 0005524 ATP binding, 0006260 DNA replication; PDB: 1Q57_E 1E0K_D 1E0J_B 1CR2_A 1CR4_A 1CR1_A 1CR0_A 1MI8_A 2R6D_B 2R6C_C ....

>PRK02496 adk adenylate kinase; Provisional

Probab=97.16  E-value=0.004  Score=56.58  Aligned_cols=24  Identities=29%  Similarity=0.602  Sum_probs=21.6

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHhh
Q psy200          221 SMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      .++|.|+||+||||+++.++..++
T Consensus         3 ~i~i~G~pGsGKst~a~~la~~~~   26 (184)
T PRK02496          3 RLIFLGPPGAGKGTQAVVLAEHLH   26 (184)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhC
Confidence            478999999999999999998864

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

Probab=97.15  E-value=0.0013  Score=63.41  Aligned_cols=97  Identities=18%  Similarity=0.298  Sum_probs=54.0

Q ss_pred             hHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCCCC
Q psy200          199 REVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKPG  278 (490)
Q Consensus       199 re~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~  278 (490)
                      .+..++.|..++.     ...+.++|+|++|+||||+++++...+.. ....++.+.-........     ..++.... 
T Consensus        65 ~~~~~~~l~~~~~-----~~~GlilisG~tGSGKTT~l~all~~i~~-~~~~iitiEdp~E~~~~~-----~~q~~v~~-  132 (264)
T cd01129          65 KPENLEIFRKLLE-----KPHGIILVTGPTGSGKTTTLYSALSELNT-PEKNIITVEDPVEYQIPG-----INQVQVNE-  132 (264)
T ss_pred             CHHHHHHHHHHHh-----cCCCEEEEECCCCCcHHHHHHHHHhhhCC-CCCeEEEECCCceecCCC-----ceEEEeCC-
Confidence            3445555555443     34568999999999999999999888742 233455553221100000     01111110 


Q ss_pred             CCcHHHHHHHHHHHHhcCCCeEEEEEecCccc
Q psy200          279 GKSERHQLGAILKYFDTKHKSILLILDEIDAL  310 (490)
Q Consensus       279 ~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l  310 (490)
                       .....+.+.+..++.  ..|-+|+|+|+-.-
T Consensus       133 -~~~~~~~~~l~~~lR--~~PD~i~vgEiR~~  161 (264)
T cd01129         133 -KAGLTFARGLRAILR--QDPDIIMVGEIRDA  161 (264)
T ss_pred             -cCCcCHHHHHHHHhc--cCCCEEEeccCCCH
Confidence             111234445555554  34779999999774

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.

>cd01394 radB RadB

Probab=97.14  E-value=0.0028  Score=59.31  Aligned_cols=40  Identities=28%  Similarity=0.388  Sum_probs=31.6

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccC
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNS  258 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~  258 (490)
                      .+..++|+|+||+|||+++..++.+... .+..++|++...
T Consensus        18 ~g~i~~i~G~~GsGKT~l~~~~a~~~~~-~g~~v~yi~~e~   57 (218)
T cd01394          18 RGTVTQVYGPPGTGKTNIAIQLAVETAG-QGKKVAYIDTEG   57 (218)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHh-cCCeEEEEECCC
Confidence            4567889999999999999999988742 345778887543

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

>TIGR02238 recomb_DMC1 meiotic recombinase Dmc1

Probab=97.14  E-value=0.0041  Score=61.41  Aligned_cols=93  Identities=22%  Similarity=0.243  Sum_probs=56.0

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhh-----cCCceEEEEeccCCCCHHHHHHHHHHHhcCCCC----------CCcH
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEI-----KDAFKTIYINCNSVRNAASVYETIVNELKLKPG----------GKSE  282 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~-----~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~----------~~s~  282 (490)
                      .+..+.|+|+||+|||+++..++-....     ..+-.++|++.-...++..+. +++..++....          -.+.
T Consensus        95 ~G~iteI~G~~GsGKTql~lqla~~~~~~~~~gg~~~~vvYIdtE~~f~~eRi~-~~a~~~g~d~~~~l~~i~~~~~~~~  173 (313)
T TIGR02238        95 SMSITEVFGEFRCGKTQLSHTLCVTAQLPREMGGGNGKVAYIDTEGTFRPDRIR-AIAERFGVDPDAVLDNILYARAYTS  173 (313)
T ss_pred             CCeEEEEECCCCCCcCHHHHHHHHHHhcchhhcCCCCeEEEEEcCCCCCHHHHH-HHHHHcCCChHHhcCcEEEecCCCH
Confidence            4567889999999999999887743321     123478999876644555443 34555543211          0123


Q ss_pred             HHHHHHHHH---HHhcCCCeEEEEEecCccccc
Q psy200          283 RHQLGAILK---YFDTKHKSILLILDEIDALES  312 (490)
Q Consensus       283 ~~~~~~l~~---~l~~~~~~~vI~IDEid~l~~  312 (490)
                      +...+.+..   .+.. .+..+||||-+..+..
T Consensus       174 e~~~~~l~~l~~~i~~-~~~~LvVIDSisal~r  205 (313)
T TIGR02238       174 EHQMELLDYLAAKFSE-EPFRLLIVDSIMALFR  205 (313)
T ss_pred             HHHHHHHHHHHHHhhc-cCCCEEEEEcchHhhh
Confidence            333333332   2333 3567999999998754

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.

>PRK13900 type IV secretion system ATPase VirB11; Provisional

Probab=97.14  E-value=0.00054  Score=68.16  Aligned_cols=98  Identities=18%  Similarity=0.166  Sum_probs=52.4

Q ss_pred             HHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcC-CCCCCcHHH
Q psy200          206 IRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKL-KPGGKSERH  284 (490)
Q Consensus       206 l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~-~~~~~s~~~  284 (490)
                      +..+|..++.  ..++++|+|++|+||||++++++..+.  .+.+++.+.-........ ......-+.. ...+...-.
T Consensus       149 ~~~~L~~~v~--~~~nili~G~tgSGKTTll~aL~~~ip--~~~ri~tiEd~~El~l~~-~~n~~~~~~~~~~~~~~~~~  223 (332)
T PRK13900        149 IKEFLEHAVI--SKKNIIISGGTSTGKTTFTNAALREIP--AIERLITVEDAREIVLSN-HPNRVHLLASKGGQGRAKVT  223 (332)
T ss_pred             HHHHHHHHHH--cCCcEEEECCCCCCHHHHHHHHHhhCC--CCCeEEEecCCCcccccc-CCCEEEEEecCCCCCcCcCc
Confidence            4455555443  367899999999999999999999875  333444442111000000 0000000000 011112223


Q ss_pred             HHHHHHHHHhcCCCeEEEEEecCccc
Q psy200          285 QLGAILKYFDTKHKSILLILDEIDAL  310 (490)
Q Consensus       285 ~~~~l~~~l~~~~~~~vI~IDEid~l  310 (490)
                      +.+.+..++.  .+|-.|++.|+-.-
T Consensus       224 ~~~ll~~~LR--~~PD~IivGEiR~~  247 (332)
T PRK13900        224 TQDLIEACLR--LRPDRIIVGELRGA  247 (332)
T ss_pred             HHHHHHHHhc--cCCCeEEEEecCCH
Confidence            4555555565  34779999999863

>cd03216 ABC_Carb_Monos_I This family represents the domain I of the carbohydrate uptake proteins that transport only monosaccharides (Monos)

Probab=97.13  E-value=0.0015  Score=58.27  Aligned_cols=99  Identities=18%  Similarity=0.215  Sum_probs=53.5

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCC--HHHHHHHHHHHhcCCCCCCcHHHH-HHHHHHHH
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRN--AASVYETIVNELKLKPGGKSERHQ-LGAILKYF  293 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~--~~~l~~~i~~~l~~~~~~~s~~~~-~~~l~~~l  293 (490)
                      ..+..+.|.|+.|+|||||++.++..+.  +.-.-++++......  ......   ..++.... .+..+. +-.+..++
T Consensus        24 ~~Ge~~~l~G~nGsGKSTLl~~i~G~~~--~~~G~v~~~g~~~~~~~~~~~~~---~~i~~~~q-LS~G~~qrl~laral   97 (163)
T cd03216          24 RRGEVHALLGENGAGKSTLMKILSGLYK--PDSGEILVDGKEVSFASPRDARR---AGIAMVYQ-LSVGERQMVEIARAL   97 (163)
T ss_pred             eCCCEEEEECCCCCCHHHHHHHHhCCCC--CCCeEEEECCEECCcCCHHHHHh---cCeEEEEe-cCHHHHHHHHHHHHH
Confidence            4677899999999999999999987654  222334554433221  111111   11111111 222222 22344444


Q ss_pred             hcCCCeEEEEEecCccc-cccCHHHHHHhHh
Q psy200          294 DTKHKSILLILDEIDAL-ESRKQTILYTIFE  323 (490)
Q Consensus       294 ~~~~~~~vI~IDEid~l-~~~~~~~L~~l~~  323 (490)
                      .  ..|-+|++||--.- .......+..++.
T Consensus        98 ~--~~p~illlDEP~~~LD~~~~~~l~~~l~  126 (163)
T cd03216          98 A--RNARLLILDEPTAALTPAEVERLFKVIR  126 (163)
T ss_pred             h--cCCCEEEEECCCcCCCHHHHHHHHHHHH
Confidence            4  34679999998654 3334555555553

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.

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=97.12  E-value=0.0033  Score=66.24  Aligned_cols=89  Identities=16%  Similarity=0.222  Sum_probs=58.1

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCCC----------------CCCc
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKP----------------GGKS  281 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~----------------~~~s  281 (490)
                      .+..++|.|+||+|||+++..++..... .+-+++|+...+  +..++.... ..++...                ...+
T Consensus       262 ~gs~~li~G~~G~GKt~l~~~f~~~~~~-~ge~~~y~s~eE--s~~~i~~~~-~~lg~~~~~~~~~g~l~~~~~~p~~~~  337 (484)
T TIGR02655       262 KDSIILATGATGTGKTLLVSKFLENACA-NKERAILFAYEE--SRAQLLRNA-YSWGIDFEEMEQQGLLKIICAYPESAG  337 (484)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHHH-CCCeEEEEEeeC--CHHHHHHHH-HHcCCChHHHhhCCcEEEEEcccccCC
Confidence            5678999999999999999999887643 234667775433  555555543 3343211                1123


Q ss_pred             HHHHHHHHHHHHhcCCCeEEEEEecCcccc
Q psy200          282 ERHQLGAILKYFDTKHKSILLILDEIDALE  311 (490)
Q Consensus       282 ~~~~~~~l~~~l~~~~~~~vI~IDEid~l~  311 (490)
                      .++....+.+.+.. .++.+|+||-+..+.
T Consensus       338 ~~~~~~~i~~~i~~-~~~~~vvIDsi~~~~  366 (484)
T TIGR02655       338 LEDHLQIIKSEIAD-FKPARIAIDSLSALA  366 (484)
T ss_pred             hHHHHHHHHHHHHH-cCCCEEEEcCHHHHH
Confidence            35566666666654 346699999999773

Members of this family are the circadian clock protein KaiC, part of the kaiABC operon that controls circadian rhythm. It may be universal in Cyanobacteria. Each member has two copies of the KaiC domain (Pfam model pfam06745), which is also found in other proteins. KaiC performs autophosphorylation and acts as its own transcriptional repressor.

>PRK08233 hypothetical protein; Provisional

Probab=97.12  E-value=0.002  Score=58.20  Aligned_cols=26  Identities=19%  Similarity=0.291  Sum_probs=23.1

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      ...|.|.|++|+||||+++.++..+.
T Consensus         3 ~~iI~I~G~~GsGKtTla~~L~~~l~   28 (182)
T PRK08233          3 TKIITIAAVSGGGKTTLTERLTHKLK   28 (182)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhhCC
Confidence            35788999999999999999999874

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

Probab=97.11  E-value=0.00086  Score=62.97  Aligned_cols=23  Identities=39%  Similarity=0.797  Sum_probs=19.0

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHh
Q psy200          221 SMYISGPPGTGKSASLNLLVSRA  243 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~l  243 (490)
                      ..+|.||||||||+++..++..+
T Consensus        19 ~~~i~GpPGTGKT~~l~~~i~~~   41 (236)
T PF13086_consen   19 ITLIQGPPGTGKTTTLASIIAQL   41 (236)
T ss_dssp             -EEEE-STTSSHHHHHHHHHHHH
T ss_pred             CEEEECCCCCChHHHHHHHHHHh
Confidence            58999999999998888888877

>COG4178 ABC-type uncharacterized transport system, permease and ATPase components [General function prediction only]

Probab=97.11  E-value=0.0023  Score=67.47  Aligned_cols=28  Identities=25%  Similarity=0.400  Sum_probs=24.8

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      +.+..++|.|++|||||+|.|+++.-..
T Consensus       417 ~~G~~llI~G~SG~GKTsLlRaiaGLWP  444 (604)
T COG4178         417 RPGERLLITGESGAGKTSLLRALAGLWP  444 (604)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHhccCc
Confidence            4678999999999999999999987654

>TIGR01351 adk adenylate kinases

Probab=97.10  E-value=0.0023  Score=59.51  Aligned_cols=23  Identities=26%  Similarity=0.631  Sum_probs=20.9

Q ss_pred             EEEECCCCCcHHHHHHHHHHHhh
Q psy200          222 MYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       222 ill~GppGtGKTtla~~l~~~l~  244 (490)
                      |+|.|+||+||||+++.+++.++
T Consensus         2 I~i~G~pGsGKsT~a~~La~~~g   24 (210)
T TIGR01351         2 LVLLGPPGSGKGTQAKRIAEKYG   24 (210)
T ss_pred             EEEECCCCCCHHHHHHHHHHHcC
Confidence            78999999999999999998754

Adenylate kinase (EC 2.7.4.3) converts ATP + AMP to ADP + ADP, that is, uses ATP as a phosphate donor for AMP. Most members of this family are known or believed to be adenylate kinase. However, some members accept other nucleotide triphosphates as donors, may be unable to use ATP, and may fail to complement adenylate kinase mutants. An example of a nucleoside-triphosphate--adenylate kinase (EC 2.7.4.10) is a GTP:AMP phosphotransferase. This family is designated subfamily rather than equivalog for this reason.

>COG1102 Cmk Cytidylate kinase [Nucleotide transport and metabolism]

Probab=97.10  E-value=0.00084  Score=58.19  Aligned_cols=43  Identities=26%  Similarity=0.487  Sum_probs=34.0

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcC
Q psy200          221 SMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKL  275 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~  275 (490)
                      .+.|.|+||+||||+++.+++.++    ++++        +...+|++++.+.++
T Consensus         2 ~ItIsG~pGsG~TTva~~lAe~~g----l~~v--------saG~iFR~~A~e~gm   44 (179)
T COG1102           2 VITISGLPGSGKTTVARELAEHLG----LKLV--------SAGTIFREMARERGM   44 (179)
T ss_pred             EEEeccCCCCChhHHHHHHHHHhC----Ccee--------eccHHHHHHHHHcCC
Confidence            467999999999999999999986    3322        456678888887765

>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=97.09  E-value=0.0045  Score=56.04  Aligned_cols=103  Identities=20%  Similarity=0.254  Sum_probs=56.4

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCC--CHHHH------HHHHHHHhcCC------CCCCcH
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVR--NAASV------YETIVNELKLK------PGGKSE  282 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~--~~~~l------~~~i~~~l~~~------~~~~s~  282 (490)
                      ..+..+.|.|+.|+|||||++.++..+.  +.---++++.....  ....+      +.+++..++..      ....+.
T Consensus        23 ~~G~~~~l~G~nGsGKStLl~~i~G~~~--~~~G~v~~~g~~~~~~~~~~~~~~i~~~~q~l~~~gl~~~~~~~~~~LS~  100 (180)
T cd03214          23 EAGEIVGILGPNGAGKSTLLKTLAGLLK--PSSGEILLDGKDLASLSPKELARKIAYVPQALELLGLAHLADRPFNELSG  100 (180)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHhCCCC--CCCcEEEECCEECCcCCHHHHHHHHhHHHHHHHHcCCHhHhcCCcccCCH
Confidence            4677899999999999999999987654  22233455543321  11111      11234444331      111222


Q ss_pred             HHH-HHHHHHHHhcCCCeEEEEEecCcc-ccccCHHHHHHhHh
Q psy200          283 RHQ-LGAILKYFDTKHKSILLILDEIDA-LESRKQTILYTIFE  323 (490)
Q Consensus       283 ~~~-~~~l~~~l~~~~~~~vI~IDEid~-l~~~~~~~L~~l~~  323 (490)
                      .+. +-.+..++.  ..|-+|++||--. |.....+.+..++.
T Consensus       101 G~~qrl~laral~--~~p~llllDEP~~~LD~~~~~~~~~~l~  141 (180)
T cd03214         101 GERQRVLLARALA--QEPPILLLDEPTSHLDIAHQIELLELLR  141 (180)
T ss_pred             HHHHHHHHHHHHh--cCCCEEEEeCCccCCCHHHHHHHHHHHH
Confidence            222 223344444  3567999999875 44444555656554

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.

>TIGR00150 HI0065_YjeE ATPase, YjeE family

Probab=97.08  E-value=0.0012  Score=56.29  Aligned_cols=44  Identities=16%  Similarity=0.265  Sum_probs=34.0

Q ss_pred             HHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhh
Q psy200          200 EVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEI  245 (490)
Q Consensus       200 e~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~  245 (490)
                      .++..++.+.|...+  ..+..++|.|+.|+||||+++.+++.++.
T Consensus         5 ~~~t~~l~~~l~~~l--~~~~~i~l~G~lGaGKTtl~~~l~~~lg~   48 (133)
T TIGR00150         5 EKAMDKFGKAFAKPL--DFGTVVLLKGDLGAGKTTLVQGLLQGLGI   48 (133)
T ss_pred             HHHHHHHHHHHHHhC--CCCCEEEEEcCCCCCHHHHHHHHHHHcCC
Confidence            345556666665543  34668999999999999999999999863

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.

>TIGR02782 TrbB_P P-type conjugative transfer ATPase TrbB

Probab=97.07  E-value=0.001  Score=65.25  Aligned_cols=92  Identities=14%  Similarity=0.186  Sum_probs=49.4

Q ss_pred             HHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhc-CCceEEEEeccCCCCHHHHHHHHHHHhcCCCCCCcHHHHH
Q psy200          208 QFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIK-DAFKTIYINCNSVRNAASVYETIVNELKLKPGGKSERHQL  286 (490)
Q Consensus       208 ~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~-~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~~~s~~~~~  286 (490)
                      .+|..++.  ..++++|+|++|+||||+++++++.+... ++.+++.+.-     ..++.-.--+.+.... ......+.
T Consensus       123 ~~L~~~v~--~~~~ilI~G~tGSGKTTll~al~~~i~~~~~~~ri~tiEd-----~~El~~~~~~~v~~~~-~~~~~~~~  194 (299)
T TIGR02782       123 DVLREAVL--ARKNILVVGGTGSGKTTLANALLAEIAKNDPTDRVVIIED-----TRELQCAAPNVVQLRT-SDDAISMT  194 (299)
T ss_pred             HHHHHHHH--cCCeEEEECCCCCCHHHHHHHHHHHhhccCCCceEEEECC-----chhhcCCCCCEEEEEe-cCCCCCHH
Confidence            44444433  35689999999999999999999887531 2344444421     1111100000000000 01111444


Q ss_pred             HHHHHHHhcCCCeEEEEEecCcc
Q psy200          287 GAILKYFDTKHKSILLILDEIDA  309 (490)
Q Consensus       287 ~~l~~~l~~~~~~~vI~IDEid~  309 (490)
                      +.+..++.  ..|-.|++.|+-.
T Consensus       195 ~~l~~aLR--~~pD~iivGEiR~  215 (299)
T TIGR02782       195 RLLKATLR--LRPDRIIVGEVRG  215 (299)
T ss_pred             HHHHHHhc--CCCCEEEEeccCC
Confidence            55555555  3467888888876

The TrbB protein is found in the trb locus of Agrobacterium Ti plasmids where it is involved in the type IV secretion system for plasmid conjugative transfer. TrbB is a homolog of the vir system VirB11 ATPase, and the Flp pilus sytem ATPase TadA.

>PRK07452 DNA polymerase III subunit delta; Validated

Probab=97.06  E-value=0.043  Score=54.72  Aligned_cols=133  Identities=17%  Similarity=0.134  Sum_probs=82.3

Q ss_pred             CeEEEEEecCcccccc---CHHHHHHhHhCCCCCCCcEEEEEecCCCChhHhhhHHhhhccCCCCeeEEeCCC---CHHH
Q psy200          298 KSILLILDEIDALESR---KQTILYTIFEWPSIPGSKLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPY---SREQ  371 (490)
Q Consensus       298 ~~~vI~IDEid~l~~~---~~~~L~~l~~~~~~~~~~vilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pl---s~~e  371 (490)
                      .+.+|+|++++.+...   ..+.|..+++..  ....+++++.++..+-...+...+...+    ....|.++   ..++
T Consensus        61 ~~rlVvv~~~~~~~~~~~~~~~~L~~~l~~~--~~~~~li~~~~~~~d~r~k~~k~l~k~~----~~~~~~~~~~~~~~~  134 (326)
T PRK07452         61 GGRLVWLKNSPLCQGCSEELLAELERTLPLI--PENTHLLLTNTKKPDGRLKSTKLLQKLA----EEKEFSLIPPWDTEG  134 (326)
T ss_pred             CceEEEEeCchhhccCCHHHHHHHHHHHcCC--CCCcEEEEEeCCCcchHHHHHHHHHHce----eEEEecCCCcccHHH
Confidence            3457888887655322   234455555432  2233444433443332223333344332    25566544   5677


Q ss_pred             HHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHhccccCCcccccCHHHHHHHHHHh
Q psy200          372 ILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITNHLIDLTYDNVKENGEVTGIGLKEVLGVISSV  447 (490)
Q Consensus       372 ~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~~~~  447 (490)
                      +..++..++...  ...+++++++.++.   ...+|+..+.+-++.....+...+      ..|+.++|...+...
T Consensus       135 l~~~i~~~~~~~--g~~i~~~a~~~L~~---~~g~dl~~l~~EleKL~ly~~~~~------~~It~~~V~~~v~~~  199 (326)
T PRK07452        135 LKQLVERTAQEL--GVKLTPEAAELLAE---AVGNDSRRLYNELEKLALYAENST------KPISAEEVKALVSNT  199 (326)
T ss_pred             HHHHHHHHHHHc--CCCCCHHHHHHHHH---HhCccHHHHHHHHHHHHHhccCCC------CccCHHHHHHHhccC
Confidence            999999999887  46699999999997   667899988888887765442222      368999998887653

>PF13479 AAA_24: AAA domain

Probab=97.06  E-value=0.0014  Score=61.17  Aligned_cols=79  Identities=22%  Similarity=0.277  Sum_probs=44.8

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCC
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFDTKHK  298 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~  298 (490)
                      +-.++|||+||+|||+++..+       +  ..+++++-.-...-..+.    ... ...-.+..++.+.+.........
T Consensus         3 ~~~~lIyG~~G~GKTt~a~~~-------~--k~l~id~E~g~~~~~~~~----~~~-~i~i~s~~~~~~~~~~l~~~~~~   68 (213)
T PF13479_consen    3 PIKILIYGPPGSGKTTLAASL-------P--KPLFIDTENGSDSLKFLD----DGD-VIPITSWEDFLEALDELEEDEAD   68 (213)
T ss_pred             ceEEEEECCCCCCHHHHHHhC-------C--CeEEEEeCCCccchhhhc----CCC-eeCcCCHHHHHHHHHHHHhccCC
Confidence            457899999999999999877       1  335555433211111110    000 00112566666666554333344


Q ss_pred             eEEEEEecCcccc
Q psy200          299 SILLILDEIDALE  311 (490)
Q Consensus       299 ~~vI~IDEid~l~  311 (490)
                      .-+||||-++.+.
T Consensus        69 y~tiVIDsis~~~   81 (213)
T PF13479_consen   69 YDTIVIDSISWLE   81 (213)
T ss_pred             CCEEEEECHHHHH
Confidence            5599999888863

>cd03283 ABC_MutS-like MutS-like homolog in eukaryotes

Probab=97.06  E-value=0.0014  Score=60.34  Aligned_cols=25  Identities=24%  Similarity=0.331  Sum_probs=22.1

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHh
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRA  243 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l  243 (490)
                      +..++|+||.|+||||+++.++...
T Consensus        25 g~~~~ltGpNg~GKSTllr~i~~~~   49 (199)
T cd03283          25 KNGILITGSNMSGKSTFLRTIGVNV   49 (199)
T ss_pred             CcEEEEECCCCCChHHHHHHHHHHH
Confidence            4789999999999999999998644

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 slid

>TIGR02858 spore_III_AA stage III sporulation protein AA

Probab=97.05  E-value=0.0063  Score=58.68  Aligned_cols=28  Identities=25%  Similarity=0.269  Sum_probs=24.7

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      +...+++|.|++|+||||+++.++..+.
T Consensus       109 ~~~~~~~i~g~~g~GKttl~~~l~~~~~  136 (270)
T TIGR02858       109 NRVLNTLIISPPQCGKTTLLRDLARILS  136 (270)
T ss_pred             CCeeEEEEEcCCCCCHHHHHHHHhCccC
Confidence            3457899999999999999999998875

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.

>KOG0479|consensus

Probab=97.05  E-value=0.043  Score=56.92  Aligned_cols=153  Identities=16%  Similarity=0.218  Sum_probs=86.3

Q ss_pred             CCCCChHHHHHHHHHHHHhhhc----cC----CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVN----NE----TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASV  265 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~----~~----~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l  265 (490)
                      ..+.|++-.++.|.-.|...+.    ++    ..-+||++|.|.+-|+-|+++|++....       .+....-.+    
T Consensus       301 PSI~GH~~vKkAillLLlGGvEk~L~NGshlRGDINiLlvGDPSvAKSQLLRyVLntApl-------AI~TTGRGS----  369 (818)
T KOG0479|consen  301 PSIYGHDYVKKAILLLLLGGVEKNLENGSHLRGDINILLVGDPSVAKSQLLRYVLNTAPL-------AIATTGRGS----  369 (818)
T ss_pred             cccccHHHHHHHHHHHHhccceeccCCCceeccceeEEEecCchHHHHHHHHHHHhcccc-------cccccCCCC----
Confidence            7899999998888777654322    11    2347999999999999999999886531       010000000    


Q ss_pred             HHHHHHHhcCCCCCCc--HHHHHHHHHHHHhcC----CCeEEEEEecCccccccCHHHHHHhHhCCC----------CCC
Q psy200          266 YETIVNELKLKPGGKS--ERHQLGAILKYFDTK----HKSILLILDEIDALESRKQTILYTIFEWPS----------IPG  329 (490)
Q Consensus       266 ~~~i~~~l~~~~~~~s--~~~~~~~l~~~l~~~----~~~~vI~IDEid~l~~~~~~~L~~l~~~~~----------~~~  329 (490)
                                ...|.+  ...-.+.=++.++.+    .-+-|+.|||||.|...+.-++...|+-..          .-+
T Consensus       370 ----------SGVGLTAAVTtD~eTGERRLEAGAMVLADRGVVCIDEFDKMsDiDRvAIHEVMEQqtVTIaKAGIHasLN  439 (818)
T KOG0479|consen  370 ----------SGVGLTAAVTTDQETGERRLEAGAMVLADRGVVCIDEFDKMSDIDRVAIHEVMEQQTVTIAKAGIHASLN  439 (818)
T ss_pred             ----------CCccceeEEeeccccchhhhhcCceEEccCceEEehhcccccchhHHHHHHHHhcceEEeEeccchhhhc
Confidence                      000000  000000001112111    113399999999999888778877776432          136


Q ss_pred             CcEEEEEecCCC----C----hhHh--hhHHhhhccCCCCeeEEeCCCCH
Q psy200          330 SKLVLVGVANAL----D----LTDR--MLPRLQANVTLQPTLMNFAPYSR  369 (490)
Q Consensus       330 ~~vilI~~tn~~----~----~~~~--l~~~l~~R~~~~~~~i~~~pls~  369 (490)
                      .++-|++++|..    +    -.+.  +-..+.+||.+  ..+.++..+.
T Consensus       440 ARCSVlAAANPvyG~Yd~~k~P~eNIgLpDSLLSRFDL--lFv~lD~~d~  487 (818)
T KOG0479|consen  440 ARCSVLAAANPVYGQYDQSKTPMENIGLPDSLLSRFDL--LFVVLDDIDA  487 (818)
T ss_pred             cceeeeeecCccccccCCCCChhhccCCcHHHHhhhcE--EEEEeccccc
Confidence            788899998832    1    1111  12456677775  2344444443

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

Probab=97.04  E-value=0.0024  Score=56.81  Aligned_cols=119  Identities=19%  Similarity=0.296  Sum_probs=59.1

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHH-HhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCC-------CCCCcHH-HHHH--
Q psy200          219 SGSMYISGPPGTGKSASLNLLVS-RAEIKDAFKTIYINCNSVRNAASVYETIVNELKLK-------PGGKSER-HQLG--  287 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~-~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~-------~~~~s~~-~~~~--  287 (490)
                      ++.++|.||+|+|||+.+...+- .+.......++++ ++...-..+.+..+...+...       ..+.... ....  
T Consensus        14 ~~~~li~aptGsGKT~~~~~~~l~~~~~~~~~~~lii-~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   92 (169)
T PF00270_consen   14 GKNVLISAPTGSGKTLAYILPALNRLQEGKDARVLII-VPTRALAEQQFERLRKFFSNTNVRVVLLHGGQSISEDQREVL   92 (169)
T ss_dssp             TSEEEEECSTTSSHHHHHHHHHHHHHHTTSSSEEEEE-ESSHHHHHHHHHHHHHHTTTTTSSEEEESTTSCHHHHHHHHH
T ss_pred             CCCEEEECCCCCccHHHHHHHHHhhhccCCCceEEEE-eecccccccccccccccccccccccccccccccccccccccc
Confidence            46799999999999999984443 3432222244444 332222333344443333221       1112211 1111  


Q ss_pred             ------------HHHHHHhc----CCCeEEEEEecCccccccCH-HHHHHhHhCC-CCCCCcEEEEEec
Q psy200          288 ------------AILKYFDT----KHKSILLILDEIDALESRKQ-TILYTIFEWP-SIPGSKLVLVGVA  338 (490)
Q Consensus       288 ------------~l~~~l~~----~~~~~vI~IDEid~l~~~~~-~~L~~l~~~~-~~~~~~vilI~~t  338 (490)
                                  .|...+..    -.+..+|||||+|.+..... ..+..++... ...+.+++++.+|
T Consensus        93 ~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~iViDE~h~l~~~~~~~~~~~i~~~~~~~~~~~~i~~SAT  161 (169)
T PF00270_consen   93 SNQADILVTTPEQLLDLISNGKINISRLSLIVIDEAHHLSDETFRAMLKSILRRLKRFKNIQIILLSAT  161 (169)
T ss_dssp             HTTSSEEEEEHHHHHHHHHTTSSTGTTESEEEEETHHHHHHTTHHHHHHHHHHHSHTTTTSEEEEEESS
T ss_pred             cccccccccCcchhhccccccccccccceeeccCcccccccccHHHHHHHHHHHhcCCCCCcEEEEeeC
Confidence                        12222322    12366999999999987532 2333333322 2224566665555

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

>PF13245 AAA_19: Part of AAA domain

Probab=97.04  E-value=0.00075  Score=51.71  Aligned_cols=25  Identities=36%  Similarity=0.671  Sum_probs=17.7

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHh
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRA  243 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l  243 (490)
                      .+.++|.||||+|||+++-.++.++
T Consensus        10 ~~~~vv~g~pGtGKT~~~~~~i~~l   34 (76)
T PF13245_consen   10 SPLFVVQGPPGTGKTTTLAARIAEL   34 (76)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHH
Confidence            5567789999999995444444444

>PRK06585 holA DNA polymerase III subunit delta; Reviewed

Probab=97.04  E-value=0.031  Score=56.14  Aligned_cols=193  Identities=12%  Similarity=0.126  Sum_probs=111.8

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHhhhcC--CceEEEEeccCCCCHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHh
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRAEIKD--AFKTIYINCNSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFD  294 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l~~~~--~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~  294 (490)
                      +..+..+|||+-.-.....++.+.+.+....  +|.+..+.+....                   ....++.+.+...--
T Consensus        18 ~~~~~yll~G~e~~li~~~~~~l~~~~~~~~~~~fn~~~~~~~e~~-------------------~~~~~~~~~~~t~sl   78 (343)
T PRK06585         18 PKIRAVLLYGPDRGLVRERARRLAKSVVPDLDDPFAVVRLDGDDLD-------------------ADPARLEDEANAISL   78 (343)
T ss_pred             CCCeEEEEeCCchHHHHHHHHHHHHHhcCCCCCCcceeeccHHHhh-------------------cCHHHHHHHHhCCCC
Confidence            3567899999998777777777776653211  2443433322110                   001122221111100


Q ss_pred             cCCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHH
Q psy200          295 TKHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILE  374 (490)
Q Consensus       295 ~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~  374 (490)
                       -+.+.+|+|.+.+.   ...+.|..++...  ....++++. ....+-...+...+. .... ...+.+.+++..++..
T Consensus        79 -F~~~rlViv~~~~~---~~~~~L~~~l~~~--~~~~~lil~-~~~~~~~~kl~k~~~-~~~~-~~~v~~~~~~~~~l~~  149 (343)
T PRK06585         79 -FGGRRLIWVRAGSK---NLAAALKALLESP--PGDAFIVIE-AGDLKKGSSLRKLFE-TAAY-AAAIPCYADDERDLAR  149 (343)
T ss_pred             -CCCceEEEEECCch---hHHHHHHHHHcCC--CCCcEEEEE-cCCCCcccHHHHHHh-cCCC-eeEEecCCCCHHHHHH
Confidence             12344777775432   2234555555433  233444443 333322222222221 1111 1367888999999999


Q ss_pred             HHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHhccccCCcccccCHHHHHHHHHHhcc
Q psy200          375 IISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITNHLIDLTYDNVKENGEVTGIGLKEVLGVISSVYC  449 (490)
Q Consensus       375 il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~~~~~~  449 (490)
                      ++..++...  ...+++++++.+++   ...||+..+.+-++.....+...       ..||.++|...+.....
T Consensus       150 ~i~~~~~~~--g~~i~~~a~~~L~~---~~g~dl~~l~~EleKL~ly~~~~-------~~It~edV~~lv~~~~e  212 (343)
T PRK06585        150 LIDDELAEA--GLRITPDARALLVA---LLGGDRLASRNEIEKLALYAHGK-------GEITLDDVRAVVGDASA  212 (343)
T ss_pred             HHHHHHHHC--CCCCCHHHHHHHHH---HhCCCHHHHHHHHHHHHHhcCCC-------CCCCHHHHHHHhCCccc
Confidence            999999987  46689999999998   67789998888888777654332       36888888887766543

>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=97.03  E-value=0.0085  Score=54.72  Aligned_cols=23  Identities=30%  Similarity=0.660  Sum_probs=21.1

Q ss_pred             EEEECCCCCcHHHHHHHHHHHhh
Q psy200          222 MYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       222 ill~GppGtGKTtla~~l~~~l~  244 (490)
                      |+|+|+||+||||+++.+++.++
T Consensus         2 I~i~G~pGsGKst~a~~La~~~~   24 (194)
T cd01428           2 ILLLGPPGSGKGTQAERLAKKYG   24 (194)
T ss_pred             EEEECCCCCCHHHHHHHHHHHcC
Confidence            78999999999999999998854

This enzyme is required for the biosynthesis of ADP and is essential for homeostasis of adenosine phosphates.

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

Probab=97.02  E-value=0.0016  Score=64.29  Aligned_cols=120  Identities=20%  Similarity=0.270  Sum_probs=68.6

Q ss_pred             ccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHH---HHh-------------c----
Q psy200          215 NNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIV---NEL-------------K----  274 (490)
Q Consensus       215 ~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~---~~l-------------~----  274 (490)
                      ....+..++|-|.||||||+++-.+.+.+..  +..++|++.-.  +...++....   ..+             .    
T Consensus         6 ~~~~G~TLLIKG~PGTGKTtfaLelL~~l~~--~~~v~YISTRV--d~d~vy~~y~~~~~~i~~~~vlDatQd~~~~~~~   81 (484)
T PF07088_consen    6 TQEPGQTLLIKGEPGTGKTTFALELLNSLKD--HGNVMYISTRV--DQDTVYEMYPWIEESIDPTNVLDATQDPFELPLD   81 (484)
T ss_pred             cCCCCcEEEEecCCCCCceeeehhhHHHHhc--cCCeEEEEecc--CHHHHHHhhhhhccccChhhhhhhccchhhcccc
Confidence            4577899999999999999999999999863  33445654332  2222322211   111             0    


Q ss_pred             --CCCCCCcHHHHHHHHHHHHhcCCCeEEEEEec----Ccccccc---CHH---HHHHhHhCCCCCCCcEEEEEecC
Q psy200          275 --LKPGGKSERHQLGAILKYFDTKHKSILLILDE----IDALESR---KQT---ILYTIFEWPSIPGSKLVLVGVAN  339 (490)
Q Consensus       275 --~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDE----id~l~~~---~~~---~L~~l~~~~~~~~~~vilI~~tn  339 (490)
                        .+......+.+.+++.+. ...+++.+|+||-    ++.+...   .++   ...++..+....+.++++|.-+.
T Consensus        82 ~~vp~~~l~~ds~~~f~~~i-~~~~k~~iI~~DSWdaiieyla~~~~~~ed~e~l~~dLv~lard~g~~LIlVsEsa  157 (484)
T PF07088_consen   82 KDVPFERLDIDSFRDFVDKI-NEAGKKPIIAFDSWDAIIEYLAEEHDEPEDIETLTNDLVELARDMGINLILVSESA  157 (484)
T ss_pred             ccCcccccCHHHHHHHHHHh-hhcccCcEEEEecHHHHHHHhhhhhcCcHHHHHHHHHHHHHHhhcCceEEEEEecC
Confidence              012223456666666643 3346677999999    5555422   122   12233333344567777775443

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

>TIGR03574 selen_PSTK L-seryl-tRNA(Sec) kinase, archaeal

Probab=97.02  E-value=0.0042  Score=59.45  Aligned_cols=33  Identities=24%  Similarity=0.397  Sum_probs=25.7

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEE
Q psy200          221 SMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYI  254 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v  254 (490)
                      .|+|+|.||+||||+++.+++.+.. .++.++.+
T Consensus         1 LIvl~G~pGSGKST~a~~La~~l~~-~~~~v~~i   33 (249)
T TIGR03574         1 LIILTGLPGVGKSTFSKELAKKLSE-KNIDVIIL   33 (249)
T ss_pred             CEEEEcCCCCCHHHHHHHHHHHHHH-cCCceEEE
Confidence            3789999999999999999998752 23445555

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.

>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=97.01  E-value=0.00084  Score=62.09  Aligned_cols=24  Identities=29%  Similarity=0.364  Sum_probs=21.4

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHH
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVS  241 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~  241 (490)
                      .+..++|+||.|+||||+++.++.
T Consensus        28 ~~~~~~l~G~Ng~GKStll~~i~~   51 (202)
T cd03243          28 SGRLLLITGPNMGGKSTYLRSIGL   51 (202)
T ss_pred             CCeEEEEECCCCCccHHHHHHHHH
Confidence            346899999999999999999984

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

>PRK04040 adenylate kinase; Provisional

Probab=97.01  E-value=0.0028  Score=57.79  Aligned_cols=26  Identities=27%  Similarity=0.523  Sum_probs=23.2

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      +..++|+|.||+||||+++.+++.+.
T Consensus         2 ~~~i~v~G~pG~GKtt~~~~l~~~l~   27 (188)
T PRK04040          2 MKVVVVTGVPGVGKTTVLNKALEKLK   27 (188)
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHHhc
Confidence            45789999999999999999999873

>cd00267 ABC_ATPase ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules

Probab=97.01  E-value=0.003  Score=55.81  Aligned_cols=98  Identities=19%  Similarity=0.236  Sum_probs=53.0

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCC--HHHHHHHHHHHhcCCCCCCcHHH-HHHHHHHHH
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRN--AASVYETIVNELKLKPGGKSERH-QLGAILKYF  293 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~--~~~l~~~i~~~l~~~~~~~s~~~-~~~~l~~~l  293 (490)
                      .++..+.|.|+.|+||||+++.++..+.  .....++++......  ...+    ...+..... .+..+ .+-.+..++
T Consensus        23 ~~g~~~~i~G~nGsGKStll~~l~g~~~--~~~G~i~~~~~~~~~~~~~~~----~~~i~~~~q-lS~G~~~r~~l~~~l   95 (157)
T cd00267          23 KAGEIVALVGPNGSGKSTLLRAIAGLLK--PTSGEILIDGKDIAKLPLEEL----RRRIGYVPQ-LSGGQRQRVALARAL   95 (157)
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHhCCCC--CCccEEEECCEEcccCCHHHH----HhceEEEee-CCHHHHHHHHHHHHH
Confidence            3567899999999999999999987654  222334555433221  1111    111111100 12222 222344444


Q ss_pred             hcCCCeEEEEEecCcccc-ccCHHHHHHhHh
Q psy200          294 DTKHKSILLILDEIDALE-SRKQTILYTIFE  323 (490)
Q Consensus       294 ~~~~~~~vI~IDEid~l~-~~~~~~L~~l~~  323 (490)
                      .  ..+-++++||...=. ......+..++.
T Consensus        96 ~--~~~~i~ilDEp~~~lD~~~~~~l~~~l~  124 (157)
T cd00267          96 L--LNPDLLLLDEPTSGLDPASRERLLELLR  124 (157)
T ss_pred             h--cCCCEEEEeCCCcCCCHHHHHHHHHHHH
Confidence            4  336699999997543 334455555544

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.

>PRK13709 conjugal transfer nickase/helicase TraI; Provisional

Probab=97.01  E-value=0.0055  Score=72.60  Aligned_cols=109  Identities=13%  Similarity=0.217  Sum_probs=60.1

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHhhh---cCCceEEEEeccCCCCHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHH-
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRAEI---KDAFKTIYINCNSVRNAASVYETIVNELKLKPGGKSERHQLGAILKY-  292 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l~~---~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~-  292 (490)
                      ...+.++|.|.+||||||+++.+...+..   ..++.++-+  ..  +... ...+ .+.     |.....+..+|... 
T Consensus       982 s~dr~~~I~G~AGTGKTT~l~~v~~~~~~l~~~~~~~V~gl--AP--TgrA-Ak~L-~e~-----Gi~A~TI~s~L~~~~ 1050 (1747)
T PRK13709        982 STDRFTVVQGYAGVGKTTQFRAVMSAVNTLPESERPRVVGL--GP--THRA-VGEM-RSA-----GVDAQTLASFLHDTQ 1050 (1747)
T ss_pred             CCCcEEEEEeCCCCCHHHHHHHHHHHHHHhhcccCceEEEE--CC--cHHH-HHHH-Hhc-----CcchhhHHHHhcccc
Confidence            34579999999999999999999887642   123333332  21  1111 1111 111     22223333333211 


Q ss_pred             -H-hc----CCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEEEecC
Q psy200          293 -F-DT----KHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVAN  339 (490)
Q Consensus       293 -l-~~----~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI~~tn  339 (490)
                       . ..    .....||||||+-.+......   .++......+.++|+||-.+
T Consensus      1051 ~~~~~~~~~~~~~~llIVDEaSMv~~~~m~---~Ll~~~~~~garvVLVGD~~ 1100 (1747)
T PRK13709       1051 LQQRSGETPDFSNTLFLLDESSMVGNTDMA---RAYALIAAGGGRAVSSGDTD 1100 (1747)
T ss_pred             cccccccCCCCCCcEEEEEccccccHHHHH---HHHHhhhcCCCEEEEecchH
Confidence             0 00    123469999999998754433   34433333467899998664

>PF05272 VirE: Virulence-associated protein E; InterPro: IPR007936 This family contains several bacterial virulence-associated protein E like proteins

Probab=97.00  E-value=0.0029  Score=58.15  Aligned_cols=89  Identities=19%  Similarity=0.239  Sum_probs=55.7

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCC
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFDTKHK  298 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~  298 (490)
                      ...++|.|+-|+|||+.++.+....-         .+....                    ...++....+..       
T Consensus        52 d~~lvl~G~QG~GKStf~~~L~~~~~---------~d~~~~--------------------~~~kd~~~~l~~-------   95 (198)
T PF05272_consen   52 DTVLVLVGKQGIGKSTFFRKLGPEYF---------SDSIND--------------------FDDKDFLEQLQG-------   95 (198)
T ss_pred             ceeeeEecCCcccHHHHHHHHhHHhc---------cCcccc--------------------CCCcHHHHHHHH-------
Confidence            35778999999999999999854421         110000                    011122222221       


Q ss_pred             eEEEEEecCccccccCHHHHHHhHhCCC------------CCCCcEEEEEecCCCCh
Q psy200          299 SILLILDEIDALESRKQTILYTIFEWPS------------IPGSKLVLVGVANALDL  343 (490)
Q Consensus       299 ~~vI~IDEid~l~~~~~~~L~~l~~~~~------------~~~~~vilI~~tn~~~~  343 (490)
                      ..||.|||++.+.....+.|..++....            ...-..++||+||..++
T Consensus        96 ~~iveldEl~~~~k~~~~~lK~~iT~~~~~~R~pY~~~~~~~~R~~~figTtN~~~~  152 (198)
T PF05272_consen   96 KWIVELDELDGLSKKDVEALKSFITRRTDTYRPPYGRDPEEFPRRAVFIGTTNDDDF  152 (198)
T ss_pred             hHheeHHHHhhcchhhHHHHHHHhcccceeeecCCcCcceeeceeEEEEeccCCcce
Confidence            3599999999999778888887764221            12345688999997654

>cd03287 ABC_MSH3_euk MutS3 homolog in eukaryotes

Probab=97.00  E-value=0.0011  Score=62.20  Aligned_cols=24  Identities=25%  Similarity=0.285  Sum_probs=21.6

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHH
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVS  241 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~  241 (490)
                      .+..++|+||.|.|||++++.++-
T Consensus        30 ~g~~~~itG~N~~GKStll~~i~~   53 (222)
T cd03287          30 GGYCQIITGPNMGGKSSYIRQVAL   53 (222)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHH
Confidence            456889999999999999999987

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

>PRK04301 radA DNA repair and recombination protein RadA; Validated

Probab=96.99  E-value=0.0059  Score=60.65  Aligned_cols=94  Identities=17%  Similarity=0.198  Sum_probs=56.1

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhc-----CCceEEEEeccCCCCHHHHHHHHHHHhcCCCC----------CCcH
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIK-----DAFKTIYINCNSVRNAASVYETIVNELKLKPG----------GKSE  282 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~-----~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~----------~~s~  282 (490)
                      .+..+.|+|+||+|||+++..++......     .+..++|+++....+...+. +++..++....          ..+.
T Consensus       101 ~g~vtei~G~~GsGKT~l~~~~~~~~~~~~~~gg~~~~~~yi~te~~f~~~rl~-~~~~~~g~~~~~~l~~i~~~~~~~~  179 (317)
T PRK04301        101 TQSITEFYGEFGSGKTQICHQLAVNVQLPEEKGGLEGKAVYIDTEGTFRPERIE-QMAEALGLDPDEVLDNIHVARAYNS  179 (317)
T ss_pred             CCcEEEEECCCCCCHhHHHHHHHHHhccccccCCCCceEEEEeCCCCcCHHHHH-HHHHHcCCChHhhhccEEEEeCCCH
Confidence            46678899999999999999998765321     12478999876644444433 33333332110          0111


Q ss_pred             H---HHHHHHHHHHhcCCCeEEEEEecCccccc
Q psy200          283 R---HQLGAILKYFDTKHKSILLILDEIDALES  312 (490)
Q Consensus       283 ~---~~~~~l~~~l~~~~~~~vI~IDEid~l~~  312 (490)
                      .   .+...+...+....+..+||||-+-.+..
T Consensus       180 ~~~~~~~~~l~~~i~~~~~~~lvVIDSisa~~~  212 (317)
T PRK04301        180 DHQMLLAEKAEELIKEGENIKLVIVDSLTAHFR  212 (317)
T ss_pred             HHHHHHHHHHHHHHhccCceeEEEEECchHHhh
Confidence            1   22333334343324567999999988753

>PRK14529 adenylate kinase; Provisional

Probab=96.99  E-value=0.0067  Score=56.71  Aligned_cols=24  Identities=29%  Similarity=0.552  Sum_probs=21.9

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHhh
Q psy200          221 SMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      .|+|.|+||+||||+++.+++.++
T Consensus         2 ~I~l~G~PGsGK~T~a~~La~~~~   25 (223)
T PRK14529          2 NILIFGPNGSGKGTQGALVKKKYD   25 (223)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHC
Confidence            478899999999999999999875

>PF01443 Viral_helicase1: Viral (Superfamily 1) RNA helicase; InterPro: IPR000606 This entry includes RNA and DNA helicases

Probab=96.99  E-value=0.00056  Score=64.61  Aligned_cols=21  Identities=33%  Similarity=0.673  Sum_probs=19.4

Q ss_pred             EEEECCCCCcHHHHHHHHHHH
Q psy200          222 MYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       222 ill~GppGtGKTtla~~l~~~  242 (490)
                      ++|.|+||+|||++++.++..
T Consensus         1 ~vv~G~pGsGKSt~i~~~~~~   21 (234)
T PF01443_consen    1 IVVHGVPGSGKSTLIKKLLKD   21 (234)
T ss_pred             CEEEcCCCCCHHHHHHHHHHh
Confidence            478999999999999999887

Some of the members are found in positive-strand single stranded RNA viruses. The helicase has multiple roles at different stages of viral RNA replication, as dissected by mutational analysis [].; GO: 0004386 helicase activity

>TIGR02788 VirB11 P-type DNA transfer ATPase VirB11

Probab=96.98  E-value=0.0027  Score=62.72  Aligned_cols=37  Identities=32%  Similarity=0.507  Sum_probs=28.9

Q ss_pred             HHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          206 IRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       206 l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      +..+|...+  ....+++|+|++|+||||++++++..+.
T Consensus       133 ~~~~l~~~v--~~~~~ili~G~tGsGKTTll~al~~~~~  169 (308)
T TIGR02788       133 IKEFLRLAI--ASRKNIIISGGTGSGKTTFLKSLVDEIP  169 (308)
T ss_pred             HHHHHHHHh--hCCCEEEEECCCCCCHHHHHHHHHccCC
Confidence            445555443  3467999999999999999999998875

The VirB11 protein is found in the vir locus of Agrobacterium Ti plasmids where it is involved in the type IV secretion system for DNA transfer. VirB11 is believed to be an ATPase. VirB11 is a homolog of the P-like conjugation system TrbB protein and the Flp pilus sytem protein TadA.

>PTZ00035 Rad51 protein; Provisional

Probab=96.97  E-value=0.0072  Score=60.34  Aligned_cols=93  Identities=22%  Similarity=0.269  Sum_probs=55.3

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhc-----CCceEEEEeccCCCCHHHHHHHHHHHhcCCC----------CCCcH
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIK-----DAFKTIYINCNSVRNAASVYETIVNELKLKP----------GGKSE  282 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~-----~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~----------~~~s~  282 (490)
                      .+..+.|+|++|+|||+++..++-.....     .+-.++|++......+.. +..++..++...          .-.+.
T Consensus       117 ~G~iteI~G~~GsGKT~l~~~l~~~~qlp~~~gg~~g~vvyIdtE~~f~~er-i~~ia~~~g~~~~~~l~nI~~~~~~~~  195 (337)
T PTZ00035        117 TGSITELFGEFRTGKTQLCHTLCVTCQLPIEQGGGEGKVLYIDTEGTFRPER-IVQIAERFGLDPEDVLDNIAYARAYNH  195 (337)
T ss_pred             CCeEEEEECCCCCchhHHHHHHHHHhccccccCCCCceEEEEEccCCCCHHH-HHHHHHHhCCChHhHhhceEEEccCCH
Confidence            45678899999999999999887654311     234678888765434443 333344433211          01123


Q ss_pred             HHHHHHHHH---HHhcCCCeEEEEEecCccccc
Q psy200          283 RHQLGAILK---YFDTKHKSILLILDEIDALES  312 (490)
Q Consensus       283 ~~~~~~l~~---~l~~~~~~~vI~IDEid~l~~  312 (490)
                      ++..+.+..   .+.. .+..+||||-+-.++.
T Consensus       196 e~~~~~l~~~~~~l~~-~~~~lvVIDSital~r  227 (337)
T PTZ00035        196 EHQMQLLSQAAAKMAE-ERFALLIVDSATALFR  227 (337)
T ss_pred             HHHHHHHHHHHHHhhc-cCccEEEEECcHHhhh
Confidence            333343332   2222 4577999999998754

>TIGR02236 recomb_radA DNA repair and recombination protein RadA

Probab=96.97  E-value=0.0066  Score=60.13  Aligned_cols=94  Identities=16%  Similarity=0.203  Sum_probs=55.1

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhc-----CCceEEEEeccCCCCHHHHHHHHHHHhcCCCC----------CCcH
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIK-----DAFKTIYINCNSVRNAASVYETIVNELKLKPG----------GKSE  282 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~-----~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~----------~~s~  282 (490)
                      .+..+.|+|+||+|||+++..++......     .+-.++|++.....+...+. +++..++....          -...
T Consensus        94 ~g~i~ei~G~~g~GKT~l~~~~~~~~~~~~~~g~~~~~~~yi~te~~f~~~rl~-~~~~~~gl~~~~~~~~i~i~~~~~~  172 (310)
T TIGR02236        94 TQAITEVFGEFGSGKTQICHQLAVNVQLPEEKGGLGGKAVYIDTENTFRPERIM-QMAEARGLDPDEVLKNIYVARAYNS  172 (310)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHhcCCcccCCCcceEEEEECCCCCCHHHHH-HHHHHcCCCHHHHhhceEEEecCCH
Confidence            45678899999999999999998775321     12278999876654555443 33333332110          0111


Q ss_pred             H---HHHHHHHHHHhcCC-CeEEEEEecCccccc
Q psy200          283 R---HQLGAILKYFDTKH-KSILLILDEIDALES  312 (490)
Q Consensus       283 ~---~~~~~l~~~l~~~~-~~~vI~IDEid~l~~  312 (490)
                      .   .+.+.+.+.+.... ...+||||-+-.+..
T Consensus       173 ~~~~~lld~l~~~i~~~~~~~~lVVIDSisa~~r  206 (310)
T TIGR02236       173 NHQMLLVEKAEDLIKELNNPVKLLIVDSLTSHFR  206 (310)
T ss_pred             HHHHHHHHHHHHHHHhcCCCceEEEEecchHhhh
Confidence            1   12333444444332 356999998887643

This family consists exclusively of archaeal RadA protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239), and archaeal RadB (TIGR02237). This protein is involved in DNA repair and recombination. The member from Pyrococcus horikoshii contains an intein.

>PLN03187 meiotic recombination protein DMC1 homolog; Provisional

Probab=96.97  E-value=0.0097  Score=59.35  Aligned_cols=93  Identities=19%  Similarity=0.193  Sum_probs=56.3

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhh-----cCCceEEEEeccCCCCHHHHHHHHHHHhcCCC----------CCCcH
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEI-----KDAFKTIYINCNSVRNAASVYETIVNELKLKP----------GGKSE  282 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~-----~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~----------~~~s~  282 (490)
                      .+....|+|++|+|||+++..++-....     ..+-.++|++.-....+..+.. ++..++...          .-.+.
T Consensus       125 ~G~ItEI~G~~GsGKTql~lqlav~~qlp~~~gg~~~~vvyIdTE~tF~peRl~~-ia~~~g~d~~~~l~~I~~~~~~~~  203 (344)
T PLN03187        125 TRCITEAFGEFRSGKTQLAHTLCVTTQLPTEMGGGNGKVAYIDTEGTFRPDRIVP-IAERFGMDADAVLDNIIYARAYTY  203 (344)
T ss_pred             CCeEEEEecCCCCChhHHHHHHHHHHhcchhhCCCCceEEEEEcCCCCCHHHHHH-HHHHcCCChhhhcCeEEEecCCCH
Confidence            4567779999999999999988754321     1134789998766555555433 444444321          01233


Q ss_pred             HHHHHHHHH---HHhcCCCeEEEEEecCccccc
Q psy200          283 RHQLGAILK---YFDTKHKSILLILDEIDALES  312 (490)
Q Consensus       283 ~~~~~~l~~---~l~~~~~~~vI~IDEid~l~~  312 (490)
                      +.....+..   .+.. .+..+||||-+-.+..
T Consensus       204 e~~~~~l~~l~~~i~~-~~~~LvVIDSital~r  235 (344)
T PLN03187        204 EHQYNLLLGLAAKMAE-EPFRLLIVDSVIALFR  235 (344)
T ss_pred             HHHHHHHHHHHHHHHh-cCCCEEEEeCcHHhhh
Confidence            333333332   3332 3467999999988754

>PRK06696 uridine kinase; Validated

Probab=96.94  E-value=0.0026  Score=59.74  Aligned_cols=59  Identities=15%  Similarity=0.192  Sum_probs=41.5

Q ss_pred             hHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCC
Q psy200          199 REVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSV  259 (490)
Q Consensus       199 re~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~  259 (490)
                      |++.+++|.+.+... ..+.+..|.|.|++|+||||+++.|++.+... +..++.++...+
T Consensus         3 ~~~~~~~la~~~~~~-~~~~~~iI~I~G~sgsGKSTlA~~L~~~l~~~-g~~v~~~~~Ddf   61 (223)
T PRK06696          3 RKQLIKELAEHILTL-NLTRPLRVAIDGITASGKTTFADELAEEIKKR-GRPVIRASIDDF   61 (223)
T ss_pred             HHHHHHHHHHHHHHh-CCCCceEEEEECCCCCCHHHHHHHHHHHHHHc-CCeEEEeccccc
Confidence            567777777777542 23456688899999999999999999998522 345555443333

>PRK06731 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=96.94  E-value=0.017  Score=55.59  Aligned_cols=148  Identities=9%  Similarity=0.133  Sum_probs=77.6

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCC-CHHHHHHHHHHHhcCCCC-CCcHHHHHHHHHHHHhc
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVR-NAASVYETIVNELKLKPG-GKSERHQLGAILKYFDT  295 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~-~~~~l~~~i~~~l~~~~~-~~s~~~~~~~l~~~l~~  295 (490)
                      ++..++|+|++|+||||+++.++..+.. ....+..+++.... ....-|......++.+.. ..+...+.+.+... ..
T Consensus        74 ~~~~i~~~G~~g~GKTtl~~~l~~~l~~-~~~~v~~i~~D~~ri~~~~ql~~~~~~~~~~~~~~~~~~~l~~~l~~l-~~  151 (270)
T PRK06731         74 EVQTIALIGPTGVGKTTTLAKMAWQFHG-KKKTVGFITTDHSRIGTVQQLQDYVKTIGFEVIAVRDEAAMTRALTYF-KE  151 (270)
T ss_pred             CCCEEEEECCCCCcHHHHHHHHHHHHHH-cCCeEEEEecCCCCHHHHHHHHHHhhhcCceEEecCCHHHHHHHHHHH-Hh
Confidence            4478999999999999999999888742 23455566655443 122223444444443322 13455555555443 32


Q ss_pred             CCCeEEEEEecCccccccC--HHHHHHhHhCCCCCCCcEEEEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHH
Q psy200          296 KHKSILLILDEIDALESRK--QTILYTIFEWPSIPGSKLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQ  371 (490)
Q Consensus       296 ~~~~~vI~IDEid~l~~~~--~~~L~~l~~~~~~~~~~vilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e  371 (490)
                      ..+.-+||||.........  .+.|..++.... ....++++.++...+....+...+..   +....+-|..++...
T Consensus       152 ~~~~D~ViIDt~Gr~~~~~~~l~el~~~~~~~~-~~~~~LVl~a~~~~~d~~~~~~~f~~---~~~~~~I~TKlDet~  225 (270)
T PRK06731        152 EARVDYILIDTAGKNYRASETVEEMIETMGQVE-PDYICLTLSASMKSKDMIEIITNFKD---IHIDGIVFTKFDETA  225 (270)
T ss_pred             cCCCCEEEEECCCCCcCCHHHHHHHHHHHhhhC-CCeEEEEEcCccCHHHHHHHHHHhCC---CCCCEEEEEeecCCC
Confidence            2345699999998875432  233334433221 22223344333221111222333332   233467777777554

>PRK09270 nucleoside triphosphate hydrolase domain-containing protein; Reviewed

Probab=96.93  E-value=0.047  Score=51.46  Aligned_cols=29  Identities=31%  Similarity=0.483  Sum_probs=25.1

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHhhh
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRAEI  245 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l~~  245 (490)
                      +.+..+.|.|++|+|||||++.++..+..
T Consensus        31 ~~~~iigi~G~~GsGKTTl~~~L~~~l~~   59 (229)
T PRK09270         31 QRRTIVGIAGPPGAGKSTLAEFLEALLQQ   59 (229)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHhhh
Confidence            45567889999999999999999998863

>PLN02200 adenylate kinase family protein

Probab=96.91  E-value=0.011  Score=55.87  Aligned_cols=27  Identities=26%  Similarity=0.415  Sum_probs=23.7

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      .+..++|.|+||+||||+++.+++.++
T Consensus        42 ~~~ii~I~G~PGSGKsT~a~~La~~~g   68 (234)
T PLN02200         42 TPFITFVLGGPGSGKGTQCEKIVETFG   68 (234)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHhC
Confidence            456789999999999999999998864

>PRK12678 transcription termination factor Rho; Provisional

Probab=96.91  E-value=0.0034  Score=65.51  Aligned_cols=95  Identities=14%  Similarity=0.159  Sum_probs=54.7

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHhhh-cCCceEEEEeccCCC-CHHHHHHHHHHHhcCCCCCCc------HHHHHHH
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRAEI-KDAFKTIYINCNSVR-NAASVYETIVNELKLKPGGKS------ERHQLGA  288 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l~~-~~~~~~~~v~~~~~~-~~~~l~~~i~~~l~~~~~~~s------~~~~~~~  288 (490)
                      +.+.-.+|+||||+|||+|++.|++.+.. ..++.++++-+..-. ...+|...+-.++-.......      ...+.-.
T Consensus       414 GkGQR~LIvgpp~aGKTtLL~~IAn~i~~n~~~~~~ivvLIgERpeEVtdm~rsVkgeVVasT~D~p~~~~~~~a~~ai~  493 (672)
T PRK12678        414 GKGQRGLIVSPPKAGKTTILQNIANAITTNNPECHLMVVLVDERPEEVTDMQRSVKGEVIASTFDRPPSDHTTVAELAIE  493 (672)
T ss_pred             ccCCEeEEeCCCCCCHHHHHHHHHHHHhhcCCCeEEEEEEEeCchhhHHHHHHhccceEEEECCCCCHHHHHHHHHHHHH
Confidence            56778999999999999999999997742 344554444333322 122232222111111111111      1122223


Q ss_pred             HHHHHhcCCCeEEEEEecCcccc
Q psy200          289 ILKYFDTKHKSILLILDEIDALE  311 (490)
Q Consensus       289 l~~~l~~~~~~~vI~IDEid~l~  311 (490)
                      +.++|...++.+|||+|.+-.+.
T Consensus       494 ~Ae~fre~G~dVlillDSlTR~A  516 (672)
T PRK12678        494 RAKRLVELGKDVVVLLDSITRLG  516 (672)
T ss_pred             HHHHHHHcCCCEEEEEeCchHHH
Confidence            44555556889999999998764

>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=96.90  E-value=0.0067  Score=54.68  Aligned_cols=25  Identities=24%  Similarity=0.280  Sum_probs=21.8

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHH
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVS  241 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~  241 (490)
                      ..+..+.|.||.|+|||||++.++.
T Consensus        19 ~~G~~~~l~G~nG~GKSTLl~~il~   43 (176)
T cd03238          19 PLNVLVVVTGVSGSGKSTLVNEGLY   43 (176)
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHhh
Confidence            4567889999999999999999863

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.

>COG0563 Adk Adenylate kinase and related kinases [Nucleotide transport and metabolism]

Probab=96.89  E-value=0.0076  Score=54.40  Aligned_cols=24  Identities=38%  Similarity=0.641  Sum_probs=21.6

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHhh
Q psy200          221 SMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      .++|.|+||+||||+|+.+++.++
T Consensus         2 riiilG~pGaGK~T~A~~La~~~~   25 (178)
T COG0563           2 RILILGPPGAGKSTLAKKLAKKLG   25 (178)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHhC
Confidence            478999999999999999999853

>TIGR03600 phage_DnaB phage replicative helicase, DnaB family, HK022 subfamily

Probab=96.87  E-value=0.012  Score=60.96  Aligned_cols=53  Identities=11%  Similarity=0.267  Sum_probs=38.0

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHH
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNE  272 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~  272 (490)
                      ++..++|.|.||+|||+++..++..+....+..+++++.- + +..++...++..
T Consensus       193 ~g~liviag~pg~GKT~~al~ia~~~a~~~g~~v~~fSlE-m-~~~~l~~Rl~~~  245 (421)
T TIGR03600       193 KGDLIVIGARPSMGKTTLALNIAENVALREGKPVLFFSLE-M-SAEQLGERLLAS  245 (421)
T ss_pred             CCceEEEEeCCCCCHHHHHHHHHHHHHHhCCCcEEEEECC-C-CHHHHHHHHHHH
Confidence            4568889999999999999999977653445677777532 2 556666555543

Members of this family are phage (or prophage-region) homologs of the bacterial homohexameric replicative helicase DnaB. Some phage may rely on host DnaB, while others encode their own verions. This model describes the largest phage-specific clade among the close homologs of DnaB, but there are, or course, other DnaB homologs from phage that fall outside the scope of this model.

>PRK00131 aroK shikimate kinase; Reviewed

Probab=96.87  E-value=0.0012  Score=59.25  Aligned_cols=27  Identities=30%  Similarity=0.340  Sum_probs=24.5

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      .+..++|+|++|+||||+++.+++.++
T Consensus         3 ~~~~i~l~G~~GsGKstla~~La~~l~   29 (175)
T PRK00131          3 KGPNIVLIGFMGAGKSTIGRLLAKRLG   29 (175)
T ss_pred             CCCeEEEEcCCCCCHHHHHHHHHHHhC
Confidence            456899999999999999999999875

>TIGR03575 selen_PSTK_euk L-seryl-tRNA(Sec) kinase, eukaryotic

Probab=96.87  E-value=0.031  Score=55.61  Aligned_cols=37  Identities=19%  Similarity=0.285  Sum_probs=28.2

Q ss_pred             EEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccC
Q psy200          222 MYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNS  258 (490)
Q Consensus       222 ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~  258 (490)
                      ++|+|.+|+||||+++.+++.+....++.+..++.-.
T Consensus         2 ~~l~Gl~GaGKST~~~~l~~~l~~~~g~~v~~~~~Dd   38 (340)
T TIGR03575         2 CVLCGLPAAGKSTLARSLSATLRRERGWAVAVITYDD   38 (340)
T ss_pred             eEEECCCCCCHHHHHHHHHHHHHhccCCeEEEEcccc
Confidence            5789999999999999999888644455555554433

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 eukaryotic proteins with this activity.

>PRK06547 hypothetical protein; Provisional

Probab=96.86  E-value=0.0017  Score=58.40  Aligned_cols=30  Identities=23%  Similarity=0.336  Sum_probs=25.8

Q ss_pred             ccCCCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          215 NNETSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       215 ~~~~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      .......|+|.|++|+||||+++.+++.++
T Consensus        11 ~~~~~~~i~i~G~~GsGKTt~a~~l~~~~~   40 (172)
T PRK06547         11 CGGGMITVLIDGRSGSGKTTLAGALAARTG   40 (172)
T ss_pred             hcCCCEEEEEECCCCCCHHHHHHHHHHHhC
Confidence            346677888999999999999999998764

>cd02027 APSK Adenosine 5'-phosphosulfate kinase (APSK) catalyzes the phosphorylation of adenosine 5'-phosphosulfate to form 3'-phosphoadenosine 5'-phosphosulfate (PAPS)

Probab=96.86  E-value=0.011  Score=51.75  Aligned_cols=33  Identities=18%  Similarity=0.339  Sum_probs=25.2

Q ss_pred             EEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEe
Q psy200          222 MYISGPPGTGKSASLNLLVSRAEIKDAFKTIYIN  255 (490)
Q Consensus       222 ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~  255 (490)
                      ++|+|.+|+||||+++.++..+. ......++++
T Consensus         2 i~i~G~~GsGKSTla~~L~~~l~-~~g~~~~~i~   34 (149)
T cd02027           2 IWLTGLSGSGKSTIARALEEKLF-QRGRPVYVLD   34 (149)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHH-HcCCCEEEEc
Confidence            78999999999999999999874 2223445553

The end-product PAPS is a biologically "activated" sulfate form important for the assimilation of inorganic sulfate.

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

Probab=96.85  E-value=0.0093  Score=56.41  Aligned_cols=27  Identities=26%  Similarity=0.415  Sum_probs=23.4

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      .+..+.|.||.|.|||||++.++.-+.
T Consensus        29 ~G~~~~iiGPNGaGKSTLlK~iLGll~   55 (254)
T COG1121          29 KGEITALIGPNGAGKSTLLKAILGLLK   55 (254)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHhCCCc
Confidence            457888999999999999999988553

>PRK14712 conjugal transfer nickase/helicase TraI; Provisional

Probab=96.85  E-value=0.0078  Score=70.50  Aligned_cols=109  Identities=13%  Similarity=0.230  Sum_probs=59.9

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHhhh---cCCceEEEEeccCCCCHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHH-
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRAEI---KDAFKTIYINCNSVRNAASVYETIVNELKLKPGGKSERHQLGAILKY-  292 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l~~---~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~-  292 (490)
                      ...+.++|.|.+||||||+++.+...+..   ..++.++-+ ++   +... ...| .+.     |.....+..+|... 
T Consensus       850 s~dr~~~IqG~AGTGKTT~l~~i~~~~~~l~e~~g~~V~gl-AP---TgkA-a~~L-~e~-----Gi~A~TIasfL~~~~  918 (1623)
T PRK14712        850 TSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRVVGL-GP---THRA-VGEM-RSA-----GVDAQTLASFLHDTQ  918 (1623)
T ss_pred             CCCceEEEEeCCCCCHHHHHHHHHHHHHHHhhccCceEEEE-ec---hHHH-HHHH-HHh-----CchHhhHHHHhcccc
Confidence            34578999999999999999888776531   223333333 11   1111 1111 111     12222233333211 


Q ss_pred             ----Hhc--CCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEEEecC
Q psy200          293 ----FDT--KHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVAN  339 (490)
Q Consensus       293 ----l~~--~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI~~tn  339 (490)
                          ...  .....||||||+-.+.......|+.++.   ..+.++++||-+.
T Consensus       919 ~~~~~~~~~~~~~~llIVDEASMV~~~~m~~ll~~~~---~~garvVLVGD~~  968 (1623)
T PRK14712        919 LQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIA---AGGGRAVASGDTD  968 (1623)
T ss_pred             chhhcccCCCCCCcEEEEEccccccHHHHHHHHHhhh---hCCCEEEEEcchh
Confidence                000  1234699999999987654444444433   3467999998664

>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=96.84  E-value=0.0038  Score=58.01  Aligned_cols=94  Identities=20%  Similarity=0.303  Sum_probs=58.5

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCC-CCHHHHHHHHHHHhcC-------CCCCCc-HHHH--
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSV-RNAASVYETIVNELKL-------KPGGKS-ERHQ--  285 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~-~~~~~l~~~i~~~l~~-------~~~~~s-~~~~--  285 (490)
                      ..+..++|.|++|+|||+|+..+++...  .+ .++++-|..- ....++++++...-..       ...... ....  
T Consensus        13 g~Gqr~~I~g~~g~GKt~Ll~~i~~~~~--~d-~~V~~~iGer~~Ev~~~~~~~~~~~~~~~t~vv~~t~~~~~~~r~~~   89 (215)
T PF00006_consen   13 GRGQRIGIFGGAGVGKTVLLQEIANNQD--AD-VVVYALIGERGREVTEFIEELKGEGALERTVVVAATSDEPPAARYRA   89 (215)
T ss_dssp             ETTSEEEEEESTTSSHHHHHHHHHHHCT--TT-EEEEEEESECHHHHHHHHHHHHHTTGGGGEEEEEEETTS-HHHHHHH
T ss_pred             ccCCEEEEEcCcccccchhhHHHHhccc--cc-ceeeeeccccchhHHHHHHHHhhcccccccccccccchhhHHHHhhh
Confidence            4678999999999999999999999874  22 3366666543 2344555555433100       011111 1111  


Q ss_pred             ---HHHHHHHHhcCCCeEEEEEecCcccccc
Q psy200          286 ---LGAILKYFDTKHKSILLILDEIDALESR  313 (490)
Q Consensus       286 ---~~~l~~~l~~~~~~~vI~IDEid~l~~~  313 (490)
                         .-.+.+++...++.++||+|++-++...
T Consensus        90 ~~~a~t~AEyfrd~G~dVlli~Dsltr~a~A  120 (215)
T PF00006_consen   90 PYTALTIAEYFRDQGKDVLLIIDSLTRWAQA  120 (215)
T ss_dssp             HHHHHHHHHHHHHTTSEEEEEEETHHHHHHH
T ss_pred             hccchhhhHHHhhcCCceeehhhhhHHHHHH
Confidence               1234455666789999999999887643

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 ....

>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=96.84  E-value=0.00087  Score=57.99  Aligned_cols=24  Identities=38%  Similarity=0.657  Sum_probs=21.4

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHhh
Q psy200          221 SMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      .++++|+||+||||+++.++..++
T Consensus         1 lii~~G~pgsGKSt~a~~l~~~~~   24 (143)
T PF13671_consen    1 LIILCGPPGSGKSTLAKRLAKRLG   24 (143)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHST
T ss_pred             CEEEECCCCCCHHHHHHHHHHHCC
Confidence            378999999999999999998764

...

>PRK09302 circadian clock protein KaiC; Reviewed

Probab=96.84  E-value=0.011  Score=62.82  Aligned_cols=90  Identities=16%  Similarity=0.191  Sum_probs=55.8

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCC---------------------
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLK---------------------  276 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~---------------------  276 (490)
                      .+..++|+|+||+|||+++..++.+.....+-.++|++...  +..++...+.. ++..                     
T Consensus        30 ~Gs~~li~G~pGsGKT~l~~qf~~~~~~~~ge~~lyis~ee--~~~~i~~~~~~-~g~d~~~~~~~g~l~~~~~~~~~~~  106 (509)
T PRK09302         30 KGRPTLVSGTAGTGKTLFALQFLVNGIKRFDEPGVFVTFEE--SPEDIIRNVAS-FGWDLQKLIDEGKLFILDASPDPSE  106 (509)
T ss_pred             CCcEEEEEeCCCCCHHHHHHHHHHHHHHhcCCCEEEEEccC--CHHHHHHHHHH-cCCCHHHHhhCCeEEEEecCccccc
Confidence            56789999999999999999987654433245677886554  44554443321 2210                     


Q ss_pred             ---CCCCcHHHHHHHHHHHHhcCCCeEEEEEecCcccc
Q psy200          277 ---PGGKSERHQLGAILKYFDTKHKSILLILDEIDALE  311 (490)
Q Consensus       277 ---~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~  311 (490)
                         ......+.+...+.+++.. .++..|+||-+..+.
T Consensus       107 ~~~~~~~~~~~l~~~l~~~i~~-~~~~~vVIDSls~l~  143 (509)
T PRK09302        107 QEEAGEYDLEALFIRIEYAIDK-IGAKRVVLDSIEALF  143 (509)
T ss_pred             ccccccccHHHHHHHHHHHHHh-hCCCEEEECCHHHHH
Confidence               0001234455555555544 345689999998764

>PRK13894 conjugal transfer ATPase TrbB; Provisional

Probab=96.84  E-value=0.056  Score=53.56  Aligned_cols=34  Identities=18%  Similarity=0.456  Sum_probs=26.4

Q ss_pred             HHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHh
Q psy200          208 QFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRA  243 (490)
Q Consensus       208 ~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l  243 (490)
                      ++|..++.  ..++++|+|++|+||||++++++..+
T Consensus       139 ~~L~~~v~--~~~~ilI~G~tGSGKTTll~aL~~~~  172 (319)
T PRK13894        139 EAIIAAVR--AHRNILVIGGTGSGKTTLVNAIINEM  172 (319)
T ss_pred             HHHHHHHH--cCCeEEEECCCCCCHHHHHHHHHHhh
Confidence            44444333  35789999999999999999998764

>TIGR01587 cas3_core CRISPR-associated helicase Cas3

Probab=96.84  E-value=0.0048  Score=62.36  Aligned_cols=39  Identities=18%  Similarity=0.319  Sum_probs=25.3

Q ss_pred             EEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEEEec
Q psy200          300 ILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVA  338 (490)
Q Consensus       300 ~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI~~t  338 (490)
                      .+|||||+|.+.......+..++......+.+++++.+|
T Consensus       126 ~~iViDE~h~~~~~~~~~l~~~l~~l~~~~~~~i~~SAT  164 (358)
T TIGR01587       126 SLLIFDEVHFYDEYTLALILAVLEVLKDNDVPILLMSAT  164 (358)
T ss_pred             CEEEEeCCCCCCHHHHHHHHHHHHHHHHcCCCEEEEecC
Confidence            489999999998654444444443322345677777776

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

>PRK09694 helicase Cas3; Provisional

Probab=96.83  E-value=0.0033  Score=70.06  Aligned_cols=41  Identities=20%  Similarity=0.361  Sum_probs=31.3

Q ss_pred             eEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEEEecC
Q psy200          299 SILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVAN  339 (490)
Q Consensus       299 ~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI~~tn  339 (490)
                      ..+|||||+|.+.......|..++++....+.++|++.+|=
T Consensus       440 ~svvIiDEVHAyD~ym~~lL~~~L~~l~~~g~~vIllSATL  480 (878)
T PRK09694        440 RSVLIVDEVHAYDAYMYGLLEAVLKAQAQAGGSVILLSATL  480 (878)
T ss_pred             cCeEEEechhhCCHHHHHHHHHHHHHHHhcCCcEEEEeCCC
Confidence            44999999999987666677777777555567788877773

>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=96.83  E-value=0.0077  Score=52.40  Aligned_cols=89  Identities=19%  Similarity=0.167  Sum_probs=49.4

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCCCCCCcHHH-HHHHHHHHHhc
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKPGGKSERH-QLGAILKYFDT  295 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~~~s~~~-~~~~l~~~l~~  295 (490)
                      ..+..+.|.|+.|+|||||++.++..+...  -.-++++...             .+..... .+..+ -+-.+..++. 
T Consensus        24 ~~Ge~~~i~G~nGsGKStLl~~l~G~~~~~--~G~i~~~~~~-------------~i~~~~~-lS~G~~~rv~laral~-   86 (144)
T cd03221          24 NPGDRIGLVGRNGAGKSTLLKLIAGELEPD--EGIVTWGSTV-------------KIGYFEQ-LSGGEKMRLALAKLLL-   86 (144)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHcCCCCCC--ceEEEECCeE-------------EEEEEcc-CCHHHHHHHHHHHHHh-
Confidence            456788999999999999999998765421  1223332110             0000000 12222 2223344444 


Q ss_pred             CCCeEEEEEecCccc-cccCHHHHHHhHh
Q psy200          296 KHKSILLILDEIDAL-ESRKQTILYTIFE  323 (490)
Q Consensus       296 ~~~~~vI~IDEid~l-~~~~~~~L~~l~~  323 (490)
                       .++-++++||--.- .......+..++.
T Consensus        87 -~~p~illlDEP~~~LD~~~~~~l~~~l~  114 (144)
T cd03221          87 -ENPNLLLLDEPTNHLDLESIEALEEALK  114 (144)
T ss_pred             -cCCCEEEEeCCccCCCHHHHHHHHHHHH
Confidence             35679999998754 3334555655554

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.

>cd03280 ABC_MutS2 MutS2 homologs in bacteria and eukaryotes

Probab=96.82  E-value=0.0018  Score=59.85  Aligned_cols=21  Identities=33%  Similarity=0.556  Sum_probs=19.8

Q ss_pred             CeEEEECCCCCcHHHHHHHHH
Q psy200          220 GSMYISGPPGTGKSASLNLLV  240 (490)
Q Consensus       220 ~~ill~GppGtGKTtla~~l~  240 (490)
                      +.++|+||.|+||||+++.++
T Consensus        29 ~~~~ltG~Ng~GKStll~~i~   49 (200)
T cd03280          29 RVLVITGPNAGGKTVTLKTLG   49 (200)
T ss_pred             eEEEEECCCCCChHHHHHHHH
Confidence            579999999999999999988

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 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, a

>TIGR02760 TraI_TIGR conjugative transfer relaxase protein TraI

Probab=96.81  E-value=0.0074  Score=73.20  Aligned_cols=130  Identities=18%  Similarity=0.236  Sum_probs=68.5

Q ss_pred             hHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHH-------HH
Q psy200          199 REVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETI-------VN  271 (490)
Q Consensus       199 re~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i-------~~  271 (490)
                      -+++.+.+..++.     ...+.++|.|++|||||++++.+.+.+. ..++.++-+ ++.......+-..+       ..
T Consensus       431 s~~Q~~Av~~il~-----s~~~v~ii~G~aGTGKTt~l~~l~~~~~-~~G~~V~~l-APTgrAA~~L~e~~g~~A~Ti~~  503 (1960)
T TIGR02760       431 SPSNKDAVSTLFT-----STKRFIIINGFGGTGSTEIAQLLLHLAS-EQGYEIQII-TAGSLSAQELRQKIPRLASTFIT  503 (1960)
T ss_pred             CHHHHHHHHHHHh-----CCCCeEEEEECCCCCHHHHHHHHHHHHH-hcCCeEEEE-eCCHHHHHHHHHHhcchhhhHHH
Confidence            3455555555553     4568999999999999999999988764 234444433 22221222222111       11


Q ss_pred             HhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEEEecC
Q psy200          272 ELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVAN  339 (490)
Q Consensus       272 ~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI~~tn  339 (490)
                      -+.....+.....+..++.. -......-||||||+..+...   .+..|++.....+.++++||-+.
T Consensus       504 ~l~~l~~~~~~~tv~~fl~~-~~~l~~~~vlIVDEAsMl~~~---~~~~Ll~~a~~~garvVlvGD~~  567 (1960)
T TIGR02760       504 WVKNLFNDDQDHTVQGLLDK-SSPFSNKDIFVVDEANKLSNN---ELLKLIDKAEQHNSKLILLNDSA  567 (1960)
T ss_pred             HHHhhcccccchhHHHhhcc-cCCCCCCCEEEEECCCCCCHH---HHHHHHHHHhhcCCEEEEEcChh
Confidence            11100111111111111110 000023459999999998654   34455544434678999997664

This protein is a component of the relaxosome complex. In the process of conjugative plasmid transfer the realaxosome binds to the plasmid at the oriT (origin of transfer) site. The relaxase protein TraI mediates the single-strand nicking and ATP-dependent unwinding (relaxation, helicase activity) of the plasmid molecule. These two activities reside in separate domains of the protein.

>cd03247 ABCC_cytochrome_bd The CYD subfamily implicated in cytochrome bd biogenesis

Probab=96.80  E-value=0.0086  Score=54.09  Aligned_cols=28  Identities=29%  Similarity=0.470  Sum_probs=24.5

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      ..+..+.|.|+.|+|||||++.++..+.
T Consensus        26 ~~Ge~~~i~G~nGsGKStLl~~l~G~~~   53 (178)
T cd03247          26 KQGEKIALLGRSGSGKSTLLQLLTGDLK   53 (178)
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHhccCC
Confidence            3577899999999999999999988754

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.

>PTZ00293 thymidine kinase; Provisional

Probab=96.79  E-value=0.001  Score=61.15  Aligned_cols=26  Identities=23%  Similarity=0.217  Sum_probs=21.7

Q ss_pred             CCeEEEECCCCCcHHH-HHHHHHHHhh
Q psy200          219 SGSMYISGPPGTGKSA-SLNLLVSRAE  244 (490)
Q Consensus       219 ~~~ill~GppGtGKTt-la~~l~~~l~  244 (490)
                      +..-+++||.|+|||+ |++.+.+...
T Consensus         4 G~i~vi~GpMfSGKTteLLr~i~~y~~   30 (211)
T PTZ00293          4 GTISVIIGPMFSGKTTELMRLVKRFTY   30 (211)
T ss_pred             eEEEEEECCCCChHHHHHHHHHHHHHH
Confidence            4577899999999999 9998876654

>KOG3928|consensus

Probab=96.79  E-value=0.058  Score=53.86  Aligned_cols=59  Identities=25%  Similarity=0.236  Sum_probs=37.5

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEE
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYI  254 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v  254 (490)
                      ..+..|+...+-+. ..+..-...+..-++|+|++|||||-++..+.+... ..++-++.+
T Consensus       155 a~lLVRkpalel~~-~~r~~d~~~P~~r~vL~Ge~GtGKSiaL~qa~h~a~-~~~wlIlhi  213 (461)
T KOG3928|consen  155 AVLLVRKPALELLL-YKRLVDPMHPVKRFVLDGEPGTGKSIALAQAVHYAA-DQKWLILHI  213 (461)
T ss_pred             chheechHHHHHHH-HhhhccccCcceEEEEeCCCCCchhhHHHHHHHHHh-cCCeEEEEC
Confidence            45667777765433 333221234667899999999999988777766553 335555554

>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=96.79  E-value=0.001  Score=56.19  Aligned_cols=22  Identities=41%  Similarity=0.593  Sum_probs=20.6

Q ss_pred             EEEECCCCCcHHHHHHHHHHHh
Q psy200          222 MYISGPPGTGKSASLNLLVSRA  243 (490)
Q Consensus       222 ill~GppGtGKTtla~~l~~~l  243 (490)
                      |+|.|++|+||||+++.+.+.+
T Consensus         1 I~i~G~~GsGKtTia~~L~~~~   22 (129)
T PF13238_consen    1 IGISGIPGSGKTTIAKELAERL   22 (129)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHH
T ss_pred             CEEECCCCCCHHHHHHHHHHHH
Confidence            6899999999999999999985

...

>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=96.79  E-value=0.0078  Score=54.11  Aligned_cols=28  Identities=36%  Similarity=0.555  Sum_probs=24.5

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      ..+..+.|.|+.|+|||||++.++..+.
T Consensus        26 ~~Ge~~~i~G~nGsGKStLl~~l~G~~~   53 (173)
T cd03246          26 EPGESLAIIGPSGSGKSTLARLILGLLR   53 (173)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHhccC
Confidence            4567899999999999999999988754

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

>smart00534 MUTSac ATPase domain of DNA mismatch repair MUTS family

Probab=96.78  E-value=0.0014  Score=59.66  Aligned_cols=20  Identities=35%  Similarity=0.416  Sum_probs=18.5

Q ss_pred             EEEECCCCCcHHHHHHHHHH
Q psy200          222 MYISGPPGTGKSASLNLLVS  241 (490)
Q Consensus       222 ill~GppGtGKTtla~~l~~  241 (490)
                      ++|+|+.|.||||+++.++-
T Consensus         2 ~~ltG~N~~GKst~l~~i~~   21 (185)
T smart00534        2 VIITGPNMGGKSTYLRQVGL   21 (185)
T ss_pred             EEEECCCCCcHHHHHHHHHH
Confidence            68999999999999999984

>TIGR00665 DnaB replicative DNA helicase

Probab=96.78  E-value=0.016  Score=60.26  Aligned_cols=52  Identities=17%  Similarity=0.254  Sum_probs=36.1

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHH
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVN  271 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~  271 (490)
                      ++..++|.|.||+|||+++..++..+....+..+++++.-.  +..++...++.
T Consensus       194 ~G~l~vi~g~pg~GKT~~~l~~a~~~a~~~g~~vl~~SlEm--~~~~i~~R~~~  245 (434)
T TIGR00665       194 PSDLIILAARPSMGKTAFALNIAENAAIKEGKPVAFFSLEM--SAEQLAMRMLS  245 (434)
T ss_pred             CCeEEEEEeCCCCChHHHHHHHHHHHHHhCCCeEEEEeCcC--CHHHHHHHHHH
Confidence            45578899999999999999998876544455666664332  45555544443

This model describes the helicase DnaB, a homohexameric protein required for DNA replication. The homohexamer can form a ring around a single strand of DNA near a replication fork. An intein of 400 residues is found at a conserved location in DnaB of Synechocystis PCC6803, Rhodothermus marinus (both experimentally confirmed), and Mycobacterium tuberculosis. The intein removes itself by a self-splicing reaction. The seed alignment contains inteins so that the model built from the seed alignment will model a low cost at common intein insertion sites.

>PTZ00088 adenylate kinase 1; Provisional

Probab=96.77  E-value=0.0049  Score=58.00  Aligned_cols=25  Identities=24%  Similarity=0.473  Sum_probs=22.4

Q ss_pred             CeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          220 GSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       220 ~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      ..++|.|+||+||||+++.+++.++
T Consensus         7 mrIvl~G~PGsGK~T~a~~La~~~g   31 (229)
T PTZ00088          7 LKIVLFGAPGVGKGTFAEILSKKEN   31 (229)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHhC
Confidence            4589999999999999999999864

>PLN02459 probable adenylate kinase

Probab=96.75  E-value=0.0049  Score=58.75  Aligned_cols=88  Identities=13%  Similarity=0.087  Sum_probs=47.1

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCC-----CHHHHHHHHHHHhcCCCCCCcHHHHHHHHHH
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVR-----NAASVYETIVNELKLKPGGKSERHQLGAILK  291 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~-----~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~  291 (490)
                      +.+..++|.|+||+||+|++..+++.++      +.++++..+.     ....+-..+-..+. ...-...+-+...+.+
T Consensus        27 ~~~~~ii~~G~PGsGK~T~a~~la~~~~------~~~is~gdllR~ei~~~t~lg~~i~~~~~-~G~lVPdeiv~~ll~~   99 (261)
T PLN02459         27 GRNVNWVFLGCPGVGKGTYASRLSKLLG------VPHIATGDLVREEIKSSGPLGAQLKEIVN-QGKLVPDEIIFSLLSK   99 (261)
T ss_pred             cCccEEEEECCCCCCHHHHHHHHHHHhC------CcEEeCcHHHHHHHhccchhHHHHHHHHH-cCCccCHHHHHHHHHH
Confidence            3344688899999999999999998864      3444433321     00011111111111 1111233444555666


Q ss_pred             HHhcC--CCeEEEEEecCcccc
Q psy200          292 YFDTK--HKSILLILDEIDALE  311 (490)
Q Consensus       292 ~l~~~--~~~~vI~IDEid~l~  311 (490)
                      .+...  ....-+|||-+.+-.
T Consensus       100 ~l~~~~~~~~~g~iLDGFPRt~  121 (261)
T PLN02459        100 RLEAGEEEGESGFILDGFPRTV  121 (261)
T ss_pred             HHhcccccCCceEEEeCCCCCH
Confidence            55432  123468899988853

>PRK14737 gmk guanylate kinase; Provisional

Probab=96.75  E-value=0.0054  Score=55.87  Aligned_cols=26  Identities=27%  Similarity=0.372  Sum_probs=23.2

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHh
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRA  243 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l  243 (490)
                      .+..++|+||+|+|||+|++.+.+..
T Consensus         3 ~~~~ivl~GpsG~GK~tl~~~l~~~~   28 (186)
T PRK14737          3 SPKLFIISSVAGGGKSTIIQALLEEH   28 (186)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHhcC
Confidence            46789999999999999999998864

>PRK10646 ADP-binding protein; Provisional

Probab=96.75  E-value=0.0091  Score=52.12  Aligned_cols=45  Identities=13%  Similarity=0.146  Sum_probs=35.6

Q ss_pred             hHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhh
Q psy200          199 REVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEI  245 (490)
Q Consensus       199 re~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~  245 (490)
                      .+++..++.+.|...+  ..+..++|.|.=|+||||+++.+++.++.
T Consensus        10 s~~~t~~l~~~la~~l--~~g~vi~L~GdLGaGKTtf~rgl~~~Lg~   54 (153)
T PRK10646         10 DEQATLDLGARVAKAC--DGATVIYLYGDLGAGKTTFSRGFLQALGH   54 (153)
T ss_pred             CHHHHHHHHHHHHHhC--CCCcEEEEECCCCCCHHHHHHHHHHHcCC
Confidence            3456667777776644  33568999999999999999999999974

>KOG0058|consensus

Probab=96.75  E-value=0.0097  Score=63.43  Aligned_cols=28  Identities=29%  Similarity=0.482  Sum_probs=24.1

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      .++..+.|+||.|.||||++..+.+-+.
T Consensus       492 ~pGe~vALVGPSGsGKSTiasLL~rfY~  519 (716)
T KOG0058|consen  492 RPGEVVALVGPSGSGKSTIASLLLRFYD  519 (716)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHHhcC
Confidence            4677899999999999999998877654

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

Probab=96.74  E-value=0.012  Score=56.59  Aligned_cols=96  Identities=16%  Similarity=0.264  Sum_probs=55.7

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCC-CCHHHHHHHHHHHhcC-------CCCCC-cHHH---
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSV-RNAASVYETIVNELKL-------KPGGK-SERH---  284 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~-~~~~~l~~~i~~~l~~-------~~~~~-s~~~---  284 (490)
                      ..++.++|.|++|+|||+|+..+++.........++++-+..- ....++++++...=..       ..... ....   
T Consensus        67 g~GQr~~If~~~G~GKTtLa~~i~~~i~~~~~~~~V~~~iGer~~Ev~e~~~~~~~~~~~~~tvvv~~t~d~~~~~r~~~  146 (274)
T cd01133          67 AKGGKIGLFGGAGVGKTVLIMELINNIAKAHGGYSVFAGVGERTREGNDLYHEMKESGVLSKTALVYGQMNEPPGARARV  146 (274)
T ss_pred             ccCCEEEEecCCCCChhHHHHHHHHHHHhcCCCEEEEEEeccCcHHHHHHHHHHHhcCCcceeEEEEECCCCCHHHHHHH
Confidence            5678999999999999999999998876332223444444332 2334555555432110       00111 1111   


Q ss_pred             --HHHHHHHHHhcC-CCeEEEEEecCccccc
Q psy200          285 --QLGAILKYFDTK-HKSILLILDEIDALES  312 (490)
Q Consensus       285 --~~~~l~~~l~~~-~~~~vI~IDEid~l~~  312 (490)
                        ..-.+.+++... ++.++|++|++-+...
T Consensus       147 ~~~a~~~AEyfr~~~g~~Vl~~~Dsltr~a~  177 (274)
T cd01133         147 ALTGLTMAEYFRDEEGQDVLLFIDNIFRFTQ  177 (274)
T ss_pred             HHHHHHHHHHHHHhcCCeEEEEEeChhHHHH
Confidence              112344555544 7888999998777653

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.

>cd03282 ABC_MSH4_euk MutS4 homolog in eukaryotes

Probab=96.74  E-value=0.002  Score=59.64  Aligned_cols=25  Identities=32%  Similarity=0.364  Sum_probs=21.5

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHH
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~  242 (490)
                      .+..++|+||.|+|||++++.++..
T Consensus        28 ~~~~~~l~G~n~~GKstll~~i~~~   52 (204)
T cd03282          28 SSRFHIITGPNMSGKSTYLKQIALL   52 (204)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHH
Confidence            4478999999999999999998644

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

>PRK03839 putative kinase; Provisional

Probab=96.73  E-value=0.0015  Score=59.08  Aligned_cols=24  Identities=33%  Similarity=0.605  Sum_probs=22.1

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHhh
Q psy200          221 SMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      .|+|.|+||+||||+++.+++.++
T Consensus         2 ~I~l~G~pGsGKsT~~~~La~~~~   25 (180)
T PRK03839          2 IIAITGTPGVGKTTVSKLLAEKLG   25 (180)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhC
Confidence            488999999999999999999875

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=96.72  E-value=0.012  Score=61.92  Aligned_cols=47  Identities=17%  Similarity=0.235  Sum_probs=32.6

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHH
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVY  266 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~  266 (490)
                      .+..++|+|+||+|||+++..++.+-....+-..+|+....  +..++.
T Consensus        20 ~g~~~Li~G~pGsGKT~la~qfl~~g~~~~ge~~lyvs~eE--~~~~l~   66 (484)
T TIGR02655        20 IGRSTLVSGTSGTGKTLFSIQFLYNGIIHFDEPGVFVTFEE--SPQDII   66 (484)
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHHHHhCCCCEEEEEEec--CHHHHH
Confidence            57789999999999999999986653222234667776542  444443

Members of this family are the circadian clock protein KaiC, part of the kaiABC operon that controls circadian rhythm. It may be universal in Cyanobacteria. Each member has two copies of the KaiC domain (Pfam model pfam06745), which is also found in other proteins. KaiC performs autophosphorylation and acts as its own transcriptional repressor.

>KOG1808|consensus

Probab=96.72  E-value=0.003  Score=73.99  Aligned_cols=148  Identities=16%  Similarity=0.215  Sum_probs=98.2

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCC
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFDTKHK  298 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~  298 (490)
                      ...++|-||.|+|||.++..++...+    ..++.++.....+..+++......-.+.   ....+  ..+..++..   
T Consensus       440 ~~pillqG~tssGKtsii~~la~~~g----~~~vrinnhehtd~qeyig~y~~~~~g~---l~fre--g~LV~Alr~---  507 (1856)
T KOG1808|consen  440 KFPILLQGPTSSGKTSIIKELARATG----KNIVRINNHEHTDLQEYIGTYVADDNGD---LVFRE--GVLVQALRN---  507 (1856)
T ss_pred             CCCeEEecCcCcCchhHHHHHHHHhc----cCceehhccccchHHHHHHhhhcCCCCC---eeeeh--hHHHHHHHh---
Confidence            45899999999999999999999875    6788898888777666665333222211   11111  123333332   


Q ss_pred             eEEEEEecCccccccCHHHHHHhHhCCC---C--------CCCcEEEEEecCCCC---hhHhhhHHhhhccCCCCeeEEe
Q psy200          299 SILLILDEIDALESRKQTILYTIFEWPS---I--------PGSKLVLVGVANALD---LTDRMLPRLQANVTLQPTLMNF  364 (490)
Q Consensus       299 ~~vI~IDEid~l~~~~~~~L~~l~~~~~---~--------~~~~vilI~~tn~~~---~~~~l~~~l~~R~~~~~~~i~~  364 (490)
                      -+.+|+||+........++|.+++++..   +        .+..+.+.++-|...   -...+.+.++.||.    .++|
T Consensus       508 G~~~vlD~lnla~~dvL~aLnrllddnRel~ipe~~rlv~~h~~f~lfatqn~~~~y~grk~lsRa~~~rf~----e~~f  583 (1856)
T KOG1808|consen  508 GDWIVLDELNLAPHDVLEALNRLLDDNRELFIPETQRLVKAHPEFMLFATQNPPGTYGGRKILSRALRNRFI----ELHF  583 (1856)
T ss_pred             CCEEEeccccccchHHHHHHHhhhhhhccccccccceeeccCcchhhhhhccCccccchhhhhhhcccccch----hhhh
Confidence            3599999999998888888888877621   1        233344444444332   12334567777875    7899


Q ss_pred             CCCCHHHHHHHHHHHHhc
Q psy200          365 APYSREQILEIISQKLKQ  382 (490)
Q Consensus       365 ~pls~~e~~~il~~~l~~  382 (490)
                      ..+..+++..++.+++..
T Consensus       584 ~~~~e~e~~~i~~~~~~i  601 (1856)
T KOG1808|consen  584 DDIGEEELEEILEHRCGI  601 (1856)
T ss_pred             hhcCchhhhhhhcccccC
Confidence            999999999888877654

>PF00406 ADK: Adenylate kinase; InterPro: IPR000850 Adenylate kinases (ADK) are phosphotransferases that catalyse the reversible reaction AMP + MgATP = ADP + MgADP an essential reaction for many processes in living cells

Probab=96.71  E-value=0.002  Score=56.55  Aligned_cols=21  Identities=43%  Similarity=0.732  Sum_probs=19.3

Q ss_pred             EECCCCCcHHHHHHHHHHHhh
Q psy200          224 ISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       224 l~GppGtGKTtla~~l~~~l~  244 (490)
                      |.||||+||||+++.+++.++
T Consensus         1 i~G~PgsGK~t~~~~la~~~~   21 (151)
T PF00406_consen    1 ILGPPGSGKGTQAKRLAKRYG   21 (151)
T ss_dssp             EEESTTSSHHHHHHHHHHHHT
T ss_pred             CcCCCCCChHHHHHHHHHhcC
Confidence            689999999999999999864

Two ADK isozymes have been identified in mammalian cells. These specifically bind AMP and favour binding to ATP over other nucleotide triphosphates (AK1 is cytosolic and AK2 is located in the mitochondria). A third ADK has been identified in bovine heart and human cells [], this is a mitochondrial GTP:AMP phosphotransferase, also specific for the phosphorylation of AMP, but can only use GTP or ITP as a substrate []. ADK has also been identified in different bacterial species and in yeast []. Two further enzymes are known to be related to the ADK family, i.e. yeast uridine monophosphokinase and slime mold UMP-CMP kinase. Within the ADK family there are several conserved regions, including the ATP-binding domains. One of the most conserved areas includes an Arg residue, whose modification inactivates the enzyme, together with an Asp that resides in the catalytic cleft of the enzyme and participates in a salt bridge.; GO: 0005524 ATP binding, 0019205 nucleobase-containing compound kinase activity, 0006139 nucleobase-containing compound metabolic process; PDB: 1ZD8_A 3TLX_D 1TEV_A 1ZAK_B 3CM0_A 3ADK_A 1ZIP_A 1ZIO_A 1ZIN_A 3NDP_A ....

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

Probab=96.71  E-value=0.0036  Score=64.21  Aligned_cols=104  Identities=20%  Similarity=0.304  Sum_probs=58.9

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHh
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNEL  273 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l  273 (490)
                      +.+..-....+.+..++.     .+.+.+|++||.|+||||++.++.+++.... ..++.+.     ++-++...=+.++
T Consensus       238 ~~Lg~~~~~~~~~~~~~~-----~p~GliLvTGPTGSGKTTTLY~~L~~ln~~~-~nI~TiE-----DPVE~~~~gI~Q~  306 (500)
T COG2804         238 EKLGMSPFQLARLLRLLN-----RPQGLILVTGPTGSGKTTTLYAALSELNTPE-RNIITIE-----DPVEYQLPGINQV  306 (500)
T ss_pred             HHhCCCHHHHHHHHHHHh-----CCCeEEEEeCCCCCCHHHHHHHHHHHhcCCC-ceEEEee-----CCeeeecCCccee
Confidence            445555555666666664     5678899999999999999999999986222 2233332     1111100000111


Q ss_pred             cC-CCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCcccccc
Q psy200          274 KL-KPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESR  313 (490)
Q Consensus       274 ~~-~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~  313 (490)
                      .. +..|.+...   .+...+.  ..|-||+|.||-.....
T Consensus       307 qVN~k~gltfa~---~LRa~LR--qDPDvImVGEIRD~ETA  342 (500)
T COG2804         307 QVNPKIGLTFAR---ALRAILR--QDPDVIMVGEIRDLETA  342 (500)
T ss_pred             ecccccCCCHHH---HHHHHhc--cCCCeEEEeccCCHHHH
Confidence            11 122333333   3344444  34789999999886543

>PRK07594 type III secretion system ATPase SsaN; Validated

Probab=96.71  E-value=0.078  Score=54.46  Aligned_cols=96  Identities=16%  Similarity=0.231  Sum_probs=57.1

Q ss_pred             cCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhc--------CCCCCCcHHHH--
Q psy200          216 NETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELK--------LKPGGKSERHQ--  285 (490)
Q Consensus       216 ~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~--------~~~~~~s~~~~--  285 (490)
                      -..+..+.|.|++|+|||++++.++....  .+..++.+.........+++......=.        ..........+  
T Consensus       152 i~~GqrigI~G~sG~GKSTLL~~I~~~~~--~d~~vi~~iGeRgrEv~efl~~~~~~~~~~rtv~vv~tsd~p~~~r~~a  229 (433)
T PRK07594        152 CGEGQRVGIFSAPGVGKSTLLAMLCNAPD--ADSNVLVLIGERGREVREFIDFTLSEETRKRCVIVVATSDRPALERVRA  229 (433)
T ss_pred             cCCCCEEEEECCCCCCccHHHHHhcCCCC--CCEEEEEEECCCchHHHHHHHHhhccCCcceEEEEEECCCCCHHHHHHH
Confidence            35678999999999999999999987653  3333333333333344455555432100        01111111222  


Q ss_pred             ---HHHHHHHHhcCCCeEEEEEecCcccccc
Q psy200          286 ---LGAILKYFDTKHKSILLILDEIDALESR  313 (490)
Q Consensus       286 ---~~~l~~~l~~~~~~~vI~IDEid~l~~~  313 (490)
                         .-.+.+++...++.++|++|++-+....
T Consensus       230 ~~~a~tiAEyfrd~G~~VLl~~Dsltr~A~A  260 (433)
T PRK07594        230 LFVATTIAEFFRDNGKRVVLLADSLTRYARA  260 (433)
T ss_pred             HHHHHHHHHHHHHCCCcEEEEEeCHHHHHHH
Confidence               2235566666688999999999887644

>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=96.70  E-value=0.0036  Score=56.47  Aligned_cols=28  Identities=29%  Similarity=0.526  Sum_probs=24.3

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      ..+..+.|.|+.|+|||||++.++..+.
T Consensus        23 ~~Ge~~~l~G~nGsGKSTLl~~l~Gl~~   50 (177)
T cd03222          23 KEGEVIGIVGPNGTGKTTAVKILAGQLI   50 (177)
T ss_pred             CCCCEEEEECCCCChHHHHHHHHHcCCC
Confidence            4567899999999999999999987654

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.

>cd01878 HflX HflX subfamily

Probab=96.69  E-value=0.035  Score=51.11  Aligned_cols=25  Identities=24%  Similarity=0.291  Sum_probs=21.8

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHH
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~  242 (490)
                      ....++|.|++|+|||+|++.+...
T Consensus        40 ~~~~I~iiG~~g~GKStLl~~l~~~   64 (204)
T cd01878          40 GIPTVALVGYTNAGKSTLFNALTGA   64 (204)
T ss_pred             CCCeEEEECCCCCCHHHHHHHHhcc
Confidence            3468889999999999999999875

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.

>cd03223 ABCD_peroxisomal_ALDP Peroxisomal ATP-binding cassette transporter (Pat) is involved in the import of very long-chain fatty acids (VLCFA) into the peroxisome

Probab=96.69  E-value=0.021  Score=50.93  Aligned_cols=28  Identities=32%  Similarity=0.523  Sum_probs=24.6

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      ..+..+.|.|+.|+|||||++.++..+.
T Consensus        25 ~~Ge~~~i~G~nGsGKSTLl~~l~G~~~   52 (166)
T cd03223          25 KPGDRLLITGPSGTGKSSLFRALAGLWP   52 (166)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHhcCCC
Confidence            4677899999999999999999988764

The peroxisomal membrane forms a permeability barrier for a wide variety of metabolites required for and formed during fatty acid beta-oxidation. To communicate with the cytoplasm and mitochondria, peroxisomes need dedicated proteins to transport such hydrophilic molecules across their membranes. X-linked adrenoleukodystrophy (X-ALD) is caused by mutations in the ALD gene, which encodes ALDP (adrenoleukodystrophy protein ), a peroxisomal integral membrane protein that is a member of the ATP-binding cassette (ABC) transporter protein family. The disease is characterized by a striking and unpredictable variation in phenotypic expression. Phenotypes include the rapidly progressive childhood cerebral form (CCALD), the milder adult form, adrenomyeloneuropathy (AMN), and variants without neurologic involvement (i.e. asympt

>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=96.68  E-value=0.003  Score=47.34  Aligned_cols=22  Identities=32%  Similarity=0.501  Sum_probs=20.6

Q ss_pred             EEEECCCCCcHHHHHHHHHHHh
Q psy200          222 MYISGPPGTGKSASLNLLVSRA  243 (490)
Q Consensus       222 ill~GppGtGKTtla~~l~~~l  243 (490)
                      +.|.|++|+||||+++.+.+.+
T Consensus         2 i~i~G~~gsGKst~~~~l~~~l   23 (69)
T cd02019           2 IAITGGSGSGKSTVAKKLAEQL   23 (69)
T ss_pred             EEEECCCCCCHHHHHHHHHHHh
Confidence            6789999999999999999986

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.

>KOG0922|consensus

Probab=96.68  E-value=0.033  Score=58.69  Aligned_cols=125  Identities=21%  Similarity=0.295  Sum_probs=70.3

Q ss_pred             HHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCC--HHHHHHHHHHHhcCCCC---
Q psy200          204 EGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRN--AASVYETIVNELKLKPG---  278 (490)
Q Consensus       204 ~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~--~~~l~~~i~~~l~~~~~---  278 (490)
                      ++|...+++      ...++|.|+.|+||||=+-.++.+.+....-.   |-|...+-  .-.+-..+..+.+....   
T Consensus        57 ~~il~~ve~------nqvlIviGeTGsGKSTQipQyL~eaG~~~~g~---I~~TQPRRVAavslA~RVAeE~~~~lG~~V  127 (674)
T KOG0922|consen   57 DQILYAVED------NQVLIVIGETGSGKSTQIPQYLAEAGFASSGK---IACTQPRRVAAVSLAKRVAEEMGCQLGEEV  127 (674)
T ss_pred             HHHHHHHHH------CCEEEEEcCCCCCccccHhHHHHhcccccCCc---EEeecCchHHHHHHHHHHHHHhCCCcCcee
Confidence            345555543      67899999999999999888887765322211   55555543  23455666666654211   


Q ss_pred             -------CC-cHHH------HHHHHHHHHhc--CCCeEEEEEecCccccccCHHHHHHhHhCC--CCCCCcEEEEEec
Q psy200          279 -------GK-SERH------QLGAILKYFDT--KHKSILLILDEIDALESRKQTILYTIFEWP--SIPGSKLVLVGVA  338 (490)
Q Consensus       279 -------~~-s~~~------~~~~l~~~l~~--~~~~~vI~IDEid~l~~~~~~~L~~l~~~~--~~~~~~vilI~~t  338 (490)
                             .. +.+.      ---.|++++..  -.+..||+|||+|.=. -..+.|+.++...  .....++|+..+|
T Consensus       128 GY~IRFed~ts~~TrikymTDG~LLRE~l~Dp~LskYsvIIlDEAHERs-l~TDiLlGlLKki~~~R~~LklIimSAT  204 (674)
T KOG0922|consen  128 GYTIRFEDSTSKDTRIKYMTDGMLLREILKDPLLSKYSVIILDEAHERS-LHTDILLGLLKKILKKRPDLKLIIMSAT  204 (674)
T ss_pred             eeEEEecccCCCceeEEEecchHHHHHHhcCCccccccEEEEechhhhh-hHHHHHHHHHHHHHhcCCCceEEEEeee
Confidence                   00 1110      01134444422  1456799999999832 2345665554322  2234567776666

>COG1936 Predicted nucleotide kinase (related to CMP and AMP kinases) [Nucleotide transport and metabolism]

Probab=96.67  E-value=0.0013  Score=57.72  Aligned_cols=23  Identities=35%  Similarity=0.569  Sum_probs=20.5

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHhh
Q psy200          221 SMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      .++|+|.||+||||+++.+. .++
T Consensus         2 ~I~ITGTPGvGKTT~~~~L~-~lg   24 (180)
T COG1936           2 LIAITGTPGVGKTTVCKLLR-ELG   24 (180)
T ss_pred             eEEEeCCCCCchHHHHHHHH-HhC
Confidence            57899999999999999998 654

>COG1136 SalX ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]

Probab=96.66  E-value=0.027  Score=52.43  Aligned_cols=27  Identities=44%  Similarity=0.581  Sum_probs=22.9

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHh
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRA  243 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l  243 (490)
                      ..+..+.|.||.|+|||||++.+..-.
T Consensus        29 ~~Ge~vaI~GpSGSGKSTLLniig~ld   55 (226)
T COG1136          29 EAGEFVAIVGPSGSGKSTLLNLLGGLD   55 (226)
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHhccc
Confidence            456789999999999999999886544

>PRK00625 shikimate kinase; Provisional

Probab=96.66  E-value=0.0019  Score=58.07  Aligned_cols=24  Identities=21%  Similarity=0.367  Sum_probs=22.3

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHhh
Q psy200          221 SMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      .|+|+|.||+||||+++.+++.++
T Consensus         2 ~I~LiG~pGsGKTT~~k~La~~l~   25 (173)
T PRK00625          2 QIFLCGLPTVGKTSFGKALAKFLS   25 (173)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhC
Confidence            589999999999999999999875

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

Probab=96.65  E-value=0.018  Score=55.51  Aligned_cols=89  Identities=17%  Similarity=0.269  Sum_probs=57.0

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCC------------------C-
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLK------------------P-  277 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~------------------~-  277 (490)
                      ..+..++|+|+||+|||+++..++...... +.+++|+....  +..++...... ++..                  . 
T Consensus        21 p~g~~~lI~G~pGsGKT~f~~qfl~~~~~~-ge~vlyvs~~e--~~~~l~~~~~~-~g~d~~~~~~~g~l~i~d~~~~~~   96 (260)
T COG0467          21 PRGSVVLITGPPGTGKTIFALQFLYEGARE-GEPVLYVSTEE--SPEELLENARS-FGWDLEVYIEKGKLAILDAFLSEK   96 (260)
T ss_pred             cCCcEEEEEcCCCCcHHHHHHHHHHHHHhc-CCcEEEEEecC--CHHHHHHHHHH-cCCCHHHHhhcCCEEEEEcccccc
Confidence            367899999999999999999998887533 56778886554  34444443322 2110                  0 


Q ss_pred             ------C--CCcHHHHHHHHHHHHhcCCCeEEEEEecCccc
Q psy200          278 ------G--GKSERHQLGAILKYFDTKHKSILLILDEIDAL  310 (490)
Q Consensus       278 ------~--~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l  310 (490)
                            .  ......+...+.++....+ ...+++|-+-.+
T Consensus        97 ~~~~~~~~~~~~~~~l~~~I~~~~~~~~-~~~~ViDsi~~~  136 (260)
T COG0467          97 GLVSIVVGDPLDLEELLDRIREIVEKEG-ADRVVIDSITEL  136 (260)
T ss_pred             ccccccccCCccHHHHHHHHHHHHHHhC-CCEEEEeCCchH
Confidence                  0  1234455666666665433 668999998854

>PF05707 Zot: Zonular occludens toxin (Zot); InterPro: IPR008900 This entry consists of bacterial and viral proteins which are very similar to the Zonular occludens toxin (Zot)

Probab=96.64  E-value=0.003  Score=57.98  Aligned_cols=19  Identities=37%  Similarity=0.485  Sum_probs=13.8

Q ss_pred             eEEEECCCCCcHHHHHHHH
Q psy200          221 SMYISGPPGTGKSASLNLL  239 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l  239 (490)
                      ..+++|.||+|||..|-..
T Consensus         2 I~~~~G~pGsGKS~~av~~   20 (193)
T PF05707_consen    2 IYLITGKPGSGKSYYAVSY   20 (193)
T ss_dssp             EEEEE--TTSSHHHHHHHH
T ss_pred             EEEEEcCCCCcHhHHHHHH
Confidence            4689999999999987544

Zot is elaborated by bacteriophage present in toxigenic strains of Vibrio cholerae. Zot is a single polypeptide chain of 44.8 kDa, with the ability to reversibly alter intestinal epithelial tight junctions, allowing the passage of macromolecules through mucosal barriers.; PDB: 2R2A_B.

>cd04160 Arfrp1 Arfrp1 subfamily

Probab=96.64  E-value=0.045  Score=48.36  Aligned_cols=23  Identities=30%  Similarity=0.320  Sum_probs=19.9

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHh
Q psy200          221 SMYISGPPGTGKSASLNLLVSRA  243 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~l  243 (490)
                      +++|.|++|+|||+|++.+....
T Consensus         1 ~i~~vG~~~~GKstLi~~l~~~~   23 (167)
T cd04160           1 SVLILGLDNAGKTTFLEQLKTLF   23 (167)
T ss_pred             CEEEEecCCCCHHHHHHHHhhhc
Confidence            47899999999999999987643

Arfrp1 (Arf-related protein 1), formerly known as ARP, is a membrane-associated Arf family member that lacks the N-terminal myristoylation motif. Arfrp1 is mainly associated with the trans-Golgi compartment and the trans-Golgi network, where it regulates the targeting of Arl1 and the GRIP domain-containing proteins, golgin-97 and golgin-245, onto Golgi membranes. It is also involved in the anterograde transport of the vesicular stomatitis virus G protein from the Golgi to the plasma membrane, and in the retrograde transport of TGN38 and Shiga toxin from endosomes to the trans-Golgi network. Arfrp1 also inhibits Arf/Sec7-dependent activation of phospholipase D. Deletion of Arfrp1 in mice causes embryonic lethality at the gastrulation stage and apoptosis of mesodermal cells, indicating its importance in development.

>cd01852 AIG1 AIG1 (avrRpt2-induced gene 1)

Probab=96.62  E-value=0.047  Score=50.08  Aligned_cols=22  Identities=36%  Similarity=0.611  Sum_probs=19.9

Q ss_pred             eEEEECCCCCcHHHHHHHHHHH
Q psy200          221 SMYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~  242 (490)
                      .|+|.|.+|+|||++++.++..
T Consensus         2 ~i~lvG~~g~GKSsl~N~ilg~   23 (196)
T cd01852           2 RLVLVGKTGAGKSATGNTILGR   23 (196)
T ss_pred             EEEEECCCCCCHHHHHHHhhCC
Confidence            5889999999999999999864

This represents Arabidoposis protein AIG1 that appears to be involved in plant resistance to bacteria. The Arabidopsis disease resistance gene RPS2 is involved in recognition of bacterial pathogens carrying the avirulence gene avrRpt2. AIG1 exhibits RPS2- and avrRpt1-dependent induction early after infection with Pseudomonas syringae carrying avrRpt2. This subfamily also includes IAN-4 protein, which has GTP-binding activity and shares sequence homology with a novel family of putative GTP-binding proteins: the immuno-associated nucleotide (IAN) family. The evolutionary conservation of the IAN family provides a unique example of a plant pathogen response gene conserved in animals. The IAN/IMAP subfamily has been proposed to regulate apoptosis in vertebrates and angiosperm plants, particularly in relation to cancer, diabetes, and infections. The human IAN genes were renamed GIMAP (GTPase of the immunity associated proteins).

>cd01853 Toc34_like Toc34-like (Translocon at the Outer-envelope membrane of Chloroplasts)

Probab=96.62  E-value=0.032  Score=53.23  Aligned_cols=26  Identities=27%  Similarity=0.498  Sum_probs=22.8

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHH
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~  242 (490)
                      ...-.|+|.|.+|+|||++++++...
T Consensus        29 ~~~~~IllvG~tGvGKSSliNaLlg~   54 (249)
T cd01853          29 DFSLTILVLGKTGVGKSSTINSIFGE   54 (249)
T ss_pred             cCCeEEEEECCCCCcHHHHHHHHhCC
Confidence            35668999999999999999999875

This family contains several Toc proteins, including Toc34, Toc33, Toc120, Toc159, Toc86, Toc125, and Toc90. The Toc complex at the outer envelope membrane of chloroplasts is a molecular machine of ~500 kDa that contains a single Toc159 protein, four Toc75 molecules, and four or five copies of Toc34. Toc64 and Toc12 are associated with the translocon, but do not appear to be part of the core complex. The Toc translocon initiates the import of nuclear-encoded preproteins from the cytosol into the organelle. Toc34 and Toc159 are both GTPases, while Toc75 is a beta-barrel integral membrane protein. Toc159 is equally distributed between a soluble cytoplasmic form and a membrane-inserted form, suggesting that assembly of the Toc complex is dynamic. Toc34 and Toc75 act sequentially to mediate docking and insertion of Toc159 resulting in assembly of the functional translocon.

>TIGR03880 KaiC_arch_3 KaiC domain protein, AF_0351 family

Probab=96.62  E-value=0.018  Score=54.13  Aligned_cols=46  Identities=17%  Similarity=0.253  Sum_probs=33.0

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHH
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVY  266 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~  266 (490)
                      .+..++|.|+||+|||+++..++..... .+..++|++...  +...+.
T Consensus        15 ~g~~~li~G~~G~GKt~~~~~~~~~~~~-~g~~~~y~s~e~--~~~~l~   60 (224)
T TIGR03880        15 EGHVIVVIGEYGTGKTTFSLQFLYQGLK-NGEKAMYISLEE--REERIL   60 (224)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHh-CCCeEEEEECCC--CHHHHH
Confidence            4678899999999999999988776432 355677776644  344443

This model represents a rather narrowly distributed archaeal protein family in which members have a single copy of the KaiC domain. This stands in contrast to the circadian clock protein KaiC itself, with two copies of the domain. Members are expected to have weak ATPase activity, by homology to the autokinase/autophosphorylase KaiC itself.

>TIGR02525 plasmid_TraJ plasmid transfer ATPase TraJ

Probab=96.61  E-value=0.0032  Score=63.44  Aligned_cols=85  Identities=15%  Similarity=0.121  Sum_probs=48.3

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHhhhc-CCceEEEEeccCCC---CHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHh
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRAEIK-DAFKTIYINCNSVR---NAASVYETIVNELKLKPGGKSERHQLGAILKYFD  294 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l~~~-~~~~~~~v~~~~~~---~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~  294 (490)
                      .+.++|+||+|+||||+++++++.+... .+..++.+.-+...   ....+..  ..+   ...+.....+.+.+..++.
T Consensus       149 ~GlilI~G~TGSGKTT~l~al~~~i~~~~~~~~IvtiEdp~E~~~~~~~~~~~--~~q---~evg~~~~~~~~~l~~aLR  223 (372)
T TIGR02525       149 AGLGLICGETGSGKSTLAASIYQHCGETYPDRKIVTYEDPIEYILGSPDDLLP--PAQ---SQIGRDVDSFANGIRLALR  223 (372)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHHHhcCCCceEEEEecCchhccCCCceeec--ccc---cccCCCccCHHHHHHHhhc
Confidence            5688999999999999999999887532 23344444211110   0000000  000   1111222344555566665


Q ss_pred             cCCCeEEEEEecCccc
Q psy200          295 TKHKSILLILDEIDAL  310 (490)
Q Consensus       295 ~~~~~~vI~IDEid~l  310 (490)
                      .  .|-+|+|+|+-.-
T Consensus       224 ~--~PD~I~vGEiRd~  237 (372)
T TIGR02525       224 R--APKIIGVGEIRDL  237 (372)
T ss_pred             c--CCCEEeeCCCCCH
Confidence            3  5789999999874

Members of this protein family are predicted ATPases associated with plasmid transfer loci in bacteria. This family is most similar to the DotB ATPase of a type-IV secretion-like system of obligate intracellular pathogens Legionella pneumophila and Coxiella burnetii (TIGR02524).

>PRK05748 replicative DNA helicase; Provisional

Probab=96.61  E-value=0.023  Score=59.28  Aligned_cols=53  Identities=13%  Similarity=0.151  Sum_probs=36.7

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHH
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNE  272 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~  272 (490)
                      ++..++|.|.||+|||+++-.++.......+..+++++.-  .+..++...++..
T Consensus       202 ~G~livIaarpg~GKT~~al~ia~~~a~~~g~~v~~fSlE--ms~~~l~~R~l~~  254 (448)
T PRK05748        202 PNDLIIVAARPSVGKTAFALNIAQNVATKTDKNVAIFSLE--MGAESLVMRMLCA  254 (448)
T ss_pred             CCceEEEEeCCCCCchHHHHHHHHHHHHhCCCeEEEEeCC--CCHHHHHHHHHHH
Confidence            4567889999999999999999887653344566665432  2556666665543

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

Probab=96.60  E-value=0.0091  Score=50.16  Aligned_cols=29  Identities=24%  Similarity=0.360  Sum_probs=24.8

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHhhh
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRAEI  245 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l~~  245 (490)
                      ..+..++|.|+-|+||||+++.+++.++.
T Consensus        13 ~~g~vi~L~GdLGaGKTtf~r~l~~~lg~   41 (123)
T PF02367_consen   13 KPGDVILLSGDLGAGKTTFVRGLARALGI   41 (123)
T ss_dssp             SS-EEEEEEESTTSSHHHHHHHHHHHTT-
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHHHcCC
Confidence            34678999999999999999999999963

They are probably essential to bacteria as members are found in all genomes so far sequenced and no equivalent genes have been found in the archaea and eukaryotes, suggesting the protein may be involved in cell wall biosynthesis. The sequence of YjeE, from Haemophilus influenzae, has been determined to 1.7-A resolution. The protein has a nucleotide-binding fold with a four-stranded parallel beta-sheet flanked by antiparallel beta-strands on each side. The topology of the beta-sheet is unique among P-loop proteins and has features of different families of enzymes. ADP has been shown to bind to the P-loop in the presence of Mg2+ and ATPase activity has been confirmed by kinetic measurements [].; PDB: 1HTW_A 1FL9_A.

>TIGR02239 recomb_RAD51 DNA repair protein RAD51

Probab=96.60  E-value=0.014  Score=57.86  Aligned_cols=92  Identities=24%  Similarity=0.282  Sum_probs=53.9

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhc-----CCceEEEEeccCCCCHHHHHHHHHHHhcCCCC----------CCcH
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIK-----DAFKTIYINCNSVRNAASVYETIVNELKLKPG----------GKSE  282 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~-----~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~----------~~s~  282 (490)
                      .+..+.|+|+||+|||+++..++......     .+-.++|++.....+... +..+...++....          ..+.
T Consensus        95 ~g~i~~i~G~~g~GKT~l~~~~~~~~~~~~~~Gg~~~~vvyIdtE~~f~~~R-l~~ia~~~~~~~~~~l~~i~~~~~~~~  173 (316)
T TIGR02239        95 TGSITEIFGEFRTGKTQLCHTLAVTCQLPIDQGGGEGKALYIDTEGTFRPER-LLAIAERYGLNPEDVLDNVAYARAYNT  173 (316)
T ss_pred             CCeEEEEECCCCCCcCHHHHHHHHHHhhhhhcCCCCceEEEEECCCCCCHHH-HHHHHHHcCCChHHhhccEEEEecCCh
Confidence            46678899999999999999887643211     123678888776545443 3333343332110          0123


Q ss_pred             HHHHHHHHHH---HhcCCCeEEEEEecCcccc
Q psy200          283 RHQLGAILKY---FDTKHKSILLILDEIDALE  311 (490)
Q Consensus       283 ~~~~~~l~~~---l~~~~~~~vI~IDEid~l~  311 (490)
                      ++....+...   +.. .+..+||||-+..++
T Consensus       174 ~~~~~~l~~~~~~~~~-~~~~LvVIDSI~al~  204 (316)
T TIGR02239       174 DHQLQLLQQAAAMMSE-SRFALLIVDSATALY  204 (316)
T ss_pred             HHHHHHHHHHHHhhcc-CCccEEEEECcHHHh
Confidence            3333333322   222 457799999998874

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).

>PRK08972 fliI flagellum-specific ATP synthase; Validated

Probab=96.57  E-value=0.008  Score=61.43  Aligned_cols=95  Identities=19%  Similarity=0.246  Sum_probs=56.5

Q ss_pred             cCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccC-CCCHHHHHHHHHHHhcCC-------CCCCc-HHH--
Q psy200          216 NETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNS-VRNAASVYETIVNELKLK-------PGGKS-ERH--  284 (490)
Q Consensus       216 ~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~-~~~~~~l~~~i~~~l~~~-------~~~~s-~~~--  284 (490)
                      -..+..+.|.|++|+|||||++.++....  .+..++ .-+.. .....+|+..++..-...       ....+ ...  
T Consensus       159 i~~GqrigI~G~sG~GKSTLL~~I~~~~~--~dv~Vi-~lIGER~rEv~efi~~~l~~~~l~rtvvv~atsd~p~~~R~~  235 (444)
T PRK08972        159 VGKGQRMGLFAGSGVGKSVLLGMMTRGTT--ADVIVV-GLVGERGREVKEFIEEILGEEGRARSVVVAAPADTSPLMRLK  235 (444)
T ss_pred             EcCCCEEEEECCCCCChhHHHHHhccCCC--CCEEEE-EEEcCChHHHHHHHHHhhccCCcccEEEEEECCCCCHHHHHH
Confidence            35678899999999999999999986543  333333 32222 223455666554431110       11111 111  


Q ss_pred             ---HHHHHHHHHhcCCCeEEEEEecCcccccc
Q psy200          285 ---QLGAILKYFDTKHKSILLILDEIDALESR  313 (490)
Q Consensus       285 ---~~~~l~~~l~~~~~~~vI~IDEid~l~~~  313 (490)
                         ..-.+.+++...++.++|++|++-++...
T Consensus       236 a~~~A~tiAEyfrd~G~~VLl~~DslTR~A~A  267 (444)
T PRK08972        236 GCETATTIAEYFRDQGLNVLLLMDSLTRYAQA  267 (444)
T ss_pred             HHHHHHHHHHHHHHcCCCEEEEEcChHHHHHH
Confidence               12235566666688999999999887644

>TIGR00041 DTMP_kinase thymidylate kinase

Probab=96.56  E-value=0.024  Score=51.90  Aligned_cols=36  Identities=22%  Similarity=0.397  Sum_probs=27.6

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEe
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYIN  255 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~  255 (490)
                      +..|+|.|++|+||||+++.+++.+.. .++.++.+.
T Consensus         3 g~~IvieG~~GsGKsT~~~~L~~~l~~-~g~~v~~~~   38 (195)
T TIGR00041         3 GMFIVIEGIDGAGKTTQANLLKKLLQE-NGYDVLFTR   38 (195)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHHHHH-cCCeEEEEe
Confidence            457889999999999999999999863 233444443

Function: phosphorylation of DTMP to form DTDP in both de novo and salvage pathways of DTTP synthesis. Catalytic activity: ATP + thymidine 5'-phosphate = ADP + thymidine 5'-diphosphate.

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

Probab=96.56  E-value=0.0041  Score=60.27  Aligned_cols=106  Identities=22%  Similarity=0.295  Sum_probs=59.9

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHh
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNEL  273 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l  273 (490)
                      +++.-.....+.+.++|...+  ...+.++|.|++|+||||++++++..+... ...++.+.-........     ...+
T Consensus       104 e~l~~~~~~~~~~~~~l~~~v--~~~~~ili~G~tGSGKTT~l~all~~i~~~-~~~iv~iEd~~E~~l~~-----~~~~  175 (270)
T PF00437_consen  104 EDLGESGSIPEEIAEFLRSAV--RGRGNILISGPTGSGKTTLLNALLEEIPPE-DERIVTIEDPPELRLPG-----PNQI  175 (270)
T ss_dssp             CCCCHTHHCHHHHHHHHHHCH--HTTEEEEEEESTTSSHHHHHHHHHHHCHTT-TSEEEEEESSS-S--SC-----SSEE
T ss_pred             hhccCchhhHHHHHHHHhhcc--ccceEEEEECCCccccchHHHHHhhhcccc-ccceEEeccccceeecc-----cceE
Confidence            555555555567777776543  347899999999999999999999988633 24555554221110000     0000


Q ss_pred             cCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccc
Q psy200          274 KLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDAL  310 (490)
Q Consensus       274 ~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l  310 (490)
                      ..... .....+.+.+..++.  ..|-+|+|+|+-.-
T Consensus       176 ~~~~~-~~~~~~~~~l~~~LR--~~pD~iiigEiR~~  209 (270)
T PF00437_consen  176 QIQTR-RDEISYEDLLKSALR--QDPDVIIIGEIRDP  209 (270)
T ss_dssp             EEEEE-TTTBSHHHHHHHHTT--S--SEEEESCE-SC
T ss_pred             EEEee-cCcccHHHHHHHHhc--CCCCcccccccCCH
Confidence            00000 123344555555565  34679999999874

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 ....

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	490
2qby_A	386	Crystal Structure Of A Heterodimer Of Cdc6ORC1 INIT		2e-09
2v1u_A	387	Structure Of The Aeropyrum Pernix Orc1 Protein In C		3e-05

>pdb|2QBY|A Chain A, Crystal Structure Of A Heterodimer Of Cdc6ORC1 INITIATORS Bound To Origin Dna (From S. Solfataricus) Length = 386

Iteration: 1
 Score = 60.8 bits (146), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 55/226 (24%), Positives = 103/226 (45%), Gaps = 8/226 (3%)
Query: 195 ELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIK--DAFKTI 252
           ELP RE Q+  I   L      E   +++I G  GTGK+A +  ++S+   K    FK +
Sbjct: 21  ELPHREDQIRKIASILAPLYREEKPNNIFIYGLTGTGKTAVVKFVLSKLHKKFLGKFKHV 80
Query: 253 YINCNSVRNAASVYETIVNELKLKP--GGKSERHQLGAILKYF-DTKHKSXXXXXXXXXX 309
           YIN   +     V   ++  L +K    G S       ++K   D   +           
Sbjct: 81  YINTRQIDTPYRVLADLLESLDVKVPFTGLSIAELYRRLVKAVRDYGSQVVIVLDEIDAF 140
Query: 310 XXSRKQTILYTIFEWPS-IPGSKLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYS 368
                  ILY +    S +  SK+  +G+ N +   D + PR++++++ +  +  F PY+
Sbjct: 141 VKKYNDDILYKLSRINSEVNKSKISFIGITNDVKFVDLLDPRVKSSLSEEEII--FPPYN 198
Query: 369 REQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDI 414
            E++ +I++++ +   K  +   + ++L A   A   GD R+A+D+
Sbjct: 199 AEELEDILTKRAQMAFKPGVLPDNVIKLCAALAAREHGDARRALDL 244

>pdb|2V1U|A Chain A, Structure Of The Aeropyrum Pernix Orc1 Protein In Complex With Dna Length = 387

Iteration: 1
 Score = 47.0 bits (110), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 56/235 (23%), Positives = 99/235 (42%), Gaps = 23/235 (9%)
Query: 196 LPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDA-----FK 250
           LP RE +L  + + L   +  E   +  + G  GTGK+A   L++ R E + +      K
Sbjct: 21  LPHREAELRRLAEVLAPALRGEKPSNALLYGLTGTGKTAVARLVLRRLEARASSLGVLVK 80
Query: 251 TIYINCNS----VRNAASVYETI---VNELKLKPGGKSERHQLGAILKYFDTKHKSXXXX 303
            IY+N        R A+++ E +   V    L  G   ER     ++K            
Sbjct: 81  PIYVNARHRETPYRVASAIAEAVGVRVPFTGLSVGEVYER-----LVKRLSRLRGIYIIV 135
Query: 304 XXXXXXXXSR--KQTILYTIFEWPSIPGSKLV--LVGVANALDLTDRMLPRLQANVTLQP 359
                    R   Q +LY I       G ++   LVG+ N+L   + + PR+++  +L  
Sbjct: 136 LDEIDFLPKRPGGQDLLYRITRINQELGDRVWVSLVGITNSLGFVENLEPRVKS--SLGE 193
Query: 360 TLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDI 414
             + F PY+  Q+ +I+  + ++     + +   + L A   A   GD R+A+D+
Sbjct: 194 VELVFPPYTAPQLRDILETRAEEAFNPGVLDPDVVPLCAALAAREHGDARRALDL 248

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	490
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	9e-57
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	5e-56
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	5e-51
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	4e-47
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	4e-46
1w5s_A	412	Origin recognition complex subunit 2 ORC2; replica	8e-40
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	5e-17
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-09
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-06
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	7e-08
2qgz_A	308	Helicase loader, putative primosome component; str	1e-04
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	1e-04
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	2e-04
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	3e-04

>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 Length = 389

 Score =  192 bits (489), Expect = 9e-57
 Identities = 62/307 (20%), Positives = 117/307 (38%), Gaps = 22/307 (7%)

Query: 195 ELPGREVQLEGIRQFLLGHVNN--ETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTI 252
            LP RE QL+ +   L   + N         + G PGTGK+ +L  L    + K   + +
Sbjct: 18  RLPHREQQLQQLDILLGNWLRNPGHHYPRATLLGRPGTGKTVTLRKLWELYKDKTTARFV 77

Query: 253 YINCNSVRNAASVYETIVNELKLKPG--GKSERHQLGAILKYFDTKHKSILLILDEIDAL 310
           YIN    RN  ++   I   L +     G S    L  ++++   +   + L+LD+   L
Sbjct: 78  YINGFIYRNFTAIIGEIARSLNIPFPRRGLSRDEFLALLVEHLRERDLYMFLVLDDAFNL 137

Query: 311 ESRKQTILYTIF-EWPSIPGSKLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSR 369
                +    +  E   +   ++ LV V +   + + + P  +    +   ++ F+PY++
Sbjct: 138 APDILSTFIRLGQEADKLGAFRIALVIVGHNDAVLNNLDPSTRG--IMGKYVIRFSPYTK 195

Query: 370 EQILEIISQKLKQTDKFNMFNASALQLLAGKVAAV------SGDIRKAIDITNHLIDLTY 423
           +QI +I+  + K       ++   LQ++A    A        GD R AIDI         
Sbjct: 196 DQIFDILLDRAKAGLAEGSYSEDILQMIADITGAQTPLDTNRGDARLAIDILYRSAYAAQ 255

Query: 424 DNVKENGEVTGIGLKEVLGVISSVYCTSQSLHCSKDEDSFPLQQKLALASLLLLKSRPNV 483
            N ++   +           +             +     PL +KL L +++      + 
Sbjct: 256 QNGRK--HIA-------PEDVRKSSKEVLFGISEEVLIGLPLHEKLFLLAIVRSLKISHT 306

Query: 484 KDVTLGK 490
             +T G 
Sbjct: 307 PYITFGD 313

>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} Length = 386

 Score =  190 bits (484), Expect = 5e-56
 Identities = 71/302 (23%), Positives = 132/302 (43%), Gaps = 18/302 (5%)

Query: 195 ELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSR--AEIKDAFKTI 252
           ELP RE Q+  I   L      E   +++I G  GTGK+A +  ++S+   +    FK +
Sbjct: 21  ELPHREDQIRKIASILAPLYREEKPNNIFIYGLTGTGKTAVVKFVLSKLHKKFLGKFKHV 80

Query: 253 YINCNSVRNAASVYETIVNELKLKPG--GKSERHQLGAILKYFDTKHKSILLILDEIDAL 310
           YIN   +     V   ++  L +K    G S       ++K        ++++LDEIDA 
Sbjct: 81  YINTRQIDTPYRVLADLLESLDVKVPFTGLSIAELYRRLVKAVRDYGSQVVIVLDEIDAF 140

Query: 311 ESRK-QTILYTIFEWPS-IPGSKLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYS 368
             +    ILY +    S +  SK+  +G+ N +   D + PR+++  +L    + F PY+
Sbjct: 141 VKKYNDDILYKLSRINSEVNKSKISFIGITNDVKFVDLLDPRVKS--SLSEEEIIFPPYN 198

Query: 369 REQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITNHLIDLTYDNVKE 428
            E++ +I++++ +   K  +   + ++L A   A   GD R+A+D+     ++      E
Sbjct: 199 AEELEDILTKRAQMAFKPGVLPDNVIKLCAALAAREHGDARRALDLLRVSGEIA-----E 253

Query: 429 NGEVTGIGLKEVLGVISSVYCTSQSLHCSKDEDSFPLQQKLALASLLLLKSRPNVKDVTL 488
             + T +  + V      +              + P   KL L +++ + S  N    T 
Sbjct: 254 RMKDTKVKEEYVYMAKEEIE----RDRVRDIILTLPFHSKLVLMAVVSISSEEN-VVSTT 308

Query: 489 GK 490
           G 
Sbjct: 309 GA 310

>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix} Length = 387

 Score =  177 bits (449), Expect = 5e-51
 Identities = 68/306 (22%), Positives = 126/306 (41%), Gaps = 24/306 (7%)

Query: 195 ELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSR-----AEIKDAF 249
            LP RE +L  + + L   +  E   +  + G  GTGK+A   L++ R     + +    
Sbjct: 20  VLPHREAELRRLAEVLAPALRGEKPSNALLYGLTGTGKTAVARLVLRRLEARASSLGVLV 79

Query: 250 KTIYINCNSVRNAASVYETIVNELKL--KPGGKSERHQLGAILKYFDTKHKSILLILDEI 307
           K IY+N         V   I   + +     G S       ++K         +++LDEI
Sbjct: 80  KPIYVNARHRETPYRVASAIAEAVGVRVPFTGLSVGEVYERLVKRLSRLRGIYIIVLDEI 139

Query: 308 DALESRK--QTILYTIFEWPSIPGSK--LVLVGVANALDLTDRMLPRLQANVTLQPTLMN 363
           D L  R   Q +LY I       G +  + LVG+ N+L   + + PR+++  +L    + 
Sbjct: 140 DFLPKRPGGQDLLYRITRINQELGDRVWVSLVGITNSLGFVENLEPRVKS--SLGEVELV 197

Query: 364 FAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITNHLIDLTY 423
           F PY+  Q+ +I+  + ++     + +   + L A   A   GD R+A+D+     ++  
Sbjct: 198 FPPYTAPQLRDILETRAEEAFNPGVLDPDVVPLCAALAAREHGDARRALDLLRVAGEIA- 256

Query: 424 DNVKENGEVTGIGLKEVLGVISSVYCTSQSLHCSKDEDSFPLQQKLALASLLLLKSRPNV 483
               E      +  + V    + +         S+   + PL  KL L S+++L+     
Sbjct: 257 ----ERRREERVRREHVYSARAEIERD----RVSEVVRTLPLHAKLVLLSIMMLED--GG 306

Query: 484 KDVTLG 489
           +  + G
Sbjct: 307 RPASTG 312

>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} Length = 384

 Score =  166 bits (422), Expect = 4e-47
 Identities = 62/303 (20%), Positives = 112/303 (36%), Gaps = 29/303 (9%)

Query: 195 ELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSR-------AEIKD 247
           E+P RE  L      +   V NE   S    G  GTGK+     + +         E   
Sbjct: 21  EIPFREDILRDAAIAIRYFVKNEVKFSNLFLGLTGTGKTFVSKYIFNEIEEVKKEDEEYK 80

Query: 248 AFKTIYINCNSVRNAA-SVYETIVNELKLKPGGKSERHQLGAILKYFDTKHKS-ILLILD 305
             K  Y+NC  V     +V  ++  +L      K   +    I K  +       ++ LD
Sbjct: 81  DVKQAYVNCREVGGTPQAVLSSLAGKLTGFSVPKHGINLGEYIDKIKNGTRNIRAIIYLD 140

Query: 306 EIDALESRK--QTILYTIFEWPSIPGSKLVLVGVANALDLTDRMLPRLQANVTLQPTLMN 363
           E+D L  R+    +LY +        + + ++ ++N +++ D M PR+ ++       + 
Sbjct: 141 EVDTLVKRRGGDIVLYQLLRSD----ANISVIMISNDINVRDYMEPRVLSS---LGPSVI 193

Query: 364 FAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITNHLIDLTY 423
           F PY  EQ+  I+S+  +       ++   L  +A   A   GD RKA+++      L  
Sbjct: 194 FKPYDAEQLKFILSKYAEYGLIKGTYDDEILSYIAAISAKEHGDARKAVNLLFRAAQL-- 251

Query: 424 DNVKENGEVTGIGLKEVLGVISSVYCTSQSLHCSKDEDSFPLQQKLALASLLLLKSRPNV 483
                 G +           +       +     +   + P   KLAL SL+  +   + 
Sbjct: 252 --ASGGGIIR-------KEHVDKAIVDYEQERLIEAVKALPFHYKLALRSLIESEDVMSA 302

Query: 484 KDV 486
             +
Sbjct: 303 HKM 305

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae} Length = 318

 Score =  162 bits (410), Expect = 4e-46
 Identities = 43/268 (16%), Positives = 84/268 (31%), Gaps = 44/268 (16%)

Query: 195 ELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIK------DA 248
            L  +      I   +   + +  +   YI+    + K   +N ++              
Sbjct: 21  LLKSQVEDFTRIFLPIYDSLMSSQNKLFYITNADDSTKFQLVNDVMDELITSSARKELPI 80

Query: 249 FKTIYINCNSVRNAASVYETIVNELKLK--PGGKSERHQLGAILKYFDTKHKSILLILDE 306
           F  I+I+   +    ++YE I   +  +   G  S       I      K +  L+++  
Sbjct: 81  FDYIHIDALELAGMDALYEKIWFAISKENLCGDISLEALNFYITNVPKAKKRKTLILIQN 140

Query: 307 IDALESRKQTILYTIFEWPSIPGSKLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAP 366
            + L    + IL    +W S   SKL ++ V          +  + +      T +    
Sbjct: 141 PENLL--SEKILQYFEKWISSKNSKLSIICVGGHNVTIREQINIMPSL-KAHFTEIKLNK 197

Query: 367 YSREQILEIISQKLKQTDKF---------------------------------NMFNASA 393
             + ++ ++I  +LK   K                                  +  N   
Sbjct: 198 VDKNELQQMIITRLKSLLKPFHVKVNDKKEMTIYNNIREGQNQKIPDNVIVINHKINNKI 257

Query: 394 LQLLAGKVAAVSGDIRKAIDITNHLIDL 421
            QL+A  VA VSG   KA  I    +++
Sbjct: 258 TQLIAKNVANVSGSTEKAFKICEAAVEI 285

>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* Length = 412

 Score =  147 bits (372), Expect = 8e-40
 Identities = 48/309 (15%), Positives = 108/309 (34%), Gaps = 31/309 (10%)

Query: 195 ELPGREVQLEGIRQFLLGHVNNETSGS-----MYISGPPGTGKSASLNLLVSR-----AE 244
           EL  R  + E + +  L  + +    S         G  G GK+      V R     A+
Sbjct: 23  ELRVRRGEAEALARIYLNRLLSGAGLSDVNMIYGSIGRVGIGKTTLAKFTVKRVSEAAAK 82

Query: 245 IKDAFKTIYINCNSVRNAASVYETIVNEL--KLKPGGKSERHQLGAILKYFDTKHKSILL 302
                K  Y+N  +  N  ++   IV +    ++  G      L A++     ++  +L+
Sbjct: 83  EGLTVKQAYVNAFNAPNLYTILSLIVRQTGYPIQVRGAPALDILKALVDNLYVENHYLLV 142

Query: 303 ILDEIDALESRKQT---ILYTIFE-----WPSIPGSKLVLVGVANALDLTDRMLPRLQAN 354
           ILDE  ++ S  +     LYT+             +++  + VA+ +     M  ++   
Sbjct: 143 ILDEFQSMLSSPRIAAEDLYTLLRVHEEIPSRDGVNRIGFLLVASDVRALSYMREKIPQV 202

Query: 355 VTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVA---AVSGDIRKA 411
            +     ++   Y   ++  I+ Q+ +   +  ++    L+L++          G  R+A
Sbjct: 203 ESQIGFKLHLPAYKSRELYTILEQRAELGLRDTVWEPRHLELISDVYGEDKGGDGSARRA 262

Query: 412 IDITNHLIDLTYDNVKENGEVTGIGLKEVLGVISSVYCTSQSLHCSKDEDSFPLQQKLAL 471
           I       ++      E      +    V   +S     + S+   +  ++  + + + L
Sbjct: 263 IVALKMACEMA-----EAMGRDSLSEDLVRKAVSENE--AASIQTHE-LEALSIHELIIL 314

Query: 472 ASLLLLKSR 480
             +      
Sbjct: 315 RLIAEATLG 323

>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 = 83.4 bits (205), Expect = 5e-17
 Identities = 71/448 (15%), Positives = 146/448 (32%), Gaps = 108/448 (24%)

Query: 113 DATSTSDAVRSVSGSRSSAKADCLRPLSPIKN-------IILDK-KSPFKAFI----RDD 160
           D     D  +S+    S  + D +       +        +L K +   + F+    R +
Sbjct: 34  DCKDVQDMPKSIL---SKEEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRIN 90

Query: 161 EDLIKRSPAKLC---SPRKLLFSEDKPK----VEEKAKDSCELPGREVQLEGIRQFLLGH 213
              +           S    ++ E + +     +  AK +     R      +RQ LL  
Sbjct: 91  YKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVS---RLQPYLKLRQALL-- 145

Query: 214 VNNETSGSMYIS--GPPGTGKSASLNLLVSRA---EIKDAFKTIYINCNSVRNAASVYET 268
              E   +  +   G  G+GK+  + L V  +   + K  FK  ++N  +  +  +V E 
Sbjct: 146 ---ELRPAKNVLIDGVLGSGKT-WVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEM 201

Query: 269 IVN-ELKLKPGGKSERHQLGAI----------LKYF--DTKHKSILLILDE------IDA 309
           +     ++ P   S       I          L+       +++ LL+L         +A
Sbjct: 202 LQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNA 261

Query: 310 LESRKQTILYT----IFEWPSIPGSKLVLVG--------------VANALDLTDRMLPRL 351
                + +L T    + ++ S   +  + +               +   LD   + LPR 
Sbjct: 262 FNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPR- 320

Query: 352 QANVTLQPTLMN-FAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRK 410
           +  +T  P  ++  A   R+ +    + K    DK      S+L +L         + RK
Sbjct: 321 EV-LTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLE------PAEYRK 373

Query: 411 -----AI-----DITNHLIDLTYDNVKENGEVTGIGLKEVLGVISSVYCTSQSLHCSKDE 460
                ++      I   L+ L + +V ++         +V+ V++       SL   K  
Sbjct: 374 MFDRLSVFPPSAHIPTILLSLIWFDVIKS---------DVMVVVNK--LHKYSL-VEKQP 421

Query: 461 DSFPLQQKLALASLLLLKSRPNVKDVTL 488
                   +++ S+ L        +  L
Sbjct: 422 KES----TISIPSIYLELKVKLENEYAL 445

>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 = 59.5 bits (143), Expect = 2e-09
 Identities = 84/476 (17%), Positives = 150/476 (31%), Gaps = 155/476 (32%)

Query: 61  LHLGSPRTPSSLLRSL-KLDSPKRKIDTALEFASPKRVFKDADATSSGAASA-VDATSTS 118
           L+L +  +P ++L  L KL     +ID             +  + S  +++  +   S  
Sbjct: 187 LNLKNCNSPETVLEMLQKL---LYQID------------PNWTSRSDHSSNIKLRIHSIQ 231

Query: 119 DAVRSVSGSRSSAKADCLRPLSPIKNIILD---KKSPFKAF--------------IRDDE 161
             +R +  S+     +CL        ++L        + AF              + D  
Sbjct: 232 AELRRLLKSKP--YENCL--------LVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFL 281

Query: 162 DLIKRSPAKLCSPRKLLFSEDKPK------VEEKAKDSCELPGREVQL----------EG 205
                +   L     +  + D+ K      ++ + +D   LP REV            E 
Sbjct: 282 SAATTTHISL-DHHSMTLTPDEVKSLLLKYLDCRPQD---LP-REVLTTNPRRLSIIAES 336

Query: 206 IRQFL-----LGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVR 260
           IR  L       HVN +   ++ I         +SLN+L   AE +  F  + +   S  
Sbjct: 337 IRDGLATWDNWKHVNCDKLTTI-I--------ESSLNVL-EPAEYRKMFDRLSVFPPSAH 386

Query: 261 NAASVY------------ETIVNELK----LKPGGKSERHQLGAILKYFDTKHKSILLIL 304
               +               +VN+L     ++   K     + +I  Y + K K     L
Sbjct: 387 IPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSI--YLELKVK-----L 439

Query: 305 DEIDALESRKQTIL--YTIFEWPSIPGSKLVLVGVANALDLTDRMLPRLQANVTLQPTLM 362
           +   AL      I+  Y I +                  D  D + P L           
Sbjct: 440 ENEYALHRS---IVDHYNIPK----------------TFDSDDLIPPYLDQ--------- 471

Query: 363 NFAPYSREQILEIIS---QKLKQTDKFNMFNASALQL--LAGKVAAVSGDIRKAIDITNH 417
               Y        I    + ++  ++  +F    L    L  K+   S     +  I N 
Sbjct: 472 ----Y----FYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSILNT 523

Query: 418 LIDL-TY-DNVKENGEVTGIGLKEVLGVISSVYCTSQSLHCSKDEDSFPLQQKLAL 471
           L  L  Y   + +N       +  +L  +  +    ++L CSK  D   L + +AL
Sbjct: 524 LQQLKFYKPYICDNDPKYERLVNAILDFLPKI---EENLICSKYTD---LLR-IAL 572

>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 = 49.1 bits (116), Expect = 3e-06
 Identities = 44/249 (17%), Positives = 71/249 (28%), Gaps = 64/249 (25%)

Query: 284 HQLGAILKYFDTKH-----KSILL--ILDEIDALESRKQTILYTIFEWPSIPGSKLVLVG 336
               A +  FD K      KSIL    +D I   +         +F        ++V   
Sbjct: 24  VFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSG-TLRLFWTLLSKQEEMVQKF 82

Query: 337 VANALD-----LTDRMLPRLQANVTLQPTLMN----------------FAPY--SREQIL 373
           V   L      L   +          QP++M                 FA Y  SR Q  
Sbjct: 83  VEEVLRINYKFLMSPI-----KTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPY 137

Query: 374 EIISQKLKQTDK------FNMFNASALQLLAGK---VAAVSGDIRKAIDITNHLIDLTYD 424
             + Q L +           +  +       GK      V    +    +   +  L   
Sbjct: 138 LKLRQALLELRPAKNVLIDGVLGS-------GKTWVALDVCLSYKVQCKMDFKIFWLNLK 190

Query: 425 NVKENGEVTGIGLKEVLGVISSVYC--------TSQSLHCSKDEDSFPLQQKLALASLLL 476
           N      V  + L+++L  I   +             +H  + E    L+ K     LL+
Sbjct: 191 NCNSPETVLEM-LQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLV 249

Query: 477 LKSRPNVKD 485
           L    NV++
Sbjct: 250 LL---NVQN 255

>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 Length = 516

 Score = 53.7 bits (129), Expect = 7e-08
 Identities = 37/231 (16%), Positives = 77/231 (33%), Gaps = 44/231 (19%)

Query: 222 MYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKPGGKS 281
             + GPPG GK+ +   LV++ E+   +  +  N + VR+   +   + N L       S
Sbjct: 80  AMLYGPPGIGKT-TAAHLVAQ-ELG--YDILEQNASDVRSKTLLNAGVKNAL----DNMS 131

Query: 282 ERHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVANAL 341
                    +  +   K  ++I+DE+D +    +  +  + +      +   L+ + N  
Sbjct: 132 VVGYFKHNEEAQNLNGKHFVIIMDEVDGMSGGDRGGVGQLAQ--FCRKTSTPLILICN-- 187

Query: 342 DLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQ-----KLKQTDKFNMFNASALQL 396
           +     +             + F       I   +       K K            +  
Sbjct: 188 ERNLPKMRPFDRVC----LDIQFRRPDANSIKSRLMTIAIREKFKLDPN-------VIDR 236

Query: 397 LAGKVAAVSGDIRKAIDITNHL-------IDLTYDNVKENGEVTGIGLKEV 440
           L   +    GDIR+ I   N L         + ++N+    E++    K +
Sbjct: 237 L---IQTTRGDIRQVI---NLLSTISTTTKTINHENIN---EISKAWEKNI 278

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3} Length = 308

 Score = 43.3 bits (102), Expect = 1e-04
 Identities = 24/130 (18%), Positives = 42/130 (32%), Gaps = 21/130 (16%)

Query: 197 PGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINC 256
             R      I  F+     +     +Y+ G  G GKS  L  +      K    T  ++ 
Sbjct: 131 ASRMEAFSAILDFV-EQYPSAEQKGLYLYGDMGIGKSYLLAAMAHELSEKKGVSTTLLHF 189

Query: 257 NSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDAL---ESR 313
            S             ++K      S + ++ A+           +LILD+I A       
Sbjct: 190 PS----------FAIDVKNAISNGSVKEEIDAVKNV-P------VLILDDIGAEQATSWV 232

Query: 314 KQTILYTIFE 323
           +  +L  I +
Sbjct: 233 RDEVLQVILQ 242

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426} Length = 202

 Score = 42.4 bits (100), Expect = 1e-04
 Identities = 21/130 (16%), Positives = 45/130 (34%), Gaps = 21/130 (16%)

Query: 197 PGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINC 256
            GR   +    +F+  +   +    +Y+ G  G GK+  L  + +    K    ++ +  
Sbjct: 32  DGRIKAIRFAERFVAEYEPGKKMKGLYLHGSFGVGKTYLLAAIANEL-AKRNVSSLIVY- 89

Query: 257 NSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDAL---ESR 313
                       +  ELK     ++   +L  I K         +L+LD++ A       
Sbjct: 90  ---------VPELFRELKHSLQDQTMNEKLDYIKKV-P------VLMLDDLGAEAMSSWV 133

Query: 314 KQTILYTIFE 323
           +  +   I +
Sbjct: 134 RDDVFGPILQ 143

>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* Length = 180

 Score = 41.6 bits (98), Expect = 2e-04
 Identities = 21/115 (18%), Positives = 40/115 (34%), Gaps = 26/115 (22%)

Query: 197 PGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKS----ASLNLLVSRAEIKDAFKTI 252
             +   L  IR F+  + N E    +   G PG GK+    A+L  +  +  I    +  
Sbjct: 17  VSQNRALLTIRVFV-HNFNPEEGKGLTFVGSPGVGKTHLAVATLKAIYEKKGI----RGY 71

Query: 253 YINCNSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEI 307
           + +             ++  LK       +   L  +L          +L+LD++
Sbjct: 72  FFDTKD----------LIFRLKHLMDEGKDTKFLKTVLNS-P------VLVLDDL 109

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	490
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	99.98
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	99.96
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	99.95
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	99.95
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	99.95
1w5s_A	412	Origin recognition complex subunit 2 ORC2; replica	99.93
4b4t_J	405	26S protease regulatory subunit 8 homolog; hydrola	99.9
4b4t_I	437	26S protease regulatory subunit 4 homolog; hydrola	99.89
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	99.88
4b4t_H	467	26S protease regulatory subunit 7 homolog; hydrola	99.88
4b4t_M	434	26S protease regulatory subunit 6A; hydrolase, AAA	99.87
4b4t_L	437	26S protease subunit RPT4; hydrolase, AAA-atpases,	99.87
4b4t_K	428	26S protease regulatory subunit 6B homolog; hydrol	99.86
2chg_A	226	Replication factor C small subunit; DNA-binding pr	99.86
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	99.86
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	99.86
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	99.85
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	99.84
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	99.84
3pvs_A	447	Replication-associated recombination protein A; ma	99.84
1hqc_A	324	RUVB; extended AAA-ATPase domain, complex with nuc	99.84
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	99.84
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	99.83
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	99.83
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	99.82
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	99.82
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	99.82
1in4_A	334	RUVB, holliday junction DNA helicase RUVB; AAA+-cl	99.82
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	99.82
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	99.82
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	99.81
1sxj_B	323	Activator 1 37 kDa subunit; clamp loader, processi	99.81
1ofh_A	310	ATP-dependent HSL protease ATP-binding subunit HSL	99.81
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	99.8
2ce7_A	476	Cell division protein FTSH; metalloprotease; HET:	99.8
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	99.8
2chq_A	319	Replication factor C small subunit; DNA-binding pr	99.8
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	99.79
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	99.79
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	99.79
3bos_A	242	Putative DNA replication factor; P-loop containing	99.78
1sxj_C	340	Activator 1 40 kDa subunit; clamp loader, processi	99.78
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	99.77
1jr3_A	373	DNA polymerase III subunit gamma; processivity, pr	99.76
2r44_A	331	Uncharacterized protein; putative ATPase, structur	99.74
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	99.74
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	99.74
2z4s_A	440	Chromosomal replication initiator protein DNAA; AA	99.73
1sxj_E	354	Activator 1 40 kDa subunit; clamp loader, processi	99.73
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	99.73
2r62_A	268	Cell division protease FTSH homolog; ATPase domain	99.73
2dhr_A	499	FTSH; AAA+ protein, hexameric Zn metalloprotease,	99.72
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	99.72
1ojl_A	304	Transcriptional regulatory protein ZRAR; response	99.72
1um8_A	376	ATP-dependent CLP protease ATP-binding subunit CL;	99.71
4fcw_A	311	Chaperone protein CLPB; AAA domain; HET: ADP; 2.35	99.71
2bjv_A	265	PSP operon transcriptional activator; AAA, transcr	99.69
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	99.67
3hws_A	363	ATP-dependent CLP protease ATP-binding subunit CL;	99.67
3pxg_A	468	Negative regulator of genetic competence CLPC/MEC;	99.66
1ixz_A	254	ATP-dependent metalloprotease FTSH; AAA domain fol	99.66
1iy2_A	278	ATP-dependent metalloprotease FTSH; AAA domain fol	99.66
1g8p_A	350	Magnesium-chelatase 38 kDa subunit; parallel beta	99.66
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	99.63
1a5t_A	334	Delta prime, HOLB; zinc finger, DNA replication; 2	99.62
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	99.62
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	99.61
3m6a_A	543	ATP-dependent protease LA 1; alpha, beta, ATP-bind	99.61
2qen_A	350	Walker-type ATPase; unknown function; HET: ADP; 2.	99.61
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	99.6
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	99.57
1g41_A	444	Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dep	99.55
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	99.54
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	99.54
3nbx_X	500	ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structu	99.53
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	99.53
2gno_A	305	DNA polymerase III, gamma subunit-related protein;	99.49
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	99.49
1ny5_A	387	Transcriptional regulator (NTRC family); AAA+ ATPa	99.46
3k1j_A	604	LON protease, ATP-dependent protease LON; ATP-bind	99.45
3dzd_A	368	Transcriptional regulator (NTRC family); sigma43 a	99.44
2fna_A	357	Conserved hypothetical protein; structural genomic	99.42
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	99.41
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	99.41
3n70_A	145	Transport activator; sigma-54, ntpase, PSI, MCSG,	99.41
2a5y_B	549	CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis	99.4
3co5_A	143	Putative two-component system transcriptional RES	99.38
3f9v_A	595	Minichromosome maintenance protein MCM; replicativ	99.33
1jr3_D	343	DNA polymerase III, delta subunit; processivity, p	99.22
1z6t_A	591	APAF-1, apoptotic protease activating factor 1; ca	99.21
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	99.12
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	99.1
3sfz_A	1249	APAF-1, apoptotic peptidase activating factor 1; a	99.09
3f8t_A	506	Predicted ATPase involved in replication control,	98.97
2kjq_A	149	DNAA-related protein; solution structure, NESG, st	98.96
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	98.91
4akg_A	2695	Glutathione S-transferase class-MU 26 kDa isozyme	98.85
2qgz_A	308	Helicase loader, putative primosome component; str	98.56
1u0j_A	267	DNA replication protein; AAA+ protein, P-loop atpa	98.35
3vkg_A	3245	Dynein heavy chain, cytoplasmic; AAA+ protein, mol	98.34
3upu_A	459	ATP-dependent DNA helicase DDA; RECA-like domain,	98.26
2r2a_A	199	Uncharacterized protein; zonular occludens toxin,	98.24
1tue_A	212	Replication protein E1; helicase, replication, E1E	98.23
4akg_A	2695	Glutathione S-transferase class-MU 26 kDa isozyme	98.17
2b8t_A	223	Thymidine kinase; deoxyribonucleoside kinase, zinc	98.0
1n0w_A	243	DNA repair protein RAD51 homolog 1; DNA repair, ho	97.94
2cvh_A	220	DNA repair and recombination protein RADB; filamen	97.92
1ye8_A	178	Protein THEP1, hypothetical UPF0334 kinase-like pr	97.87
2w0m_A	235	SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus	97.81
2vhj_A	331	Ntpase P4, P4; non- hydrolysable ATP analogue, hyd	97.8
2orw_A	184	Thymidine kinase; TMTK, TP4A, transferase; HET: 4T	97.78
2z43_A	324	DNA repair and recombination protein RADA; archaea	97.7
3hr8_A	356	Protein RECA; alpha and beta proteins (A/B, A+B),	97.68
1w4r_A	195	Thymidine kinase; type II, human, cytosolic, phosp	97.68
1v5w_A	343	DMC1, meiotic recombination protein DMC1/LIM15 hom	97.68
1xp8_A	366	RECA protein, recombinase A; recombination, radior	97.66
2zr9_A	349	Protein RECA, recombinase A; recombination, RECA m	97.64
3e1s_A	574	Exodeoxyribonuclease V, subunit RECD; alpha and be	97.64
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	97.62
3kl4_A	433	SRP54, signal recognition 54 kDa protein; signal r	97.61
3dm5_A	443	SRP54, signal recognition 54 kDa protein; protein-	97.6
1cr0_A	296	DNA primase/helicase; RECA-type protein fold, tran	97.58
2r6a_A	454	DNAB helicase, replicative helicase; replication,	97.58
2dr3_A	247	UPF0273 protein PH0284; RECA superfamily ATPase, h	97.54
3lda_A	400	DNA repair protein RAD51; DNA binding protein, ATP	97.54
2q6t_A	444	DNAB replication FORK helicase; hydrolase; 2.90A {	97.52
2fz4_A	237	DNA repair protein RAD25; RECA-like domain, DNA da	97.5
2ehv_A	251	Hypothetical protein PH0186; KAIC, RECA ATPase, un	97.5
4a1f_A	338	DNAB helicase, replicative DNA helicase; hydrolase	97.45
1u94_A	356	RECA protein, recombinase A; homologous recombinat	97.44
4a74_A	231	DNA repair and recombination protein RADA; hydrola	97.43
1sky_E	473	F1-ATPase, F1-ATP synthase; F1FO ATP synthase, alp	97.42
1pzn_A	349	RAD51, DNA repair and recombination protein RAD51,	97.41
1w36_D	608	RECD, exodeoxyribonuclease V alpha chain; recombin	97.39
2i3b_A	189	HCR-ntpase, human cancer-related ntpase; AAA, ross	97.38
3io5_A	333	Recombination and repair protein; storage dimer, i	97.36
3bh0_A	315	DNAB-like replicative helicase; ATPase, replicatio	97.36
3tlx_A	243	Adenylate kinase 2; structural genomics, structura	97.33
3llm_A	235	ATP-dependent RNA helicase A; alpha-beta-alpha, st	97.31
3sr0_A	206	Adenylate kinase; phosphoryl transfer analogue, AL	97.3
2i1q_A	322	DNA repair and recombination protein RADA; ATPase,	97.29
2px0_A	296	Flagellar biosynthesis protein FLHF; SRP GTPase, f	97.28
3umf_A	217	Adenylate kinase; rossmann fold, transferase; 2.05	97.27
3cmw_A	1706	Protein RECA, recombinase A; homologous recombinat	97.27
1ex7_A	186	Guanylate kinase; substrate-induced FIT, domain mo	97.21
2j9r_A	214	Thymidine kinase; TK1, DNK, lasso, transferase, AT	97.18
1xx6_A	191	Thymidine kinase; NESG, northeast structural genom	97.18
1nlf_A	279	Regulatory protein REPA; replicative DNA helicase	97.17
2zts_A	251	Putative uncharacterized protein PH0186; KAIC like	97.15
3ice_A	422	Transcription termination factor RHO; transcriptio	97.13
3bgw_A	444	DNAB-like replicative helicase; ATPase, replicatio	97.11
3e2i_A	219	Thymidine kinase; Zn-binding, ATP-binding, DNA syn	97.09
2iut_A	574	DNA translocase FTSK; nucleotide-binding, chromoso	97.08
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	97.07
1q57_A	503	DNA primase/helicase; dntpase, DNA replication, tr	97.06
1vma_A	306	Cell division protein FTSY; TM0570, structural gen	97.06
3vkg_A	3245	Dynein heavy chain, cytoplasmic; AAA+ protein, mol	97.05
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	97.03
3be4_A	217	Adenylate kinase; malaria, cryptosporidium parvum	96.98
2ga8_A	359	Hypothetical 39.9 kDa protein; YFR007W, YFH7, unkn	96.96
1qhx_A	178	CPT, protein (chloramphenicol phosphotransferase);	96.95
3cmw_A	1706	Protein RECA, recombinase A; homologous recombinat	96.93
1g5t_A	196	COB(I)alamin adenosyltransferase; P-loop protein,	96.89
2r8r_A	228	Sensor protein; KDPD, PFAM02702, MCSG, structural	96.87
3a4m_A	260	L-seryl-tRNA(SEC) kinase; P-loop motif, walker A m	96.87
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	96.87
3dl0_A	216	Adenylate kinase; phosphotransferase, zinc coordin	96.86
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	96.78
2v3c_C	432	SRP54, signal recognition 54 kDa protein; nucleoti	96.78
3trf_A	185	Shikimate kinase, SK; amino acid biosynthesis, tra	96.74
3vaa_A	199	Shikimate kinase, SK; structural genomics, center	96.72
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	96.7
1tev_A	196	UMP-CMP kinase; ploop, NMP binding region, LID reg	96.7
4eun_A	200	Thermoresistant glucokinase; putative sugar kinase	96.68
1gvn_B	287	Zeta; postsegregational killing system, plasmid; 1	96.68
3uie_A	200	Adenylyl-sulfate kinase 1, chloroplastic; rossmann	96.67
2orv_A	234	Thymidine kinase; TP4A (P1-(5'-adenosyl)P4-(5'- (2	96.66
2p5t_B	253	PEZT; postsegregational killing system, phosphoryl	96.65
3kb2_A	173	SPBC2 prophage-derived uncharacterized protein YOR	96.64
3bor_A	237	Human initiation factor 4A-II; translation initiat	96.64
3jvv_A	356	Twitching mobility protein; hexameric P-loop ATPas	96.64
3e70_C	328	DPA, signal recognition particle receptor; FTSY, S	96.63
2ius_A	512	DNA translocase FTSK; nucleotide-binding, chromoso	96.62
4gp7_A	171	Metallophosphoesterase; polynucleotide kinase phos	96.6
3b6e_A	216	Interferon-induced helicase C domain-containing P;	96.59
3iij_A	180	Coilin-interacting nuclear ATPase protein; alpha a	96.59
3zvl_A	416	Bifunctional polynucleotide phosphatase/kinase; hy	96.58
1rz3_A	201	Hypothetical protein rbstp0775; MCSG, structural g	96.57
1kag_A	173	SKI, shikimate kinase I; transferase, structural g	96.54
3l0o_A	427	Transcription termination factor RHO; helicase, RH	96.53
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	96.53
2xb4_A	223	Adenylate kinase; ATP-binding, nucleotide-binding,	96.53
1y63_A	184	LMAJ004144AAA protein; structural genomics, protei	96.5
1kht_A	192	Adenylate kinase; phosphotransferase, signaling pr	96.49
1via_A	175	Shikimate kinase; structural genomics, transferase	96.47
1zuh_A	168	Shikimate kinase; alpha-beta protein, transferase;	96.47
3c8u_A	208	Fructokinase; YP_612366.1, putative fructose trans	96.47
3vkw_A	446	Replicase large subunit; alpha/beta domain, helica	96.46
2rhm_A	193	Putative kinase; P-loop containing nucleoside trip	96.46
2j37_W	504	Signal recognition particle 54 kDa protein (SRP54)	96.45
3lw7_A	179	Adenylate kinase related protein (ADKA-like); AMP,	96.43
2iyv_A	184	Shikimate kinase, SK; transferase, aromatic amino	96.41
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	96.41
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	96.4
2cdn_A	201	Adenylate kinase; phosphoryl transfer, associative	96.39
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	96.36
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	96.34
1aky_A	220	Adenylate kinase; ATP:AMP phosphotransferase, myok	96.34
2c95_A	196	Adenylate kinase 1; transferase, AP4A, nucleotide	96.34
3cm0_A	186	Adenylate kinase; ATP-binding, cytoplasm, nucleoti	96.33
2z0h_A	197	DTMP kinase, thymidylate kinase; ATP-binding, nucl	96.32
1e6c_A	173	Shikimate kinase; phosphoryl transfer, ADP, shikim	96.32
3lxw_A	247	GTPase IMAP family member 1; immunity, structural	96.32
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	96.31
3lfu_A	647	DNA helicase II; SF1 helicase, ATP-binding, DNA da	96.31
3t61_A	202	Gluconokinase; PSI-biology, structural genomics, p	96.3
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	96.3
1ly1_A	181	Polynucleotide kinase; PNK, phosphatase, transfera	96.29
1kgd_A	180	CASK, peripheral plasma membrane CASK; maguk, guan	96.28
2pbr_A	195	DTMP kinase, thymidylate kinase; transferase, nucl	96.27
2qor_A	204	Guanylate kinase; phosphotransferase, purine metab	96.26
1nks_A	194	Adenylate kinase; thermophilic, transferase; HET:	96.25
2v54_A	204	DTMP kinase, thymidylate kinase; nucleotide biosyn	96.24
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	96.24
2ze6_A	253	Isopentenyl transferase; crown GALL tumor, cytokin	96.23
2pez_A	179	Bifunctional 3'-phosphoadenosine 5'- phosphosulfat	96.23
2vli_A	183	Antibiotic resistance protein; transferase, tunica	96.23
1zp6_A	191	Hypothetical protein ATU3015; alpha-beta protein.,	96.22
2plr_A	213	DTMP kinase, probable thymidylate kinase; TMP-bind	96.2
2bwj_A	199	Adenylate kinase 5; phosphoryl transfer reaction,	96.2
1knq_A	175	Gluconate kinase; ALFA/beta structure, transferase	96.2
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	96.19
4b3f_X	646	DNA-binding protein smubp-2; hydrolase, helicase;	96.18
1j8m_F	297	SRP54, signal recognition 54 kDa protein; signalin	96.17
2xxa_A	433	Signal recognition particle protein; protein trans	96.16
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	96.16
3tau_A	208	Guanylate kinase, GMP kinase; structural genomics,	96.15
1qf9_A	194	UMP/CMP kinase, protein (uridylmonophosphate/cytid	96.12
1zd8_A	227	GTP:AMP phosphotransferase mitochondrial; ATP:AMP	96.12
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	96.11
1ukz_A	203	Uridylate kinase; transferase; HET: ADP AMP; 1.90A	96.11
1ak2_A	233	Adenylate kinase isoenzyme-2; nucleoside monophosp	96.1
2yvu_A	186	Probable adenylyl-sulfate kinase; transferase, str	96.1
1zak_A	222	Adenylate kinase; ATP:AMP-phosphotransferase, tran	96.09
1m7g_A	211	Adenylylsulfate kinase; APS kinase, transferase, s	96.09
2wwf_A	212	Thymidilate kinase, putative; transferase, malaria	96.08
2ck3_D	482	ATP synthase subunit beta\, mitochondrial; hydrola	96.06
2qe7_A	502	ATP synthase subunit alpha; blockage of ATP hydrol	96.05
2pt5_A	168	Shikimate kinase, SK; aromatic amino acid biosynth	96.03
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	96.02
2bbw_A	246	Adenylate kinase 4, AK4; nucleotide kinase, nucleo	96.02
2ck3_A	510	ATP synthase subunit alpha\, mitochondrial; hydrol	96.01
1tf7_A	525	KAIC; homohexamer, hexamer, circadian clock protei	96.01
3tr0_A	205	Guanylate kinase, GMP kinase; purines, pyrimidines	96.01
4eaq_A	229	DTMP kinase, thymidylate kinase; structural genomi	96.0
1nn5_A	215	Similar to deoxythymidylate kinase (thymidylate K;	96.0
3fb4_A	216	Adenylate kinase; psychrophIle, phosphotransferase	96.0
2ffh_A	425	Protein (FFH); SRP54, signal recognition particle,	95.99
1zd9_A	188	ADP-ribosylation factor-like 10B; transport protei	95.99
1zj6_A	187	ADP-ribosylation factor-like protein 5; ARL, GTP-b	95.98
2jaq_A	205	Deoxyguanosine kinase; transferase, deoxyribonucle	95.94
1ls1_A	295	Signal recognition particle protein; FFH, SRP54, S	95.93
3ney_A	197	55 kDa erythrocyte membrane protein; structural ge	95.92
3a00_A	186	Guanylate kinase, GMP kinase; domain movement, dim	95.9
2j41_A	207	Guanylate kinase; GMP, GMK, transferase, ATP-bindi	95.9
1fx0_B	498	ATP synthase beta chain; latent ATPase, thermal st	95.89
2r9v_A	515	ATP synthase subunit alpha; TM1612, structural gen	95.89
1rif_A	282	DAR protein, DNA helicase UVSW; bacteriophage, REC	95.87
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	95.86
1zu4_A	320	FTSY; GTPase, signal recognition particle, SRP, re	95.86
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	95.85
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	95.84
1lvg_A	198	Guanylate kinase, GMP kinase; transferase; HET: AD	95.83
1cke_A	227	CK, MSSA, protein (cytidine monophosphate kinase);	95.81
2yhs_A	503	FTSY, cell division protein FTSY; cell cycle, prot	95.81
3crm_A	323	TRNA delta(2)-isopentenylpyrophosphate transferase	95.8
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	95.8
3nwj_A	250	ATSK2; P loop, shikimate, nucleoside monophosphate	95.79
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	95.76
1odf_A	290	YGR205W, hypothetical 33.3 kDa protein in ADE3-Ser	95.75
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	95.74
3oaa_A	513	ATP synthase subunit alpha; rossmann fold, hydrola	95.73
1tf7_A	525	KAIC; homohexamer, hexamer, circadian clock protei	95.68
1r8s_A	164	ADP-ribosylation factor 1; protein transport/excha	95.67
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	95.66
2bdt_A	189	BH3686; alpha-beta protein, structural genomics, P	95.64
1e4v_A	214	Adenylate kinase; transferase(phosphotransferase);	95.64
1upt_A	171	ARL1, ADP-ribosylation factor-like protein 1; hydr	95.63
3r20_A	233	Cytidylate kinase; structural genomics, seattle st	95.59
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	95.59
2if2_A	204	Dephospho-COA kinase; alpha-beta protein, structur	95.58
2h57_A	190	ADP-ribosylation factor-like protein 6; GTP, GTPas	95.58
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	95.57
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	95.57
3gmt_A	230	Adenylate kinase; ssgcid, ATP-BIN cytoplasm, nucle	95.57
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	95.52
1s96_A	219	Guanylate kinase, GMP kinase; E.coli, dimer, SAD,	95.52
1svm_A	377	Large T antigen; AAA+ fold, viral protein; HET: AT	95.51
3asz_A	211	Uridine kinase; cytidine phosphorylation, transfer	95.5
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	95.49
2hf9_A	226	Probable hydrogenase nickel incorporation protein	95.48
4e22_A	252	Cytidylate kinase; P-loop, CMP/ATP binding, transf	95.47
1znw_A	207	Guanylate kinase, GMP kinase; ATP:GMP-phosphotrans	95.47
3foz_A	316	TRNA delta(2)-isopentenylpyrophosphate transferas;	95.46
3vr4_D	465	V-type sodium ATPase subunit D; V-ATPase, rotary m	95.44
1htw_A	158	HI0065; nucleotide-binding fold, structural genomi	95.44
3tqc_A	321	Pantothenate kinase; biosynthesis of cofactors, pr	95.43
3dz8_A	191	RAS-related protein RAB-3B; GDP, GTPase, structura	95.43
3a8t_A	339	Adenylate isopentenyltransferase; rossmann fold pr	95.41
1z6g_A	218	Guanylate kinase; structural genomics, SGC, struct	95.41
2h17_A	181	ADP-ribosylation factor-like protein 5A; GDP, GTPa	95.41
4a4z_A	997	Antiviral helicase SKI2; hydrolase, ATPase, mRNA d	95.39
3mfy_A	588	V-type ATP synthase alpha chain; A-type ATP syntha	95.37
1nrj_B	218	SR-beta, signal recognition particle receptor beta	95.34
4edh_A	213	DTMP kinase, thymidylate kinase; structural genomi	95.32
1fzq_A	181	ADP-ribosylation factor-like protein 3; protein-GD	95.31
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	95.3
2grj_A	192	Dephospho-COA kinase; TM1387, EC 2.7.1.24, dephosp	95.27
3v9p_A	227	DTMP kinase, thymidylate kinase; ssgcid, STRU geno	95.26
1uj2_A	252	Uridine-cytidine kinase 2; alpha/beta mononucleoti	95.25
2wsm_A	221	Hydrogenase expression/formation protein (HYPB); m	95.24
2z83_A	459	Helicase/nucleoside triphosphatase; hydrolase, mem	95.23
3exa_A	322	TRNA delta(2)-isopentenylpyrophosphate transferase	95.22
2eyu_A	261	Twitching motility protein PILT; pilus retraction	95.2
1moz_A	183	ARL1, ADP-ribosylation factor-like protein 1; GTP-	95.2
2xgj_A	1010	ATP-dependent RNA helicase DOB1; hydrolase-RNA com	95.16
3ake_A	208	Cytidylate kinase; CMP kinase, CMP complex, open c	95.16
1fx0_A	507	ATP synthase alpha chain; latent ATPase, thermal s	95.12
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	95.11
2qt1_A	207	Nicotinamide riboside kinase 1; non-protein kinase	95.1
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	95.1
3b9q_A	302	Chloroplast SRP receptor homolog, alpha subunit CP	95.08
3l9o_A	1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	95.07
3hjn_A	197	DTMP kinase, thymidylate kinase; ATP-binding, nucl	95.05
3gqb_B	464	V-type ATP synthase beta chain; A3B3, V-ATPase, AT	95.01
1rj9_A	304	FTSY, signal recognition protein; SRP-GTPase domai	95.01
1uf9_A	203	TT1252 protein; P-loop, nucleotide binding domain,	95.01
3vr4_A	600	V-type sodium ATPase catalytic subunit A; V-ATPase	95.0
2gk6_A	624	Regulator of nonsense transcripts 1; UPF1, helicas	95.0
3def_A	262	T7I23.11 protein; chloroplast, TOC33, GTPase, hydr	95.0
3ld9_A	223	DTMP kinase, thymidylate kinase; ssgcid, NIH, niai	94.99
1gtv_A	214	TMK, thymidylate kinase; transferase, transferase	94.99
1xjc_A	169	MOBB protein homolog; structural genomics, midwest	94.98
1jjv_A	206	Dephospho-COA kinase; P-loop nucleotide-binding fo	94.96
3aez_A	312	Pantothenate kinase; transferase, homodimer, COA b	94.95
2c61_A	469	A-type ATP synthase non-catalytic subunit B; hydro	94.95
3lnc_A	231	Guanylate kinase, GMP kinase; ALS collaborative cr	94.94
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	94.88
2v9p_A	305	Replication protein E1; AAA+ molecular motor, DNA	94.87
3iqw_A	334	Tail-anchored protein targeting factor GET3; ATPas	94.86
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	94.85
3kw6_A	78	26S protease regulatory subunit 8; structural geno	94.85
4tmk_A	213	Protein (thymidylate kinase); ATP:DTMP phosphotran	94.85
1p9r_A	418	General secretion pathway protein E; bacterial typ	94.84
3p32_A	355	Probable GTPase RV1496/MT1543; structural genomics	94.84
2og2_A	359	Putative signal recognition particle receptor; nuc	94.83
1q3t_A	236	Cytidylate kinase; nucleotide monophosphate kinase	94.83
1vht_A	218	Dephospho-COA kinase; structural genomics, transfe	94.83
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	94.78
2oap_1	511	GSPE-2, type II secretion system protein; hexameri	94.77
2b6h_A	192	ADP-ribosylation factor 5; membrane trafficking, G	94.77
2bov_A	206	RAla, RAS-related protein RAL-A; C3BOT, exoenzyme,	94.75
1sq5_A	308	Pantothenate kinase; P-loop, transferase; HET: PAU	94.73
1ltq_A	301	Polynucleotide kinase; phosphatase, alpha/beta, P-	94.71
2f7s_A	217	C25KG, RAS-related protein RAB-27B; G-protein, str	94.7
4hlc_A	205	DTMP kinase, thymidylate kinase; TMK, MRSA, pipiri	94.7
2jeo_A	245	Uridine-cytidine kinase 1; UCK, transferase, ATP-b	94.69
1m8p_A	573	Sulfate adenylyltransferase; rossmann fold, phosph	94.69
1f6b_A	198	SAR1; gtpases, N-terminal helix, Mg-containing com	94.68
2qmh_A	205	HPR kinase/phosphorylase; V267F mutation, ATP-bind	94.66
1ksh_A	186	ARF-like protein 2; small GTPase, small GTP-bindin	94.64
2ewv_A	372	Twitching motility protein PILT; pilus retraction	94.64
3d3q_A	340	TRNA delta(2)-isopentenylpyrophosphate transferase	94.64
3lv8_A	236	DTMP kinase, thymidylate kinase; structural genomi	94.64
3tif_A	235	Uncharacterized ABC transporter ATP-binding prote;	94.63
1np6_A	174	Molybdopterin-guanine dinucleotide biosynthesis pr	94.63
2ged_A	193	SR-beta, signal recognition particle receptor beta	94.62
2h92_A	219	Cytidylate kinase; rossmann fold, transferase; HET	94.6
2oca_A	510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	94.6
3clv_A	208	RAB5 protein, putative; malaria, GTPase, structura	94.59
3eph_A	409	TRNA isopentenyltransferase; transferase, alternat	94.58
3iev_A	308	GTP-binding protein ERA; ERA, GTPase, KH domain, a	94.58
1g8f_A	511	Sulfate adenylyltransferase; alpha-beta protein, b	94.57
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	94.55
2f6r_A	281	COA synthase, bifunctional coenzyme A synthase; 18	94.53
2pcj_A	224	ABC transporter, lipoprotein-releasing system ATP-	94.49
3h1t_A	590	Type I site-specific restriction-modification syst	94.43
2cbz_A	237	Multidrug resistance-associated protein 1; ABC pro	94.43
4bas_A	199	ADP-ribosylation factor, putative (small GTPase, p	94.42
2wjy_A	800	Regulator of nonsense transcripts 1; nonsense medi	94.39
3b85_A	208	Phosphate starvation-inducible protein; PHOH2, ATP	94.38
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	94.37
3dmq_A	968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	94.36
2whx_A	618	Serine protease/ntpase/helicase NS3; transcription	94.35
1b0u_A	262	Histidine permease; ABC transporter, transport pro	94.33
1sgw_A	214	Putative ABC transporter; structural genomics, P p	94.3
2krk_A	86	26S protease regulatory subunit 8; structural geno	94.26
2gza_A	361	Type IV secretion system protein VIRB11; ATPase, h	94.25
2pt7_A	330	CAG-ALFA; ATPase, protein-protein complex, type IV	94.23
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	94.22
2zu0_C	267	Probable ATP-dependent transporter SUFC; iron-sulf	94.21
3kta_A	182	Chromosome segregation protein SMC; structural mai	94.21
3cr8_A	552	Sulfate adenylyltranferase, adenylylsulfate kinase	94.19
1wf3_A	301	GTP-binding protein; GTPase, riken structural geno	94.19
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	94.16
2olj_A	263	Amino acid ABC transporter; ABC domain, ATPase, hy	94.15
2d2e_A	250	SUFC protein; ABC-ATPase, SUF protein, 310-helix,	94.13
1g6h_A	257	High-affinity branched-chain amino acid transport	94.11
2onk_A	240	Molybdate/tungstate ABC transporter, ATP-binding p	94.1
2pze_A	229	Cystic fibrosis transmembrane conductance regulat;	94.1
1yrb_A	262	ATP(GTP)binding protein; GTPase, P-loop, rossman f	94.09
1tq4_A	413	IIGP1, interferon-inducible GTPase; interferon gam	94.09
1ji0_A	240	ABC transporter; ATP binding protein, structural g	94.08
3gfo_A	275	Cobalt import ATP-binding protein CBIO 1; structur	94.06
1a7j_A	290	Phosphoribulokinase; transferase, calvin cycle; 2.	94.05
2ff7_A	247	Alpha-hemolysin translocation ATP-binding protein	94.03
1mv5_A	243	LMRA, multidrug resistance ABC transporter ATP-bin	94.02
2ihy_A	279	ABC transporter, ATP-binding protein; ATPase, ABC	94.01
2ghi_A	260	Transport protein; multidrug resistance protein, M	94.01
1vpl_A	256	ABC transporter, ATP-binding protein; TM0544, stru	93.99
2qi9_C	249	Vitamin B12 import ATP-binding protein BTUD; inner	93.98
2ixe_A	271	Antigen peptide transporter 1; ABC ATPase, hydrola	93.96
3fdi_A	201	Uncharacterized protein; cytidylate kinase like pr	93.96
2ocp_A	241	DGK, deoxyguanosine kinase; protein-nucleotide com	93.94
3bfv_A	271	CAPA1, CAPB2, membrane protein CAPA1, protein tyro	93.94
4g1u_C	266	Hemin import ATP-binding protein HMUV; membrane tr	93.94
3fvq_A	359	Fe(3+) IONS import ATP-binding protein FBPC; nucle	93.93
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	93.92
1yks_A	440	Genome polyprotein [contains: flavivirin protease	93.87
2f9l_A	199	RAB11B, member RAS oncogene family; RAB11B GTPase,	93.87
3gqb_A	578	V-type ATP synthase alpha chain; A3B3, V-ATPase, A	93.84
2yz2_A	266	Putative ABC transporter ATP-binding protein TM_0;	93.84
1oix_A	191	RAS-related protein RAB-11A; small G protein, intr	93.79
2it1_A	362	362AA long hypothetical maltose/maltodextrin trans	93.77
2yyz_A	359	Sugar ABC transporter, ATP-binding protein; sugar	93.75
2nq2_C	253	Hypothetical ABC transporter ATP-binding protein H	93.75
3rlf_A	381	Maltose/maltodextrin import ATP-binding protein M;	93.74
2dyk_A	161	GTP-binding protein; GTPase, ribosome-binding prot	93.73
1z47_A	355	CYSA, putative ABC-transporter ATP-binding protein	93.71
2xzl_A	802	ATP-dependent helicase NAM7; hydrolase-RNA complex	93.71
2obl_A	347	ESCN; ATPase, hydrolase; 1.80A {Escherichia coli O	93.7
2f1r_A	171	Molybdopterin-guanine dinucleotide biosynthesis pr	93.69
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	93.67
3cio_A	299	ETK, tyrosine-protein kinase ETK; WZC, escherichia	93.67
3sop_A	270	Neuronal-specific septin-3; hydrolase; HET: GDP; 2	93.66
1v43_A	372	Sugar-binding transport ATP-binding protein; ATPas	93.64
2zpa_A	671	Uncharacterized protein YPFI; RNA modification enz	93.54
2dpy_A	438	FLII, flagellum-specific ATP synthase; beta barrel	93.53
3thx_A	934	DNA mismatch repair protein MSH2; ABC family ATPas	93.53
1z2a_A	168	RAS-related protein RAB-23; RAB GTPase, vesicular	93.52
3d31_A	348	Sulfate/molybdate ABC transporter, ATP-binding pro	93.51
3io3_A	348	DEHA2D07832P; chaperone, membrane traffic, ATPase;	93.5
1g29_1	372	MALK, maltose transport protein MALK; ATPase, acti	93.5
2wji_A	165	Ferrous iron transport protein B homolog; membrane	93.45
3tmk_A	216	Thymidylate kinase; phosphotransferase; HET: T5A;	93.43
2zej_A	184	Dardarin, leucine-rich repeat kinase 2; parkinson'	93.42
1kao_A	167	RAP2A; GTP-binding protein, small G protein, GDP,	93.4
3end_A	307	Light-independent protochlorophyllide reductase ir	93.38
3tqf_A	181	HPR(Ser) kinase; transferase, hydrolase; 2.80A {Co	93.38
2wv9_A	673	Flavivirin protease NS2B regulatory subunit, FLAV	93.38
2yv5_A	302	YJEQ protein; hydrolase, GTPase, permutation, stru	93.33
1f2t_A	149	RAD50 ABC-ATPase; DNA double-strand break repair,	93.32
1x6v_B	630	Bifunctional 3'-phosphoadenosine 5'- phosphosulfat	93.3
2ce2_X	166	GTPase HRAS; signaling protein, guanine nucleotide	93.28
2nzj_A	175	GTP-binding protein REM 1; GDP/GTP binding, GTP hy	93.26
1wms_A	177	RAB-9, RAB9, RAS-related protein RAB-9A; GTPase, p	93.21
3nh6_A	306	ATP-binding cassette SUB-family B member 6, mitoc;	93.21
1u8z_A	168	RAS-related protein RAL-A; GNP, GTP, GMPPNP, GPPNH	93.21
1ek0_A	170	Protein (GTP-binding protein YPT51); vesicular tra	93.2
2qm8_A	337	GTPase/ATPase; G protein, G3E, metallochaperone, c	93.19
2axn_A	520	6-phosphofructo-2-kinase/fructose-2,6- biphosphata	93.17
2bbs_A	290	Cystic fibrosis transmembrane conductance regulato	93.16
1z08_A	170	RAS-related protein RAB-21; RAB GTPase, vesicular	93.16
2pjz_A	263	Hypothetical protein ST1066; ATP binding protein,	93.15
1z0j_A	170	RAB-22, RAS-related protein RAB-22A; RAB GTPase, R	93.15
1p5z_B	263	DCK, deoxycytidine kinase; nucleoside kinase, P-lo	93.15
3o47_A	329	ADP-ribosylation factor GTPase-activating protein	93.14
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	93.14
4dhe_A	223	Probable GTP-binding protein ENGB; melioidosis, RA	93.11
4dzz_A	206	Plasmid partitioning protein PARF; deviant walker	93.07
3la6_A	286	Tyrosine-protein kinase WZC; P-loop protein, nucle	93.06
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	93.05
2o8b_B	1022	DNA mismatch repair protein MSH6; DNA damage respo	93.04
1oxx_K	353	GLCV, glucose, ABC transporter, ATP binding protei	93.03
1ky3_A	182	GTP-binding protein YPT7P; vesicular traffic, GTP	93.02
1c1y_A	167	RAS-related protein RAP-1A; GTP-binding proteins,	93.02
2lkc_A	178	Translation initiation factor IF-2; NMR {Geobacill	93.01
3hdt_A	223	Putative kinase; structura genomics, PSI-2, protei	92.99
1u0l_A	301	Probable GTPase ENGC; permutation, OB-fold, zinc-f	92.96
1g16_A	170	RAS-related protein SEC4; G protein RAB, signaling	92.95
3gd7_A	390	Fusion complex of cystic fibrosis transmembrane co	92.94
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	92.93
1m2o_B	190	GTP-binding protein SAR1, GTP binding protein; zin	92.92
2erx_A	172	GTP-binding protein DI-RAS2; GTP hydrolysis, trans	92.9
1r2q_A	170	RAS-related protein RAB-5A; GTPase, GNP, atomic re	92.89
2www_A	349	Methylmalonic aciduria type A protein, mitochondri	92.87
2gks_A	546	Bifunctional SAT/APS kinase; transferase, sulfuryl	92.83
2gj8_A	172	MNME, tRNA modification GTPase TRME; G-domain dime	92.83
3q85_A	169	GTP-binding protein REM 2; G-domain, CAV2 beta, si	92.83
3bc1_A	195	RAS-related protein RAB-27A; RAB27, GTPase, RAB, s	92.79

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}

Probab=99.98  E-value=7.7e-32  Score=263.27  Aligned_cols=252  Identities=18%  Similarity=0.174  Sum_probs=205.1

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhc------CCceEEEEeccCCCCHHHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIK------DAFKTIYINCNSVRNAASVYE  267 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~------~~~~~~~v~~~~~~~~~~l~~  267 (490)
                      +.|.||+++++.|..+|...+..+.+++++|+||||||||++++.+++++...      ..+.++++||....+...++.
T Consensus        20 ~~L~~Re~E~~~i~~~L~~~i~~~~~~~lli~GpPGTGKT~~v~~v~~~L~~~~~~~~~~~~~~v~INc~~~~t~~~~~~   99 (318)
T 3te6_A           20 ELLKSQVEDFTRIFLPIYDSLMSSQNKLFYITNADDSTKFQLVNDVMDELITSSARKELPIFDYIHIDALELAGMDALYE   99 (318)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTTCCCEEEEECCCSHHHHHHHHHHHHHHHHTTTTTSSCCEEEEEEETTCCC--HHHHH
T ss_pred             cccCCHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHHHHHHHHHhhhccCCceEEEEEeccccCCHHHHHH
Confidence            44899999999999999999999999999999999999999999999999632      257899999999999999999


Q ss_pred             HHHHHhcCCC--CCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEEEecCCCChhH
Q psy200          268 TIVNELKLKP--GGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVANALDLTD  345 (490)
Q Consensus       268 ~i~~~l~~~~--~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI~~tn~~~~~~  345 (490)
                      .|+.+|....  .+.....+...|.......++++||||||+|.|.  .|+.|+.+++|.....+++++|+++|..++++
T Consensus       100 ~I~~~L~g~~~~~~~~~~~L~~~f~~~~~~~~~~~ii~lDE~d~l~--~q~~L~~l~~~~~~~~s~~~vI~i~n~~d~~~  177 (318)
T 3te6_A          100 KIWFAISKENLCGDISLEALNFYITNVPKAKKRKTLILIQNPENLL--SEKILQYFEKWISSKNSKLSIICVGGHNVTIR  177 (318)
T ss_dssp             HHHHHHSCCC--CCCCHHHHHHHHHHSCGGGSCEEEEEEECCSSSC--CTHHHHHHHHHHHCSSCCEEEEEECCSSCCCH
T ss_pred             HHHHHhcCCCCCchHHHHHHHHHHHHhhhccCCceEEEEecHHHhh--cchHHHHHHhcccccCCcEEEEEEecCcccch
Confidence            9999996542  2233444444444322234678999999999998  78999999998766788999999999988877


Q ss_pred             h-hhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCC---------------------------------CCCCH
Q psy200          346 R-MLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKF---------------------------------NMFNA  391 (490)
Q Consensus       346 ~-l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~---------------------------------~~~~~  391 (490)
                      + +.+++++||+.  ..|.|.||+.+|+.+|+.+++......                                 ..+++
T Consensus       178 ~~L~~~v~SR~~~--~~i~F~pYt~~el~~Il~~Rl~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~  255 (318)
T 3te6_A          178 EQINIMPSLKAHF--TEIKLNKVDKNELQQMIITRLKSLLKPFHVKVNDKKEMTIYNNIREGQNQKIPDNVIVINHKINN  255 (318)
T ss_dssp             HHHHTCHHHHTTE--EEEECCCCCHHHHHHHHHHHHHHHCCCEEEEECTTCCEEECCCC--------CTTEEEECEECCH
T ss_pred             hhcchhhhccCCc--eEEEeCCCCHHHHHHHHHHHHHhhhccccccccccccccccccccccccccccccccccccccCH
Confidence            5 46788999864  479999999999999999999874211                                 14799


Q ss_pred             HHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHhcccc----CCcccccCHHHHHHHHHHhcc
Q psy200          392 SALQLLAGKVAAVSGDIRKAIDITNHLIDLTYDNVKE----NGEVTGIGLKEVLGVISSVYC  449 (490)
Q Consensus       392 ~~i~~i~~~i~~~~Gd~r~ai~ll~~a~~~a~~~~~~----~~~~~~It~~~v~~a~~~~~~  449 (490)
                      ++|+.++++++..+||+|.||++|++|+++|+.+...    ......|+.+++.+++++++.
T Consensus       256 ~ai~~~A~~vA~~~GD~R~Al~ilr~A~~~ae~e~~~k~~~~~~~~~i~~~~~~~~~~~~~~  317 (318)
T 3te6_A          256 KITQLIAKNVANVSGSTEKAFKICEAAVEISKKDFVRKGGLQKGKLVVSQEMVPRYFSEAIN  317 (318)
T ss_dssp             HHHHHHHHHHHHHHCSHHHHHHHHHHHHHHHHHHHHHHTTEETTEECCSEECCTHHHHHHHC
T ss_pred             HHHHHHHHHHHhhCChHHHHHHHHHHHHHHHHHHHHhccCCCCCcEEeeHHHHHHHHHHHhc
Confidence            9999999999999999999999999999999875221    112457888888888887653

>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix}

Probab=99.96  E-value=2.3e-28  Score=247.82  Aligned_cols=275  Identities=24%  Similarity=0.359  Sum_probs=225.8

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhc-----CCceEEEEeccCCCCHHHHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIK-----DAFKTIYINCNSVRNAASVYET  268 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~-----~~~~~~~v~~~~~~~~~~l~~~  268 (490)
                      +.|+||+++++.+..++...+....+.+++|+||+|+|||++++.+++.+...     .++.+++++|....+...++..
T Consensus        19 ~~~~gr~~~~~~l~~~l~~~~~~~~~~~vll~G~~G~GKT~l~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~   98 (387)
T 2v1u_A           19 DVLPHREAELRRLAEVLAPALRGEKPSNALLYGLTGTGKTAVARLVLRRLEARASSLGVLVKPIYVNARHRETPYRVASA   98 (387)
T ss_dssp             SCCTTCHHHHHHHHHTTGGGTSSCCCCCEEECBCTTSSHHHHHHHHHHHHHHHHHHHTCCEEEEEEETTTSCSHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHHHHcCCCCCcEEEECCCCCCHHHHHHHHHHHHHHHHhccCCCeEEEEEECCcCCCHHHHHHH
Confidence            78999999999999999877666778899999999999999999999988432     2578999999999999999999


Q ss_pred             HHHHhcCC--CCCCcHHHHHHHHHHHHhcCCCeEEEEEecCcccccc--CHHHHHHhHhCCCC-C-CCcEEEEEecCCCC
Q psy200          269 IVNELKLK--PGGKSERHQLGAILKYFDTKHKSILLILDEIDALESR--KQTILYTIFEWPSI-P-GSKLVLVGVANALD  342 (490)
Q Consensus       269 i~~~l~~~--~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~--~~~~L~~l~~~~~~-~-~~~vilI~~tn~~~  342 (490)
                      ++..++..  ..+.+..++.+.+...+...+++++|||||+|.+...  .++.|+.++++... . ..++++|+++|..+
T Consensus        99 l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~~~~~vlilDEi~~l~~~~~~~~~l~~l~~~~~~~~~~~~~~~I~~t~~~~  178 (387)
T 2v1u_A           99 IAEAVGVRVPFTGLSVGEVYERLVKRLSRLRGIYIIVLDEIDFLPKRPGGQDLLYRITRINQELGDRVWVSLVGITNSLG  178 (387)
T ss_dssp             HHHHHSCCCCSSCCCHHHHHHHHHHHHTTSCSEEEEEEETTTHHHHSTTHHHHHHHHHHGGGCC-----CEEEEECSCST
T ss_pred             HHHHhCCCCCCCCCCHHHHHHHHHHHHhccCCeEEEEEccHhhhcccCCCChHHHhHhhchhhcCCCceEEEEEEECCCc
Confidence            99998753  3345567777777777766677999999999999877  67888888876532 2 66889999999776


Q ss_pred             hhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHH
Q psy200          343 LTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITNHLIDLT  422 (490)
Q Consensus       343 ~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll~~a~~~a  422 (490)
                      +...+.+.+.+||..  ..+.|+||+.+++..++..++........+++++++.+++......|++|.++++|+.|+..+
T Consensus       179 ~~~~l~~~l~~r~~~--~~i~l~~l~~~~~~~il~~~~~~~~~~~~~~~~~~~~l~~~~~~~~G~~r~~~~~l~~a~~~a  256 (387)
T 2v1u_A          179 FVENLEPRVKSSLGE--VELVFPPYTAPQLRDILETRAEEAFNPGVLDPDVVPLCAALAAREHGDARRALDLLRVAGEIA  256 (387)
T ss_dssp             TSSSSCHHHHTTTTS--EECCBCCCCHHHHHHHHHHHHHHHBCTTTBCSSHHHHHHHHHHSSSCCHHHHHHHHHHHHHHH
T ss_pred             hHhhhCHHHHhcCCC--eEEeeCCCCHHHHHHHHHHHHHhhccCCCCCHHHHHHHHHHHHHhccCHHHHHHHHHHHHHHH
Confidence            667778889999863  379999999999999999998753224568889999999844444599999999999999998


Q ss_pred             HhccccCCcccccCHHHHHHHHHHhccCccccccccccCCCChHhHHHHHHHHHHhc
Q psy200          423 YDNVKENGEVTGIGLKEVLGVISSVYCTSQSLHCSKDEDSFPLQQKLALASLLLLKS  479 (490)
Q Consensus       423 ~~~~~~~~~~~~It~~~v~~a~~~~~~~~~~~~~~~~l~~L~~~qk~vL~al~~~~~  479 (490)
                      ...+     ...|+.+++..++..+.....    ...+.+++.+++.+|+|++.+..
T Consensus       257 ~~~~-----~~~i~~~~v~~a~~~~~~~~~----~~~~~~l~~~~~~~l~a~~~~~~  304 (387)
T 2v1u_A          257 ERRR-----EERVRREHVYSARAEIERDRV----SEVVRTLPLHAKLVLLSIMMLED  304 (387)
T ss_dssp             HHTT-----CSCBCHHHHHHHHHHHHHHHH----HHHHHSSCHHHHHHHHHHHHHSS
T ss_pred             HHcC-----CCCcCHHHHHHHHHHHhhchH----HHHHHcCCHHHHHHHHHHHHHhc
Confidence            8776     568999999999998865544    56789999999999999997765

>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=99.95  E-value=3.5e-26  Score=232.02  Aligned_cols=273  Identities=23%  Similarity=0.271  Sum_probs=220.1

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCC--eEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSG--SMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVN  271 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~--~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~  271 (490)
                      +.++||+++++.|..++...+.+..+.  +++|+||+|+|||++++.+++.+....++.+++++|....+...++..++.
T Consensus        17 ~~l~gr~~~~~~l~~~l~~~~~~~~~~~~~~li~G~~G~GKTtl~~~l~~~~~~~~~~~~~~i~~~~~~~~~~~~~~l~~   96 (389)
T 1fnn_A           17 KRLPHREQQLQQLDILLGNWLRNPGHHYPRATLLGRPGTGKTVTLRKLWELYKDKTTARFVYINGFIYRNFTAIIGEIAR   96 (389)
T ss_dssp             SCCTTCHHHHHHHHHHHHHHHHSTTSSCCEEEEECCTTSSHHHHHHHHHHHHTTSCCCEEEEEETTTCCSHHHHHHHHHH
T ss_pred             CCCCChHHHHHHHHHHHHHHHcCCCCCCCeEEEECCCCCCHHHHHHHHHHHHhhhcCeeEEEEeCccCCCHHHHHHHHHH
Confidence            679999999999999999877666666  899999999999999999999885332578999999998888999999999


Q ss_pred             HhcCCC--CCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCHHHHHHhHhCCCCCC---CcEEEEEecCCCChhHh
Q psy200          272 ELKLKP--GGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPSIPG---SKLVLVGVANALDLTDR  346 (490)
Q Consensus       272 ~l~~~~--~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~---~~vilI~~tn~~~~~~~  346 (490)
                      .++...  .+.+...+.+.+...+...+++.||||||+|++....+..|..+++.  ...   .++.+|++++..++...
T Consensus        97 ~l~~~~~~~~~~~~~~~~~l~~~l~~~~~~~vlilDE~~~l~~~~~~~L~~~~~~--~~~~~~~~~~iI~~~~~~~~~~~  174 (389)
T 1fnn_A           97 SLNIPFPRRGLSRDEFLALLVEHLRERDLYMFLVLDDAFNLAPDILSTFIRLGQE--ADKLGAFRIALVIVGHNDAVLNN  174 (389)
T ss_dssp             HTTCCCCSSCCCHHHHHHHHHHHHHHTTCCEEEEEETGGGSCHHHHHHHHHHTTC--HHHHSSCCEEEEEEESSTHHHHT
T ss_pred             HhCccCCCCCCCHHHHHHHHHHHHhhcCCeEEEEEECccccchHHHHHHHHHHHh--CCCCCcCCEEEEEEECCchHHHH
Confidence            886532  34456777777777776667789999999999944333444443321  112   57888888887766677


Q ss_pred             hhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHh------hCCHHHHHHHHHHHHH
Q psy200          347 MLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAV------SGDIRKAIDITNHLID  420 (490)
Q Consensus       347 l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~------~Gd~r~ai~ll~~a~~  420 (490)
                      +.+++.+||..  ..+.|+|++.+++.+++..++...+....+++++++.+++.....      .|++|.++++|+.|+.
T Consensus       175 l~~~~~~r~~~--~~i~~~pl~~~~~~~~l~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~G~~r~~~~~l~~a~~  252 (389)
T 1fnn_A          175 LDPSTRGIMGK--YVIRFSPYTKDQIFDILLDRAKAGLAEGSYSEDILQMIADITGAQTPLDTNRGDARLAIDILYRSAY  252 (389)
T ss_dssp             SCHHHHHHHTT--CEEECCCCBHHHHHHHHHHHHHHHBCTTSSCHHHHHHHHHHHSBSSTTCTTSCCHHHHHHHHHHHHH
T ss_pred             hCHHhhhcCCC--ceEEeCCCCHHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHhhcccCCCCCCcHHHHHHHHHHHHH
Confidence            78888888863  369999999999999999998763223468999999999843333      7999999999999999


Q ss_pred             HHHhccccCCcccccCHHHHHHHHHHhccCccccccccccCCCChHhHHHHHHHHHHhc
Q psy200          421 LTYDNVKENGEVTGIGLKEVLGVISSVYCTSQSLHCSKDEDSFPLQQKLALASLLLLKS  479 (490)
Q Consensus       421 ~a~~~~~~~~~~~~It~~~v~~a~~~~~~~~~~~~~~~~l~~L~~~qk~vL~al~~~~~  479 (490)
                      .|..++     ...|+.+++..++..+.....    ...+..|+.+++.+|++|+.+.+
T Consensus       253 ~a~~~~-----~~~i~~~~v~~~~~~~~~~~~----~~~l~~l~~~~~~~L~~l~~~~~  302 (389)
T 1fnn_A          253 AAQQNG-----RKHIAPEDVRKSSKEVLFGIS----EEVLIGLPLHEKLFLLAIVRSLK  302 (389)
T ss_dssp             HHHHTT-----CSSCCHHHHHHHHHHHSCCCC----HHHHHHSCHHHHHHHHHHHHHHH
T ss_pred             HHHHhC-----CCCcCHHHHHHHHHHHhhhhH----HHHHHcCCHHHHHHHHHHHHHHh
Confidence            998877     568999999999999886666    67889999999999999998763

>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=99.95  E-value=1.6e-26  Score=234.28  Aligned_cols=263  Identities=24%  Similarity=0.293  Sum_probs=215.0

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhc------C-CceEEEEeccCCC-CHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIK------D-AFKTIYINCNSVR-NAASV  265 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~------~-~~~~~~v~~~~~~-~~~~l  265 (490)
                      ++|+||+++++.|..++..++....+++++|+||+|+|||++++.+++.+...      . ++.+++++|.... +...+
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            78999999999999999988777778899999999999999999999987422      1 5789999999888 88999


Q ss_pred             HHHHHHHhcC---CCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccC-HHH-HHHhHhCCCCCCCcEEEEEecCC
Q psy200          266 YETIVNELKL---KPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRK-QTI-LYTIFEWPSIPGSKLVLVGVANA  340 (490)
Q Consensus       266 ~~~i~~~l~~---~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~-~~~-L~~l~~~~~~~~~~vilI~~tn~  340 (490)
                      +..++..+..   ...+.+...+.+.+.+.+... +. ||||||+|++.... ++. +..++++.    .++.+|+++|.
T Consensus       100 ~~~l~~~l~~~~~~~~~~~~~~~~~~l~~~l~~~-~~-vlilDEi~~l~~~~~~~~~l~~l~~~~----~~~~iI~~t~~  173 (384)
T 2qby_B          100 LSSLAGKLTGFSVPKHGINLGEYIDKIKNGTRNI-RA-IIYLDEVDTLVKRRGGDIVLYQLLRSD----ANISVIMISND  173 (384)
T ss_dssp             HHHHHHHHHCSCCCSSSSCTHHHHHHHHHHHSSS-CE-EEEEETTHHHHHSTTSHHHHHHHHTSS----SCEEEEEECSS
T ss_pred             HHHHHHHhcCCCCCCCCCCHHHHHHHHHHHhccC-CC-EEEEECHHHhccCCCCceeHHHHhcCC----cceEEEEEECC
Confidence            9999988832   223344566666666666543 23 99999999998763 777 88887765    67889999987


Q ss_pred             CChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHHHHHHHHH
Q psy200          341 LDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITNHLID  420 (490)
Q Consensus       341 ~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll~~a~~  420 (490)
                      .++...+.+.+.+||..   .+.|+|++.+++.+++..++........+++++++.+++......||+|.++++|+.|+.
T Consensus       174 ~~~~~~l~~~l~sr~~~---~i~l~~l~~~~~~~il~~~~~~~~~~~~~~~~~~~~i~~~~~~~~G~~r~a~~~l~~a~~  250 (384)
T 2qby_B          174 INVRDYMEPRVLSSLGP---SVIFKPYDAEQLKFILSKYAEYGLIKGTYDDEILSYIAAISAKEHGDARKAVNLLFRAAQ  250 (384)
T ss_dssp             TTTTTTSCHHHHHTCCC---EEEECCCCHHHHHHHHHHHHHHTSCTTSCCSHHHHHHHHHHHTTCCCHHHHHHHHHHHHH
T ss_pred             CchHhhhCHHHHhcCCC---eEEECCCCHHHHHHHHHHHHHhhcccCCcCHHHHHHHHHHHHhccCCHHHHHHHHHHHHH
Confidence            76667778888888863   899999999999999999987422235688999999998555555999999999999998


Q ss_pred             HHHhccccCCcccccCHHHHHHHHHHhccCccccccccccCCCChHhHHHHHHHHH
Q psy200          421 LTYDNVKENGEVTGIGLKEVLGVISSVYCTSQSLHCSKDEDSFPLQQKLALASLLL  476 (490)
Q Consensus       421 ~a~~~~~~~~~~~~It~~~v~~a~~~~~~~~~~~~~~~~l~~L~~~qk~vL~al~~  476 (490)
                      .|.  +     ...|+.+++..++.+......    ...+..|+.+++.+|++|+.
T Consensus       251 ~a~--~-----~~~i~~~~v~~~~~~~~~~~~----~~~~~~l~~~~~~~l~al~~  295 (384)
T 2qby_B          251 LAS--G-----GGIIRKEHVDKAIVDYEQERL----IEAVKALPFHYKLALRSLIE  295 (384)
T ss_dssp             HTT--S-----SSCCCHHHHHHHHHHHHHHHH----HHHHHSSCHHHHHHHHHHHT
T ss_pred             Hhc--C-----CCccCHHHHHHHHHHHhcchH----HHHHHcCCHHHHHHHHHHHH
Confidence            887  3     458999999999999875544    56778999999999999986

>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=99.95  E-value=2.1e-26  Score=233.02  Aligned_cols=276  Identities=24%  Similarity=0.368  Sum_probs=217.8

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcC--CceEEEEeccCCCCHHHHHHHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKD--AFKTIYINCNSVRNAASVYETIVN  271 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~--~~~~~~v~~~~~~~~~~l~~~i~~  271 (490)
                      +.|+||+++++.|..++...+....+..++|+||+|+|||++++.+++.+....  ++.+++++|....+...++..++.
T Consensus        20 ~~~~gr~~e~~~l~~~l~~~~~~~~~~~vli~G~~G~GKTtl~~~l~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~i~~   99 (386)
T 2qby_A           20 DELPHREDQIRKIASILAPLYREEKPNNIFIYGLTGTGKTAVVKFVLSKLHKKFLGKFKHVYINTRQIDTPYRVLADLLE   99 (386)
T ss_dssp             SCCTTCHHHHHHHHHSSGGGGGTCCCCCEEEEECTTSSHHHHHHHHHHHHHHHTCSSCEEEEEEHHHHCSHHHHHHHHTT
T ss_pred             CCCCChHHHHHHHHHHHHHHHcCCCCCeEEEECCCCCCHHHHHHHHHHHHHHHhcCCceEEEEECCCCCCHHHHHHHHHH
Confidence            779999999999999998766667788999999999999999999999875322  578999999888788888888888


Q ss_pred             HhcCCC--CCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccC-HHHHHHhHhCC-CCCCCcEEEEEecCCCChhHhh
Q psy200          272 ELKLKP--GGKSERHQLGAILKYFDTKHKSILLILDEIDALESRK-QTILYTIFEWP-SIPGSKLVLVGVANALDLTDRM  347 (490)
Q Consensus       272 ~l~~~~--~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~-~~~L~~l~~~~-~~~~~~vilI~~tn~~~~~~~l  347 (490)
                      .++...  .+.+..+..+.+.+.+...++++||||||+|++.... ++.+..++.+. .....++.+|++++..++...+
T Consensus       100 ~l~~~~~~~~~~~~~~~~~l~~~l~~~~~~~vlilDE~~~l~~~~~~~~l~~l~~~~~~~~~~~~~~I~~~~~~~~~~~~  179 (386)
T 2qby_A          100 SLDVKVPFTGLSIAELYRRLVKAVRDYGSQVVIVLDEIDAFVKKYNDDILYKLSRINSEVNKSKISFIGITNDVKFVDLL  179 (386)
T ss_dssp             TTSCCCCSSSCCHHHHHHHHHHHHHTCCSCEEEEEETHHHHHHSSCSTHHHHHHHHHHSCCC--EEEEEEESCGGGGGGC
T ss_pred             HhCCCCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcChhhhhccCcCHHHHHHhhchhhcCCCeEEEEEEECCCChHhhh
Confidence            776532  3345667677777777666678999999999997553 45555554432 1145678888899877666777


Q ss_pred             hHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHhccc
Q psy200          348 LPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITNHLIDLTYDNVK  427 (490)
Q Consensus       348 ~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll~~a~~~a~~~~~  427 (490)
                      .+.+.+||..  ..+.|+|++.+++.+++.+++........+++++++.+++......|+++.++++|+.++..+..++ 
T Consensus       180 ~~~~~~r~~~--~~i~l~~l~~~~~~~il~~~~~~~~~~~~~~~~~~~~l~~~~~~~~G~~r~~~~ll~~a~~~a~~~~-  256 (386)
T 2qby_A          180 DPRVKSSLSE--EEIIFPPYNAEELEDILTKRAQMAFKPGVLPDNVIKLCAALAAREHGDARRALDLLRVSGEIAERMK-  256 (386)
T ss_dssp             TTHHHHTTTT--EEEEECCCCHHHHHHHHHHHHHHHBCSSCSCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTT-
T ss_pred             CHHHhccCCC--eeEEeCCCCHHHHHHHHHHHHHhhccCCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHhcC-
Confidence            7788888753  4799999999999999999887543345689999999998544444999999999999999988777 


Q ss_pred             cCCcccccCHHHHHHHHHHhccCccccccccccCCCChHhHHHHHHHHHHhcC
Q psy200          428 ENGEVTGIGLKEVLGVISSVYCTSQSLHCSKDEDSFPLQQKLALASLLLLKSR  480 (490)
Q Consensus       428 ~~~~~~~It~~~v~~a~~~~~~~~~~~~~~~~l~~L~~~qk~vL~al~~~~~~  480 (490)
                          ...|+.+++..++..+.....    ...+..++.+++.+|+||+.+.+.
T Consensus       257 ----~~~i~~~~v~~a~~~~~~~~~----~~~~~~l~~~~~~il~ai~~~~~~  301 (386)
T 2qby_A          257 ----DTKVKEEYVYMAKEEIERDRV----RDIILTLPFHSKLVLMAVVSISSE  301 (386)
T ss_dssp             ----CSSCCHHHHHHHHHHHHHHHH----HHHHHTSCHHHHHHHHHHHHHC--
T ss_pred             ----CCccCHHHHHHHHHHHhhchH----HHHHHcCCHHHHHHHHHHHHHHhc
Confidence                568999999999998865444    466789999999999999976543

>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=99.93  E-value=1.5e-24  Score=221.83  Aligned_cols=274  Identities=17%  Similarity=0.221  Sum_probs=210.4

Q ss_pred             CCCCChHHHHHHHHHHH-Hhhhcc--CCCCeEEE--ECCCCCcHHHHHHHHHHHhhhc-----CCceEEEEeccCCCCHH
Q psy200          194 CELPGREVQLEGIRQFL-LGHVNN--ETSGSMYI--SGPPGTGKSASLNLLVSRAEIK-----DAFKTIYINCNSVRNAA  263 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L-~~~~~~--~~~~~ill--~GppGtGKTtla~~l~~~l~~~-----~~~~~~~v~~~~~~~~~  263 (490)
                      +.|+||+++++.|..++ .....+  ..+..++|  +|++|+|||++++.+++.+...     .++.+++++|....+..
T Consensus        22 ~~l~gR~~el~~l~~~l~~~~~~~~~~~~~~~li~i~G~~G~GKT~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  101 (412)
T 1w5s_A           22 PELRVRRGEAEALARIYLNRLLSGAGLSDVNMIYGSIGRVGIGKTTLAKFTVKRVSEAAAKEGLTVKQAYVNAFNAPNLY  101 (412)
T ss_dssp             SSCSSSCHHHHHHHHHHHHHHHTSSCBCCEEEEEECTTCCSSSHHHHHHHHHHHHHHHHHHTTCCEEEEEEEGGGCCSHH
T ss_pred             CCCCChHHHHHHHHHHHhHHHhcCCCCCCCEEEEeCcCcCCCCHHHHHHHHHHHHHHHHhccCCceeEEEEECCCCCCHH
Confidence            67999999999999999 766555  46778999  9999999999999999987532     25788999998888889


Q ss_pred             HHHHHHHHHhcCCC--CCCcHHHHHHHHHHHHhcCCCeEEEEEecCcccccc---CHHHHHHhHhCC---CCCC--CcEE
Q psy200          264 SVYETIVNELKLKP--GGKSERHQLGAILKYFDTKHKSILLILDEIDALESR---KQTILYTIFEWP---SIPG--SKLV  333 (490)
Q Consensus       264 ~l~~~i~~~l~~~~--~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~---~~~~L~~l~~~~---~~~~--~~vi  333 (490)
                      .++..++..++...  .+.+...+...+...+...++++||||||+|++...   .++.+..++.+.   ...+  .++.
T Consensus       102 ~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~~~~~llvlDe~~~l~~~~~~~~~~l~~l~~~~~~~~~~~~~~~v~  181 (412)
T 1w5s_A          102 TILSLIVRQTGYPIQVRGAPALDILKALVDNLYVENHYLLVILDEFQSMLSSPRIAAEDLYTLLRVHEEIPSRDGVNRIG  181 (412)
T ss_dssp             HHHHHHHHHHTCCCCCTTCCHHHHHHHHHHHHHHHTCEEEEEEESTHHHHSCTTSCHHHHHHHHTHHHHSCCTTSCCBEE
T ss_pred             HHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHHHhcCCeEEEEEeCHHHHhhccCcchHHHHHHHHHHHhcccCCCCceEE
Confidence            99999999987643  234556666777666654467999999999999763   455555444332   1113  7888


Q ss_pred             EEEecCCCChhHhhh---HHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhh---CC
Q psy200          334 LVGVANALDLTDRML---PRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVS---GD  407 (490)
Q Consensus       334 lI~~tn~~~~~~~l~---~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~---Gd  407 (490)
                      +|++++..++...+.   +.+.+++.   ..+.|.|++.+++.+++.+++...+....+++++++.+++......   |+
T Consensus       182 lI~~~~~~~~~~~l~~~~~~~~~~~~---~~i~l~~l~~~e~~~ll~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~G~  258 (412)
T 1w5s_A          182 FLLVASDVRALSYMREKIPQVESQIG---FKLHLPAYKSRELYTILEQRAELGLRDTVWEPRHLELISDVYGEDKGGDGS  258 (412)
T ss_dssp             EEEEEEETHHHHHHHHHCHHHHTTCS---EEEECCCCCHHHHHHHHHHHHHHHBCTTSCCHHHHHHHHHHHCGGGTSCCC
T ss_pred             EEEEeccccHHHHHhhhcchhhhhcC---CeeeeCCCCHHHHHHHHHHHHHhcCCCCCCChHHHHHHHHHHHHhccCCCc
Confidence            888887666666666   77777775   3499999999999999998876543334588999999998443333   99


Q ss_pred             HHHHHHHHHHHHHHHHhccccCCcccccCHHHHHHHHHHhc-cCccccccccccCCCChHhHHHHHHHHHHhc
Q psy200          408 IRKAIDITNHLIDLTYDNVKENGEVTGIGLKEVLGVISSVY-CTSQSLHCSKDEDSFPLQQKLALASLLLLKS  479 (490)
Q Consensus       408 ~r~ai~ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~~~~~-~~~~~~~~~~~l~~L~~~qk~vL~al~~~~~  479 (490)
                      ++.+++++..++..+..++     ...|+.+++..++.... ....    ...+..||.+++.+|++++.+..
T Consensus       259 p~~~~~l~~~a~~~a~~~~-----~~~i~~~~v~~~~~~~~~~~~~----~~~l~~l~~~~~~~l~aia~l~~  322 (412)
T 1w5s_A          259 ARRAIVALKMACEMAEAMG-----RDSLSEDLVRKAVSENEAASIQ----THELEALSIHELIILRLIAEATL  322 (412)
T ss_dssp             HHHHHHHHHHHHHHHHHTT-----CSSCCHHHHHHHHHHC----------CCSSSSSCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHcC-----CCCCCHHHHHHHHHHHhccchH----HHHHHcCCHHHHHHHHHHHHHHh
Confidence            9999999999998888777     56899999999998776 4444    57788999999999999997653

>4b4t_J 26S protease regulatory subunit 8 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=99.90  E-value=2.1e-22  Score=201.03  Aligned_cols=220  Identities=17%  Similarity=0.214  Sum_probs=167.8

Q ss_pred             CCCCChHHHHHHHHHHHHhhhc---------cCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVN---------NETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAAS  264 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~---------~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~  264 (490)
                      +++.|.++++++|.+.+...+.         -..++++|||||||||||++|++++++++    ..++.++++.+.+   
T Consensus       148 ~dIgGl~~~k~~l~e~v~~Pl~~pe~f~~~gi~~prGvLL~GPPGTGKTllAkAiA~e~~----~~f~~v~~s~l~s---  220 (405)
T 4b4t_J          148 DMVGGLTKQIKEIKEVIELPVKHPELFESLGIAQPKGVILYGPPGTGKTLLARAVAHHTD----CKFIRVSGAELVQ---  220 (405)
T ss_dssp             GGSCSCHHHHHHHHHHTHHHHHCHHHHHHHTCCCCCCEEEESCSSSSHHHHHHHHHHHHT----CEEEEEEGGGGSC---
T ss_pred             HHhCCHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCceEEeCCCCCCHHHHHHHHHHhhC----CCceEEEhHHhhc---
Confidence            7899999999999987765332         23678999999999999999999999976    7889999887643   


Q ss_pred             HHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccC-----------HHHHHHhHhC--CCCCCCc
Q psy200          265 VYETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRK-----------QTILYTIFEW--PSIPGSK  331 (490)
Q Consensus       265 l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~-----------~~~L~~l~~~--~~~~~~~  331 (490)
                                 .+.|.+...+.+.|..+..  ..|+||||||+|.+....           +..+..++..  .......
T Consensus       221 -----------k~vGese~~vr~lF~~Ar~--~aP~IIFiDEiDai~~~R~~~~~~~~~~~~~~l~~lL~~lDg~~~~~~  287 (405)
T 4b4t_J          221 -----------KYIGEGSRMVRELFVMARE--HAPSIIFMDEIDSIGSTRVEGSGGGDSEVQRTMLELLNQLDGFETSKN  287 (405)
T ss_dssp             -----------SSTTHHHHHHHHHHHHHHH--TCSEEEEEESSSCCTTSCSCSSSGGGGHHHHHHHHHHHHHHTTTCCCC
T ss_pred             -----------cccchHHHHHHHHHHHHHH--hCCceEeeecchhhccCCCCCCCCCcHHHHHHHHHHHHhhhccCCCCC
Confidence                       6777888888888887766  569999999999997542           1233333322  1234568


Q ss_pred             EEEEEecCCCChhHhhhHHhhh--ccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhC-CH
Q psy200          332 LVLVGVANALDLTDRMLPRLQA--NVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSG-DI  408 (490)
Q Consensus       332 vilI~~tn~~~~~~~l~~~l~~--R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~G-d~  408 (490)
                      ++||++||+.   +.+++++.+  ||.   ..|.|+.++.++..+||+.++......   .+..++.|++   .+.| ..
T Consensus       288 V~vIaATNrp---d~LDpAllRpGRfD---~~I~i~lPd~~~R~~Il~~~~~~~~l~---~dvdl~~lA~---~t~G~SG  355 (405)
T 4b4t_J          288 IKIIMATNRL---DILDPALLRPGRID---RKIEFPPPSVAARAEILRIHSRKMNLT---RGINLRKVAE---KMNGCSG  355 (405)
T ss_dssp             EEEEEEESCS---SSSCHHHHSTTSSC---CEEECCCCCHHHHHHHHHHHHTTSBCC---SSCCHHHHHH---HCCSCCH
T ss_pred             eEEEeccCCh---hhCCHhHcCCCcCc---eEEEcCCcCHHHHHHHHHHHhcCCCCC---ccCCHHHHHH---HCCCCCH
Confidence            9999999964   456677765  777   589999999999999999888765222   2223677777   3344 33


Q ss_pred             HHHHHHHHHHHHHHHhccccCCcccccCHHHHHHHHHHhccC
Q psy200          409 RKAIDITNHLIDLTYDNVKENGEVTGIGLKEVLGVISSVYCT  450 (490)
Q Consensus       409 r~ai~ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~~~~~~~  450 (490)
                      ..+-++|..|...|.+++     ...|+.+||..|+.++...
T Consensus       356 ADi~~l~~eA~~~Air~~-----~~~vt~~Df~~Al~~v~~~  392 (405)
T 4b4t_J          356 ADVKGVCTEAGMYALRER-----RIHVTQEDFELAVGKVMNK  392 (405)
T ss_dssp             HHHHHHHHHHHHHHHHTT-----CSBCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHcC-----CCCcCHHHHHHHHHHHhCc
Confidence            445568999999998887     6789999999999988653

>4b4t_I 26S protease regulatory subunit 4 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=99.89  E-value=4.7e-22  Score=198.94  Aligned_cols=223  Identities=13%  Similarity=0.135  Sum_probs=167.9

Q ss_pred             CCCCChHHHHHHHHHHHHhhhc---------cCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVN---------NETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAAS  264 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~---------~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~  264 (490)
                      +++.|.++++++|.+.+...+.         ...++++|||||||||||++|+++|++++    ..++.++++.+.+   
T Consensus       182 ~DIgGld~~k~~L~e~v~~Pl~~pe~f~~~Gi~~prGvLLyGPPGTGKTlLAkAiA~e~~----~~fi~v~~s~l~s---  254 (437)
T 4b4t_I          182 SDIGGLESQIQEIKESVELPLTHPELYEEMGIKPPKGVILYGAPGTGKTLLAKAVANQTS----ATFLRIVGSELIQ---  254 (437)
T ss_dssp             GGTCSCHHHHHHHHHHHHHHHHCCHHHHHHTCCCCSEEEEESSTTTTHHHHHHHHHHHHT----CEEEEEESGGGCC---
T ss_pred             eecCcHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCCCceECCCCchHHHHHHHHHHHhC----CCEEEEEHHHhhh---
Confidence            7899999999999998765432         23678999999999999999999999986    7888998876633   


Q ss_pred             HHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccC-----------HHHHHHhHhC--CCCCCCc
Q psy200          265 VYETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRK-----------QTILYTIFEW--PSIPGSK  331 (490)
Q Consensus       265 l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~-----------~~~L~~l~~~--~~~~~~~  331 (490)
                                 .+.|.+...+...|..+..  ..|+||||||+|.+...+           ...+..++..  .......
T Consensus       255 -----------k~vGesek~ir~lF~~Ar~--~aP~IIfiDEiDai~~~R~~~~~~~~~~~~~~l~~LL~~lDg~~~~~~  321 (437)
T 4b4t_I          255 -----------KYLGDGPRLCRQIFKVAGE--NAPSIVFIDEIDAIGTKRYDSNSGGEREIQRTMLELLNQLDGFDDRGD  321 (437)
T ss_dssp             -----------SSSSHHHHHHHHHHHHHHH--TCSEEEEEEEESSSSCCCSCSSCSSCCHHHHHHHHHHHHHHHCCCSSS
T ss_pred             -----------ccCchHHHHHHHHHHHHHh--cCCcEEEEehhhhhcccCCCCCCCccHHHHHHHHHHHHHhhCcCCCCC
Confidence                       6777788888888877665  569999999999997542           1233333321  1234568


Q ss_pred             EEEEEecCCCChhHhhhHHhhh--ccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHH
Q psy200          332 LVLVGVANALDLTDRMLPRLQA--NVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIR  409 (490)
Q Consensus       332 vilI~~tn~~~~~~~l~~~l~~--R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r  409 (490)
                      ++||++||+.   +.+++++.+  ||.   ..|.|+.++.++..+||+.++......   .+..++.|++...++  .-.
T Consensus       322 ViVIaATNrp---d~LDpALlRpGRfD---~~I~v~lPd~~~R~~Il~~~l~~~~l~---~dvdl~~LA~~T~Gf--SGA  390 (437)
T 4b4t_I          322 VKVIMATNKI---ETLDPALIRPGRID---RKILFENPDLSTKKKILGIHTSKMNLS---EDVNLETLVTTKDDL--SGA  390 (437)
T ss_dssp             EEEEEEESCS---TTCCTTSSCTTTEE---EEECCCCCCHHHHHHHHHHHHTTSCBC---SCCCHHHHHHHCCSC--CHH
T ss_pred             EEEEEeCCCh---hhcCHHHhcCCcee---EEEEcCCcCHHHHHHHHHHHhcCCCCC---CcCCHHHHHHhCCCC--CHH
Confidence            9999999964   556677765  776   589999999999999999888765211   122367777633222  234


Q ss_pred             HHHHHHHHHHHHHHhccccCCcccccCHHHHHHHHHHhccCcc
Q psy200          410 KAIDITNHLIDLTYDNVKENGEVTGIGLKEVLGVISSVYCTSQ  452 (490)
Q Consensus       410 ~ai~ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~~~~~~~~~  452 (490)
                      .+-++|..|...|.+++     ...|+.+||..|+..+.....
T Consensus       391 DI~~l~~eA~~~Air~~-----~~~It~eDf~~Al~rv~~~~~  428 (437)
T 4b4t_I          391 DIQAMCTEAGLLALRER-----RMQVTAEDFKQAKERVMKNKV  428 (437)
T ss_dssp             HHHHHHHHHHHHHHHTT-----CSCBCHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHcC-----CCccCHHHHHHHHHHHhCCCC
Confidence            55578999999998888     678999999999998876544

>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable holliday junction DNA helicase; HET: ADP; 2.69A {Campylobacter jejuni subsp}

Probab=99.88  E-value=7.8e-21  Score=189.25  Aligned_cols=242  Identities=17%  Similarity=0.158  Sum_probs=183.6

Q ss_pred             CCCCcchHHHhhcCCCCCCChHHHHHHHHHHHHhhhc-cCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEecc
Q psy200          179 FSEDKPKVEEKAKDSCELPGREVQLEGIRQFLLGHVN-NETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCN  257 (490)
Q Consensus       179 ~~~~~~~~~~~~l~~~~lvgre~~~~~l~~~L~~~~~-~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~  257 (490)
                      .|.++|.+...    ++++|++..++.+..++..... .....+++|+||+|||||++|+++++.+.    ..++.++|.
T Consensus        18 ~~~~~~~p~~~----~~iiG~~~~~~~l~~~l~~~~~~~~~~~~vll~G~~GtGKT~la~~ia~~~~----~~~~~~~~~   89 (338)
T 3pfi_A           18 TYETSLRPSNF----DGYIGQESIKKNLNVFIAAAKKRNECLDHILFSGPAGLGKTTLANIISYEMS----ANIKTTAAP   89 (338)
T ss_dssp             -----CCCCSG----GGCCSCHHHHHHHHHHHHHHHHTTSCCCCEEEECSTTSSHHHHHHHHHHHTT----CCEEEEEGG
T ss_pred             hhhhccCCCCH----HHhCChHHHHHHHHHHHHHHHhcCCCCCeEEEECcCCCCHHHHHHHHHHHhC----CCeEEecch
Confidence            56677777766    8899999999999999986533 34567899999999999999999998864    568889887


Q ss_pred             CCCCHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCHHHHHHhHhCCCC----------
Q psy200          258 SVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPSI----------  327 (490)
Q Consensus       258 ~~~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~----------  327 (490)
                      .....                    ..+.    ..+.......+|||||||.+....+..|+..++....          
T Consensus        90 ~~~~~--------------------~~~~----~~~~~~~~~~vl~lDEi~~l~~~~~~~Ll~~l~~~~~~~~~~~~~~~  145 (338)
T 3pfi_A           90 MIEKS--------------------GDLA----AILTNLSEGDILFIDEIHRLSPAIEEVLYPAMEDYRLDIIIGSGPAA  145 (338)
T ss_dssp             GCCSH--------------------HHHH----HHHHTCCTTCEEEEETGGGCCHHHHHHHHHHHHTSCC---------C
T ss_pred             hccch--------------------hHHH----HHHHhccCCCEEEEechhhcCHHHHHHHHHHHHhccchhhcccCccc
Confidence            65322                    2222    2222234567999999999998888888887764321          


Q ss_pred             -----CCCcEEEEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHH
Q psy200          328 -----PGSKLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVA  402 (490)
Q Consensus       328 -----~~~~vilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~  402 (490)
                           ...++++|++||..   ..+.+.+.+||+   ..+.|.+++.+++..++.+.+...  ...+++++++.+++   
T Consensus       146 ~~~~~~~~~~~~i~atn~~---~~l~~~L~~R~~---~~i~l~~~~~~e~~~il~~~~~~~--~~~~~~~~~~~l~~---  214 (338)
T 3pfi_A          146 QTIKIDLPKFTLIGATTRA---GMLSNPLRDRFG---MQFRLEFYKDSELALILQKAALKL--NKTCEEKAALEIAK---  214 (338)
T ss_dssp             CCCCCCCCCCEEEEEESCG---GGSCHHHHTTCS---EEEECCCCCHHHHHHHHHHHHHHT--TCEECHHHHHHHHH---
T ss_pred             cceecCCCCeEEEEeCCCc---cccCHHHHhhcC---EEeeCCCcCHHHHHHHHHHHHHhc--CCCCCHHHHHHHHH---
Confidence                 11248899999853   446788999986   489999999999999999988876  35689999999987   


Q ss_pred             HhhCCHHHHHHHHHHHHHHHHhccccCCcccccCHHHHHHHHHHhccCccccccccccCCCChHhHHHHHHHHHH
Q psy200          403 AVSGDIRKAIDITNHLIDLTYDNVKENGEVTGIGLKEVLGVISSVYCTSQSLHCSKDEDSFPLQQKLALASLLLL  477 (490)
Q Consensus       403 ~~~Gd~r~ai~ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~~~~~~~~~~~~~~~~l~~L~~~qk~vL~al~~~  477 (490)
                      .+.|++|.+.++++++...+...+     ...|+.+++..++......         ...+...++.++.+++..
T Consensus       215 ~~~G~~r~l~~~l~~~~~~a~~~~-----~~~i~~~~~~~~~~~~~~~---------~~~l~~~e~~~l~~l~~~  275 (338)
T 3pfi_A          215 RSRSTPRIALRLLKRVRDFADVND-----EEIITEKRANEALNSLGVN---------ELGFDAMDLRYLELLTAA  275 (338)
T ss_dssp             TTTTCHHHHHHHHHHHHHHHHHTT-----CSEECHHHHHHHHHHHTCC---------TTCCCHHHHHHHHHHHHS
T ss_pred             HHCcCHHHHHHHHHHHHHHHHhhc-----CCccCHHHHHHHHHHhCCc---------ccCCCHHHHHHHHHHHHh
Confidence            789999999999999998888776     5689999999998774321         234566667788888765

>4b4t_H 26S protease regulatory subunit 7 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=99.88  E-value=3.1e-21  Score=194.90  Aligned_cols=219  Identities=16%  Similarity=0.176  Sum_probs=166.2

Q ss_pred             CCCCChHHHHHHHHHHHHhhh---------ccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHV---------NNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAAS  264 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~---------~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~  264 (490)
                      +++.|.++++++|.+.+...+         .-..++++|||||||||||++|+++|++++    ..++.++++.+.+   
T Consensus       209 ~DIgGl~~~k~~L~e~V~~pl~~pe~f~~~Gi~pprGILLyGPPGTGKTlLAkAiA~e~~----~~fi~vs~s~L~s---  281 (467)
T 4b4t_H          209 SDVGGCKDQIEKLREVVELPLLSPERFATLGIDPPKGILLYGPPGTGKTLCARAVANRTD----ATFIRVIGSELVQ---  281 (467)
T ss_dssp             SSCTTCHHHHHHHHHHTHHHHHCHHHHHHHTCCCCSEEEECSCTTSSHHHHHHHHHHHHT----CEEEEEEGGGGCC---
T ss_pred             HHhccHHHHHHHHHHHHHHHhcCHHHHHHCCCCCCCceEeeCCCCCcHHHHHHHHHhccC----CCeEEEEhHHhhc---
Confidence            789999999999998765432         224789999999999999999999999986    7889998887643   


Q ss_pred             HHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccC-----------HHHHHHhHhC--CCCCCCc
Q psy200          265 VYETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRK-----------QTILYTIFEW--PSIPGSK  331 (490)
Q Consensus       265 l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~-----------~~~L~~l~~~--~~~~~~~  331 (490)
                                 .+.|.+...+...|..+..  ..|+||||||+|.+...+           ...+..++..  .......
T Consensus       282 -----------k~vGesek~ir~lF~~Ar~--~aP~IIfiDEiDai~~~R~~~~~~~~~~~~~~l~~lL~~lDg~~~~~~  348 (467)
T 4b4t_H          282 -----------KYVGEGARMVRELFEMART--KKACIIFFDEIDAVGGARFDDGAGGDNEVQRTMLELITQLDGFDPRGN  348 (467)
T ss_dssp             -----------CSSSHHHHHHHHHHHHHHH--TCSEEEEEECCTTTSBCCSSSSCGGGGHHHHHHHHHHHHHHSSCCTTT
T ss_pred             -----------ccCCHHHHHHHHHHHHHHh--cCCceEeecccccccccccCcCCCccHHHHHHHHHHHHHhhccCCCCc
Confidence                       6777888888888887665  569999999999997542           1222233221  1235568


Q ss_pred             EEEEEecCCCChhHhhhHHhhh--ccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhC-CH
Q psy200          332 LVLVGVANALDLTDRMLPRLQA--NVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSG-DI  408 (490)
Q Consensus       332 vilI~~tn~~~~~~~l~~~l~~--R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~G-d~  408 (490)
                      ++||++||+.   +.+++++.+  ||.   ..|.|+.++.++..+||+.++........+   .++.|++.   +.| ..
T Consensus       349 ViVIaATNrp---d~LDpALlRpGRFD---~~I~i~lPd~~~R~~Ilk~~l~~~~l~~dv---dl~~LA~~---T~GfSG  416 (467)
T 4b4t_H          349 IKVMFATNRP---NTLDPALLRPGRID---RKVEFSLPDLEGRANIFRIHSKSMSVERGI---RWELISRL---CPNSTG  416 (467)
T ss_dssp             EEEEEECSCT---TSBCHHHHSTTTCC---EEECCCCCCHHHHHHHHHHHHTTSCBCSSC---CHHHHHHH---CCSCCH
T ss_pred             EEEEeCCCCc---ccCChhhhcccccc---EEEEeCCcCHHHHHHHHHHHhcCCCCCCCC---CHHHHHHH---CCCCCH
Confidence            9999999964   556677765  787   589999999999999999888765222222   36677763   333 33


Q ss_pred             HHHHHHHHHHHHHHHhccccCCcccccCHHHHHHHHHHhcc
Q psy200          409 RKAIDITNHLIDLTYDNVKENGEVTGIGLKEVLGVISSVYC  449 (490)
Q Consensus       409 r~ai~ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~~~~~~  449 (490)
                      ..+-++|..|...|.+++     ...|+.+||..|+.++..
T Consensus       417 ADI~~l~~eAa~~Air~~-----~~~it~~Df~~Al~kV~~  452 (467)
T 4b4t_H          417 AELRSVCTEAGMFAIRAR-----RKVATEKDFLKAVDKVIS  452 (467)
T ss_dssp             HHHHHHHHHHHHHHHHHT-----CSSBCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHcC-----CCccCHHHHHHHHHHHhc
Confidence            455568999999998887     678999999999998764

>4b4t_M 26S protease regulatory subunit 6A; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=99.87  E-value=2e-21  Score=196.92  Aligned_cols=222  Identities=14%  Similarity=0.200  Sum_probs=166.3

Q ss_pred             CCCCChHHHHHHHHHHHHhhhc---------cCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVN---------NETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAAS  264 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~---------~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~  264 (490)
                      +++.|.++++++|.+.+...+.         -..++++|||||||||||++|++++++++    ..++.++++.+.+   
T Consensus       181 ~digGl~~~k~~l~e~v~~pl~~pe~f~~~g~~~prGvLLyGPPGTGKTllAkAiA~e~~----~~f~~v~~s~l~~---  253 (434)
T 4b4t_M          181 SDVGGLDKQIEELVEAIVLPMKRADKFKDMGIRAPKGALMYGPPGTGKTLLARACAAQTN----ATFLKLAAPQLVQ---  253 (434)
T ss_dssp             GGSCSCHHHHHHHHHHTHHHHHCSHHHHHHCCCCCCEEEEESCTTSSHHHHHHHHHHHHT----CEEEEEEGGGGCS---
T ss_pred             HhcCcHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCeeEEECcCCCCHHHHHHHHHHHhC----CCEEEEehhhhhh---
Confidence            7899999999999987655432         23678999999999999999999999986    7889998877633   


Q ss_pred             HHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccC-----------HHHHHHhHhC--CCCCCCc
Q psy200          265 VYETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRK-----------QTILYTIFEW--PSIPGSK  331 (490)
Q Consensus       265 l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~-----------~~~L~~l~~~--~~~~~~~  331 (490)
                                 .+.|.+...+...|..+..  ..|+||||||+|.+...+           ...+..++..  ......+
T Consensus       254 -----------~~vGese~~ir~lF~~A~~--~aP~IifiDEiDal~~~R~~~~~~~~~~~~~~~~~lL~~ldg~~~~~~  320 (434)
T 4b4t_M          254 -----------MYIGEGAKLVRDAFALAKE--KAPTIIFIDELDAIGTKRFDSEKSGDREVQRTMLELLNQLDGFSSDDR  320 (434)
T ss_dssp             -----------SCSSHHHHHHHHHHHHHHH--HCSEEEEEECTHHHHCCCSSGGGGTTHHHHHHHHHHHHHHTTSCSSCS
T ss_pred             -----------cccchHHHHHHHHHHHHHh--cCCeEEeecchhhhhhccCCCCCCCchHHHHHHHHHHHHhhccCCCCC
Confidence                       6777788888888877665  458999999999996542           1122233221  1224567


Q ss_pred             EEEEEecCCCChhHhhhHHhhh--ccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhC-CH
Q psy200          332 LVLVGVANALDLTDRMLPRLQA--NVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSG-DI  408 (490)
Q Consensus       332 vilI~~tn~~~~~~~l~~~l~~--R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~G-d~  408 (490)
                      ++||++||+.   +.+++++.+  ||.   ..|.|+.++.++..+||+.++........+   .++.|++   .+.| ..
T Consensus       321 ViVIaaTNrp---~~LD~AllRpGRfD---~~I~i~lPd~~~R~~Il~~~~~~~~~~~dv---dl~~lA~---~t~G~sG  388 (434)
T 4b4t_M          321 VKVLAATNRV---DVLDPALLRSGRLD---RKIEFPLPSEDSRAQILQIHSRKMTTDDDI---NWQELAR---STDEFNG  388 (434)
T ss_dssp             SEEEEECSSC---CCCCTTTCSTTSEE---EEEECCCCCHHHHHHHHHHHHHHSCBCSCC---CHHHHHH---HCSSCCH
T ss_pred             EEEEEeCCCc---hhcCHhHhcCCcee---EEEEeCCcCHHHHHHHHHHHhcCCCCCCcC---CHHHHHH---hCCCCCH
Confidence            9999999964   456667755  777   589999999999999999888775222222   2677776   3333 34


Q ss_pred             HHHHHHHHHHHHHHHhccccCCcccccCHHHHHHHHHHhccCcc
Q psy200          409 RKAIDITNHLIDLTYDNVKENGEVTGIGLKEVLGVISSVYCTSQ  452 (490)
Q Consensus       409 r~ai~ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~~~~~~~~~  452 (490)
                      ..+-++|..|...|.+++     ...|+.+||..|+..+.+...
T Consensus       389 ADi~~l~~eA~~~a~r~~-----~~~i~~~Df~~Al~~v~~~~~  427 (434)
T 4b4t_M          389 AQLKAVTVEAGMIALRNG-----QSSVKHEDFVEGISEVQARKS  427 (434)
T ss_dssp             HHHHHHHHHHHHHHHHHT-----CSSBCHHHHHHHHHSCSSSCC
T ss_pred             HHHHHHHHHHHHHHHHcC-----CCCcCHHHHHHHHHHHhCCCC
Confidence            455578999999998888     678999999999998876543

>4b4t_L 26S protease subunit RPT4; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=99.87  E-value=2.3e-21  Score=196.64  Aligned_cols=220  Identities=15%  Similarity=0.176  Sum_probs=165.0

Q ss_pred             CCCCChHHHHHHHHHHHHhhhc---------cCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVN---------NETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAAS  264 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~---------~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~  264 (490)
                      +++.|.++++++|.+.+...+.         -..++++|||||||||||++|++++++++    +.++.++++.+.+   
T Consensus       181 ~digGl~~~k~~l~e~v~~pl~~p~~f~~~g~~~prGvLL~GPPGtGKTllAkAiA~e~~----~~~~~v~~s~l~s---  253 (437)
T 4b4t_L          181 DGIGGLTEQIRELREVIELPLKNPEIFQRVGIKPPKGVLLYGPPGTGKTLLAKAVAATIG----ANFIFSPASGIVD---  253 (437)
T ss_dssp             GGGCSCHHHHHHHHHHHHHHHHCHHHHHHHCCCCCCEEEEESCTTSSHHHHHHHHHHHHT----CEEEEEEGGGTCC---
T ss_pred             hHhCChHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCeEEEECCCCCcHHHHHHHHHHHhC----CCEEEEehhhhcc---
Confidence            7899999999999998875433         23678999999999999999999999986    7889999887644   


Q ss_pred             HHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccC-----------HHHHHHhHhC--CCCCCCc
Q psy200          265 VYETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRK-----------QTILYTIFEW--PSIPGSK  331 (490)
Q Consensus       265 l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~-----------~~~L~~l~~~--~~~~~~~  331 (490)
                                 .+.|.+...+...|..+..  ..|+||||||+|.+...+           ...+..++..  .......
T Consensus       254 -----------k~~Gese~~ir~~F~~A~~--~~P~IifiDEiDai~~~R~~~~~~~~~~~~~~l~~lL~~lDg~~~~~~  320 (437)
T 4b4t_L          254 -----------KYIGESARIIREMFAYAKE--HEPCIIFMDEVDAIGGRRFSEGTSADREIQRTLMELLTQMDGFDNLGQ  320 (437)
T ss_dssp             -----------SSSSHHHHHHHHHHHHHHH--SCSEEEEEECCCSSSCCCSSSCCSSTTHHHHHHHHHHHHHHSSSCTTS
T ss_pred             -----------ccchHHHHHHHHHHHHHHh--cCCceeeeecccccccccccCCCCcchHHHHHHHHHHHHhhcccCCCC
Confidence                       6677777777777776655  569999999999997542           1222233221  1224567


Q ss_pred             EEEEEecCCCChhHhhhHHhhh--ccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhC-CH
Q psy200          332 LVLVGVANALDLTDRMLPRLQA--NVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSG-DI  408 (490)
Q Consensus       332 vilI~~tn~~~~~~~l~~~l~~--R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~G-d~  408 (490)
                      ++||++||+.   +.+++++.+  ||.   ..|.|+.++.++..+||+.++......   .+..++.+++   .+.| ..
T Consensus       321 vivI~ATNrp---~~LDpAllRpGRfD---~~I~i~lPd~~~R~~Il~~~~~~~~~~---~d~dl~~lA~---~t~G~sG  388 (437)
T 4b4t_L          321 TKIIMATNRP---DTLDPALLRPGRLD---RKVEIPLPNEAGRLEIFKIHTAKVKKT---GEFDFEAAVK---MSDGFNG  388 (437)
T ss_dssp             SEEEEEESST---TSSCTTTTSTTSEE---EEECCCCCCHHHHHHHHHHHHHTSCBC---SCCCHHHHHH---TCCSCCH
T ss_pred             eEEEEecCCc---hhhCHHHhCCCccc---eeeecCCcCHHHHHHHHHHHhcCCCCC---cccCHHHHHH---hCCCCCH
Confidence            8999999964   456666654  465   589999999999999999888765222   2223677776   3344 34


Q ss_pred             HHHHHHHHHHHHHHHhccccCCcccccCHHHHHHHHHHhccC
Q psy200          409 RKAIDITNHLIDLTYDNVKENGEVTGIGLKEVLGVISSVYCT  450 (490)
Q Consensus       409 r~ai~ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~~~~~~~  450 (490)
                      ..+-++|..|...|.+++     ...|+.+||..|+..+...
T Consensus       389 ADi~~l~~eA~~~air~~-----~~~i~~~d~~~Al~~v~~~  425 (437)
T 4b4t_L          389 ADIRNCATEAGFFAIRDD-----RDHINPDDLMKAVRKVAEV  425 (437)
T ss_dssp             HHHHHHHHHHHHHHHHTT-----CSSBCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHcC-----CCCCCHHHHHHHHHHHHhc
Confidence            455568999999998887     6789999999999988754

>4b4t_K 26S protease regulatory subunit 6B homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=99.86  E-value=1.3e-20  Score=190.75  Aligned_cols=220  Identities=15%  Similarity=0.154  Sum_probs=164.0

Q ss_pred             CCCCChHHHHHHHHHHHHhhhc---------cCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVN---------NETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAAS  264 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~---------~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~  264 (490)
                      +++.|.+++++.|.+.+...+.         -..++++|||||||||||++|+++|++++    +.++.++++.+.+   
T Consensus       172 ~digGl~~~k~~l~e~v~~pl~~p~~~~~~g~~~prGiLL~GPPGtGKT~lakAiA~~~~----~~~~~v~~~~l~~---  244 (428)
T 4b4t_K          172 ADVGGLDMQKQEIREAVELPLVQADLYEQIGIDPPRGVLLYGPPGTGKTMLVKAVANSTK----AAFIRVNGSEFVH---  244 (428)
T ss_dssp             GGSCSCHHHHHHHHHHHHHHHHCHHHHHHHCCCCCCEEEEESCTTTTHHHHHHHHHHHHT----CEEEEEEGGGTCC---
T ss_pred             HHhccHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCceEEEECCCCCCHHHHHHHHHHHhC----CCeEEEecchhhc---
Confidence            7899999999999998765432         23678999999999999999999999986    7889999887643   


Q ss_pred             HHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccC-----------HHHHHHhHhCC--CCCCCc
Q psy200          265 VYETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRK-----------QTILYTIFEWP--SIPGSK  331 (490)
Q Consensus       265 l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~-----------~~~L~~l~~~~--~~~~~~  331 (490)
                                 .+.|.+...+...|..+..  ..|+||||||+|.+...+           ...+..++.+.  .....+
T Consensus       245 -----------~~~Ge~e~~ir~lF~~A~~--~aP~IifiDEiD~i~~~R~~~~~~~~~~~~r~l~~lL~~ldg~~~~~~  311 (428)
T 4b4t_K          245 -----------KYLGEGPRMVRDVFRLARE--NAPSIIFIDEVDSIATKRFDAQTGSDREVQRILIELLTQMDGFDQSTN  311 (428)
T ss_dssp             -----------SSCSHHHHHHHHHHHHHHH--TCSEEEEEECTHHHHCSCSSSCSCCCCHHHHHHHHHHHHHHHSCSSCS
T ss_pred             -----------cccchhHHHHHHHHHHHHH--cCCCeeechhhhhhhccccCCCCCCChHHHHHHHHHHHHhhCCCCCCC
Confidence                       6677778888888877665  468999999999987542           12333333211  124567


Q ss_pred             EEEEEecCCCChhHhhhHHhhh--ccCCCCeeEEeC-CCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCH
Q psy200          332 LVLVGVANALDLTDRMLPRLQA--NVTLQPTLMNFA-PYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDI  408 (490)
Q Consensus       332 vilI~~tn~~~~~~~l~~~l~~--R~~~~~~~i~~~-pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~  408 (490)
                      ++||++||+.   +.+++++.+  ||.   ..|.|+ +++.++...||+.++......   .+..++.+++...++  ..
T Consensus       312 v~vI~aTN~~---~~LD~AllRpGRfd---~~I~~p~lPd~~~R~~Il~~~~~~~~l~---~~~dl~~lA~~t~G~--sg  380 (428)
T 4b4t_K          312 VKVIMATNRA---DTLDPALLRPGRLD---RKIEFPSLRDRRERRLIFGTIASKMSLA---PEADLDSLIIRNDSL--SG  380 (428)
T ss_dssp             EEEEEEESCS---SSCCHHHHSSSSEE---EEEECCSSCCHHHHHHHHHHHHHSSCBC---TTCCHHHHHHHTTTC--CH
T ss_pred             EEEEEecCCh---hhcChhhhcCCcce---EEEEcCCCCCHHHHHHHHHHHhcCCCCC---cccCHHHHHHHCCCC--CH
Confidence            9999999964   456677765  676   478895 788999999999888765211   222367777733332  33


Q ss_pred             HHHHHHHHHHHHHHHhccccCCcccccCHHHHHHHHHHhcc
Q psy200          409 RKAIDITNHLIDLTYDNVKENGEVTGIGLKEVLGVISSVYC  449 (490)
Q Consensus       409 r~ai~ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~~~~~~  449 (490)
                      ..+-++|..|...|.+++     ...|+.+||.+|+.....
T Consensus       381 adi~~l~~eA~~~a~r~~-----~~~i~~~d~~~A~~~~~~  416 (428)
T 4b4t_K          381 AVIAAIMQEAGLRAVRKN-----RYVILQSDLEEAYATQVK  416 (428)
T ss_dssp             HHHHHHHHHHHHHHHHTT-----CSSBCHHHHHHHHHHHSC
T ss_pred             HHHHHHHHHHHHHHHHCC-----CCCCCHHHHHHHHHHhhC
Confidence            455578999999998888     678999999999987653

>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=99.86  E-value=1.4e-20  Score=174.83  Aligned_cols=214  Identities=19%  Similarity=0.241  Sum_probs=160.1

Q ss_pred             CCCCcchHHHhhcCCCCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhc-CCceEEEEecc
Q psy200          179 FSEDKPKVEEKAKDSCELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIK-DAFKTIYINCN  257 (490)
Q Consensus       179 ~~~~~~~~~~~~l~~~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~-~~~~~~~v~~~  257 (490)
                      +|.+.|.+...    ++++|+++.++.|..++..    ....+++|+||+|+|||++++.+++.+... ....++.++|.
T Consensus         6 ~~~~~~~p~~~----~~~~g~~~~~~~l~~~l~~----~~~~~~ll~G~~G~GKT~l~~~l~~~~~~~~~~~~~~~~~~~   77 (226)
T 2chg_A            6 IWVEKYRPRTL----DEVVGQDEVIQRLKGYVER----KNIPHLLFSGPPGTGKTATAIALARDLFGENWRDNFIEMNAS   77 (226)
T ss_dssp             CHHHHTSCSSG----GGCCSCHHHHHHHHHHHHT----TCCCCEEEECSTTSSHHHHHHHHHHHHHGGGGGGGEEEEETT
T ss_pred             hHHHhcCCCCH----HHHcCcHHHHHHHHHHHhC----CCCCeEEEECCCCCCHHHHHHHHHHHHhccccccceEEeccc
Confidence            45555655555    7899999999999999864    344569999999999999999999987422 23457788876


Q ss_pred             CCCCHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHhc----CCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEE
Q psy200          258 SVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFDT----KHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLV  333 (490)
Q Consensus       258 ~~~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~----~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vi  333 (490)
                      ......                    .+...+......    .+++.+|||||+|.+....++.|..+++..   ...+.
T Consensus        78 ~~~~~~--------------------~~~~~~~~~~~~~~~~~~~~~vliiDe~~~l~~~~~~~l~~~l~~~---~~~~~  134 (226)
T 2chg_A           78 DERGID--------------------VVRHKIKEFARTAPIGGAPFKIIFLDEADALTADAQAALRRTMEMY---SKSCR  134 (226)
T ss_dssp             CTTCHH--------------------HHHHHHHHHHTSCCSTTCSCEEEEEETGGGSCHHHHHHHHHHHHHT---TTTEE
T ss_pred             cccChH--------------------HHHHHHHHHhcccCCCccCceEEEEeChhhcCHHHHHHHHHHHHhc---CCCCe
Confidence            653322                    222222222221    256789999999999877777788777643   33566


Q ss_pred             EEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHH
Q psy200          334 LVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAID  413 (490)
Q Consensus       334 lI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~  413 (490)
                      +|+++|.   ...+.+.+.+||.    .+.|.+++.+++.+++.+++...+  ..+++++++.+++   .+.|++|.+++
T Consensus       135 ~i~~~~~---~~~~~~~l~~r~~----~i~~~~~~~~~~~~~l~~~~~~~~--~~~~~~~~~~l~~---~~~g~~r~l~~  202 (226)
T 2chg_A          135 FILSCNY---VSRIIEPIQSRCA----VFRFKPVPKEAMKKRLLEICEKEG--VKITEDGLEALIY---ISGGDFRKAIN  202 (226)
T ss_dssp             EEEEESC---GGGSCHHHHTTSE----EEECCCCCHHHHHHHHHHHHHHHT--CCBCHHHHHHHHH---HHTTCHHHHHH
T ss_pred             EEEEeCC---hhhcCHHHHHhCc----eeecCCCCHHHHHHHHHHHHHHcC--CCCCHHHHHHHHH---HcCCCHHHHHH
Confidence            6777763   3456788888885    799999999999999999887653  4588999999886   77899999999


Q ss_pred             HHHHHHHHHHhccccCCcccccCHHHHHHHHH
Q psy200          414 ITNHLIDLTYDNVKENGEVTGIGLKEVLGVIS  445 (490)
Q Consensus       414 ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~~  445 (490)
                      +++.++..+   .       .|+.++|.+++.
T Consensus       203 ~l~~~~~~~---~-------~I~~~~v~~~~~  224 (226)
T 2chg_A          203 ALQGAAAIG---E-------VVDADTIYQITA  224 (226)
T ss_dssp             HHHHHHHTC---S-------CBCHHHHHHHHH
T ss_pred             HHHHHHhcC---c-------eecHHHHHHHhc
Confidence            998887543   2       799999999875

>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET: ADP; 2.95A {Homo sapiens} PDB: 2xsz_D*

Probab=99.86  E-value=5.1e-20  Score=185.48  Aligned_cols=236  Identities=14%  Similarity=0.127  Sum_probs=167.0

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccC-CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCC----CHHHHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNE-TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVR----NAASVYET  268 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~-~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~----~~~~l~~~  268 (490)
                      ++|+|++..++.+..++....... .+++++|+||||||||++|+++++.+.  ....++.++|..+.    ....++..
T Consensus        44 ~~ivG~~~~~~~l~~l~~~~~~~~~~~~~vLl~GppGtGKT~la~~la~~l~--~~~~~~~~~~~~~~~~~~~~~~~~~~  121 (368)
T 3uk6_A           44 QGMVGQLAARRAAGVVLEMIREGKIAGRAVLIAGQPGTGKTAIAMGMAQALG--PDTPFTAIAGSEIFSLEMSKTEALTQ  121 (368)
T ss_dssp             TTEESCHHHHHHHHHHHHHHHTTCCTTCEEEEEESTTSSHHHHHHHHHHHHC--SSCCEEEEEGGGGSCSSSCHHHHHHH
T ss_pred             hhccChHHHHHHHHHHHHHHHcCCCCCCEEEEECCCCCCHHHHHHHHHHHhc--ccCCcccccchhhhhcccchhHHHHH
Confidence            789999999887665554332222 346999999999999999999999986  44567777766532    23334443


Q ss_pred             HHHHhcC-------------------------------CCCCCcHHHHHHHHHHHHh---cCCC----eEEEEEecCccc
Q psy200          269 IVNELKL-------------------------------KPGGKSERHQLGAILKYFD---TKHK----SILLILDEIDAL  310 (490)
Q Consensus       269 i~~~l~~-------------------------------~~~~~s~~~~~~~l~~~l~---~~~~----~~vI~IDEid~l  310 (490)
                      .+.....                               ...+.....+...+..+..   ..++    +.||||||+|.+
T Consensus       122 ~~~~~~~~~~~~~~~~~~~~~~ld~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~g~~~~~~~vl~IDEi~~l  201 (368)
T 3uk6_A          122 AFRRSIGVRIKAGAVHTVSLHEIDVINSRTQGFLALFSGDTGEIKSEVREQINAKVAEWREEGKAEIIPGVLFIDEVHML  201 (368)
T ss_dssp             HHHHSBEECC------CEEHHHHHHHTC----CCSCC-------CHHHHHHHHHHHHHHHHHTC---CBCEEEEESGGGS
T ss_pred             HHHHHHHHHhhhhccccccHhhhhhhhcccccchhhccCcccccHHHHHHHHHHHHHHhhhhccccccCceEEEhhcccc
Confidence            3333110                               1111223444444444332   1122    569999999999


Q ss_pred             cccCHHHHHHhHhCCCCCCCcEEEEEecCC--------CChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhc
Q psy200          311 ESRKQTILYTIFEWPSIPGSKLVLVGVANA--------LDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQ  382 (490)
Q Consensus       311 ~~~~~~~L~~l~~~~~~~~~~vilI~~tn~--------~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~  382 (490)
                      ....++.|+.+++..   ...++++++.+.        .+....+.+.+.+||.    .+.|.||+.+++.+++..++..
T Consensus       202 ~~~~~~~L~~~le~~---~~~~~ii~t~~~~~~i~~t~~~~~~~l~~~l~sR~~----~i~~~~~~~~e~~~il~~~~~~  274 (368)
T 3uk6_A          202 DIESFSFLNRALESD---MAPVLIMATNRGITRIRGTSYQSPHGIPIDLLDRLL----IVSTTPYSEKDTKQILRIRCEE  274 (368)
T ss_dssp             BHHHHHHHHHHTTCT---TCCEEEEEESCSEEECBTSSCEEETTCCHHHHTTEE----EEEECCCCHHHHHHHHHHHHHH
T ss_pred             ChHHHHHHHHHhhCc---CCCeeeeecccceeeeeccCCCCcccCCHHHHhhcc----EEEecCCCHHHHHHHHHHHHHH
Confidence            887777777776543   334555555421        1224556788999996    6899999999999999999987


Q ss_pred             cCCCCCCCHHHHHHHHHHHHHhh-CCHHHHHHHHHHHHHHHHhccccCCcccccCHHHHHHHHHHhc
Q psy200          383 TDKFNMFNASALQLLAGKVAAVS-GDIRKAIDITNHLIDLTYDNVKENGEVTGIGLKEVLGVISSVY  448 (490)
Q Consensus       383 ~~~~~~~~~~~i~~i~~~i~~~~-Gd~r~ai~ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~~~~~  448 (490)
                      .  ...+++++++.|++   ... |++|.++++|+.|...|..++     ...|+.++|.+++..+.
T Consensus       275 ~--~~~~~~~~l~~l~~---~~~~G~~r~~~~ll~~a~~~A~~~~-----~~~It~~~v~~a~~~~~  331 (368)
T 3uk6_A          275 E--DVEMSEDAYTVLTR---IGLETSLRYAIQLITAASLVCRKRK-----GTEVQVDDIKRVYSLFL  331 (368)
T ss_dssp             T--TCCBCHHHHHHHHH---HHHHSCHHHHHHHHHHHHHHHHHTT-----CSSBCHHHHHHHHHHSB
T ss_pred             c--CCCCCHHHHHHHHH---HhcCCCHHHHHHHHHHHHHHHHHhC-----CCCCCHHHHHHHHHHhc
Confidence            5  35689999999998   444 999999999999999998887     67999999999998754

>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=99.86  E-value=2.8e-20  Score=184.01  Aligned_cols=228  Identities=15%  Similarity=0.189  Sum_probs=163.4

Q ss_pred             CCCCChHHHHHHHHHHHHhhhc--------cCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVN--------NETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASV  265 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~--------~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l  265 (490)
                      ++++|.++.++.|.+++...+.        ....+++||+||||||||++|+++++++.    ..+++++|..+      
T Consensus        18 ~di~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~vLl~GppGtGKT~la~aia~~~~----~~~~~v~~~~l------   87 (322)
T 3eie_A           18 EDVAGLEGAKEALKEAVILPVKFPHLFKGNRKPTSGILLYGPPGTGKSYLAKAVATEAN----STFFSVSSSDL------   87 (322)
T ss_dssp             GGSCSCHHHHHHHHHHTHHHHHCGGGCCTTCCCCCEEEEECSSSSCHHHHHHHHHHHHT----CEEEEEEHHHH------
T ss_pred             HHhcChHHHHHHHHHHHHHHHhCHHHHhcCCCCCCeEEEECCCCCcHHHHHHHHHHHHC----CCEEEEchHHH------
Confidence            7899999999999998843221        12457899999999999999999999875    67888887542      


Q ss_pred             HHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccC-----------HHHHHHhHhCCCCCCCcEEE
Q psy200          266 YETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRK-----------QTILYTIFEWPSIPGSKLVL  334 (490)
Q Consensus       266 ~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~-----------~~~L~~l~~~~~~~~~~vil  334 (490)
                              ...+.+.....+...+..+..  ..+.||||||||.|....           +..++..++........++|
T Consensus        88 --------~~~~~g~~~~~~~~~f~~a~~--~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~v~v  157 (322)
T 3eie_A           88 --------VSKWMGESEKLVKQLFAMARE--NKPSIIFIDQVDALTGTRGEGESEASRRIKTELLVQMNGVGNDSQGVLV  157 (322)
T ss_dssp             --------HTTTGGGHHHHHHHHHHHHHH--TSSEEEEEECGGGGSCC------CCTHHHHHHHHHHHGGGGTSCCCEEE
T ss_pred             --------hhcccchHHHHHHHHHHHHHh--cCCeEEEechhhhhhccCCCCcchHHHHHHHHHHHHhccccccCCceEE
Confidence                    113333444455555554443  457899999999997643           23344444433334568999


Q ss_pred             EEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhC-CHHHHHH
Q psy200          335 VGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSG-DIRKAID  413 (490)
Q Consensus       335 I~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~G-d~r~ai~  413 (490)
                      |++||.   ++.+++.+.+||.   ..+.+.+++.++..+|+..++...  ...+++..++.|++   ...| ..+.+-+
T Consensus       158 i~atn~---~~~ld~al~~Rf~---~~i~~~~p~~~~r~~il~~~~~~~--~~~~~~~~l~~la~---~t~g~sg~di~~  226 (322)
T 3eie_A          158 LGATNI---PWQLDSAIRRRFE---RRIYIPLPDLAARTTMFEINVGDT--PCVLTKEDYRTLGA---MTEGYSGSDIAV  226 (322)
T ss_dssp             EEEESC---GGGSCHHHHHHCC---EEEECCCCCHHHHHHHHHHHHTTC--CCCCCHHHHHHHHH---TTTTCCHHHHHH
T ss_pred             EEecCC---hhhCCHHHHcccC---eEEEeCCCCHHHHHHHHHHHhccC--CCCCCHHHHHHHHH---HcCCCCHHHHHH
Confidence            999984   4557788888997   489999999999999999998765  45578999999987   4444 3455556


Q ss_pred             HHHHHHHHHHhccccC--------------------------------------CcccccCHHHHHHHHHHhccCcc
Q psy200          414 ITNHLIDLTYDNVKEN--------------------------------------GEVTGIGLKEVLGVISSVYCTSQ  452 (490)
Q Consensus       414 ll~~a~~~a~~~~~~~--------------------------------------~~~~~It~~~v~~a~~~~~~~~~  452 (490)
                      +|+.|+..+.++....                                      .....|+++||..|+..+.++..
T Consensus       227 l~~~a~~~a~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~it~~df~~al~~~~ps~~  303 (322)
T 3eie_A          227 VVKDALMQPIRKIQSATHFKDVSTEDDETRKLTPCSPGDDGAIEMSWTDIEADELKEPDLTIKDFLKAIKSTRPTVN  303 (322)
T ss_dssp             HHHHHTTHHHHHHHHCEEEEECC----CCCCEEECCSSCTTEEEEEGGGSCSSCBCCCCCCHHHHHHHHHHSCCSSC
T ss_pred             HHHHHHHHHHHHHhhhhhhhhhccccccccccccccccccccccccccccccccccCCCCCHHHHHHHHHhcCCCCC
Confidence            8888876665543110                                      01246999999999998887654

>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=99.85  E-value=8e-20  Score=183.01  Aligned_cols=228  Identities=15%  Similarity=0.193  Sum_probs=161.1

Q ss_pred             CCCCChHHHHHHHHHHHHhhhc--------cCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVN--------NETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASV  265 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~--------~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l  265 (490)
                      ++++|.++.++.|.+++...+.        ....+++||+||||||||++|+++++++.    ..++.++|..+      
T Consensus        51 ~di~G~~~~~~~l~~~v~~~~~~~~~~~~~~~~~~~iLL~GppGtGKT~la~ala~~~~----~~~~~v~~~~l------  120 (355)
T 2qp9_X           51 EDVAGLEGAKEALKEAVILPVKFPHLFKGNRKPTSGILLYGPPGTGKSYLAKAVATEAN----STFFSVSSSDL------  120 (355)
T ss_dssp             GGSCCGGGHHHHHHHHTHHHHHCGGGGCSSCCCCCCEEEECSTTSCHHHHHHHHHHHHT----CEEEEEEHHHH------
T ss_pred             HHhCCHHHHHHHHHHHHHHHHhCHHHHhcCCCCCceEEEECCCCCcHHHHHHHHHHHhC----CCEEEeeHHHH------
Confidence            7899999999999988753321        12457899999999999999999999985    67888877532      


Q ss_pred             HHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccC-----------HHHHHHhHhCCCCCCCcEEE
Q psy200          266 YETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRK-----------QTILYTIFEWPSIPGSKLVL  334 (490)
Q Consensus       266 ~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~-----------~~~L~~l~~~~~~~~~~vil  334 (490)
                              ...+.+.....+...|..+..  ..++||||||+|.+....           +..|+..++........++|
T Consensus       121 --------~~~~~g~~~~~~~~~f~~a~~--~~~~vl~iDEid~l~~~r~~~~~~~~~~~~~~ll~~l~~~~~~~~~v~v  190 (355)
T 2qp9_X          121 --------VSKWMGESEKLVKQLFAMARE--NKPSIIFIDQVDALTGTRGEGESEASRRIKTELLVQMNGVGNDSQGVLV  190 (355)
T ss_dssp             --------HSCC---CHHHHHHHHHHHHH--TSSEEEEEECGGGGTC------CTHHHHHHHHHHHHHHHCC---CCEEE
T ss_pred             --------hhhhcchHHHHHHHHHHHHHH--cCCeEEEEechHhhcccCCCCcchHHHHHHHHHHHHhhcccccCCCeEE
Confidence                    113334455555555554433  457899999999997542           23444444433334567999


Q ss_pred             EEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhC-CHHHHHH
Q psy200          335 VGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSG-DIRKAID  413 (490)
Q Consensus       335 I~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~G-d~r~ai~  413 (490)
                      |++||.   .+.+++.+.+||.   ..+.+.+++.++...||..++...  ...+++..++.|++   .+.| ..+.+-+
T Consensus       191 I~atn~---~~~ld~al~rRf~---~~i~i~~P~~~~r~~il~~~l~~~--~~~~~~~~l~~la~---~t~G~sg~dl~~  259 (355)
T 2qp9_X          191 LGATNI---PWQLDSAIRRRFE---RRIYIPLPDLAARTTMFEINVGDT--PSVLTKEDYRTLGA---MTEGYSGSDIAV  259 (355)
T ss_dssp             EEEESC---GGGSCHHHHHTCC---EEEECCCCCHHHHHHHHHHHHTTS--CBCCCHHHHHHHHH---HTTTCCHHHHHH
T ss_pred             EeecCC---cccCCHHHHcccC---EEEEeCCcCHHHHHHHHHHHHhhC--CCCCCHHHHHHHHH---HcCCCCHHHHHH
Confidence            999985   4566788888997   489999999999999999998765  34568899999998   4445 4555666


Q ss_pred             HHHHHHHHHHhccccC--------------------------------------CcccccCHHHHHHHHHHhccCcc
Q psy200          414 ITNHLIDLTYDNVKEN--------------------------------------GEVTGIGLKEVLGVISSVYCTSQ  452 (490)
Q Consensus       414 ll~~a~~~a~~~~~~~--------------------------------------~~~~~It~~~v~~a~~~~~~~~~  452 (490)
                      +|+.|+..|..+....                                      .....|+++||..|+..+.++..
T Consensus       260 l~~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~df~~Al~~~~ps~~  336 (355)
T 2qp9_X          260 VVKDALMQPIRKIQSATHFKDVSTEDDETRKLTPSSPGDDGAIEMSWTDIEADELKEPDLTIKDFLKAIKSTRPTVN  336 (355)
T ss_dssp             HHHHHHHHHHHHHHHCSEEEECCC-----CCEEEECTTSSSEEECCGGGSCGGGBCCCCBCHHHHHHHHHHSCCSSC
T ss_pred             HHHHHHHHHHHHHHHhhhhhhhccccccccccCcCCccccchhhcccccccccccccCCccHHHHHHHHHHcCCCCC
Confidence            8888887776542100                                      01235999999999999887654

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii}

Probab=99.84  E-value=6.6e-20  Score=178.04  Aligned_cols=220  Identities=15%  Similarity=0.196  Sum_probs=159.7

Q ss_pred             CCCCChHHHHHHHHHHHHhhhcc---------CCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVNN---------ETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAAS  264 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~---------~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~  264 (490)
                      ++++|.+++++.|.+++...+..         ..+.+++|+||||||||++|+++++.+.    ..+++++|.....   
T Consensus        17 ~~i~G~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ll~G~~GtGKT~la~~la~~~~----~~~~~v~~~~~~~---   89 (285)
T 3h4m_A           17 EDIGGLEKQMQEIREVVELPLKHPELFEKVGIEPPKGILLYGPPGTGKTLLAKAVATETN----ATFIRVVGSELVK---   89 (285)
T ss_dssp             GGSCSCHHHHHHHHHHTHHHHHCHHHHHHHCCCCCSEEEEESSSSSSHHHHHHHHHHHTT----CEEEEEEGGGGCC---
T ss_pred             HHhcCHHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCeEEEECCCCCcHHHHHHHHHHHhC----CCEEEEehHHHHH---
Confidence            67999999999999988654322         4678999999999999999999999875    6788888766532   


Q ss_pred             HHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCcccccc-----------CHHHHHHhHhCC--CCCCCc
Q psy200          265 VYETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESR-----------KQTILYTIFEWP--SIPGSK  331 (490)
Q Consensus       265 l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~-----------~~~~L~~l~~~~--~~~~~~  331 (490)
                                 .+.+.....+...+..+..  ..+.||||||+|.+...           .+..+..+++..  ......
T Consensus        90 -----------~~~~~~~~~~~~~~~~~~~--~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~l~~ll~~~~~~~~~~~  156 (285)
T 3h4m_A           90 -----------KFIGEGASLVKDIFKLAKE--KAPSIIFIDEIDAIAAKRTDALTGGDREVQRTLMQLLAEMDGFDARGD  156 (285)
T ss_dssp             -----------CSTTHHHHHHHHHHHHHHH--TCSEEEEEETTHHHHBCCSSSCCGGGGHHHHHHHHHHHHHHTTCSSSS
T ss_pred             -----------hccchHHHHHHHHHHHHHH--cCCeEEEEECHHHhcccCccccCCccHHHHHHHHHHHHHhhCCCCCCC
Confidence                       2333333444444444433  45789999999998532           245555555431  124467


Q ss_pred             EEEEEecCCCChhHhhhHHhhh--ccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhC-CH
Q psy200          332 LVLVGVANALDLTDRMLPRLQA--NVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSG-DI  408 (490)
Q Consensus       332 vilI~~tn~~~~~~~l~~~l~~--R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~G-d~  408 (490)
                      +++|+++|..   +.+.+.+.+  ||.   ..+.|.+++.++..+++..++......   .+..++.++.   ...| ..
T Consensus       157 ~~vI~ttn~~---~~l~~~l~~~~Rf~---~~i~~~~p~~~~r~~il~~~~~~~~~~---~~~~~~~l~~---~~~g~~~  224 (285)
T 3h4m_A          157 VKIIGATNRP---DILDPAILRPGRFD---RIIEVPAPDEKGRLEILKIHTRKMNLA---EDVNLEEIAK---MTEGCVG  224 (285)
T ss_dssp             EEEEEECSCG---GGBCHHHHSTTSEE---EEEECCCCCHHHHHHHHHHHHTTSCBC---TTCCHHHHHH---HCTTCCH
T ss_pred             EEEEEeCCCc---hhcCHHHcCCCcCC---eEEEECCCCHHHHHHHHHHHHhcCCCC---CcCCHHHHHH---HcCCCCH
Confidence            9999999853   556677776  776   479999999999999999988765221   2233566665   3445 45


Q ss_pred             HHHHHHHHHHHHHHHhccccCCcccccCHHHHHHHHHHhccC
Q psy200          409 RKAIDITNHLIDLTYDNVKENGEVTGIGLKEVLGVISSVYCT  450 (490)
Q Consensus       409 r~ai~ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~~~~~~~  450 (490)
                      +.+..+|..|...|..++     ...|+.++|.+|+.++...
T Consensus       225 ~~i~~l~~~a~~~a~~~~-----~~~I~~~d~~~al~~~~~~  261 (285)
T 3h4m_A          225 AELKAICTEAGMNAIREL-----RDYVTMDDFRKAVEKIMEK  261 (285)
T ss_dssp             HHHHHHHHHHHHHHHHTT-----CSSBCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhc-----cCcCCHHHHHHHHHHHHhc
Confidence            666678999999998887     6789999999999998754

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens}

Probab=99.84  E-value=2.5e-19  Score=177.01  Aligned_cols=229  Identities=16%  Similarity=0.175  Sum_probs=164.7

Q ss_pred             CCCCChHHHHHHHHHHHHhhhc--------cCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVN--------NETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASV  265 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~--------~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l  265 (490)
                      ++++|.++.++.|.+.+...+.        ...+++++|+||||||||++|+++++++   .+..++.+++....+    
T Consensus        12 ~di~G~~~~k~~l~~~v~~p~~~~~~~~~~~~~~~~iLL~GppGtGKT~la~ala~~~---~~~~~~~i~~~~l~~----   84 (322)
T 1xwi_A           12 SDVAGLEGAKEALKEAVILPIKFPHLFTGKRTPWRGILLFGPPGTGKSYLAKAVATEA---NNSTFFSISSSDLVS----   84 (322)
T ss_dssp             GGSCSCHHHHHHHHHHHHHHHHCGGGSCTTCCCCSEEEEESSSSSCHHHHHHHHHHHT---TSCEEEEEECCSSCC----
T ss_pred             HHhcCHHHHHHHHHHHHHHHHhCHHHHhCCCCCCceEEEECCCCccHHHHHHHHHHHc---CCCcEEEEEhHHHHh----
Confidence            6799999999999988754322        1245799999999999999999999987   235788898876532    


Q ss_pred             HHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccC-----------HHHHHHhHhCCCCCCCcEEE
Q psy200          266 YETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRK-----------QTILYTIFEWPSIPGSKLVL  334 (490)
Q Consensus       266 ~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~-----------~~~L~~l~~~~~~~~~~vil  334 (490)
                                .+.+.+...+...+..+..  .+++||||||+|.+....           ...++..++.......+++|
T Consensus        85 ----------~~~g~~~~~~~~lf~~a~~--~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~ll~~ld~~~~~~~~v~v  152 (322)
T 1xwi_A           85 ----------KWLGESEKLVKNLFQLARE--NKPSIIFIDEIDSLCGSRSENESEAARRIKTEFLVQMQGVGVDNDGILV  152 (322)
T ss_dssp             ----------SSCCSCHHHHHHHHHHHHH--TSSEEEEEETTTGGGCCSSSCCTTHHHHHHHHHHHHHHCSSSCCTTEEE
T ss_pred             ----------hhhhHHHHHHHHHHHHHHh--cCCcEEEeecHHHhccccccccchHHHHHHHHHHHHHhcccccCCCEEE
Confidence                      4455666666666665544  458899999999996432           12233333332234578999


Q ss_pred             EEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCC-HHHHHH
Q psy200          335 VGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGD-IRKAID  413 (490)
Q Consensus       335 I~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd-~r~ai~  413 (490)
                      |++||..   +.+++.+.+||.   ..+.+++++.++..+|+..++...  ...+++..++.|++   .+.|. .+.+-.
T Consensus       153 I~atn~~---~~ld~al~rRf~---~~i~i~~P~~~~r~~il~~~l~~~--~~~l~~~~l~~la~---~t~G~sgadl~~  221 (322)
T 1xwi_A          153 LGATNIP---WVLDSAIRRRFE---KRIYIPLPEPHARAAMFKLHLGTT--QNSLTEADFRELGR---KTDGYSGADISI  221 (322)
T ss_dssp             EEEESCT---TTSCHHHHHTCC---EEEECCCCCHHHHHHHHHHHHTTC--CBCCCHHHHHHHHH---TCTTCCHHHHHH
T ss_pred             EEecCCc---ccCCHHHHhhcC---eEEEeCCcCHHHHHHHHHHHHhcC--CCCCCHHHHHHHHH---HcCCCCHHHHHH
Confidence            9999854   456778888997   489999999999999999988765  34568889999987   44454 444556


Q ss_pred             HHHHHHHHHHhccccC--------------------------------------------CcccccCHHHHHHHHHHhcc
Q psy200          414 ITNHLIDLTYDNVKEN--------------------------------------------GEVTGIGLKEVLGVISSVYC  449 (490)
Q Consensus       414 ll~~a~~~a~~~~~~~--------------------------------------------~~~~~It~~~v~~a~~~~~~  449 (490)
                      +|+.|+..+.++....                                            .....|+++||..|+..+.+
T Consensus       222 l~~~A~~~a~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~df~~al~~~~p  301 (322)
T 1xwi_A          222 IVRDALMQPVRKVQSATHFKKVRGPSRADPNHLVDDLLTPCSPGDPGAIEMTWMDVPGDKLLEPVVSMSDMLRSLSNTKP  301 (322)
T ss_dssp             HHHHHHTHHHHHHHHCSEEEEEEEECSSCTTSEEEEEEEECCSSSTTEEECCGGGSCGGGBCCCCBCHHHHHHHHHTCCC
T ss_pred             HHHHHHHHHHHHHHhhhhhhhhccccccccccccccccccccccccchhhccccccccccccCCCcCHHHHHHHHHhCCC
Confidence            8888876665432100                                            01236999999999998876


Q ss_pred             Ccc
Q psy200          450 TSQ  452 (490)
Q Consensus       450 ~~~  452 (490)
                      +..
T Consensus       302 s~~  304 (322)
T 1xwi_A          302 TVN  304 (322)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            544

>3pvs_A Replication-associated recombination protein A; maintenance of genome stability Pro recombination; 2.50A {Escherichia coli}

Probab=99.84  E-value=4.1e-20  Score=189.99  Aligned_cols=218  Identities=16%  Similarity=0.212  Sum_probs=159.6

Q ss_pred             CCCCcchHHHhhcCCCCCCChHHHH---HHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEe
Q psy200          179 FSEDKPKVEEKAKDSCELPGREVQL---EGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYIN  255 (490)
Q Consensus       179 ~~~~~~~~~~~~l~~~~lvgre~~~---~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~  255 (490)
                      +|.+.|.+...    ++++|++..+   ..|...+..    +...+++|+||||||||++|+.+++.+.    ..++.++
T Consensus        15 pla~r~rP~~l----~~ivGq~~~~~~~~~L~~~i~~----~~~~~vLL~GppGtGKTtlAr~ia~~~~----~~f~~l~   82 (447)
T 3pvs_A           15 PLAARMRPENL----AQYIGQQHLLAAGKPLPRAIEA----GHLHSMILWGPPGTGKTTLAEVIARYAN----ADVERIS   82 (447)
T ss_dssp             CHHHHTCCCST----TTCCSCHHHHSTTSHHHHHHHH----TCCCEEEEECSTTSSHHHHHHHHHHHTT----CEEEEEE
T ss_pred             ChHHHhCCCCH----HHhCCcHHHHhchHHHHHHHHc----CCCcEEEEECCCCCcHHHHHHHHHHHhC----CCeEEEE
Confidence            34445555545    8999999998   677777754    5557899999999999999999999864    5677787


Q ss_pred             ccCCCCHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHh--cCCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEE
Q psy200          256 CNSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFD--TKHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLV  333 (490)
Q Consensus       256 ~~~~~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~--~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vi  333 (490)
                      +...                     ....+.+.+..+..  ..++..+|||||||.+....++.|+..++.     ..++
T Consensus        83 a~~~---------------------~~~~ir~~~~~a~~~~~~~~~~iLfIDEI~~l~~~~q~~LL~~le~-----~~v~  136 (447)
T 3pvs_A           83 AVTS---------------------GVKEIREAIERARQNRNAGRRTILFVDEVHRFNKSQQDAFLPHIED-----GTIT  136 (447)
T ss_dssp             TTTC---------------------CHHHHHHHHHHHHHHHHTTCCEEEEEETTTCC------CCHHHHHT-----TSCE
T ss_pred             eccC---------------------CHHHHHHHHHHHHHhhhcCCCcEEEEeChhhhCHHHHHHHHHHHhc-----CceE
Confidence            6543                     12223333332221  135678999999999998888888888773     3577


Q ss_pred             EEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccC-----CCCCCCHHHHHHHHHHHHHhhCCH
Q psy200          334 LVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTD-----KFNMFNASALQLLAGKVAAVSGDI  408 (490)
Q Consensus       334 lI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~-----~~~~~~~~~i~~i~~~i~~~~Gd~  408 (490)
                      +|++|+.. ....+.+.+.+||.    .+.|.+++.+++..++.+.+....     ....+++++++.|++   .+.||+
T Consensus       137 lI~att~n-~~~~l~~aL~sR~~----v~~l~~l~~edi~~il~~~l~~~~~~~~~~~~~i~~~al~~L~~---~~~Gd~  208 (447)
T 3pvs_A          137 FIGATTEN-PSFELNSALLSRAR----VYLLKSLSTEDIEQVLTQAMEDKTRGYGGQDIVLPDETRRAIAE---LVNGDA  208 (447)
T ss_dssp             EEEEESSC-GGGSSCHHHHTTEE----EEECCCCCHHHHHHHHHHHHHCTTTSSTTSSEECCHHHHHHHHH---HHCSCH
T ss_pred             EEecCCCC-cccccCHHHhCcee----EEeeCCcCHHHHHHHHHHHHHHHhhhhccccCcCCHHHHHHHHH---HCCCCH
Confidence            77777532 23456788999985    799999999999999999988631     235689999999998   589999


Q ss_pred             HHHHHHHHHHHHHHHhc--cccCCcccccCHHHHHHHHHHh
Q psy200          409 RKAIDITNHLIDLTYDN--VKENGEVTGIGLKEVLGVISSV  447 (490)
Q Consensus       409 r~ai~ll~~a~~~a~~~--~~~~~~~~~It~~~v~~a~~~~  447 (490)
                      |.++++|+.++..+...  +     ...|+.++|.+++...
T Consensus       209 R~lln~Le~a~~~a~~~~~~-----~~~It~e~v~~~l~~~  244 (447)
T 3pvs_A          209 RRALNTLEMMADMAEVDDSG-----KRVLKPELLTEIAGER  244 (447)
T ss_dssp             HHHHHHHHHHHHHSCBCTTS-----CEECCHHHHHHHHTCC
T ss_pred             HHHHHHHHHHHHhcccccCC-----CCccCHHHHHHHHhhh
Confidence            99999999999887633  3     3579999999988754

>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=99.84  E-value=6.9e-20  Score=181.15  Aligned_cols=235  Identities=15%  Similarity=0.188  Sum_probs=176.5

Q ss_pred             CCCCChHHHHHHHHHHHHhhhc-cCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVN-NETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNE  272 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~-~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~  272 (490)
                      ++++|++..++.+..++..... .....+++|+||+|||||++|+++++.+.    ..+++++|........+       
T Consensus        12 ~~~ig~~~~~~~l~~~l~~~~~~~~~~~~vll~G~~GtGKT~la~~i~~~~~----~~~~~~~~~~~~~~~~l-------   80 (324)
T 1hqc_A           12 DEYIGQERLKQKLRVYLEAAKARKEPLEHLLLFGPPGLGKTTLAHVIAHELG----VNLRVTSGPAIEKPGDL-------   80 (324)
T ss_dssp             TTCCSCHHHHHHHHHHHHHHHHHCSCCCCCEEECCTTCCCHHHHHHHHHHHT----CCEEEECTTTCCSHHHH-------
T ss_pred             HHhhCHHHHHHHHHHHHHHHHccCCCCCcEEEECCCCCCHHHHHHHHHHHhC----CCEEEEeccccCChHHH-------
Confidence            7899999999999998876433 23567899999999999999999999875    57788888776443222       


Q ss_pred             hcCCCCCCcHHHHHHHHHHHHhc-CCCeEEEEEecCccccccCHHHHHHhHhCCCC---------------CCCcEEEEE
Q psy200          273 LKLKPGGKSERHQLGAILKYFDT-KHKSILLILDEIDALESRKQTILYTIFEWPSI---------------PGSKLVLVG  336 (490)
Q Consensus       273 l~~~~~~~s~~~~~~~l~~~l~~-~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~---------------~~~~vilI~  336 (490)
                                   ...    +.. ...+.+|||||+|.+....+..|+.+++....               ....+++|+
T Consensus        81 -------------~~~----l~~~~~~~~~l~lDEi~~l~~~~~~~L~~~l~~~~~~~v~~~~~~~~~~~~~~~~~~~i~  143 (324)
T 1hqc_A           81 -------------AAI----LANSLEEGDILFIDEIHRLSRQAEEHLYPAMEDFVMDIVIGQGPAARTIRLELPRFTLIG  143 (324)
T ss_dssp             -------------HHH----HTTTCCTTCEEEETTTTSCCHHHHHHHHHHHHHSEEEECCSSSSSCCCEEEECCCCEEEE
T ss_pred             -------------HHH----HHHhccCCCEEEEECCcccccchHHHHHHHHHhhhhHHhccccccccccccCCCCEEEEE
Confidence                         222    221 23456999999999988778878777654310               113578889


Q ss_pred             ecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHHHHH
Q psy200          337 VANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITN  416 (490)
Q Consensus       337 ~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll~  416 (490)
                      ++|..   ..+.+.+.+||.   ..+.|.+++.+++..++...+...  ...+++++++.+++   .+.|++|.+.++++
T Consensus       144 ~t~~~---~~~~~~l~~R~~---~~i~l~~~~~~e~~~~l~~~~~~~--~~~~~~~~~~~l~~---~~~G~~r~l~~~l~  212 (324)
T 1hqc_A          144 ATTRP---GLITAPLLSRFG---IVEHLEYYTPEELAQGVMRDARLL--GVRITEEAALEIGR---RSRGTMRVAKRLFR  212 (324)
T ss_dssp             EESCC---SSCSCSTTTTCS---CEEECCCCCHHHHHHHHHHHHHTT--TCCCCHHHHHHHHH---HSCSCHHHHHHHHH
T ss_pred             eCCCc---ccCCHHHHhccc---EEEecCCCCHHHHHHHHHHHHHhc--CCCCCHHHHHHHHH---HccCCHHHHHHHHH
Confidence            99854   344567788885   379999999999999999988765  35689999999987   56899999999999


Q ss_pred             HHHHHHHhccccCCcccccCHHHHHHHHHHhccCccccccccccCCCChHhHHHHHHHHHHhcCC
Q psy200          417 HLIDLTYDNVKENGEVTGIGLKEVLGVISSVYCTSQSLHCSKDEDSFPLQQKLALASLLLLKSRP  481 (490)
Q Consensus       417 ~a~~~a~~~~~~~~~~~~It~~~v~~a~~~~~~~~~~~~~~~~l~~L~~~qk~vL~al~~~~~~~  481 (490)
                      .+...+...+     ...|+.+++..++......         ...+...++.++.+++....+.
T Consensus       213 ~~~~~a~~~~-----~~~i~~~~~~~~~~~~~~~---------~~~l~~~e~~~i~~~~~~~~g~  263 (324)
T 1hqc_A          213 RVRDFAQVAG-----EEVITRERALEALAALGLD---------ELGLEKRDREILEVLILRFGGG  263 (324)
T ss_dssp             HHTTTSTTTS-----CSCCCHHHHHHHHHHHTCC---------TTCCCHHHHHHHHHHHHHSCSS
T ss_pred             HHHHHHHHhc-----CCCCCHHHHHHHHHHhccc---------ccCCCHHHHHHHHHHHHHhcCC
Confidence            9887776555     4579999999988775321         2456777778888777665443

>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens}

Probab=99.84  E-value=2.1e-19  Score=182.41  Aligned_cols=236  Identities=14%  Similarity=0.205  Sum_probs=162.5

Q ss_pred             CCCcchHHHhhcCCCCCCChHHHHHHHHHHHHhhhc--------cCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceE
Q psy200          180 SEDKPKVEEKAKDSCELPGREVQLEGIRQFLLGHVN--------NETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKT  251 (490)
Q Consensus       180 ~~~~~~~~~~~l~~~~lvgre~~~~~l~~~L~~~~~--------~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~  251 (490)
                      |...|.+...    ++++|++..++.|.+++.....        .....++||+||+|||||++|+++++++.    ..+
T Consensus       105 ~~~~~~~~~~----~~iiG~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~vLL~GppGtGKT~la~aia~~~~----~~~  176 (389)
T 3vfd_A          105 IVDNGTAVKF----DDIAGQDLAKQALQEIVILPSLRPELFTGLRAPARGLLLFGPPGNGKTMLAKAVAAESN----ATF  176 (389)
T ss_dssp             TBCCSCCCCG----GGSCSCHHHHHHHHHHTHHHHHCTTTSCGGGCCCSEEEEESSTTSCHHHHHHHHHHHTT----CEE
T ss_pred             hhccCCCCCh----HHhCCHHHHHHHHHHHHHHhccCHHHhcccCCCCceEEEECCCCCCHHHHHHHHHHhhc----CcE
Confidence            4444444444    7899999999999998854332        23468999999999999999999999864    788


Q ss_pred             EEEeccCCCCHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccC-----------HHHHHH
Q psy200          252 IYINCNSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRK-----------QTILYT  320 (490)
Q Consensus       252 ~~v~~~~~~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~-----------~~~L~~  320 (490)
                      ++++|..+..              .+.+.....+...+..+..  ..+.||||||||.|....           +..|..
T Consensus       177 ~~v~~~~l~~--------------~~~g~~~~~~~~~~~~a~~--~~~~il~iDEid~l~~~~~~~~~~~~~~~~~~ll~  240 (389)
T 3vfd_A          177 FNISAASLTS--------------KYVGEGEKLVRALFAVARE--LQPSIIFIDQVDSLLCERREGEHDASRRLKTEFLI  240 (389)
T ss_dssp             EEECSCCC---------------------CHHHHHHHHHHHHH--SSSEEEEEETGGGGC--------CTHHHHHHHHHH
T ss_pred             EEeeHHHhhc--------------cccchHHHHHHHHHHHHHh--cCCeEEEEECchhhcccCCCccchHHHHHHHHHHH
Confidence            9999987643              2223334444445544433  356899999999995432           122222


Q ss_pred             hHh-CCCCCCCcEEEEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHH
Q psy200          321 IFE-WPSIPGSKLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAG  399 (490)
Q Consensus       321 l~~-~~~~~~~~vilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~  399 (490)
                      .++ .......+++||++||.   .+.+.+.+.+||.   ..+.|.+++.++...++..++...  ...++++.++.|++
T Consensus       241 ~l~~~~~~~~~~v~vI~atn~---~~~l~~~l~~R~~---~~i~i~~p~~~~r~~il~~~~~~~--~~~l~~~~~~~la~  312 (389)
T 3vfd_A          241 EFDGVQSAGDDRVLVMGATNR---PQELDEAVLRRFI---KRVYVSLPNEETRLLLLKNLLCKQ--GSPLTQKELAQLAR  312 (389)
T ss_dssp             HHHHHC-----CEEEEEEESC---GGGCCHHHHTTCC---EEEECCCCCHHHHHHHHHHHHTTS--CCCSCHHHHHHHHH
T ss_pred             HhhcccccCCCCEEEEEecCC---chhcCHHHHcCcc---eEEEcCCcCHHHHHHHHHHHHHhc--CCCCCHHHHHHHHH
Confidence            222 22224568999999985   4566788888987   379999999999999999988775  45688999999887


Q ss_pred             HHHHhhCCHHHHH-HHHHHHHHHHHhccccC-------CcccccCHHHHHHHHHHhccC
Q psy200          400 KVAAVSGDIRKAI-DITNHLIDLTYDNVKEN-------GEVTGIGLKEVLGVISSVYCT  450 (490)
Q Consensus       400 ~i~~~~Gd~r~ai-~ll~~a~~~a~~~~~~~-------~~~~~It~~~v~~a~~~~~~~  450 (490)
                         ...|..+..+ .+|..|+..+.++....       .....|+.+||..++..+.+.
T Consensus       313 ---~~~g~~~~~l~~L~~~a~~~~~rel~~~~~~~~~~~~~~~i~~~d~~~al~~~~~s  368 (389)
T 3vfd_A          313 ---MTDGYSGSDLTALAKDAALGPIRELKPEQVKNMSASEMRNIRLSDFTESLKKIKRS  368 (389)
T ss_dssp             ---HTTTCCHHHHHHHHHHHTTHHHHTSCCC---CCSSSCCCCCCHHHHHHHHHHCCCS
T ss_pred             ---HcCCCCHHHHHHHHHHHHHHHHHhhhhhhhhccchhhcCCcCHHHHHHHHHHcCCC
Confidence               5667666555 47888877776652211       124579999999999887654

>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A {Escherichia coli} SCOP: c.37.1.20

Probab=99.83  E-value=3.5e-19  Score=170.32  Aligned_cols=218  Identities=12%  Similarity=0.156  Sum_probs=157.4

Q ss_pred             CCCCChHHHHHHHHHHHHhhhc--------cCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVN--------NETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASV  265 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~--------~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l  265 (490)
                      ++++|.+..++.|.+.+.....        ...+.+++|+||+|||||++++++++.+.    ..+++++|..+..    
T Consensus        12 ~~i~G~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKT~la~~la~~~~----~~~~~i~~~~~~~----   83 (257)
T 1lv7_A           12 ADVAGCDEAKEEVAELVEYLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGEAK----VPFFTISGSDFVE----   83 (257)
T ss_dssp             GGSCSCHHHHHHTHHHHHHHHCGGGC-----CCCCEEEEECCTTSCHHHHHHHHHHHHT----CCEEEECSCSSTT----
T ss_pred             HHhcCcHHHHHHHHHHHHHHhCHHHHHHcCCCCCCeEEEECcCCCCHHHHHHHHHHHcC----CCEEEEeHHHHHH----
Confidence            7899999999988887654211        12466899999999999999999999874    5678888876532    


Q ss_pred             HHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCH-----------HHHHHh---HhCCCCCCCc
Q psy200          266 YETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQ-----------TILYTI---FEWPSIPGSK  331 (490)
Q Consensus       266 ~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~-----------~~L~~l---~~~~~~~~~~  331 (490)
                                ...+.....+...+..+..  ..+++|||||+|.+....+           ..+..+   ++.. .....
T Consensus        84 ----------~~~~~~~~~~~~~~~~a~~--~~~~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~-~~~~~  150 (257)
T 1lv7_A           84 ----------MFVGVGASRVRDMFEQAKK--AAPCIIFIDEIDAVGRQRGAGLGGGHDEREQTLNQMLVEMDGF-EGNEG  150 (257)
T ss_dssp             ----------SCCCCCHHHHHHHHHHHHT--TCSEEEEETTHHHHTCCCSTTSCCTTCHHHHHHHHHHHHHHTC-CSSSC
T ss_pred             ----------HhhhhhHHHHHHHHHHHHH--cCCeeehhhhhhhhccCCCCCcCCCchHHHHHHHHHHHHhhCc-ccCCC
Confidence                      2334455556666665443  4578999999998865421           223333   2221 23567


Q ss_pred             EEEEEecCCCChhHhhhHHhhh--ccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhC-CH
Q psy200          332 LVLVGVANALDLTDRMLPRLQA--NVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSG-DI  408 (490)
Q Consensus       332 vilI~~tn~~~~~~~l~~~l~~--R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~G-d~  408 (490)
                      +++|++||..+   .+++.+.+  ||.   ..+.+.+++.++..+|+..++....   ...+..+..++.   .+.| +.
T Consensus       151 ~~vI~~tn~~~---~l~~~l~r~~rf~---~~i~i~~P~~~~r~~il~~~~~~~~---l~~~~~~~~la~---~~~G~~~  218 (257)
T 1lv7_A          151 IIVIAATNRPD---VLDPALLRPGRFD---RQVVVGLPDVRGREQILKVHMRRVP---LAPDIDAAIIAR---GTPGFSG  218 (257)
T ss_dssp             EEEEEEESCTT---TSCGGGGSTTSSC---EEEECCCCCHHHHHHHHHHHHTTSC---BCTTCCHHHHHH---TCTTCCH
T ss_pred             EEEEEeeCCch---hCCHHHcCCCcCC---eEEEeCCCCHHHHHHHHHHHHhcCC---CCccccHHHHHH---HcCCCCH
Confidence            89999998653   44555555  676   4799999999999999998886542   112223556665   6788 99


Q ss_pred             HHHHHHHHHHHHHHHhccccCCcccccCHHHHHHHHHHhcc
Q psy200          409 RKAIDITNHLIDLTYDNVKENGEVTGIGLKEVLGVISSVYC  449 (490)
Q Consensus       409 r~ai~ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~~~~~~  449 (490)
                      +.+.++|++|...|..++     ...|+.+||.+|+..+..
T Consensus       219 ~dl~~l~~~a~~~a~~~~-----~~~i~~~~~~~a~~~~~~  254 (257)
T 1lv7_A          219 ADLANLVNEAALFAARGN-----KRVVSMVEFEKAKDKIMM  254 (257)
T ss_dssp             HHHHHHHHHHHHHHHHTT-----CSSBCHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHHHhC-----CCcccHHHHHHHHHHHhc
Confidence            999999999999998887     578999999999998753

>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=99.83  E-value=9.6e-20  Score=182.19  Aligned_cols=236  Identities=17%  Similarity=0.164  Sum_probs=165.5

Q ss_pred             cCCCCcchHHHhhcCCCCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhc--CCceEEEEe
Q psy200          178 LFSEDKPKVEEKAKDSCELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIK--DAFKTIYIN  255 (490)
Q Consensus       178 ~~~~~~~~~~~~~l~~~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~--~~~~~~~v~  255 (490)
                      .+|.++|.+...    ++++|+++.++.|..++..    +...+++|+||+|+|||++++++++.+...  ..+.++.++
T Consensus        25 ~~~~~k~~p~~~----~~i~g~~~~~~~l~~~l~~----~~~~~~ll~G~~G~GKT~la~~la~~l~~~~~~~~~~~~~~   96 (353)
T 1sxj_D           25 QPWVEKYRPKNL----DEVTAQDHAVTVLKKTLKS----ANLPHMLFYGPPGTGKTSTILALTKELYGPDLMKSRILELN   96 (353)
T ss_dssp             -CHHHHTCCSST----TTCCSCCTTHHHHHHHTTC----TTCCCEEEECSTTSSHHHHHHHHHHHHHHHHHHTTSEEEEC
T ss_pred             ccHHHhcCCCCH----HHhhCCHHHHHHHHHHHhc----CCCCEEEEECCCCCCHHHHHHHHHHHhCCCcccccceEEEc
Confidence            367778887776    8999999999888888753    444569999999999999999999987532  335678888


Q ss_pred             ccCCCCHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEE
Q psy200          256 CNSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLV  335 (490)
Q Consensus       256 ~~~~~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI  335 (490)
                      +........+ ......+...........    .. .....+...||||||+|.+....++.|..+++...   ....+|
T Consensus        97 ~~~~~~~~~~-~~~~~~~~~~~~~~~~~~----~~-~~~~~~~~~vliiDE~~~l~~~~~~~Ll~~le~~~---~~~~~i  167 (353)
T 1sxj_D           97 ASDERGISIV-REKVKNFARLTVSKPSKH----DL-ENYPCPPYKIIILDEADSMTADAQSALRRTMETYS---GVTRFC  167 (353)
T ss_dssp             SSSCCCHHHH-TTHHHHHHHSCCCCCCTT----HH-HHSCCCSCEEEEETTGGGSCHHHHHHHHHHHHHTT---TTEEEE
T ss_pred             cccccchHHH-HHHHHHHhhhcccccchh----hc-ccCCCCCceEEEEECCCccCHHHHHHHHHHHHhcC---CCceEE
Confidence            8765433322 211111110000000000    00 11122456799999999998888888888877542   234455


Q ss_pred             EecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHHHH
Q psy200          336 GVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDIT  415 (490)
Q Consensus       336 ~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll  415 (490)
                      .++|.   ...+.+.+.+||.    .+.|.+++.+++..++..++...  ...+++++++.|++   ...||+|.+++++
T Consensus       168 l~~~~---~~~l~~~l~sR~~----~i~~~~~~~~~~~~~l~~~~~~~--~~~i~~~~l~~l~~---~~~G~~r~~~~~l  235 (353)
T 1sxj_D          168 LICNY---VTRIIDPLASQCS----KFRFKALDASNAIDRLRFISEQE--NVKCDDGVLERILD---ISAGDLRRGITLL  235 (353)
T ss_dssp             EEESC---GGGSCHHHHHHSE----EEECCCCCHHHHHHHHHHHHHTT--TCCCCHHHHHHHHH---HTSSCHHHHHHHH
T ss_pred             EEeCc---hhhCcchhhccCc----eEEeCCCCHHHHHHHHHHHHHHh--CCCCCHHHHHHHHH---HcCCCHHHHHHHH
Confidence            55663   4567888999985    79999999999999999988765  35689999999997   5679999999999


Q ss_pred             HHHHHHHHhccccCCcccccCHHHHHHHHHH
Q psy200          416 NHLIDLTYDNVKENGEVTGIGLKEVLGVISS  446 (490)
Q Consensus       416 ~~a~~~a~~~~~~~~~~~~It~~~v~~a~~~  446 (490)
                      +.+...+...+.    ...|+.++|.+++..
T Consensus       236 ~~~~~~~~~~~~----~~~It~~~v~~~~~~  262 (353)
T 1sxj_D          236 QSASKGAQYLGD----GKNITSTQVEELAGV  262 (353)
T ss_dssp             HHTHHHHHHHCS----CCCCCHHHHHHHHTC
T ss_pred             HHHHHhcCCCcc----CccccHHHHHHHhCC
Confidence            998877654431    126999998887653

>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=99.82  E-value=6e-20  Score=181.78  Aligned_cols=211  Identities=17%  Similarity=0.183  Sum_probs=150.9

Q ss_pred             ccCCCCcchHHHhhcCCCCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEec
Q psy200          177 LLFSEDKPKVEEKAKDSCELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINC  256 (490)
Q Consensus       177 ~~~~~~~~~~~~~~l~~~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~  256 (490)
                      ..+|.++|.+...    ++++|+++.++.|..++..   +..++.++++||+|+|||++++++++.+.    ..++++++
T Consensus        13 ~~~~~~k~rP~~~----~~ivg~~~~~~~l~~~l~~---~~~~~~~L~~G~~G~GKT~la~~la~~l~----~~~~~i~~   81 (324)
T 3u61_B           13 EHILEQKYRPSTI----DECILPAFDKETFKSITSK---GKIPHIILHSPSPGTGKTTVAKALCHDVN----ADMMFVNG   81 (324)
T ss_dssp             CSSHHHHSCCCST----TTSCCCHHHHHHHHHHHHT---TCCCSEEEECSSTTSSHHHHHHHHHHHTT----EEEEEEET
T ss_pred             cchHHHhhCCCCH----HHHhCcHHHHHHHHHHHHc---CCCCeEEEeeCcCCCCHHHHHHHHHHHhC----CCEEEEcc
Confidence            3478888988877    9999999999999999873   34556778889999999999999999874    68899987


Q ss_pred             cCCCCHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHhc---CCCeEEEEEecCcccc-ccCHHHHHHhHhCCCCCCCcE
Q psy200          257 NSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFDT---KHKSILLILDEIDALE-SRKQTILYTIFEWPSIPGSKL  332 (490)
Q Consensus       257 ~~~~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~---~~~~~vI~IDEid~l~-~~~~~~L~~l~~~~~~~~~~v  332 (490)
                      ....                     ...+.+.+..+...   .+.+.+|||||+|.+. ...++.|..+++..   ...+
T Consensus        82 ~~~~---------------------~~~i~~~~~~~~~~~~~~~~~~vliiDEi~~l~~~~~~~~L~~~le~~---~~~~  137 (324)
T 3u61_B           82 SDCK---------------------IDFVRGPLTNFASAASFDGRQKVIVIDEFDRSGLAESQRHLRSFMEAY---SSNC  137 (324)
T ss_dssp             TTCC---------------------HHHHHTHHHHHHHBCCCSSCEEEEEEESCCCGGGHHHHHHHHHHHHHH---GGGC
T ss_pred             cccC---------------------HHHHHHHHHHHHhhcccCCCCeEEEEECCcccCcHHHHHHHHHHHHhC---CCCc
Confidence            6542                     22233333333322   2367899999999998 77788888887643   2456


Q ss_pred             EEEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHH-------HHHHhccCCCCCCCH-HHHHHHHHHHHHh
Q psy200          333 VLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEII-------SQKLKQTDKFNMFNA-SALQLLAGKVAAV  404 (490)
Q Consensus       333 ilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il-------~~~l~~~~~~~~~~~-~~i~~i~~~i~~~  404 (490)
                      .+|+++|.   ...+.+.+++||.    .+.|.+++.+++.+++       ...+...  ...+++ ++++.+++   .+
T Consensus       138 ~iI~~~n~---~~~l~~~l~sR~~----~i~~~~~~~~e~~~il~~~~~~l~~~~~~~--~~~~~~~~~~~~l~~---~~  205 (324)
T 3u61_B          138 SIIITANN---IDGIIKPLQSRCR----VITFGQPTDEDKIEMMKQMIRRLTEICKHE--GIAIADMKVVAALVK---KN  205 (324)
T ss_dssp             EEEEEESS---GGGSCTTHHHHSE----EEECCCCCHHHHHHHHHHHHHHHHHHHHHH--TCCBSCHHHHHHHHH---HT
T ss_pred             EEEEEeCC---ccccCHHHHhhCc----EEEeCCCCHHHHHHHHHHHHHHHHHHHHHc--CCCCCcHHHHHHHHH---hC
Confidence            77778884   3467788999995    7999999988854443       3334443  345777 99999987   68


Q ss_pred             hCCHHHHHHHHHHHHHHHHhccccCCcccccCHHHHHHHHH
Q psy200          405 SGDIRKAIDITNHLIDLTYDNVKENGEVTGIGLKEVLGVIS  445 (490)
Q Consensus       405 ~Gd~r~ai~ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~~  445 (490)
                      .||+|.+++.|+.+.    ..       ..|+.+++..++.
T Consensus       206 ~gd~R~a~~~L~~~~----~~-------~~i~~~~v~~~~~  235 (324)
T 3u61_B          206 FPDFRKTIGELDSYS----SK-------GVLDAGILSLVTN  235 (324)
T ss_dssp             CSCTTHHHHHHHHHG----GG-------TCBCC--------
T ss_pred             CCCHHHHHHHHHHHh----cc-------CCCCHHHHHHHhC
Confidence            899999999998876    22       2466666665443

>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=99.82  E-value=1.3e-18  Score=174.42  Aligned_cols=228  Identities=13%  Similarity=0.175  Sum_probs=160.3

Q ss_pred             CCCCChHHHHHHHHHHHHhhh--------ccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHV--------NNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASV  265 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~--------~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l  265 (490)
                      ++++|++..++.|.+++...+        ......+++|+||+|||||++|+++++.+.    ..+++++|.....    
T Consensus        84 ~~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~vLl~GppGtGKT~la~aia~~~~----~~~~~i~~~~l~~----  155 (357)
T 3d8b_A           84 EDIAGVEFAKATIKEIVVWPMLRPDIFTGLRGPPKGILLFGPPGTGKTLIGKCIASQSG----ATFFSISASSLTS----  155 (357)
T ss_dssp             GGSCSCHHHHHHHHHHTHHHHHCTTTSCGGGSCCSEEEEESSTTSSHHHHHHHHHHHTT----CEEEEEEGGGGCC----
T ss_pred             HHhCChHHHHHHHHHHHHHHhhChHhHhhccCCCceEEEECCCCCCHHHHHHHHHHHcC----CeEEEEehHHhhc----
Confidence            679999999999999886432        124578999999999999999999999864    6889999876532    


Q ss_pred             HHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccC-----------HHHHHHhHh-CCCCCCCcEE
Q psy200          266 YETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRK-----------QTILYTIFE-WPSIPGSKLV  333 (490)
Q Consensus       266 ~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~-----------~~~L~~l~~-~~~~~~~~vi  333 (490)
                                .+.+.....+...+..+..  ..+.||||||||.|....           +..+...++ .......+++
T Consensus       156 ----------~~~g~~~~~~~~~~~~a~~--~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~lL~~l~~~~~~~~~~v~  223 (357)
T 3d8b_A          156 ----------KWVGEGEKMVRALFAVARC--QQPAVIFIDEIDSLLSQRGDGEHESSRRIKTEFLVQLDGATTSSEDRIL  223 (357)
T ss_dssp             ----------SSTTHHHHHHHHHHHHHHH--TCSEEEEEETHHHHTBC------CHHHHHHHHHHHHHHC----CCCCEE
T ss_pred             ----------cccchHHHHHHHHHHHHHh--cCCeEEEEeCchhhhccCCCCcchHHHHHHHHHHHHHhcccccCCCCEE
Confidence                      2233333334444443332  457899999999996542           122222232 2223456899


Q ss_pred             EEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhC-CHHHHH
Q psy200          334 LVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSG-DIRKAI  412 (490)
Q Consensus       334 lI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~G-d~r~ai  412 (490)
                      ||++||.   .+.+.+.+.+||.   ..+.+..++.++..+++...+...  ...++++.++.|++   ...| ..+.+.
T Consensus       224 vI~atn~---~~~l~~~l~~Rf~---~~i~i~~p~~~~r~~il~~~~~~~--~~~l~~~~l~~la~---~t~G~s~~dl~  292 (357)
T 3d8b_A          224 VVGATNR---PQEIDEAARRRLV---KRLYIPLPEASARKQIVINLMSKE--QCCLSEEEIEQIVQ---QSDAFSGADMT  292 (357)
T ss_dssp             EEEEESC---GGGBCHHHHTTCC---EEEECCCCCHHHHHHHHHHHHHTS--CBCCCHHHHHHHHH---HTTTCCHHHHH
T ss_pred             EEEecCC---hhhCCHHHHhhCc---eEEEeCCcCHHHHHHHHHHHHhhc--CCCccHHHHHHHHH---HcCCCCHHHHH
Confidence            9999985   3456778888987   478999999999999999988765  34578999999987   4455 334444


Q ss_pred             HHHHHHHHHHHhccccC-------CcccccCHHHHHHHHHHhccCcc
Q psy200          413 DITNHLIDLTYDNVKEN-------GEVTGIGLKEVLGVISSVYCTSQ  452 (490)
Q Consensus       413 ~ll~~a~~~a~~~~~~~-------~~~~~It~~~v~~a~~~~~~~~~  452 (490)
                      .+|+.|+..+.++....       .....|+.+||..|+..+.+...
T Consensus       293 ~l~~~a~~~~ir~l~~~~~~~~~~~~~~~i~~~d~~~al~~~~ps~~  339 (357)
T 3d8b_A          293 QLCREASLGPIRSLQTADIATITPDQVRPIAYIDFENAFRTVRPSVS  339 (357)
T ss_dssp             HHHHHHHTHHHHHCCC----------CCCBCHHHHHHHHHHHGGGCC
T ss_pred             HHHHHHHHHHHHHhhhhhhccccccccCCcCHHHHHHHHHhcCCCCC
Confidence            68888877666532110       11457999999999999886544

>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=99.82  E-value=2.7e-20  Score=195.66  Aligned_cols=231  Identities=15%  Similarity=0.195  Sum_probs=159.5

Q ss_pred             cCCCCcchHHHhhcCCCCCCChHHHHHHHHHHHHhhhcc-------------CCCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          178 LFSEDKPKVEEKAKDSCELPGREVQLEGIRQFLLGHVNN-------------ETSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       178 ~~~~~~~~~~~~~l~~~~lvgre~~~~~l~~~L~~~~~~-------------~~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      ..|.++|.+...    ++++|++++++.|..||..+...             +..+.++|+||+|||||++|++++++++
T Consensus        27 ~lW~ekyrP~~~----~dliG~~~~~~~L~~~l~~~~~~~~~~~~~~g~~~~~~~~~lLL~GppGtGKTtla~~la~~l~  102 (516)
T 1sxj_A           27 KLWTVKYAPTNL----QQVCGNKGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAAHLVAQELG  102 (516)
T ss_dssp             CCHHHHTCCSSG----GGCCSCHHHHHHHHHHHHTHHHHHHTTTCCCCTTSTTSCSEEEEECSTTSSHHHHHHHHHHHTT
T ss_pred             CCcccccCCCCH----HHhcCCHHHHHHHHHHHHHhHhhchhhccccCccCCCCCcEEEEECCCCCCHHHHHHHHHHHcC
Confidence            478889998877    89999999999999999875321             1457999999999999999999999974


Q ss_pred             hcCCceEEEEeccCCCCHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCH---HHHHHh
Q psy200          245 IKDAFKTIYINCNSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQ---TILYTI  321 (490)
Q Consensus       245 ~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~---~~L~~l  321 (490)
                          +.+++++|........+ ...+..+...   .....++......+...+++.||||||+|.+....+   ..|..+
T Consensus       103 ----~~~i~in~s~~~~~~~~-~~~i~~~~~~---~~~~~~~~~~~~~~~~~~~~~vliIDEid~l~~~~~~~l~~L~~~  174 (516)
T 1sxj_A          103 ----YDILEQNASDVRSKTLL-NAGVKNALDN---MSVVGYFKHNEEAQNLNGKHFVIIMDEVDGMSGGDRGGVGQLAQF  174 (516)
T ss_dssp             ----CEEEEECTTSCCCHHHH-HHTGGGGTTB---CCSTTTTTC----CCSSTTSEEEEECSGGGCCTTSTTHHHHHHHH
T ss_pred             ----CCEEEEeCCCcchHHHH-HHHHHHHhcc---ccHHHHHhhhhhhhhccCCCeEEEEECCCccchhhHHHHHHHHHH
Confidence                78999999988664432 2222111110   000011110101112235678999999999987765   455555


Q ss_pred             HhCCCCCCCcEEEEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHH
Q psy200          322 FEWPSIPGSKLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKV  401 (490)
Q Consensus       322 ~~~~~~~~~~vilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i  401 (490)
                      ++.   ....+++|+.+...    ..++.+.+|+.    .+.|.+++.+++.++|...+...+  ..+++++++.|++  
T Consensus       175 l~~---~~~~iIli~~~~~~----~~l~~l~~r~~----~i~f~~~~~~~~~~~L~~i~~~~~--~~i~~~~l~~la~--  239 (516)
T 1sxj_A          175 CRK---TSTPLILICNERNL----PKMRPFDRVCL----DIQFRRPDANSIKSRLMTIAIREK--FKLDPNVIDRLIQ--  239 (516)
T ss_dssp             HHH---CSSCEEEEESCTTS----STTGGGTTTSE----EEECCCCCHHHHHHHHHHHHHHHT--CCCCTTHHHHHHH--
T ss_pred             HHh---cCCCEEEEEcCCCC----ccchhhHhceE----EEEeCCCCHHHHHHHHHHHHHHcC--CCCCHHHHHHHHH--
Confidence            543   34556666654321    12344666653    899999999999999999887763  4578899999987  


Q ss_pred             HHhhCCHHHHHHHHHHHHHHHHhccccCCcccccCHHHHHHHHHH
Q psy200          402 AAVSGDIRKAIDITNHLIDLTYDNVKENGEVTGIGLKEVLGVISS  446 (490)
Q Consensus       402 ~~~~Gd~r~ai~ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~~~  446 (490)
                       ...||+|.++++++.+..     +     ...|+.+++..++..
T Consensus       240 -~s~GdiR~~i~~L~~~~~-----~-----~~~It~~~v~~~~~~  273 (516)
T 1sxj_A          240 -TTRGDIRQVINLLSTIST-----T-----TKTINHENINEISKA  273 (516)
T ss_dssp             -HTTTCHHHHHHHHTHHHH-----H-----SSCCCTTHHHHHHHH
T ss_pred             -HcCCcHHHHHHHHHHHHh-----c-----CCCCchHHHHHHHHh
Confidence             678999999999876642     2     235777777666553

>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=99.82  E-value=3.6e-18  Score=169.70  Aligned_cols=237  Identities=18%  Similarity=0.237  Sum_probs=173.7

Q ss_pred             CCCCChHHHHHHHHHHHHhhhc-cCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVN-NETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNE  272 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~-~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~  272 (490)
                      ++++|++..++.|...+..... +....+++|+||+|+|||||++.++..++    ..+...++.....           
T Consensus        25 ~~~~g~~~~~~~l~~~i~~~~~~~~~~~~~ll~Gp~G~GKTTLa~~ia~~l~----~~~~~~sg~~~~~-----------   89 (334)
T 1in4_A           25 DEFIGQENVKKKLSLALEAAKMRGEVLDHVLLAGPPGLGKTTLAHIIASELQ----TNIHVTSGPVLVK-----------   89 (334)
T ss_dssp             GGCCSCHHHHHHHHHHHHHHHHHTCCCCCEEEESSTTSSHHHHHHHHHHHHT----CCEEEEETTTCCS-----------
T ss_pred             HHccCcHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCcHHHHHHHHHHHhC----CCEEEEechHhcC-----------
Confidence            7889999999888888765322 23457899999999999999999999985    2333444332211           


Q ss_pred             hcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCHHHHHHhHhCCCC---------------CCCcEEEEEe
Q psy200          273 LKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPSI---------------PGSKLVLVGV  337 (490)
Q Consensus       273 l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~---------------~~~~vilI~~  337 (490)
                               ..++...+.    ...+..|+||||++.+....++.|+..++....               .-..+.++++
T Consensus        90 ---------~~~l~~~~~----~~~~~~v~~iDE~~~l~~~~~e~L~~~~~~~~~~i~~~~~~~~~~i~~~l~~~~li~a  156 (334)
T 1in4_A           90 ---------QGDMAAILT----SLERGDVLFIDEIHRLNKAVEELLYSAIEDFQIDIMIGKGPSAKSIRIDIQPFTLVGA  156 (334)
T ss_dssp             ---------HHHHHHHHH----HCCTTCEEEEETGGGCCHHHHHHHHHHHHTSCCCC---------------CCCEEEEE
T ss_pred             ---------HHHHHHHHH----HccCCCEEEEcchhhcCHHHHHHHHHHHHhcccceeeccCcccccccccCCCeEEEEe
Confidence                     122222211    112345999999999987666777665543211               0124667777


Q ss_pred             cCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHHHHHH
Q psy200          338 ANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITNH  417 (490)
Q Consensus       338 tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll~~  417 (490)
                      ++.   ...+.+.+++||++   .+.|++++.+++.+++.+.+...  ...++++++..|++   ...|++|.++++|++
T Consensus       157 t~~---~~~Ls~~l~sR~~l---~~~Ld~~~~~~l~~iL~~~~~~~--~~~~~~~~~~~ia~---~~~G~~R~a~~ll~~  225 (334)
T 1in4_A          157 TTR---SGLLSSPLRSRFGI---ILELDFYTVKELKEIIKRAASLM--DVEIEDAAAEMIAK---RSRGTPRIAIRLTKR  225 (334)
T ss_dssp             ESC---GGGSCHHHHTTCSE---EEECCCCCHHHHHHHHHHHHHHT--TCCBCHHHHHHHHH---TSTTCHHHHHHHHHH
T ss_pred             cCC---cccCCHHHHHhcCc---eeeCCCCCHHHHHHHHHHHHHHc--CCCcCHHHHHHHHH---hcCCChHHHHHHHHH
Confidence            764   45677889999974   68999999999999999887765  35689999999987   678999999999999


Q ss_pred             HHHHHHhccccCCcccccCHHHHHHHHHHhccCccccccccccCCCChHhHHHHHHHHHHhcCCCC
Q psy200          418 LIDLTYDNVKENGEVTGIGLKEVLGVISSVYCTSQSLHCSKDEDSFPLQQKLALASLLLLKSRPNV  483 (490)
Q Consensus       418 a~~~a~~~~~~~~~~~~It~~~v~~a~~~~~~~~~~~~~~~~l~~L~~~qk~vL~al~~~~~~~~~  483 (490)
                      +...|...+     ...|+.+++.+++..+..+         -.+++.+.+.+|.+++..++++.+
T Consensus       226 ~~~~a~~~~-----~~~It~~~v~~al~~~~~~---------~~~l~~~~~~~l~~~~~~~~~~~~  277 (334)
T 1in4_A          226 VRDMLTVVK-----ADRINTDIVLKTMEVLNID---------DEGLDEFDRKILKTIIEIYRGGPV  277 (334)
T ss_dssp             HHHHHHHHT-----CSSBCHHHHHHHHHHHTCC---------TTCCCHHHHHHHHHHHHHSTTCCB
T ss_pred             HHHHHHHcC-----CCCcCHHHHHHHHHHhCCC---------cCCCCHHHHHHHHHHHHHhCCCcc
Confidence            998888776     5689999999999986422         147888999999999988765543

>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=99.82  E-value=4.3e-19  Score=169.88  Aligned_cols=221  Identities=15%  Similarity=0.127  Sum_probs=145.7

Q ss_pred             CCCCChHHHHHHHHHHHHhhhc--------cCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVN--------NETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASV  265 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~--------~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l  265 (490)
                      ++++|.++.++.|.+++.....        ...+++++|+||||||||++|+++++++.    ..+++++|.....    
T Consensus         6 ~~i~G~~~~~~~l~~~~~~~~~~~~~~~~g~~~~~~vll~G~~GtGKT~la~~la~~~~----~~~~~~~~~~~~~----   77 (262)
T 2qz4_A            6 KDVAGMHEAKLEVREFVDYLKSPERFLQLGAKVPKGALLLGPPGCGKTLLAKAVATEAQ----VPFLAMAGAEFVE----   77 (262)
T ss_dssp             TSSCSCHHHHHHHHHHHHHHHCCC------CCCCCEEEEESCTTSSHHHHHHHHHHHHT----CCEEEEETTTTSS----
T ss_pred             HHhCCHHHHHHHHHHHHHHHHCHHHHHHcCCCCCceEEEECCCCCCHHHHHHHHHHHhC----CCEEEechHHHHh----
Confidence            6799999999999887754211        13567899999999999999999999875    6788898877532    


Q ss_pred             HHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCcccccc------------CHHHHHHhHhCC--CCCCCc
Q psy200          266 YETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESR------------KQTILYTIFEWP--SIPGSK  331 (490)
Q Consensus       266 ~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~------------~~~~L~~l~~~~--~~~~~~  331 (490)
                                .+.+.....+...+..+..  ..+.||||||+|.+...            .+..+..++...  ......
T Consensus        78 ----------~~~~~~~~~~~~~~~~a~~--~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~l~~ll~~~~~~~~~~~  145 (262)
T 2qz4_A           78 ----------VIGGLGAARVRSLFKEARA--RAPCIVYIDEIDAVGKKRSTTMSGFSNTEEEQTLNQLLVEMDGMGTTDH  145 (262)
T ss_dssp             ----------SSTTHHHHHHHHHHHHHHH--TCSEEEEEECC-------------------CHHHHHHHHHHHTCCTTCC
T ss_pred             ----------hccChhHHHHHHHHHHHHh--cCCeEEEEeCcchhhccccccccCccchhHHHHHHHHHHHhhCcCCCCC
Confidence                      2223334444455555443  34789999999999532            233444444321  123457


Q ss_pred             EEEEEecCCCChhHhhhHHhhh--ccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHH-HHHHHHHHHHHhhCC-
Q psy200          332 LVLVGVANALDLTDRMLPRLQA--NVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNAS-ALQLLAGKVAAVSGD-  407 (490)
Q Consensus       332 vilI~~tn~~~~~~~l~~~l~~--R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~-~i~~i~~~i~~~~Gd-  407 (490)
                      +++|+++|..   +.+++.+.+  ||.   ..+.|.+++.++..+++.+++...+  ...+.+ .++.+++   ...|. 
T Consensus       146 ~~vi~~tn~~---~~ld~~l~~~~R~~---~~i~i~~p~~~~r~~il~~~~~~~~--~~~~~~~~~~~l~~---~~~g~~  214 (262)
T 2qz4_A          146 VIVLASTNRA---DILDGALMRPGRLD---RHVFIDLPTLQERREIFEQHLKSLK--LTQSSTFYSQRLAE---LTPGFS  214 (262)
T ss_dssp             EEEEEEESCG---GGGGSGGGSTTSCC---EEEECCSCCHHHHHHHHHHHHHHTT--CCBTHHHHHHHHHH---TCTTCC
T ss_pred             EEEEecCCCh---hhcCHHHhcCCcCC---eEEEeCCcCHHHHHHHHHHHHHhCC--CCcchhhHHHHHHH---HCCCCC
Confidence            8999999853   445667766  786   4799999999999999999988762  333443 3456665   34443 


Q ss_pred             HHHHHHHHHHHHHHHHhccccCCcccccCHHHHHHHHHHhccC
Q psy200          408 IRKAIDITNHLIDLTYDNVKENGEVTGIGLKEVLGVISSVYCT  450 (490)
Q Consensus       408 ~r~ai~ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~~~~~~~  450 (490)
                      .+.+.++++.|...|..++     ...|+.+++..|+.++...
T Consensus       215 ~~~l~~l~~~a~~~a~~~~-----~~~i~~~d~~~a~~~~~~~  252 (262)
T 2qz4_A          215 GADIANICNEAALHAAREG-----HTSVHTLNFEYAVERVLAG  252 (262)
T ss_dssp             HHHHHHHHHHHHTC-------------CCBCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHcC-----CCCCCHHHHHHHHHHhccC
Confidence            3466678999988888776     5689999999999987644

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster}

Probab=99.82  E-value=2.6e-18  Score=167.85  Aligned_cols=226  Identities=14%  Similarity=0.209  Sum_probs=159.3

Q ss_pred             CCCCChHHHHHHHHHHHHhhhc--------cCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVN--------NETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASV  265 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~--------~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l  265 (490)
                      ++++|++..++.|.+++.....        ...+++++|+||||||||++|+++++.+.    ..++.++|.....    
T Consensus        21 ~~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~vll~Gp~GtGKT~la~~la~~~~----~~~~~i~~~~l~~----   92 (297)
T 3b9p_A           21 TDIAGQDVAKQALQEMVILPSVRPELFTGLRAPAKGLLLFGPPGNGKTLLARAVATECS----ATFLNISAASLTS----   92 (297)
T ss_dssp             GGSCCCHHHHHHHHHHTHHHHHCGGGSCGGGCCCSEEEEESSSSSCHHHHHHHHHHHTT----CEEEEEESTTTSS----
T ss_pred             HHhCChHHHHHHHHHHHHhhhhCHHHHhcCCCCCCeEEEECcCCCCHHHHHHHHHHHhC----CCeEEeeHHHHhh----
Confidence            7899999999999988754321        23568999999999999999999999874    6788899876532    


Q ss_pred             HHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCH-----------HHHHHhHhCC-C-CCCCcE
Q psy200          266 YETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQ-----------TILYTIFEWP-S-IPGSKL  332 (490)
Q Consensus       266 ~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~-----------~~L~~l~~~~-~-~~~~~v  332 (490)
                                .+.+.........+..+..  ..+.+|||||+|.+....+           ..|...++.. . ..+.++
T Consensus        93 ----------~~~~~~~~~~~~~~~~~~~--~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~v  160 (297)
T 3b9p_A           93 ----------KYVGDGEKLVRALFAVARH--MQPSIIFIDEVDSLLSERSSSEHEASRRLKTEFLVEFDGLPGNPDGDRI  160 (297)
T ss_dssp             ----------SSCSCHHHHHHHHHHHHHH--TCSEEEEEETGGGTSBCC-----CCSHHHHHHHHHHHHHCC------CE
T ss_pred             ----------cccchHHHHHHHHHHHHHH--cCCcEEEeccHHHhccccccCcchHHHHHHHHHHHHHhcccccCCCCcE
Confidence                      3333444444444444333  4578999999999965431           1233333322 1 123578


Q ss_pred             EEEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHH
Q psy200          333 VLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAI  412 (490)
Q Consensus       333 ilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai  412 (490)
                      ++|++||..   +.+++.+.+||.   ..+.+..++.++...++..++...  ...+++++++.+++   .+.|..+..+
T Consensus       161 ~vi~~tn~~---~~l~~~l~~R~~---~~i~~~~p~~~~r~~il~~~~~~~--~~~~~~~~~~~la~---~~~g~~~~~l  229 (297)
T 3b9p_A          161 VVLAATNRP---QELDEAALRRFT---KRVYVSLPDEQTRELLLNRLLQKQ--GSPLDTEALRRLAK---ITDGYSGSDL  229 (297)
T ss_dssp             EEEEEESCG---GGBCHHHHHHCC---EEEECCCCCHHHHHHHHHHHHGGG--SCCSCHHHHHHHHH---HTTTCCHHHH
T ss_pred             EEEeecCCh---hhCCHHHHhhCC---eEEEeCCcCHHHHHHHHHHHHHhc--CCCCCHHHHHHHHH---HcCCCCHHHH
Confidence            999999853   456777888887   479999999999999999988775  34578899999987   5567766555


Q ss_pred             -HHHHHHHHHHHhccccC-------CcccccCHHHHHHHHHHhccC
Q psy200          413 -DITNHLIDLTYDNVKEN-------GEVTGIGLKEVLGVISSVYCT  450 (490)
Q Consensus       413 -~ll~~a~~~a~~~~~~~-------~~~~~It~~~v~~a~~~~~~~  450 (490)
                       .+|+.|+..+.++....       .....|+.+||..|+..+.++
T Consensus       230 ~~l~~~a~~~a~r~~~~~~~~~~~~~~~~~i~~~d~~~a~~~~~~s  275 (297)
T 3b9p_A          230 TALAKDAALEPIRELNVEQVKCLDISAMRAITEQDFHSSLKRIRRS  275 (297)
T ss_dssp             HHHHHHHTTHHHHTCC--------CCCCCCCCHHHHHHHTTSCCCS
T ss_pred             HHHHHHHHHHHHHHHhhhhcccccccccCCcCHHHHHHHHHHcCCC
Confidence             68888887777654211       113579999999999876654

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A*

Probab=99.81  E-value=5.8e-19  Score=173.32  Aligned_cols=221  Identities=15%  Similarity=0.134  Sum_probs=154.7

Q ss_pred             CCCCChHHHHHHHHHHHHhhhc-----------cCCCCeEEEECCCCCcHHHHHHHHHHHhhhcC---CceEEEEeccCC
Q psy200          194 CELPGREVQLEGIRQFLLGHVN-----------NETSGSMYISGPPGTGKSASLNLLVSRAEIKD---AFKTIYINCNSV  259 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~-----------~~~~~~ill~GppGtGKTtla~~l~~~l~~~~---~~~~~~v~~~~~  259 (490)
                      .+++|+++.++.|.+++.....           .....+++|+||||||||++|+++++.+....   ...++++++..+
T Consensus        31 ~~i~G~~~~~~~l~~~~~~~~~~~~~~~~g~~~~~~~~~vll~G~~GtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~l  110 (309)
T 3syl_A           31 RELIGLKPVKDRIRETAALLLVERARQKLGLAHETPTLHMSFTGNPGTGKTTVALKMAGLLHRLGYVRKGHLVSVTRDDL  110 (309)
T ss_dssp             HHSSSCHHHHHHHHHHHHHHHHHHHHHHHTCCSSCCCCEEEEEECTTSSHHHHHHHHHHHHHHTTSSSSCCEEEECGGGT
T ss_pred             HHccChHHHHHHHHHHHHHHHhHHHHHHcCCCCCCCCceEEEECCCCCCHHHHHHHHHHHHHhcCCcCCCcEEEEcHHHh
Confidence            4699999999999988765321           34566899999999999999999999886322   236888887655


Q ss_pred             CCHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCcccccc---------CHHHHHHhHhCCCCCCC
Q psy200          260 RNAASVYETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESR---------KQTILYTIFEWPSIPGS  330 (490)
Q Consensus       260 ~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~---------~~~~L~~l~~~~~~~~~  330 (490)
                      ..              ...+.........|..+     .+.||||||+|.+...         .+..|+.+++.   ...
T Consensus       111 ~~--------------~~~g~~~~~~~~~~~~~-----~~~vl~iDEid~l~~~~~~~~~~~~~~~~Ll~~l~~---~~~  168 (309)
T 3syl_A          111 VG--------------QYIGHTAPKTKEVLKRA-----MGGVLFIDEAYYLYRPDNERDYGQEAIEILLQVMEN---NRD  168 (309)
T ss_dssp             CC--------------SSTTCHHHHHHHHHHHH-----TTSEEEEETGGGSCCCC---CCTHHHHHHHHHHHHH---CTT
T ss_pred             hh--------------hcccccHHHHHHHHHhc-----CCCEEEEEChhhhccCCCcccccHHHHHHHHHHHhc---CCC
Confidence            22              33344444444444433     2349999999998532         23455555553   345


Q ss_pred             cEEEEEecCCC--ChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHH-----H
Q psy200          331 KLVLVGVANAL--DLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVA-----A  403 (490)
Q Consensus       331 ~vilI~~tn~~--~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~-----~  403 (490)
                      ++++|+++|..  +....+.+.+++||.   ..+.|++++.+++..++.+++...  ...+++++++.+++.+.     .
T Consensus       169 ~~~~i~~~~~~~~~~~~~~~~~l~~R~~---~~i~~~~~~~~~~~~il~~~l~~~--~~~~~~~~~~~l~~~~~~~~~~~  243 (309)
T 3syl_A          169 DLVVILAGYADRMENFFQSNPGFRSRIA---HHIEFPDYSDEELFEIAGHMLDDQ--NYQMTPEAETALRAYIGLRRNQP  243 (309)
T ss_dssp             TCEEEEEECHHHHHHHHHHSTTHHHHEE---EEEEECCCCHHHHHHHHHHHHHHT--TCEECHHHHHHHHHHHHHHTTSS
T ss_pred             CEEEEEeCChHHHHHHHhhCHHHHHhCC---eEEEcCCcCHHHHHHHHHHHHHHc--CCCCCHHHHHHHHHHHHHhccCC
Confidence            67788888743  223344689999996   489999999999999999999876  45689999999998554     5


Q ss_pred             hhCCHHHHHHHHHHHHHHHHhccccCCcccccCHHHHHH
Q psy200          404 VSGDIRKAIDITNHLIDLTYDNVKENGEVTGIGLKEVLG  442 (490)
Q Consensus       404 ~~Gd~r~ai~ll~~a~~~a~~~~~~~~~~~~It~~~v~~  442 (490)
                      +.||+|.+.++|++++..+..+.... ....++.+++..
T Consensus       244 ~~gn~r~l~~~l~~a~~~~~~r~~~~-~~~~~~~~~l~~  281 (309)
T 3syl_A          244 HFANARSIRNALDRARLRQANRLFTA-SSGPLDARALST  281 (309)
T ss_dssp             SCCHHHHHHHHHHHHHHHHHHHHHHC----CEEHHHHHE
T ss_pred             CCCcHHHHHHHHHHHHHHHHHHHHhc-cCCCCCHHHHhh
Confidence            67999999999999987554331100 023455555543

>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=99.81  E-value=4.4e-19  Score=175.00  Aligned_cols=216  Identities=19%  Similarity=0.252  Sum_probs=159.1

Q ss_pred             CCCCcchHHHhhcCCCCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhc-CCceEEEEecc
Q psy200          179 FSEDKPKVEEKAKDSCELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIK-DAFKTIYINCN  257 (490)
Q Consensus       179 ~~~~~~~~~~~~l~~~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~-~~~~~~~v~~~  257 (490)
                      +|.++|.+...    ++++|+++.++.|..++..    +...+++|+||+|+|||++++.+++.+... ..+.++++++.
T Consensus        10 ~~~~~~~p~~~----~~~~g~~~~~~~l~~~l~~----~~~~~~ll~G~~G~GKt~la~~l~~~l~~~~~~~~~~~~~~~   81 (323)
T 1sxj_B           10 PWVEKYRPQVL----SDIVGNKETIDRLQQIAKD----GNMPHMIISGMPGIGKTTSVHCLAHELLGRSYADGVLELNAS   81 (323)
T ss_dssp             CHHHHTCCSSG----GGCCSCTHHHHHHHHHHHS----CCCCCEEEECSTTSSHHHHHHHHHHHHHGGGHHHHEEEECTT
T ss_pred             cHHHhcCCCCH----HHHHCCHHHHHHHHHHHHc----CCCCeEEEECcCCCCHHHHHHHHHHHhcCCcccCCEEEecCc
Confidence            56667777666    7899999999999998864    444459999999999999999999987421 12457888876


Q ss_pred             CCCCHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHh----c-CCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcE
Q psy200          258 SVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFD----T-KHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKL  332 (490)
Q Consensus       258 ~~~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~----~-~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~v  332 (490)
                      ....                    ...+.+.+.....    . .+++.||||||+|.+....++.|..+++..   ...+
T Consensus        82 ~~~~--------------------~~~i~~~~~~~~~~~~~~~~~~~~viiiDe~~~l~~~~~~~L~~~le~~---~~~~  138 (323)
T 1sxj_B           82 DDRG--------------------IDVVRNQIKHFAQKKLHLPPGKHKIVILDEADSMTAGAQQALRRTMELY---SNST  138 (323)
T ss_dssp             SCCS--------------------HHHHHTHHHHHHHBCCCCCTTCCEEEEEESGGGSCHHHHHTTHHHHHHT---TTTE
T ss_pred             cccC--------------------hHHHHHHHHHHHhccccCCCCCceEEEEECcccCCHHHHHHHHHHHhcc---CCCc
Confidence            5422                    2233333333221    0 245789999999999877777777777643   3356


Q ss_pred             EEEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHH
Q psy200          333 VLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAI  412 (490)
Q Consensus       333 ilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai  412 (490)
                      ++|++++.   ...+.+.+.+||.    .+.|.+++.+++.+++..++...  ...+++++++.+++   ...||+|.++
T Consensus       139 ~~il~~~~---~~~l~~~l~sr~~----~i~~~~~~~~~~~~~l~~~~~~~--~~~~~~~~~~~l~~---~~~G~~r~a~  206 (323)
T 1sxj_B          139 RFAFACNQ---SNKIIEPLQSQCA----ILRYSKLSDEDVLKRLLQIIKLE--DVKYTNDGLEAIIF---TAEGDMRQAI  206 (323)
T ss_dssp             EEEEEESC---GGGSCHHHHTTSE----EEECCCCCHHHHHHHHHHHHHHH--TCCBCHHHHHHHHH---HHTTCHHHHH
T ss_pred             eEEEEeCC---hhhchhHHHhhce----EEeecCCCHHHHHHHHHHHHHHc--CCCCCHHHHHHHHH---HcCCCHHHHH
Confidence            66666763   4567788999985    89999999999999999988765  34588999999987   6689999999


Q ss_pred             HHHHHHHHHHHhccccCCcccccCHHHHHHHHHHh
Q psy200          413 DITNHLIDLTYDNVKENGEVTGIGLKEVLGVISSV  447 (490)
Q Consensus       413 ~ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~~~~  447 (490)
                      ++++.+...   .+       .|+.++|.+++...
T Consensus       207 ~~l~~~~~~---~~-------~i~~~~v~~~~~~~  231 (323)
T 1sxj_B          207 NNLQSTVAG---HG-------LVNADNVFKIVDSP  231 (323)
T ss_dssp             HHHHHHHHH---HS-------SBCHHHHHHHHTSC
T ss_pred             HHHHHHHhc---CC-------CcCHHHHHHHHCCC
Confidence            999877632   12       58888887776543

>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=99.81  E-value=9.8e-19  Score=171.52  Aligned_cols=236  Identities=16%  Similarity=0.208  Sum_probs=158.4

Q ss_pred             CCCCChHHHHHHHHHHHHhhhc----------cCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVN----------NETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAA  263 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~----------~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~  263 (490)
                      +.++|+++.++.|...+...+.          ...+.+++|+||||||||++|+++++.+.    ..+++++|...... 
T Consensus        15 ~~i~G~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKT~la~~la~~l~----~~~~~i~~~~~~~~-   89 (310)
T 1ofh_A           15 QHIIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAKLAN----APFIKVEATKFTEV-   89 (310)
T ss_dssp             TTCCSCHHHHHHHHHHHHHHHHTTSSCHHHHHHCCCCCEEEECCTTSSHHHHHHHHHHHHT----CCEEEEEGGGGSSC-
T ss_pred             hhcCChHHHHHHHHHHHHHHHhhhhhcccccccCCCceEEEECCCCCCHHHHHHHHHHHhC----CCEEEEcchhcccC-
Confidence            7899999999999988865211          23567999999999999999999999874    57888998876431 


Q ss_pred             HHHHHHHHHhcCCCCCCcH-HHHHHHHHH---HHhcCCCeEEEEEecCccccccC------------HHHHHHhHhCCC-
Q psy200          264 SVYETIVNELKLKPGGKSE-RHQLGAILK---YFDTKHKSILLILDEIDALESRK------------QTILYTIFEWPS-  326 (490)
Q Consensus       264 ~l~~~i~~~l~~~~~~~s~-~~~~~~l~~---~l~~~~~~~vI~IDEid~l~~~~------------~~~L~~l~~~~~-  326 (490)
                                  .+.+... ..+.+.+..   .+...+.+.||||||+|.+....            ++.|+.+++... 
T Consensus        90 ------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vl~iDEi~~l~~~~~~~~~~~~~~~~~~~Ll~~le~~~~  157 (310)
T 1ofh_A           90 ------------GYVGKEVDSIIRDLTDSAGGAIDAVEQNGIVFIDEIDKICKKGEYSGADVSREGVQRDLLPLVEGSTV  157 (310)
T ss_dssp             ------------CSGGGSTTHHHHHHHHTTTTCHHHHHHHCEEEEECGGGGSCCSSCCSSHHHHHHHHHHHHHHHHCCEE
T ss_pred             ------------CccCccHHHHHHHHHHHhhHHHhhccCCCEEEEEChhhcCccccccccchhHHHHHHHHHHHhcCCeE
Confidence                        0001111 111111110   01110124599999999998765            677777776321 


Q ss_pred             ------CCCCcEEEEEecCC-CChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHH-----------HHhccCCCCC
Q psy200          327 ------IPGSKLVLVGVANA-LDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQ-----------KLKQTDKFNM  388 (490)
Q Consensus       327 ------~~~~~vilI~~tn~-~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~-----------~l~~~~~~~~  388 (490)
                            .....+++|++++. ......+.+.+.+||.   ..+.|++++.+++..++.+           .+...+....
T Consensus       158 ~~~~~~~~~~~~~~i~~~~~~~~~~~~l~~~l~~R~~---~~i~~~~~~~~~~~~il~~~~~~~~~~~~~~~~~~~~~~~  234 (310)
T 1ofh_A          158 STKHGMVKTDHILFIASGAFQVARPSDLIPELQGRLP---IRVELTALSAADFERILTEPHASLTEQYKALMATEGVNIA  234 (310)
T ss_dssp             EETTEEEECTTCEEEEEECCSSSCGGGSCHHHHHTCC---EEEECCCCCHHHHHHHHHSSTTCHHHHHHHHHHHTTCEEE
T ss_pred             ecccccccCCcEEEEEcCCcccCCcccCCHHHHhhCC---ceEEcCCcCHHHHHHHHHhhHHHHHHHHHHHHHhcCCeec
Confidence                  02346788887642 1234567889999997   3799999999999999983           1222222346


Q ss_pred             CCHHHHHHHHHHHHHh-----hCCHHHHHHHHHHHHHHHHhcccc-CCcccccCHHHHHHHHHHhcc
Q psy200          389 FNASALQLLAGKVAAV-----SGDIRKAIDITNHLIDLTYDNVKE-NGEVTGIGLKEVLGVISSVYC  449 (490)
Q Consensus       389 ~~~~~i~~i~~~i~~~-----~Gd~r~ai~ll~~a~~~a~~~~~~-~~~~~~It~~~v~~a~~~~~~  449 (490)
                      +++++++.|++.....     .||+|.+.++|++++..+...... ......|+.+++..++.....
T Consensus       235 ~~~~a~~~l~~~~~~~~~~~~~g~~R~l~~~l~~~~~~~~~~~~~~~~~~~~i~~~~v~~~l~~~~~  301 (310)
T 1ofh_A          235 FTTDAVKKIAEAAFRVNEKTENIGARRLHTVMERLMDKISFSASDMNGQTVNIDAAYVADALGEVVE  301 (310)
T ss_dssp             ECHHHHHHHHHHHHHHHHHSCCCTTHHHHHHHHHHSHHHHHHGGGCTTCEEEECHHHHHHHTCSSSS
T ss_pred             cCHHHHHHHHHHhhhhcccccccCcHHHHHHHHHHHHhhhcCCccccCCEEEEeeHHHHHHHHhhhh
Confidence            8999999999843322     599999999999987554322210 011225999999999987643

>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=99.80  E-value=1e-18  Score=164.31  Aligned_cols=233  Identities=16%  Similarity=0.210  Sum_probs=151.3

Q ss_pred             CCCCcchHHHhhcCCCCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccC
Q psy200          179 FSEDKPKVEEKAKDSCELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNS  258 (490)
Q Consensus       179 ~~~~~~~~~~~~l~~~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~  258 (490)
                      .|.+.|.+...    ++++|++++++.|..++..   ...++.++|+||+|+|||++++.+++.+....  .+....|..
T Consensus        12 ~~~~~~~p~~~----~~~~g~~~~~~~l~~~l~~---~~~~~~~ll~G~~G~GKT~l~~~~~~~~~~~~--~~~~~~~~~   82 (250)
T 1njg_A           12 VLARKWRPQTF----ADVVGQEHVLTALANGLSL---GRIHHAYLFSGTRGVGKTSIARLLAKGLNCET--GITATPCGV   82 (250)
T ss_dssp             CHHHHTCCCSG----GGCCSCHHHHHHHHHHHHH---TCCCSEEEEECSTTSCHHHHHHHHHHHHHCTT--CSCSSCCSC
T ss_pred             HHhhccCCccH----HHHhCcHHHHHHHHHHHHc---CCCCeEEEEECCCCCCHHHHHHHHHHHhcCCC--CCCCCCCcc
Confidence            34445555444    7899999999999999874   33456899999999999999999999875221  111112221


Q ss_pred             CCCHHHHHHHHHHH-hcCCCCC-CcHHHHHHHHHHHHh--cCCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEE
Q psy200          259 VRNAASVYETIVNE-LKLKPGG-KSERHQLGAILKYFD--TKHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVL  334 (490)
Q Consensus       259 ~~~~~~l~~~i~~~-l~~~~~~-~s~~~~~~~l~~~l~--~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vil  334 (490)
                      ......+....... +...... .....+...+.....  ..+++.+|||||+|.+....++.|..+++..   ...+++
T Consensus        83 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vlviDe~~~l~~~~~~~l~~~l~~~---~~~~~~  159 (250)
T 1njg_A           83 CDNCREIEQGRFVDLIEIDAASRTKVEDTRDLLDNVQYAPARGRFKVYLIDEVHMLSRHSFNALLKTLEEP---PEHVKF  159 (250)
T ss_dssp             SHHHHHHHTTCCSSEEEEETTCGGGHHHHHHHHHSCCCSCSSSSSEEEEEETGGGSCHHHHHHHHHHHHSC---CTTEEE
T ss_pred             cHHHHHHhccCCcceEEecCcccccHHHHHHHHHHhhhchhcCCceEEEEECcccccHHHHHHHHHHHhcC---CCceEE
Confidence            11100000000000 0000000 112222222221111  1245789999999999876677777776632   346777


Q ss_pred             EEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHHH
Q psy200          335 VGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDI  414 (490)
Q Consensus       335 I~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~l  414 (490)
                      |++++.   ...+.+.+.+|+    ..+.|.+++.+++.+++..++...  ...+++++++.+++   .+.|+++.++++
T Consensus       160 i~~t~~---~~~~~~~l~~r~----~~i~l~~l~~~e~~~~l~~~~~~~--~~~~~~~~~~~l~~---~~~G~~~~~~~~  227 (250)
T 1njg_A          160 LLATTD---PQKLPVTILSRC----LQFHLKALDVEQIRHQLEHILNEE--HIAHEPRALQLLAR---AAEGSLRDALSL  227 (250)
T ss_dssp             EEEESC---GGGSCHHHHTTS----EEEECCCCCHHHHHHHHHHHHHHT--TCCBCHHHHHHHHH---HHTTCHHHHHHH
T ss_pred             EEEeCC---hHhCCHHHHHHh----hhccCCCCCHHHHHHHHHHHHHhc--CCCCCHHHHHHHHH---HcCCCHHHHHHH
Confidence            777764   344566777886    389999999999999999998765  35678999999887   668999999999


Q ss_pred             HHHHHHHHHhccccCCcccccCHHHHHHHH
Q psy200          415 TNHLIDLTYDNVKENGEVTGIGLKEVLGVI  444 (490)
Q Consensus       415 l~~a~~~a~~~~~~~~~~~~It~~~v~~a~  444 (490)
                      ++.++..    +     ...|+.++|.+++
T Consensus       228 ~~~~~~~----~-----~~~i~~~~v~~~~  248 (250)
T 1njg_A          228 TDQAIAS----G-----DGQVSTQAVSAML  248 (250)
T ss_dssp             HHHHHTT----T-----TSSBCHHHHHHHS
T ss_pred             HHHHHhc----c-----CceecHHHHHHHh
Confidence            9888532    2     2379999998875

>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=99.80  E-value=2.8e-18  Score=176.67  Aligned_cols=220  Identities=16%  Similarity=0.177  Sum_probs=157.5

Q ss_pred             CCCCChHHHHHHHHHHHHhhh--------ccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHV--------NNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASV  265 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~--------~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l  265 (490)
                      ++++|.++.+++|.+.+....        ....+++++|+||||||||+++++++.++.    ..+++++|..+..    
T Consensus        16 ~di~G~~~~~~~l~e~v~~l~~~~~~~~~g~~~p~gvLL~GppGtGKT~Laraia~~~~----~~f~~is~~~~~~----   87 (476)
T 2ce7_A           16 KDVGGAEEAIEELKEVVEFLKDPSKFNRIGARMPKGILLVGPPGTGKTLLARAVAGEAN----VPFFHISGSDFVE----   87 (476)
T ss_dssp             GGCCSCHHHHHHHHHHHHHHHCTHHHHTTTCCCCSEEEEECCTTSSHHHHHHHHHHHHT----CCEEEEEGGGTTT----
T ss_pred             HHhCCcHHHHHHHHHHHHHhhChHHHhhcCCCCCCeEEEECCCCCCHHHHHHHHHHHcC----CCeeeCCHHHHHH----
Confidence            679999999988888765421        112457899999999999999999999875    6788998877633    


Q ss_pred             HHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCH-----------HHHHHhHhCC--CCCCCcE
Q psy200          266 YETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQ-----------TILYTIFEWP--SIPGSKL  332 (490)
Q Consensus       266 ~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~-----------~~L~~l~~~~--~~~~~~v  332 (490)
                                .+.+.....+...|..+..  +.++||||||+|.+....+           ..+..++...  ......+
T Consensus        88 ----------~~~g~~~~~~r~lf~~A~~--~~p~ILfIDEid~l~~~r~~~~~g~~~~~~~~l~~LL~~ld~~~~~~~v  155 (476)
T 2ce7_A           88 ----------LFVGVGAARVRDLFAQAKA--HAPCIVFIDEIDAVGRHRGAGLGGGHDEREQTLNQLLVEMDGFDSKEGI  155 (476)
T ss_dssp             ----------CCTTHHHHHHHHHHHHHHH--TCSEEEEEETGGGTCCC---------CHHHHHHHHHHHHHHHSCGGGTE
T ss_pred             ----------HHhcccHHHHHHHHHHHHh--cCCCEEEEechhhhhhhcccccCcCcHHHHHHHHHHHHHHhccCCCCCE
Confidence                      2333445556666666554  4589999999999975432           2333333211  1134579


Q ss_pred             EEEEecCCCChhHhhhHHhhh--ccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCH-H
Q psy200          333 VLVGVANALDLTDRMLPRLQA--NVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDI-R  409 (490)
Q Consensus       333 ilI~~tn~~~~~~~l~~~l~~--R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~-r  409 (490)
                      +||++||..   +.+++.+.+  ||.   ..+.|.+++.++..+|++.++.....   .++..++.++.   .+.|.. +
T Consensus       156 iVIaaTn~~---~~Ld~allR~gRFd---~~i~i~~Pd~~~R~~Il~~~~~~~~l---~~~v~l~~la~---~t~G~sga  223 (476)
T 2ce7_A          156 IVMAATNRP---DILDPALLRPGRFD---KKIVVDPPDMLGRKKILEIHTRNKPL---AEDVNLEIIAK---RTPGFVGA  223 (476)
T ss_dssp             EEEEEESCG---GGSCGGGGSTTSSC---EEEECCCCCHHHHHHHHHHHHTTSCB---CTTCCHHHHHH---TCTTCCHH
T ss_pred             EEEEecCCh---hhhchhhcccCcce---eEeecCCCCHHHHHHHHHHHHHhCCC---cchhhHHHHHH---hcCCCcHH
Confidence            999999964   344555554  776   48999999999999999988876421   12223666766   678877 6


Q ss_pred             HHHHHHHHHHHHHHhccccCCcccccCHHHHHHHHHHhccC
Q psy200          410 KAIDITNHLIDLTYDNVKENGEVTGIGLKEVLGVISSVYCT  450 (490)
Q Consensus       410 ~ai~ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~~~~~~~  450 (490)
                      .+.++|.+|...|...+     ...|+.++|..|+..+...
T Consensus       224 dL~~lv~~Aal~A~~~~-----~~~I~~~dl~~al~~v~~~  259 (476)
T 2ce7_A          224 DLENLVNEAALLAAREG-----RDKITMKDFEEAIDRVIAG  259 (476)
T ss_dssp             HHHHHHHHHHHHHHHTT-----CSSBCHHHHHHHHHHHC--
T ss_pred             HHHHHHHHHHHHHHHcC-----CCeecHHHHHHHHHHHhcC
Confidence            78889999999888777     5689999999999998754

>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=99.80  E-value=6.5e-19  Score=174.08  Aligned_cols=198  Identities=19%  Similarity=0.263  Sum_probs=148.1

Q ss_pred             CCCCcchHHHhhcCCCCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcC-CceEEEEecc
Q psy200          179 FSEDKPKVEEKAKDSCELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKD-AFKTIYINCN  257 (490)
Q Consensus       179 ~~~~~~~~~~~~l~~~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~-~~~~~~v~~~  257 (490)
                      +|.++|.+...    ++++|+++.++.|..++..    +...+++|+||+|+|||++++++++.+.... ...++++++.
T Consensus        14 ~~~~k~~p~~~----~~~~g~~~~~~~l~~~l~~----~~~~~~ll~G~~G~GKT~la~~l~~~l~~~~~~~~~~~~~~~   85 (327)
T 1iqp_A           14 PWVEKYRPQRL----DDIVGQEHIVKRLKHYVKT----GSMPHLLFAGPPGVGKTTAALALARELFGENWRHNFLELNAS   85 (327)
T ss_dssp             CHHHHTCCCST----TTCCSCHHHHHHHHHHHHH----TCCCEEEEESCTTSSHHHHHHHHHHHHHGGGHHHHEEEEETT
T ss_pred             chhhccCCCCH----HHhhCCHHHHHHHHHHHHc----CCCCeEEEECcCCCCHHHHHHHHHHHhcCCcccCceEEeecc
Confidence            67778887766    8999999999999988864    4455699999999999999999999874221 2356777765


Q ss_pred             CCCCHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHhc----CCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEE
Q psy200          258 SVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFDT----KHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLV  333 (490)
Q Consensus       258 ~~~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~----~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vi  333 (490)
                      ....                    ...+.+.+......    .+++.+|||||+|.+....++.|..+++..   ...++
T Consensus        86 ~~~~--------------------~~~~~~~~~~~~~~~~~~~~~~~vliiDe~~~l~~~~~~~L~~~le~~---~~~~~  142 (327)
T 1iqp_A           86 DERG--------------------INVIREKVKEFARTKPIGGASFKIIFLDEADALTQDAQQALRRTMEMF---SSNVR  142 (327)
T ss_dssp             CHHH--------------------HHTTHHHHHHHHHSCCGGGCSCEEEEEETGGGSCHHHHHHHHHHHHHT---TTTEE
T ss_pred             ccCc--------------------hHHHHHHHHHHHhhCCcCCCCCeEEEEeCCCcCCHHHHHHHHHHHHhc---CCCCe
Confidence            4211                    11111122222111    145779999999999887888888888753   23566


Q ss_pred             EEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHH
Q psy200          334 LVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAID  413 (490)
Q Consensus       334 lI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~  413 (490)
                      +|+++|.   ...+.+.+.+||.    .+.|.|++.+++..++...+...  ...+++++++.+++   .+.||+|.+++
T Consensus       143 ~i~~~~~---~~~l~~~l~sr~~----~~~~~~l~~~~~~~~l~~~~~~~--~~~~~~~~~~~l~~---~~~g~~r~~~~  210 (327)
T 1iqp_A          143 FILSCNY---SSKIIEPIQSRCA----IFRFRPLRDEDIAKRLRYIAENE--GLELTEEGLQAILY---IAEGDMRRAIN  210 (327)
T ss_dssp             EEEEESC---GGGSCHHHHHTEE----EEECCCCCHHHHHHHHHHHHHTT--TCEECHHHHHHHHH---HHTTCHHHHHH
T ss_pred             EEEEeCC---ccccCHHHHhhCc----EEEecCCCHHHHHHHHHHHHHhc--CCCCCHHHHHHHHH---HCCCCHHHHHH
Confidence            6666763   3557788889985    79999999999999999988765  34589999999987   67899999999


Q ss_pred             HHHHHH
Q psy200          414 ITNHLI  419 (490)
Q Consensus       414 ll~~a~  419 (490)
                      +++.+.
T Consensus       211 ~l~~~~  216 (327)
T 1iqp_A          211 ILQAAA  216 (327)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            998765

>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=99.80  E-value=3.7e-19  Score=175.19  Aligned_cols=217  Identities=19%  Similarity=0.240  Sum_probs=154.7

Q ss_pred             cCCCCcchHHHhhcCCCCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcC-CceEEEEec
Q psy200          178 LFSEDKPKVEEKAKDSCELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKD-AFKTIYINC  256 (490)
Q Consensus       178 ~~~~~~~~~~~~~l~~~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~-~~~~~~v~~  256 (490)
                      .+|.++|.+...    ++++|++..++.|..++..    +...+++|+||+|+|||++++.+++.+.... ...+++++|
T Consensus         5 ~~~~~k~~p~~~----~~~~g~~~~~~~l~~~l~~----~~~~~~ll~G~~G~GKt~la~~l~~~l~~~~~~~~~~~~~~   76 (319)
T 2chq_A            5 EIWVEKYRPRTL----DEVVGQDEVIQRLKGYVER----KNIPHLLFSGPPGTGKTATAIALARDLFGENWRDNFIEMNA   76 (319)
T ss_dssp             -CTTTTTSCSSG----GGSCSCHHHHHHHHTTTTT----TCCCCEEEESSSSSSHHHHHHHHHHHHHTTCHHHHCEEEET
T ss_pred             ccHHHhcCCCCH----HHHhCCHHHHHHHHHHHhC----CCCCeEEEECcCCcCHHHHHHHHHHHhcCCcccCCeEEEeC
Confidence            378889988877    8899999999888877753    4445699999999999999999999874211 235678887


Q ss_pred             cCCCCHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHH-hcCCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEE
Q psy200          257 NSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYF-DTKHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLV  335 (490)
Q Consensus       257 ~~~~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l-~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI  335 (490)
                      .......                 ........+.... -..+++.||||||+|.+....++.|..+++.   ....+++|
T Consensus        77 ~~~~~~~-----------------~~~~~~~~~~~~~~~~~~~~~vliiDe~~~l~~~~~~~L~~~le~---~~~~~~~i  136 (319)
T 2chq_A           77 SDERGID-----------------VVRHKIKEFARTAPIGGAPFKIIFLDEADALTADAQAALRRTMEM---YSKSCRFI  136 (319)
T ss_dssp             TSTTCTT-----------------TSSHHHHHHHHSCCSSSCCCEEEEEETGGGSCHHHHHTTGGGTSS---SSSSEEEE
T ss_pred             ccccChH-----------------HHHHHHHHHHhcCCCCCCCceEEEEeCCCcCCHHHHHHHHHHHHh---cCCCCeEE
Confidence            7542110                 1111111111100 0124578999999999987666666555543   34567777


Q ss_pred             EecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHHHH
Q psy200          336 GVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDIT  415 (490)
Q Consensus       336 ~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll  415 (490)
                      +++|.   ...+.+.+.+||.    .+.|.+++.+++..++..++...  ...+++++++.++.   .+.||+|.+++++
T Consensus       137 ~~~~~---~~~l~~~l~sr~~----~i~~~~~~~~~~~~~l~~~~~~~--~~~i~~~~l~~l~~---~~~G~~r~~~~~l  204 (319)
T 2chq_A          137 LSCNY---VSRIIEPIQSRCA----VFRFKPVPKEAMKKRLLEICEKE--GVKITEDGLEALIY---ISGGDFRKAINAL  204 (319)
T ss_dssp             EEESC---GGGSCHHHHTTCE----EEECCCCCHHHHHHHHHHHHHTT--CCCBCHHHHHHHHH---TTTTCHHHHHHHH
T ss_pred             EEeCC---hhhcchHHHhhCe----EEEecCCCHHHHHHHHHHHHHHc--CCCCCHHHHHHHHH---HcCCCHHHHHHHH
Confidence            77774   3467788999985    89999999999999999998876  35689999999987   7789999999998


Q ss_pred             HHHHHHHHhccccCCcccccCHHHHHHHH
Q psy200          416 NHLIDLTYDNVKENGEVTGIGLKEVLGVI  444 (490)
Q Consensus       416 ~~a~~~a~~~~~~~~~~~~It~~~v~~a~  444 (490)
                      +.+...    +      ..|+.+++.+++
T Consensus       205 ~~~~~~----~------~~i~~~~v~~~~  223 (319)
T 2chq_A          205 QGAAAI----G------EVVDADTIYQIT  223 (319)
T ss_dssp             HHHHHS----S------SCBCHHHHHHHT
T ss_pred             HHHHHc----C------CCCCHHHHHHHH
Confidence            877532    1      246666665543

>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=99.79  E-value=2.5e-18  Score=177.10  Aligned_cols=229  Identities=17%  Similarity=0.176  Sum_probs=156.4

Q ss_pred             CCCCChHHHHHHHHHHHHhhhc--------cCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVN--------NETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASV  265 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~--------~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l  265 (490)
                      ++++|.+..++.|.+++...+.        ...++++||+||||||||++|+++++++   .+..++.++|..+.+    
T Consensus       134 ~di~G~~~~k~~l~~~v~~p~~~~~~~~~~~~~~~~vLL~GppGtGKT~lA~aia~~~---~~~~~~~v~~~~l~~----  206 (444)
T 2zan_A          134 SDVAGLEGAKEALKEAVILPIKFPHLFTGKRTPWRGILLFGPPGTGKSYLAKAVATEA---NNSTFFSISSSDLVS----  206 (444)
T ss_dssp             GGSCSCHHHHHHHHHHHTHHHHCTTTTSGGGCCCSEEEEECSTTSSHHHHHHHHHHHC---CSSEEEEECCC--------
T ss_pred             HHhcCHHHHHHHHHHHHHHHhhCHHHhhccCCCCceEEEECCCCCCHHHHHHHHHHHc---CCCCEEEEeHHHHHh----
Confidence            7899999999999988743211        2356899999999999999999999987   235788888875422    


Q ss_pred             HHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccC--------HHHHHHhHhCC---CCCCCcEEE
Q psy200          266 YETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRK--------QTILYTIFEWP---SIPGSKLVL  334 (490)
Q Consensus       266 ~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~--------~~~L~~l~~~~---~~~~~~vil  334 (490)
                                .+.+.+...+...|..+..  ..+.||||||||.+....        ...+..++...   .....+++|
T Consensus       207 ----------~~~g~~~~~~~~~f~~a~~--~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~lL~~l~~~~~~~~~v~v  274 (444)
T 2zan_A          207 ----------KWLGESEKLVKNLFQLARE--NKPSIIFIDEIDSLCGSRSENESEAARRIKTEFLVQMQGVGVDNDGILV  274 (444)
T ss_dssp             ---------------CCCTHHHHHHHHHH--SCSEEEEESCTTTTCCCSSCCCCGGGHHHHHHHHTTTTCSSCCCSSCEE
T ss_pred             ----------hhcchHHHHHHHHHHHHHH--cCCeEEEEechHhhccCCCCccccHHHHHHHHHHHHHhCcccCCCCEEE
Confidence                      1222223334444444333  457899999999995431        22333343322   224578999


Q ss_pred             EEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhC-CHHHHHH
Q psy200          335 VGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSG-DIRKAID  413 (490)
Q Consensus       335 I~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~G-d~r~ai~  413 (490)
                      |++||..   +.+++.+.+||.   ..+.+++++.++...|+..++...  ...+++..++.|++   .+.| ..+.+-.
T Consensus       275 I~atn~~---~~ld~al~rRf~---~~i~i~~P~~~~r~~il~~~l~~~--~~~l~~~~l~~la~---~t~G~sgadl~~  343 (444)
T 2zan_A          275 LGATNIP---WVLDSAIRRRFE---KRIYIPLPEAHARAAMFRLHLGST--QNSLTEADFQELGR---KTDGYSGADISI  343 (444)
T ss_dssp             EEEESCG---GGSCHHHHTTCC---EEEECCCCCHHHHHHHHHHHHTTS--CEECCHHHHHHHHH---HTTTCCHHHHHH
T ss_pred             EecCCCc---cccCHHHHhhcc---eEEEeCCcCHHHHHHHHHHHHhcC--CCCCCHHHHHHHHH---HcCCCCHHHHHH
Confidence            9999854   567788888997   489999999999999999988765  33468889999988   4455 3445556


Q ss_pred             HHHHHHHHHHhccccC--------------------------------------------CcccccCHHHHHHHHHHhcc
Q psy200          414 ITNHLIDLTYDNVKEN--------------------------------------------GEVTGIGLKEVLGVISSVYC  449 (490)
Q Consensus       414 ll~~a~~~a~~~~~~~--------------------------------------------~~~~~It~~~v~~a~~~~~~  449 (490)
                      +|+.|+..+.++....                                            .....|+++||..|+..+.+
T Consensus       344 l~~~a~~~a~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~df~~a~~~~~p  423 (444)
T 2zan_A          344 IVRDALMQPVRKVQSATHFKKVRGPSRADPNCIVNDLLTPCSPGDPGAIEMTWMDVPGDKLLEPVVSMWDMLRSLSSTKP  423 (444)
T ss_dssp             HHHHHHTHHHHHHHHCSEEEEECCBCSSCTTSBCSCEEEEECTTSTTEEECCTTTSCTTCBCCCCEEHHHHHHHHHTCCC
T ss_pred             HHHHHHHHHHHHHHhhhhhhhhccccccccccccccccccCCCCcccchhcccccCchhhccCCccCHHHHHHHHHhCCC
Confidence            7778776665432100                                            01246999999999998877


Q ss_pred             Ccc
Q psy200          450 TSQ  452 (490)
Q Consensus       450 ~~~  452 (490)
                      +..
T Consensus       424 s~~  426 (444)
T 2zan_A          424 TVN  426 (444)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            644

>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=99.79  E-value=3.3e-18  Score=177.06  Aligned_cols=132  Identities=17%  Similarity=0.159  Sum_probs=107.4

Q ss_pred             EEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEEEe---------cCCCChhHhhhHHhhhccCCCCeeEEeCCCCHH
Q psy200          300 ILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGV---------ANALDLTDRMLPRLQANVTLQPTLMNFAPYSRE  370 (490)
Q Consensus       300 ~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI~~---------tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~  370 (490)
                      .|+||||+|.|....++.|+..++...   ..++++++         ++.......+.+.+++||.    .+.|.+|+.+
T Consensus       297 ~VliIDEa~~l~~~a~~aLlk~lEe~~---~~~~il~tn~~~~~i~~~~~~~~~~~l~~~i~sR~~----~~~~~~~~~~  369 (456)
T 2c9o_A          297 GVLFVDEVHMLDIECFTYLHRALESSI---APIVIFASNRGNCVIRGTEDITSPHGIPLDLLDRVM----IIRTMLYTPQ  369 (456)
T ss_dssp             CEEEEESGGGCBHHHHHHHHHHTTSTT---CCEEEEEECCSEEECBTTSSCEEETTCCHHHHTTEE----EEECCCCCHH
T ss_pred             eEEEEechhhcCHHHHHHHHHHhhccC---CCEEEEecCCccccccccccccccccCChhHHhhcc----eeeCCCCCHH
Confidence            599999999998888888888877442   33544454         3323345667889999997    6899999999


Q ss_pred             HHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHh-hCCHHHHHHHHHHHHHHHHhccccCCcccccCHHHHHHHHHHhc
Q psy200          371 QILEIISQKLKQTDKFNMFNASALQLLAGKVAAV-SGDIRKAIDITNHLIDLTYDNVKENGEVTGIGLKEVLGVISSVY  448 (490)
Q Consensus       371 e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~-~Gd~r~ai~ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~~~~~  448 (490)
                      ++.++|.+++...  ...+++++++.|++   .. .|++|.++++|+.|...|..++     ...|+.++|.+++.-+.
T Consensus       370 e~~~iL~~~~~~~--~~~~~~~~~~~i~~---~a~~g~~r~a~~ll~~a~~~A~~~~-----~~~v~~~~v~~~~~~~~  438 (456)
T 2c9o_A          370 EMKQIIKIRAQTE--GINISEEALNHLGE---IGTKTTLRYSVQLLTPANLLAKING-----KDSIEKEHVEEISELFY  438 (456)
T ss_dssp             HHHHHHHHHHHHH--TCCBCHHHHHHHHH---HHHHSCHHHHHHTHHHHHHHHHHTT-----CSSBCHHHHHHHHHHSC
T ss_pred             HHHHHHHHHHHHh--CCCCCHHHHHHHHH---HccCCCHHHHHHHHHHHHHHHhhcC-----CCccCHHHHHHHHHHhc
Confidence            9999999998766  35689999999987   34 6999999999999999999888     67899999999987654

>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=99.79  E-value=4.1e-19  Score=173.87  Aligned_cols=227  Identities=17%  Similarity=0.220  Sum_probs=152.4

Q ss_pred             CCCCChHHHHHHHHHHHHhhh---------ccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHV---------NNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAAS  264 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~---------~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~  264 (490)
                      ++++|.++.++.|.+++...+         ....+.+++|+||||||||++|+++++.+.    ..++.++|..      
T Consensus        15 ~di~G~~~~~~~l~~~v~~~~~~~~~~~~~~~~~~~~vLL~Gp~GtGKT~la~ala~~~~----~~~i~v~~~~------   84 (301)
T 3cf0_A           15 EDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANECQ----ANFISIKGPE------   84 (301)
T ss_dssp             GGSCSCHHHHHHHHHHHHHHHHCHHHHHHHCCCCCSEEEEECSSSSSHHHHHHHHHHHTT----CEEEEECHHH------
T ss_pred             HHhCCHHHHHHHHHHHHHHHhhCHHHHHHcCCCCCceEEEECCCCcCHHHHHHHHHHHhC----CCEEEEEhHH------
Confidence            679999999999999886532         124678899999999999999999999874    6778887643      


Q ss_pred             HHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccC--------------HHHHHHhHhCCCCCCC
Q psy200          265 VYETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRK--------------QTILYTIFEWPSIPGS  330 (490)
Q Consensus       265 l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~--------------~~~L~~l~~~~~~~~~  330 (490)
                      +...+.        +.....+...|..+..  ..+++|||||+|.+....              +..|+..++-. ....
T Consensus        85 l~~~~~--------g~~~~~~~~~f~~a~~--~~p~il~iDEid~l~~~~~~~~~~~~~~~~~~~~~lL~~l~~~-~~~~  153 (301)
T 3cf0_A           85 LLTMWF--------GESEANVREIFDKARQ--AAPCVLFFDELDSIAKARGGNIGDGGGAADRVINQILTEMDGM-STKK  153 (301)
T ss_dssp             HHHHHH--------TTCTTHHHHHHHHHHH--TCSEEEEECSTTHHHHHHTTTTCCSSCSCCHHHHHHHHHHHSS-CTTS
T ss_pred             HHhhhc--------CchHHHHHHHHHHHHh--cCCeEEEEEChHHHhhccCCCcCCcchHHHHHHHHHHHHhhcc-cCCC
Confidence            222221        1233445555555443  457899999999986431              23444444422 2456


Q ss_pred             cEEEEEecCCCChhHhhhHHhhh--ccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCH
Q psy200          331 KLVLVGVANALDLTDRMLPRLQA--NVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDI  408 (490)
Q Consensus       331 ~vilI~~tn~~~~~~~l~~~l~~--R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~  408 (490)
                      +++||++||..   +.+++.+.+  ||.   ..+.|++++.++..+|+..++........++   ++.++....++.|+ 
T Consensus       154 ~v~vi~atn~~---~~ld~al~r~gRf~---~~i~i~~p~~~~r~~il~~~l~~~~~~~~~~---~~~la~~~~g~sg~-  223 (301)
T 3cf0_A          154 NVFIIGATNRP---DIIDPAILRPGRLD---QLIYIPLPDEKSRVAILKANLRKSPVAKDVD---LEFLAKMTNGFSGA-  223 (301)
T ss_dssp             SEEEEEEESCG---GGSCGGGGSTTSSC---EEEECCCCCHHHHHHHHHHHHTTSCBCSSCC---HHHHHHTCSSCCHH-
T ss_pred             CEEEEEecCCc---cccChHHhcCCccc---eEEecCCcCHHHHHHHHHHHHccCCCCccch---HHHHHHHcCCCCHH-
Confidence            79999999954   445666665  776   4899999999999999999987653222233   45566534444443 


Q ss_pred             HHHHHHHHHHHHHHHhcccc--------------------CCcccccCHHHHHHHHHHhccCcc
Q psy200          409 RKAIDITNHLIDLTYDNVKE--------------------NGEVTGIGLKEVLGVISSVYCTSQ  452 (490)
Q Consensus       409 r~ai~ll~~a~~~a~~~~~~--------------------~~~~~~It~~~v~~a~~~~~~~~~  452 (490)
                       .+-++|++|+..|..+...                    ......|+.+||..|+..+.++..
T Consensus       224 -dl~~l~~~a~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~al~~~~~s~~  286 (301)
T 3cf0_A          224 -DLTEICQRACKLAIRESIESEIRRERERQTNPSAMEVEEDDPVPEIRRDHFEEAMRFARRSVS  286 (301)
T ss_dssp             -HHHHHHHHHHHHHHHHHHHHHC--------------------CCCBCHHHHHHHHTTCCCSSC
T ss_pred             -HHHHHHHHHHHHHHHHHHHhhhhhhhhcccccccccccccccCCccCHHHHHHHHHHcCCCCC
Confidence             5556788877766543210                    001246999999999988765433

>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=99.78  E-value=1.5e-18  Score=163.50  Aligned_cols=209  Identities=11%  Similarity=0.197  Sum_probs=144.6

Q ss_pred             CCCCCh---HHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHH
Q psy200          194 CELPGR---EVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIV  270 (490)
Q Consensus       194 ~~lvgr---e~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~  270 (490)
                      +++++.   +..++.+..++.    .....+++|+||+|+|||++++.+++.+... .+.++++++......        
T Consensus        28 ~~~~~~~~~~~~~~~l~~~~~----~~~~~~~ll~G~~G~GKT~la~~l~~~~~~~-~~~~~~~~~~~~~~~--------   94 (242)
T 3bos_A           28 TSYYPAAGNDELIGALKSAAS----GDGVQAIYLWGPVKSGRTHLIHAACARANEL-ERRSFYIPLGIHASI--------   94 (242)
T ss_dssp             TTSCC--CCHHHHHHHHHHHH----TCSCSEEEEECSTTSSHHHHHHHHHHHHHHT-TCCEEEEEGGGGGGS--------
T ss_pred             hhccCCCCCHHHHHHHHHHHh----CCCCCeEEEECCCCCCHHHHHHHHHHHHHHc-CCeEEEEEHHHHHHH--------
Confidence            556653   456666666554    3467899999999999999999999988633 567888887654210        


Q ss_pred             HHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccC--HHHHHHhHhCCCCCCCcEEEEEecCCCChhHhhh
Q psy200          271 NELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRK--QTILYTIFEWPSIPGSKLVLVGVANALDLTDRML  348 (490)
Q Consensus       271 ~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~--~~~L~~l~~~~~~~~~~vilI~~tn~~~~~~~l~  348 (490)
                            .            .+.+....++.+|||||++.+....  ++.|+.+++.....+...+++++....+....+.
T Consensus        95 ------~------------~~~~~~~~~~~vliiDe~~~~~~~~~~~~~l~~~l~~~~~~~~~~ii~~~~~~~~~~~~~~  156 (242)
T 3bos_A           95 ------S------------TALLEGLEQFDLICIDDVDAVAGHPLWEEAIFDLYNRVAEQKRGSLIVSASASPMEAGFVL  156 (242)
T ss_dssp             ------C------------GGGGTTGGGSSEEEEETGGGGTTCHHHHHHHHHHHHHHHHHCSCEEEEEESSCTTTTTCCC
T ss_pred             ------H------------HHHHHhccCCCEEEEeccccccCCHHHHHHHHHHHHHHHHcCCCeEEEEcCCCHHHHHHhh
Confidence                  0            0001111335699999999998765  6777776543221222213333332222222334


Q ss_pred             HHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHhcccc
Q psy200          349 PRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITNHLIDLTYDNVKE  428 (490)
Q Consensus       349 ~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll~~a~~~a~~~~~~  428 (490)
                      +.+.+||..+ ..+.|.+++.+++.+++..++...  ...+++++++.+++   .+.||+|.++++++.+...+..++  
T Consensus       157 ~~l~~r~~~~-~~i~l~~~~~~~~~~~l~~~~~~~--~~~~~~~~~~~l~~---~~~g~~r~l~~~l~~~~~~a~~~~--  228 (242)
T 3bos_A          157 PDLVSRMHWG-LTYQLQPMMDDEKLAALQRRAAMR--GLQLPEDVGRFLLN---RMARDLRTLFDVLDRLDKASMVHQ--  228 (242)
T ss_dssp             HHHHHHHHHS-EEEECCCCCGGGHHHHHHHHHHHT--TCCCCHHHHHHHHH---HTTTCHHHHHHHHHHHHHHHHHHT--
T ss_pred             hhhhhHhhcC-ceEEeCCCCHHHHHHHHHHHHHHc--CCCCCHHHHHHHHH---HccCCHHHHHHHHHHHHHHHHHhC--
Confidence            7777787311 279999999999999999998765  35689999999987   678999999999999998886555  


Q ss_pred             CCcccccCHHHHHHHHH
Q psy200          429 NGEVTGIGLKEVLGVIS  445 (490)
Q Consensus       429 ~~~~~~It~~~v~~a~~  445 (490)
                          ..|+.+++.+++.
T Consensus       229 ----~~It~~~v~~~l~  241 (242)
T 3bos_A          229 ----RKLTIPFVKEMLR  241 (242)
T ss_dssp             ----CCCCHHHHHHHHT
T ss_pred             ----CCCcHHHHHHHhh
Confidence                3699999998874

>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=99.78  E-value=1.4e-18  Score=173.21  Aligned_cols=221  Identities=21%  Similarity=0.247  Sum_probs=159.5

Q ss_pred             ccCCCCcchHHHhhcCCCCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcC-CceEEEEe
Q psy200          177 LLFSEDKPKVEEKAKDSCELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKD-AFKTIYIN  255 (490)
Q Consensus       177 ~~~~~~~~~~~~~~l~~~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~-~~~~~~v~  255 (490)
                      ..+|.++|.+...    ++++|++..++.|..++..    +...+++|+||+|+||||+++++++.+.... ...++.++
T Consensus        12 ~~~~~~k~rp~~~----~~~~g~~~~~~~L~~~i~~----g~~~~~ll~Gp~G~GKTtla~~la~~l~~~~~~~~~~~~~   83 (340)
T 1sxj_C           12 NLPWVEKYRPETL----DEVYGQNEVITTVRKFVDE----GKLPHLLFYGPPGTGKTSTIVALAREIYGKNYSNMVLELN   83 (340)
T ss_dssp             CCCHHHHTCCSSG----GGCCSCHHHHHHHHHHHHT----TCCCCEEEECSSSSSHHHHHHHHHHHHHTTSHHHHEEEEC
T ss_pred             CCchHHHhCCCcH----HHhcCcHHHHHHHHHHHhc----CCCceEEEECCCCCCHHHHHHHHHHHHcCCCccceEEEEc
Confidence            3478888888777    8899999999988888864    4444599999999999999999999875221 12466676


Q ss_pred             ccCCCCHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHhc----CCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCc
Q psy200          256 CNSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFDT----KHKSILLILDEIDALESRKQTILYTIFEWPSIPGSK  331 (490)
Q Consensus       256 ~~~~~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~----~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~  331 (490)
                      +.....                    ...+.+.+......    .+...|+||||+|.+....++.|..+++...   ..
T Consensus        84 ~~~~~~--------------------~~~ir~~i~~~~~~~~~~~~~~~viiiDe~~~l~~~~~~~L~~~le~~~---~~  140 (340)
T 1sxj_C           84 ASDDRG--------------------IDVVRNQIKDFASTRQIFSKGFKLIILDEADAMTNAAQNALRRVIERYT---KN  140 (340)
T ss_dssp             TTSCCS--------------------HHHHHTHHHHHHHBCCSSSCSCEEEEETTGGGSCHHHHHHHHHHHHHTT---TT
T ss_pred             Cccccc--------------------HHHHHHHHHHHHhhcccCCCCceEEEEeCCCCCCHHHHHHHHHHHhcCC---CC
Confidence            654322                    23333333332211    1346799999999998888888888887542   34


Q ss_pred             EEEEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHH
Q psy200          332 LVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKA  411 (490)
Q Consensus       332 vilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~a  411 (490)
                      ..+|.++|.   ...+.+.+.+||.    .+.|.+++.+++.+++.+.+...  ...+++++++.+++   ...|++|.+
T Consensus       141 ~~~il~~n~---~~~i~~~i~sR~~----~~~~~~l~~~~~~~~l~~~~~~~--~~~i~~~~~~~i~~---~s~G~~r~~  208 (340)
T 1sxj_C          141 TRFCVLANY---AHKLTPALLSQCT----RFRFQPLPQEAIERRIANVLVHE--KLKLSPNAEKALIE---LSNGDMRRV  208 (340)
T ss_dssp             EEEEEEESC---GGGSCHHHHTTSE----EEECCCCCHHHHHHHHHHHHHTT--TCCBCHHHHHHHHH---HHTTCHHHH
T ss_pred             eEEEEEecC---ccccchhHHhhce----eEeccCCCHHHHHHHHHHHHHHc--CCCCCHHHHHHHHH---HcCCCHHHH
Confidence            555666763   4677889999985    79999999999999999988765  35689999999987   678999999


Q ss_pred             HHHHHHHHHHHHhccccCCcccccCHHHHHHHHH
Q psy200          412 IDITNHLIDLTYDNVKENGEVTGIGLKEVLGVIS  445 (490)
Q Consensus       412 i~ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~~  445 (490)
                      +++++.+...+...+     ...|+.+++..++.
T Consensus       209 ~~~l~~~~~~~~~~~-----~~~it~~~v~~~~~  237 (340)
T 1sxj_C          209 LNVLQSCKATLDNPD-----EDEISDDVIYECCG  237 (340)
T ss_dssp             HHHTTTTTTTTCSSS-----CCCBCHHHHHHHTT
T ss_pred             HHHHHHHHHhcCCcc-----cccccHHHHHHHhC
Confidence            999877653332222     23577777765543

>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=99.77  E-value=2.9e-18  Score=177.92  Aligned_cols=226  Identities=15%  Similarity=0.201  Sum_probs=161.1

Q ss_pred             CCCCChHHHHHHHHHHHHhhhc---------cCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVN---------NETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAAS  264 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~---------~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~  264 (490)
                      ++++|.+.+++.|.+++...+.         ...+.++||+||||||||++|+++++++.    ..+++++|..+.    
T Consensus       204 ~~i~G~~~~~~~l~~~i~~~l~~~~~~~~~g~~~~~~vLL~GppGtGKT~lAraia~~~~----~~fv~vn~~~l~----  275 (489)
T 3hu3_A          204 DDIGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANETG----AFFFLINGPEIM----  275 (489)
T ss_dssp             GGCCSCHHHHHHHHHHTHHHHHCHHHHHHHTCCCCCEEEEECSTTSSHHHHHHHHHHHCS----SEEEEEEHHHHH----
T ss_pred             HHcCCHHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCcEEEECcCCCCHHHHHHHHHHHhC----CCEEEEEchHhh----
Confidence            6799999999999998875421         35678899999999999999999998864    788999986542    


Q ss_pred             HHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccC-----------HHHHHHhHhCCCCCCCcEE
Q psy200          265 VYETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRK-----------QTILYTIFEWPSIPGSKLV  333 (490)
Q Consensus       265 l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~-----------~~~L~~l~~~~~~~~~~vi  333 (490)
                                ..+.+.....+...|..+..  +++.+|||||||.+....           +..|+.+++.. .....++
T Consensus       276 ----------~~~~g~~~~~~~~~f~~A~~--~~p~iLfLDEId~l~~~~~~~~~~~~~~~~~~LL~~ld~~-~~~~~v~  342 (489)
T 3hu3_A          276 ----------SKLAGESESNLRKAFEEAEK--NAPAIIFIDELDAIAPKREKTHGEVERRIVSQLLTLMDGL-KQRAHVI  342 (489)
T ss_dssp             ----------TSCTTHHHHHHHHHHHHHHH--TCSEEEEEESHHHHCBCTTSCCCHHHHHHHHHHHHHHHHS-CTTSCEE
T ss_pred             ----------hhhcchhHHHHHHHHHHHHh--cCCcEEEecchhhhccccccccchHHHHHHHHHHHHhhcc-ccCCceE
Confidence                      13334455556666666554  458899999999987642           24455555532 2456899


Q ss_pred             EEEecCCCChhHhhhHHhhh--ccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCC-HHH
Q psy200          334 LVGVANALDLTDRMLPRLQA--NVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGD-IRK  410 (490)
Q Consensus       334 lI~~tn~~~~~~~l~~~l~~--R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd-~r~  410 (490)
                      ||++||..   +.+.+.+.+  ||.   ..+.|.+++.++..++|..++....   ...+..++.++.   ...|. .+.
T Consensus       343 vIaaTn~~---~~Ld~al~r~gRf~---~~i~i~~P~~~eR~~IL~~~~~~~~---l~~~~~l~~la~---~t~g~s~~d  410 (489)
T 3hu3_A          343 VMAATNRP---NSIDPALRRFGRFD---REVDIGIPDATGRLEILQIHTKNMK---LADDVDLEQVAN---ETHGHVGAD  410 (489)
T ss_dssp             EEEEESCG---GGBCGGGGSTTSSC---EEEECCCCCHHHHHHHHHHHTTTSC---BCTTCCHHHHHH---TCTTCCHHH
T ss_pred             EEEecCCc---cccCHHHhCCCcCc---eEEEeCCCCHHHHHHHHHHHHhcCC---CcchhhHHHHHH---HccCCcHHH
Confidence            99999954   445677776  665   4799999999999999998877652   122334566666   44454 444


Q ss_pred             HHHHHHHHHHHHHhccccCC------------cccccCHHHHHHHHHHhccCcc
Q psy200          411 AIDITNHLIDLTYDNVKENG------------EVTGIGLKEVLGVISSVYCTSQ  452 (490)
Q Consensus       411 ai~ll~~a~~~a~~~~~~~~------------~~~~It~~~v~~a~~~~~~~~~  452 (490)
                      +-.+|..|...+..+.....            ....|+++||..|+..+.++..
T Consensus       411 L~~L~~~A~~~a~r~~~~~i~~~~~~~~~~~~~~~~vt~edf~~Al~~~~ps~~  464 (489)
T 3hu3_A          411 LAALCSEAALQAIRKKMDLIDLEDETIDAEVMNSLAVTMDDFRWALSQSNPSAL  464 (489)
T ss_dssp             HHHHHHHHHHHHHHTTTTTCCTTCSSCCHHHHHHCCBCHHHHHHHHTSHHHHHH
T ss_pred             HHHHHHHHHHHHHHhccccccccccccchhhcccCcCCHHHHHHHHHhCCchhh
Confidence            55688999888877653210            1235899999999988765443

>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=99.76  E-value=1.3e-17  Score=168.06  Aligned_cols=229  Identities=17%  Similarity=0.230  Sum_probs=152.7

Q ss_pred             CCCCcchHHHhhcCCCCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccC
Q psy200          179 FSEDKPKVEEKAKDSCELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNS  258 (490)
Q Consensus       179 ~~~~~~~~~~~~l~~~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~  258 (490)
                      .|.++|.+...    ++++|++++++.|..++..   +..++.++|+||+|+|||++++.+++.+......  ....|..
T Consensus         5 ~l~~k~rp~~~----~~~vg~~~~~~~L~~~l~~---~~~~~~~ll~G~~G~GKT~la~~la~~l~~~~~~--~~~~~~~   75 (373)
T 1jr3_A            5 VLARKWRPQTF----ADVVGQEHVLTALANGLSL---GRIHHAYLFSGTRGVGKTSIARLLAKGLNCETGI--TATPCGV   75 (373)
T ss_dssp             CHHHHTCCCST----TTSCSCHHHHHHHHHHHHH---TCCCSEEEEESCTTSSHHHHHHHHHHHHSCTTCS--CSSCCSS
T ss_pred             HHHHhhCCCch----hhccCcHHHHHHHHHHHHh---CCCCeEEEEECCCCCCHHHHHHHHHHHhCCCCCC--CCCCCcc
Confidence            34455666555    7899999999999998864   3445678999999999999999999988532111  1112222


Q ss_pred             CCCHHHHHHHHHHH----h-cCC-CCCCcHHHHHHHHHHHHh--cCCCeEEEEEecCccccccCHHHHHHhHhCCCCCCC
Q psy200          259 VRNAASVYETIVNE----L-KLK-PGGKSERHQLGAILKYFD--TKHKSILLILDEIDALESRKQTILYTIFEWPSIPGS  330 (490)
Q Consensus       259 ~~~~~~l~~~i~~~----l-~~~-~~~~s~~~~~~~l~~~l~--~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~  330 (490)
                      +.+.    ..+...    + ... ........+.+.+.....  ..+++.||||||+|.+....++.|..+++.   ...
T Consensus        76 ~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~vliiDe~~~l~~~~~~~Ll~~le~---~~~  148 (373)
T 1jr3_A           76 CDNC----REIEQGRFVDLIEIDAASRTKVEDTRDLLDNVQYAPARGRFKVYLIDEVHMLSRHSFNALLKTLEE---PPE  148 (373)
T ss_dssp             SHHH----HHHHTSCCSSCEEEETTCSCCSSCHHHHHHHTTSCCSSSSSEEEEEECGGGSCHHHHHHHHHHHHS---CCS
T ss_pred             cHHH----HHHhccCCCceEEecccccCCHHHHHHHHHHHhhccccCCeEEEEEECcchhcHHHHHHHHHHHhc---CCC
Confidence            2111    111100    0 000 000112223333332221  124578999999999988777888887764   344


Q ss_pred             cEEEEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHH
Q psy200          331 KLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRK  410 (490)
Q Consensus       331 ~vilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~  410 (490)
                      .+++|++++.   ...+.+.+.+||.    .+.|.+++.+++..++.+++...  ...+++++++.+++   ...|+++.
T Consensus       149 ~~~~Il~~~~---~~~l~~~l~sr~~----~i~~~~l~~~~~~~~l~~~~~~~--~~~~~~~a~~~l~~---~~~G~~r~  216 (373)
T 1jr3_A          149 HVKFLLATTD---PQKLPVTILSRCL----QFHLKALDVEQIRHQLEHILNEE--HIAHEPRALQLLAR---AAEGSLRD  216 (373)
T ss_dssp             SEEEEEEESC---GGGSCHHHHTTSE----EEECCCCCHHHHHHHHHHHHHHH--TCCBCHHHHHHHHH---HSSSCHHH
T ss_pred             ceEEEEEeCC---hHhCcHHHHhhee----EeeCCCCCHHHHHHHHHHHHHHc--CCCCCHHHHHHHHH---HCCCCHHH
Confidence            6777777763   3456778888874    89999999999999999998776  34578999999987   66899999


Q ss_pred             HHHHHHHHHHHHHhccccCCcccccCHHHHHHHH
Q psy200          411 AIDITNHLIDLTYDNVKENGEVTGIGLKEVLGVI  444 (490)
Q Consensus       411 ai~ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~  444 (490)
                      ++++++.++..+  .+       .|+.++|.+++
T Consensus       217 ~~~~l~~~~~~~--~~-------~i~~~~v~~~~  241 (373)
T 1jr3_A          217 ALSLTDQAIASG--DG-------QVSTQAVSAML  241 (373)
T ss_dssp             HHHHHHHHHHHT--TT-------CBCHHHHHHHT
T ss_pred             HHHHHHHHHHhc--CC-------cccHHHHHHHh
Confidence            999998886432  22       56776666553

>2r44_A Uncharacterized protein; putative ATPase, structural genomics, joint center for struc genomics, JCSG; HET: MSE PG4; 2.00A {Cytophaga hutchinsonii atcc 33406}

Probab=99.74  E-value=1.1e-16  Score=158.71  Aligned_cols=238  Identities=13%  Similarity=0.129  Sum_probs=168.4

Q ss_pred             CCCcchHHHhhcCCCCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCC
Q psy200          180 SEDKPKVEEKAKDSCELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSV  259 (490)
Q Consensus       180 ~~~~~~~~~~~l~~~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~  259 (490)
                      |.+.+.+...    +.++|+++.++.+...+..      +++++|+||||||||++++++++.+.    ..++.++|...
T Consensus        17 ~~~~~~~~~~----~~i~g~~~~~~~l~~~l~~------~~~vll~G~pGtGKT~la~~la~~~~----~~~~~i~~~~~   82 (331)
T 2r44_A           17 KIKEVIDEVG----KVVVGQKYMINRLLIGICT------GGHILLEGVPGLAKTLSVNTLAKTMD----LDFHRIQFTPD   82 (331)
T ss_dssp             HHHHHHHHHT----TTCCSCHHHHHHHHHHHHH------TCCEEEESCCCHHHHHHHHHHHHHTT----CCEEEEECCTT
T ss_pred             HHHHHHHHhc----cceeCcHHHHHHHHHHHHc------CCeEEEECCCCCcHHHHHHHHHHHhC----CCeEEEecCCC
Confidence            3334555544    8999999999888887754      46899999999999999999999875    45677887655


Q ss_pred             CCHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcC-CCeEEEEEecCccccccCHHHHHHhHhCCC--------CCCC
Q psy200          260 RNAASVYETIVNELKLKPGGKSERHQLGAILKYFDTK-HKSILLILDEIDALESRKQTILYTIFEWPS--------IPGS  330 (490)
Q Consensus       260 ~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~-~~~~vI~IDEid~l~~~~~~~L~~l~~~~~--------~~~~  330 (490)
                      ....+++....  +. ...+. .         .+..+ -...+|||||++.+....+..|...++...        ....
T Consensus        83 ~~~~~l~g~~~--~~-~~~~~-~---------~~~~g~l~~~vl~iDEi~~~~~~~~~~Ll~~l~~~~~~~~g~~~~~~~  149 (331)
T 2r44_A           83 LLPSDLIGTMI--YN-QHKGN-F---------EVKKGPVFSNFILADEVNRSPAKVQSALLECMQEKQVTIGDTTYPLDN  149 (331)
T ss_dssp             CCHHHHHEEEE--EE-TTTTE-E---------EEEECTTCSSEEEEETGGGSCHHHHHHHHHHHHHSEEEETTEEEECCS
T ss_pred             CChhhcCCcee--ec-CCCCc-e---------EeccCcccccEEEEEccccCCHHHHHHHHHHHhcCceeeCCEEEECCC
Confidence            44444322110  00 00000 0         00000 012499999999998888888888776321        1244


Q ss_pred             cEEEEEecCCCChhH--hhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccC--------------------CCCC
Q psy200          331 KLVLVGVANALDLTD--RMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTD--------------------KFNM  388 (490)
Q Consensus       331 ~vilI~~tn~~~~~~--~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~--------------------~~~~  388 (490)
                      ++++|+++|..+...  .+.+.+.+||.+   .+.+.+++.++..+++..++....                    ....
T Consensus       150 ~~~viat~np~~~~~~~~l~~~l~~Rf~~---~i~i~~p~~~~~~~il~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~v~  226 (331)
T 2r44_A          150 PFLVLATQNPVEQEGTYPLPEAQVDRFMM---KIHLTYLDKESELEVMRRVSNMNFNYQVQKIVSKNDVLEIRNEINKVT  226 (331)
T ss_dssp             SCEEEEEECTTCCSCCCCCCHHHHTTSSE---EEECCCCCHHHHHHHHHHHHCTTCCCCCCCCSCHHHHHHHHHHHHTCB
T ss_pred             CEEEEEecCCCcccCcccCCHHHHhheeE---EEEcCCCCHHHHHHHHHhccccCcchhccccCCHHHHHHHHHHhccCC
Confidence            678888888654322  267889999973   699999999999999998876431                    1345


Q ss_pred             CCHHHHHHHHHHHHHh--hC---------------CHHHHHHHHHHHHHHHHhccccCCcccccCHHHHHHHHHHhccCc
Q psy200          389 FNASALQLLAGKVAAV--SG---------------DIRKAIDITNHLIDLTYDNVKENGEVTGIGLKEVLGVISSVYCTS  451 (490)
Q Consensus       389 ~~~~~i~~i~~~i~~~--~G---------------d~r~ai~ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~~~~~~~~  451 (490)
                      +++++++.+++.....  .|               +.|.++++++.|...|...+     ...|+.+|+..++..++...
T Consensus       227 ~~~~~~~~i~~~~~~~r~~~~~~~~~~~~~~~~~~s~R~~~~ll~~a~a~A~l~g-----~~~v~~~dv~~~~~~vl~~r  301 (331)
T 2r44_A          227 ISESLEKYIIELVFATRFPAEYGLEAEASYILYGASTRAAINLNRVAKAMAFFNN-----RDYVLPEDIKEVAYDILNHR  301 (331)
T ss_dssp             CCHHHHHHHHHHHHHHHSGGGGTCHHHHHHEEECCCHHHHHHHHHHHHHHHHHTT-----CSBCCHHHHHHHHHHHHTTT
T ss_pred             CCHHHHHHHHHHHHHHhccccccccccccccccCcChhHHHHHHHHHHHHHHHcC-----CCCCCHHHHHHHHHHHhHhh
Confidence            7888899888754321  12               69999999999999998888     66899999999999988766


Q ss_pred             c
Q psy200          452 Q  452 (490)
Q Consensus       452 ~  452 (490)
                      .
T Consensus       302 ~  302 (331)
T 2r44_A          302 I  302 (331)
T ss_dssp             S
T ss_pred             c
Confidence            5

>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=99.74  E-value=4.2e-18  Score=184.44  Aligned_cols=226  Identities=15%  Similarity=0.215  Sum_probs=157.7

Q ss_pred             CCCCChHHHHHHHHHHHHhhhc---------cCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVN---------NETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAAS  264 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~---------~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~  264 (490)
                      +++.|.++++++|.+++...+.         ...+++||||||||||||++|++++++++    ..+++++|..+     
T Consensus       204 ~dIgGl~~~~~~l~e~v~~pl~~p~~f~~~g~~~p~GILL~GPPGTGKT~LAraiA~elg----~~~~~v~~~~l-----  274 (806)
T 3cf2_A          204 DDIGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANETG----AFFFLINGPEI-----  274 (806)
T ss_dssp             GGCCSCCTTHHHHHHHHHHHHHCCGGGTSCCCCCCCEEEEECCTTSCHHHHHHHHHTTTT----CEEEEEEHHHH-----
T ss_pred             hhhcCHHHHHHHHHHHHHHHccCHHHHhhcCCCCCCeEEEECCCCCCHHHHHHHHHHHhC----CeEEEEEhHHh-----
Confidence            6799999999999988764332         13678999999999999999999999875    78888987643     


Q ss_pred             HHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccC--------HHHHHHhHhCC--CCCCCcEEE
Q psy200          265 VYETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRK--------QTILYTIFEWP--SIPGSKLVL  334 (490)
Q Consensus       265 l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~--------~~~L~~l~~~~--~~~~~~vil  334 (490)
                               ...+.|.+...+...|..+..  ..|+||||||+|.+....        ...+.+++.+.  .....+++|
T Consensus       275 ---------~sk~~gese~~lr~lF~~A~~--~~PsIIfIDEiDal~~~r~~~~~~~~~riv~~LL~~mdg~~~~~~V~V  343 (806)
T 3cf2_A          275 ---------MSKLAGESESNLRKAFEEAEK--NAPAIIFIDELDAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHVIV  343 (806)
T ss_dssp             ---------HSSCTTHHHHHHHHHHHHHTT--SCSEEEEEESGGGTCCTTTTCCCTTHHHHHHHHHTHHHHCCGGGCEEE
T ss_pred             ---------hcccchHHHHHHHHHHHHHHH--cCCeEEEEehhcccccccCCCCChHHHHHHHHHHHHHhcccccCCEEE
Confidence                     225666777778877776654  569999999999997542        12233332211  123467999


Q ss_pred             EEecCCCChhHhhhHHhhh--ccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCH-HHH
Q psy200          335 VGVANALDLTDRMLPRLQA--NVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDI-RKA  411 (490)
Q Consensus       335 I~~tn~~~~~~~l~~~l~~--R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~-r~a  411 (490)
                      |++||+.   +.+++.+++  ||.   ..|.+..++.++..+||+.++....   ...+..++.+++   .+.|-. ..+
T Consensus       344 IaaTN~~---d~LD~ALrR~GRFd---~~I~i~~Pd~~~R~~IL~~~l~~~~---~~~dvdl~~lA~---~T~GfsgaDL  411 (806)
T 3cf2_A          344 MAATNRP---NSIDPALRRFGRFD---REVDIGIPDATGRLEILQIHTKNMK---LADDVDLEQVAN---ETHGHVGADL  411 (806)
T ss_dssp             EEECSST---TTSCTTTTSTTSSC---EEEECCCCCHHHHHHHHHHTCSSSE---ECTTCCHHHHHH---HCCSCCHHHH
T ss_pred             EEecCCh---hhcCHHHhCCcccc---eEEecCCCCHHHHHHHHHHHhcCCC---CCcccCHHHHHH---hcCCCCHHHH
Confidence            9999965   445666665  666   5899999999999999998776541   112334677776   344432 334


Q ss_pred             HHHHHHHHHHHHhccccC------------CcccccCHHHHHHHHHHhccCc
Q psy200          412 IDITNHLIDLTYDNVKEN------------GEVTGIGLKEVLGVISSVYCTS  451 (490)
Q Consensus       412 i~ll~~a~~~a~~~~~~~------------~~~~~It~~~v~~a~~~~~~~~  451 (490)
                      ..+|+.|...|..+....            .....|+.+||..|+..+.+..
T Consensus       412 ~~Lv~eA~~~A~~r~~~~i~~~~~~~~~e~~~~~~v~~~Df~~Al~~~~ps~  463 (806)
T 3cf2_A          412 AALCSEAALQAIRKKMDLIDLEDETIDAEVMNSLAVTMDDFRWALSQSNPSA  463 (806)
T ss_dssp             HHHHHHHHHHHHHHHHHHGGGTCCCCSHHHHHHCEECTTHHHHHHSSSSCCC
T ss_pred             HHHHHHHHHHHHHhccccccccccccchhhhccceeeHHHHHHHHHhCCCcc
Confidence            457777776665432110            0134688999999998876544

>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=99.74  E-value=1.2e-16  Score=158.04  Aligned_cols=223  Identities=17%  Similarity=0.256  Sum_probs=147.7

Q ss_pred             CCCC-C--hHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHH
Q psy200          194 CELP-G--REVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIV  270 (490)
Q Consensus       194 ~~lv-g--re~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~  270 (490)
                      ++|+ |  +......+..++..  ......+++|+||+|+|||++++++++.+... +..+++++|..      +...+.
T Consensus        11 ~~fv~g~~~~~a~~~~~~~~~~--~~~~~~~lll~G~~GtGKT~la~~i~~~~~~~-~~~~~~i~~~~------~~~~~~   81 (324)
T 1l8q_A           11 ENFIVGEGNRLAYEVVKEALEN--LGSLYNPIFIYGSVGTGKTHLLQAAGNEAKKR-GYRVIYSSADD------FAQAMV   81 (324)
T ss_dssp             SSCCCCTTTHHHHHHHHHHHHT--TTTSCSSEEEECSSSSSHHHHHHHHHHHHHHT-TCCEEEEEHHH------HHHHHH
T ss_pred             ccCCCCCcHHHHHHHHHHHHhC--cCCCCCeEEEECCCCCcHHHHHHHHHHHHHHC-CCEEEEEEHHH------HHHHHH
Confidence            4454 4  33444444554443  11246799999999999999999999988532 56788997654      233333


Q ss_pred             HHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccc--cCHHHHHHhHhCCCCCCCcEEEEEecCCCChhHhhh
Q psy200          271 NELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALES--RKQTILYTIFEWPSIPGSKLVLVGVANALDLTDRML  348 (490)
Q Consensus       271 ~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~--~~~~~L~~l~~~~~~~~~~vilI~~tn~~~~~~~l~  348 (490)
                      ..+..    ....    .+...+.   ++.+|||||+|.+..  ..+..++.+++.....+ ..+++++++.......+.
T Consensus        82 ~~~~~----~~~~----~~~~~~~---~~~vL~iDEi~~l~~~~~~~~~l~~~l~~~~~~~-~~iii~~~~~~~~l~~l~  149 (324)
T 1l8q_A           82 EHLKK----GTIN----EFRNMYK---SVDLLLLDDVQFLSGKERTQIEFFHIFNTLYLLE-KQIILASDRHPQKLDGVS  149 (324)
T ss_dssp             HHHHH----TCHH----HHHHHHH---TCSEEEEECGGGGTTCHHHHHHHHHHHHHHHHTT-CEEEEEESSCGGGCTTSC
T ss_pred             HHHHc----CcHH----HHHHHhc---CCCEEEEcCcccccCChHHHHHHHHHHHHHHHCC-CeEEEEecCChHHHHHhh
Confidence            33221    0111    1222222   256999999999986  45666666654322222 345555555433233567


Q ss_pred             HHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHHHHHHHHHH---HHh-
Q psy200          349 PRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITNHLIDL---TYD-  424 (490)
Q Consensus       349 ~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll~~a~~~---a~~-  424 (490)
                      +++.+||..+ ..+.|.| +.+++..++..++...  ...+++++++.|++   .. ||+|.+.++|..++..   +.. 
T Consensus       150 ~~L~sR~~~~-~~i~l~~-~~~e~~~il~~~~~~~--~~~l~~~~l~~l~~---~~-g~~r~l~~~l~~~~~~~~~~l~~  221 (324)
T 1l8q_A          150 DRLVSRFEGG-ILVEIEL-DNKTRFKIIKEKLKEF--NLELRKEVIDYLLE---NT-KNVREIEGKIKLIKLKGFEGLER  221 (324)
T ss_dssp             HHHHHHHHTS-EEEECCC-CHHHHHHHHHHHHHHT--TCCCCHHHHHHHHH---HC-SSHHHHHHHHHHHHHHCHHHHHH
T ss_pred             hHhhhcccCc-eEEEeCC-CHHHHHHHHHHHHHhc--CCCCCHHHHHHHHH---hC-CCHHHHHHHHHHHHHcCHHHhcc
Confidence            8888888532 2699999 9999999999998865  45789999999998   45 9999999999888765   000 


Q ss_pred             ccccCCccccc-CHHHHHHHHHHhccC
Q psy200          425 NVKENGEVTGI-GLKEVLGVISSVYCT  450 (490)
Q Consensus       425 ~~~~~~~~~~I-t~~~v~~a~~~~~~~  450 (490)
                      ..     ...| +.+++.+++.+.+..
T Consensus       222 ~~-----~~~i~t~~~i~~~~~~~~~~  243 (324)
T 1l8q_A          222 KE-----RKERDKLMQIVEFVANYYAV  243 (324)
T ss_dssp             HH-----HHHHHHHHHHHHHHHHHHSC
T ss_pred             cc-----ccCCCCHHHHHHHHHHHhCC
Confidence            12     2468 999999999987753

>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=99.73  E-value=3.4e-17  Score=168.45  Aligned_cols=201  Identities=17%  Similarity=0.250  Sum_probs=142.9

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHhhhc-CCceEEEEeccCCCCHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCC
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRAEIK-DAFKTIYINCNSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFDTKH  297 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l~~~-~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~  297 (490)
                      .++++|+||+|+|||||++++++.+... ++..+++++|..      +...+...+...    ...    .+...+.  .
T Consensus       130 ~~~lll~Gp~G~GKTtLa~aia~~l~~~~~~~~v~~v~~~~------~~~~~~~~~~~~----~~~----~~~~~~~--~  193 (440)
T 2z4s_A          130 YNPLFIYGGVGLGKTHLLQSIGNYVVQNEPDLRVMYITSEK------FLNDLVDSMKEG----KLN----EFREKYR--K  193 (440)
T ss_dssp             SCCEEEECSSSSSHHHHHHHHHHHHHHHCCSSCEEEEEHHH------HHHHHHHHHHTT----CHH----HHHHHHT--T
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHHHhCCCCeEEEeeHHH------HHHHHHHHHHcc----cHH----HHHHHhc--C
Confidence            6799999999999999999999988532 356788887654      333444433221    111    2222222  1


Q ss_pred             CeEEEEEecCccccc--cCHHHHHHhHhCCCCCCCcEEEEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHH
Q psy200          298 KSILLILDEIDALES--RKQTILYTIFEWPSIPGSKLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEI  375 (490)
Q Consensus       298 ~~~vI~IDEid~l~~--~~~~~L~~l~~~~~~~~~~vilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~i  375 (490)
                      .+.||||||+|.+..  ..++.|+.+++.....+ ..+++++.+.......+.+++.+||..+ ..+.|.+++.+++..+
T Consensus       194 ~~~vL~IDEi~~l~~~~~~q~~l~~~l~~l~~~~-~~iIitt~~~~~~l~~l~~~L~sR~~~g-~~i~l~~p~~e~r~~i  271 (440)
T 2z4s_A          194 KVDILLIDDVQFLIGKTGVQTELFHTFNELHDSG-KQIVICSDREPQKLSEFQDRLVSRFQMG-LVAKLEPPDEETRKSI  271 (440)
T ss_dssp             TCSEEEEECGGGGSSCHHHHHHHHHHHHHHHTTT-CEEEEEESSCGGGCSSCCHHHHHHHHSS-BCCBCCCCCHHHHHHH
T ss_pred             CCCEEEEeCcccccCChHHHHHHHHHHHHHHHCC-CeEEEEECCCHHHHHHHHHHHHhhccCC-eEEEeCCCCHHHHHHH
Confidence            466999999999987  45677777765432223 3455554443332334667888888533 3689999999999999


Q ss_pred             HHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHhccccCCcccccCHHHHHHHHHHhc
Q psy200          376 ISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITNHLIDLTYDNVKENGEVTGIGLKEVLGVISSVY  448 (490)
Q Consensus       376 l~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~~~~~  448 (490)
                      +...+...  ...+++++++.|+.   .+.||+|.+.++|.++...+...+      ..|+.+++.+++.+..
T Consensus       272 L~~~~~~~--~~~i~~e~l~~la~---~~~gn~R~l~~~L~~~~~~a~~~~------~~It~~~~~~~l~~~~  333 (440)
T 2z4s_A          272 ARKMLEIE--HGELPEEVLNFVAE---NVDDNLRRLRGAIIKLLVYKETTG------KEVDLKEAILLLKDFI  333 (440)
T ss_dssp             HHHHHHHH--TCCCCTTHHHHHHH---HCCSCHHHHHHHHHHHHHHHHHSS------SCCCHHHHHHHTSTTT
T ss_pred             HHHHHHHc--CCCCCHHHHHHHHH---hcCCCHHHHHHHHHHHHHHHHHhC------CCCCHHHHHHHHHHHh
Confidence            99998765  35578999999987   678999999999999998887665      3588888888887655

>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=99.73  E-value=2.5e-17  Score=164.86  Aligned_cols=204  Identities=16%  Similarity=0.190  Sum_probs=140.4

Q ss_pred             CCCCcchHHHhhcCCCCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCc---------
Q psy200          179 FSEDKPKVEEKAKDSCELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAF---------  249 (490)
Q Consensus       179 ~~~~~~~~~~~~l~~~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~---------  249 (490)
                      +|.++|+|...    ++++|++..++.|..++.   ..+...+++|+||+|+||||+++.++..+.....-         
T Consensus         3 ~w~~kyrP~~~----~~~vg~~~~~~~l~~~~~---~~~~~~~~ll~Gp~G~GKTtl~~~la~~l~~~~~g~i~~~~~~~   75 (354)
T 1sxj_E            3 LWVDKYRPKSL----NALSHNEELTNFLKSLSD---QPRDLPHLLLYGPNGTGKKTRCMALLESIFGPGVYRLKIDVRQF   75 (354)
T ss_dssp             -CTTTTCCCSG----GGCCSCHHHHHHHHTTTT---CTTCCCCEEEECSTTSSHHHHHHTHHHHHSCTTCCC--------
T ss_pred             cchhccCCCCH----HHhcCCHHHHHHHHHHHh---hCCCCCeEEEECCCCCCHHHHHHHHHHHHcCCCCCeEEecceee
Confidence            68999998887    899999998887777661   23444459999999999999999999975311110         


Q ss_pred             ----------------eEEEEeccCCCCHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHh-----------c-CCCeEE
Q psy200          250 ----------------KTIYINCNSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFD-----------T-KHKSIL  301 (490)
Q Consensus       250 ----------------~~~~v~~~~~~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~-----------~-~~~~~v  301 (490)
                                      .++.+++.....                  .....+.+.+.....           . .+++.|
T Consensus        76 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~------------------~~~~~~~~~i~~~~~~~~~~~~~~ls~l~~~~~v  137 (354)
T 1sxj_E           76 VTASNRKLELNVVSSPYHLEITPSDMGN------------------NDRIVIQELLKEVAQMEQVDFQDSKDGLAHRYKC  137 (354)
T ss_dssp             ----------CCEECSSEEEECCC----------------------CCHHHHHHHHHHHTTTTC------------CCEE
T ss_pred             cccccccceeeeecccceEEecHhhcCC------------------cchHHHHHHHHHHHHhccccccccccccCCCCeE
Confidence                            112222111100                  000012222222111           0 235779


Q ss_pred             EEEecCccccccCHHHHHHhHhCCCCCCCcEEEEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHh
Q psy200          302 LILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLK  381 (490)
Q Consensus       302 I~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~  381 (490)
                      |||||++.|....++.|..+++...   ....+|.+++..   ..+.+.+++||.    .+.|.+++.+++.+++...+.
T Consensus       138 lilDE~~~L~~~~~~~L~~~le~~~---~~~~~Il~t~~~---~~l~~~l~sR~~----~~~~~~~~~~~~~~~l~~~~~  207 (354)
T 1sxj_E          138 VIINEANSLTKDAQAALRRTMEKYS---KNIRLIMVCDSM---SPIIAPIKSQCL----LIRCPAPSDSEISTILSDVVT  207 (354)
T ss_dssp             EEEECTTSSCHHHHHHHHHHHHHST---TTEEEEEEESCS---CSSCHHHHTTSE----EEECCCCCHHHHHHHHHHHHH
T ss_pred             EEEeCccccCHHHHHHHHHHHHhhc---CCCEEEEEeCCH---HHHHHHHHhhce----EEecCCcCHHHHHHHHHHHHH
Confidence            9999999988777888888877532   235556566643   346778999984    899999999999999999988


Q ss_pred             ccCCCCCCC-HHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHH
Q psy200          382 QTDKFNMFN-ASALQLLAGKVAAVSGDIRKAIDITNHLIDLT  422 (490)
Q Consensus       382 ~~~~~~~~~-~~~i~~i~~~i~~~~Gd~r~ai~ll~~a~~~a  422 (490)
                      .++  ..++ +++++.|++   ...||+|.++++++.+....
T Consensus       208 ~~~--~~~~~~~~l~~i~~---~~~G~~r~a~~~l~~~~~~~  244 (354)
T 1sxj_E          208 NER--IQLETKDILKRIAQ---ASNGNLRVSLLMLESMALNN  244 (354)
T ss_dssp             HHT--CEECCSHHHHHHHH---HHTTCHHHHHHHHTHHHHTT
T ss_pred             HcC--CCCCcHHHHHHHHH---HcCCCHHHHHHHHHHHHHhC
Confidence            763  4577 899999987   67899999999999887544

>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=99.73  E-value=1.2e-16  Score=154.00  Aligned_cols=209  Identities=17%  Similarity=0.224  Sum_probs=136.8

Q ss_pred             CCCCChHHHHHHHHHH---HHhhhc---cCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHH
Q psy200          194 CELPGREVQLEGIRQF---LLGHVN---NETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYE  267 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~---L~~~~~---~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~  267 (490)
                      ..++|....++.+...   +...+.   ....++++|+||+|||||++|+++++.+.    ..++.++|....       
T Consensus        33 ~~~i~~~~~~~~i~~~~~~l~~~l~~~~~~~~~~vLl~G~~GtGKT~la~~ia~~~~----~~~~~i~~~~~~-------  101 (272)
T 1d2n_A           33 NGIIKWGDPVTRVLDDGELLVQQTKNSDRTPLVSVLLEGPPHSGKTALAAKIAEESN----FPFIKICSPDKM-------  101 (272)
T ss_dssp             TCCCCCSHHHHHHHHHHHHHHHHHHHCSSCSEEEEEEECSTTSSHHHHHHHHHHHHT----CSEEEEECGGGC-------
T ss_pred             cCCCCccHHHHHHHHHHHHHHHHHhccCCCCCeEEEEECCCCCcHHHHHHHHHHHhC----CCEEEEeCHHHh-------
Confidence            5677887777666663   333332   45668999999999999999999999864    677888876421       


Q ss_pred             HHHHHhcCCCCCCcH----HHHHHHHHHHHhcCCCeEEEEEecCccccc------cCH----HHHHHhHhCCCCCCCcEE
Q psy200          268 TIVNELKLKPGGKSE----RHQLGAILKYFDTKHKSILLILDEIDALES------RKQ----TILYTIFEWPSIPGSKLV  333 (490)
Q Consensus       268 ~i~~~l~~~~~~~s~----~~~~~~l~~~l~~~~~~~vI~IDEid~l~~------~~~----~~L~~l~~~~~~~~~~vi  333 (490)
                                .+...    ..+...+..+..  .++.+|||||+|.+..      ..+    +.|..+++.....+..++
T Consensus       102 ----------~g~~~~~~~~~~~~~~~~~~~--~~~~vl~iDEid~l~~~~~~~~~~~~~~l~~L~~~~~~~~~~~~~~~  169 (272)
T 1d2n_A          102 ----------IGFSETAKCQAMKKIFDDAYK--SQLSCVVVDDIERLLDYVPIGPRFSNLVLQALLVLLKKAPPQGRKLL  169 (272)
T ss_dssp             ----------TTCCHHHHHHHHHHHHHHHHT--SSEEEEEECCHHHHTTCBTTTTBCCHHHHHHHHHHTTCCCSTTCEEE
T ss_pred             ----------cCCchHHHHHHHHHHHHHHHh--cCCcEEEEEChhhhhccCCCChhHHHHHHHHHHHHhcCccCCCCCEE
Confidence                      11222    222333333322  4578999999999832      222    333344443333566888


Q ss_pred             EEEecCCCChhHhhhH-HhhhccCCCCeeEEeCCCCH-HHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHH--hhCCHH
Q psy200          334 LVGVANALDLTDRMLP-RLQANVTLQPTLMNFAPYSR-EQILEIISQKLKQTDKFNMFNASALQLLAGKVAA--VSGDIR  409 (490)
Q Consensus       334 lI~~tn~~~~~~~l~~-~l~~R~~~~~~~i~~~pls~-~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~--~~Gd~r  409 (490)
                      +|+++|..   +.+.+ .+.+||.   ..+.|++++. +++..++.+.       ..+++++++.+++...+  +.|++|
T Consensus       170 ii~ttn~~---~~l~~~~l~~rf~---~~i~~p~l~~r~~i~~i~~~~-------~~~~~~~~~~l~~~~~g~~~~g~ir  236 (272)
T 1d2n_A          170 IIGTTSRK---DVLQEMEMLNAFS---TTIHVPNIATGEQLLEALELL-------GNFKDKERTTIAQQVKGKKVWIGIK  236 (272)
T ss_dssp             EEEEESCH---HHHHHTTCTTTSS---EEEECCCEEEHHHHHHHHHHH-------TCSCHHHHHHHHHHHTTSEEEECHH
T ss_pred             EEEecCCh---hhcchhhhhcccc---eEEcCCCccHHHHHHHHHHhc-------CCCCHHHHHHHHHHhcCCCccccHH
Confidence            99999854   33333 5677876   4799999987 7777777652       23688999999884322  244899


Q ss_pred             HHHHHHHHHHHHHHhccccCCcccccCHHHHHHHHHHhc
Q psy200          410 KAIDITNHLIDLTYDNVKENGEVTGIGLKEVLGVISSVY  448 (490)
Q Consensus       410 ~ai~ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~~~~~  448 (490)
                      .++++++.|...+.          ....+++.+++.+..
T Consensus       237 ~l~~~l~~a~~~~~----------~~~~~~~~~~l~~~~  265 (272)
T 1d2n_A          237 KLLMLIEMSLQMDP----------EYRVRKFLALLREEG  265 (272)
T ss_dssp             HHHHHHHHHTTSCG----------GGHHHHHHHHHHHTS
T ss_pred             HHHHHHHHHhhhch----------HHHHHHHHHHHHHcC
Confidence            99999988865432          234666666666554

>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=99.73  E-value=1e-19  Score=175.06  Aligned_cols=223  Identities=15%  Similarity=0.147  Sum_probs=144.7

Q ss_pred             CCCCChHHHHHHHHHHHHhhh--------ccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHV--------NNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASV  265 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~--------~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l  265 (490)
                      ++++|.+..++.|.+++....        ....+.+++|+||+|||||++|+++++++.    ..+++++|..+..    
T Consensus        11 ~~i~G~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKT~la~~la~~~~----~~~~~v~~~~~~~----   82 (268)
T 2r62_A           11 KDMAGNEEAKEEVVEIVDFLKYPERYANLGAKIPKGVLLVGPPGTGKTLLAKAVAGEAH----VPFFSMGGSSFIE----   82 (268)
T ss_dssp             TTSSSCTTTHHHHHHHHHHHHCHHHHHHHSCCCCSCCCCBCSSCSSHHHHHHHHHHHHT----CCCCCCCSCTTTT----
T ss_pred             HHhCCcHHHHHHHHHHHHHHHChHHHHHCCCCCCceEEEECCCCCcHHHHHHHHHHHhC----CCEEEechHHHHH----
Confidence            678999888888887765321        123456799999999999999999999875    4566777765432    


Q ss_pred             HHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCH------------HHHHHhH---hCCCCCCC
Q psy200          266 YETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQ------------TILYTIF---EWPSIPGS  330 (490)
Q Consensus       266 ~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~------------~~L~~l~---~~~~~~~~  330 (490)
                                ...+.....+...|..+..  ..+.||||||+|.+.....            ..+..++   +.......
T Consensus        83 ----------~~~~~~~~~~~~~~~~a~~--~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~  150 (268)
T 2r62_A           83 ----------MFVGLGASRVRDLFETAKK--QAPSIIFIDEIDAIGKSRAAGGVVSGNDEREQTLNQLLAEMDGFGSENA  150 (268)
T ss_dssp             ----------SCSSSCSSSSSTTHHHHHH--SCSCEEEESCGGGTTC----------CCCSCSSTTTTTTTTTCSSCSCS
T ss_pred             ----------hhcchHHHHHHHHHHHHHh--cCCeEEEEeChhhhcccccccccCCCchhHHHHHHHHHHHhhCcccCCC
Confidence                      1111222222233443333  3467999999999975421            1122222   21122345


Q ss_pred             cEEEEEecCCCChhHhhhHHhhh--ccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCH
Q psy200          331 KLVLVGVANALDLTDRMLPRLQA--NVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDI  408 (490)
Q Consensus       331 ~vilI~~tn~~~~~~~l~~~l~~--R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~  408 (490)
                      .+++|+++|..+   .+++.+.+  ||.   ..+.|.+++.++..+++..++.....   .++..++.+++...++  ..
T Consensus       151 ~v~vi~ttn~~~---~ld~~l~r~~Rf~---~~i~i~~p~~~~r~~il~~~~~~~~~---~~~~~~~~la~~~~g~--~g  219 (268)
T 2r62_A          151 PVIVLAATNRPE---ILDPALMRPGRFD---RQVLVDKPDFNGRVEILKVHIKGVKL---ANDVNLQEVAKLTAGL--AG  219 (268)
T ss_dssp             CCEEEECBSCCT---TSCGGGGSSSSSC---CCCBCCCCCTTTHHHHHHHHTSSSCC---CSSCCTTTTTSSSCSS--CH
T ss_pred             CEEEEEecCCch---hcCHhHcCCCCCC---eEEEecCcCHHHHHHHHHHHHhcCCC---CCccCHHHHHHHcCCC--CH
Confidence            689999998653   34455555  665   36899999999999999988865421   1222345565522222  23


Q ss_pred             HHHHHHHHHHHHHHHhccccCCcccccCHHHHHHHHHHhccCcc
Q psy200          409 RKAIDITNHLIDLTYDNVKENGEVTGIGLKEVLGVISSVYCTSQ  452 (490)
Q Consensus       409 r~ai~ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~~~~~~~~~  452 (490)
                      +.+.++|++|...|...+     ...|+.+++..++..+.+...
T Consensus       220 ~dl~~l~~~a~~~a~~~~-----~~~i~~~~~~~a~~~~~~~~~  258 (268)
T 2r62_A          220 ADLANIINEAALLAGRNN-----QKEVRQQHLKEAVERGIAGLE  258 (268)
T ss_dssp             HHHHHHHHHHHHTTSSSC-----CCSCCHHHHHTSCTTCCCCCC
T ss_pred             HHHHHHHHHHHHHHHHhc-----cCCcCHHHHHHHHHHHhhcch
Confidence            677789999998887766     568999999999887765544

>2dhr_A FTSH; AAA+ protein, hexameric Zn metalloprotease, hydrolase; HET: ADP; 3.90A {Thermus thermophilus}

Probab=99.72  E-value=7.7e-17  Score=166.87  Aligned_cols=217  Identities=18%  Similarity=0.218  Sum_probs=151.3

Q ss_pred             CCCCChHHHHHHHHHHHHhhhc--------cCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVN--------NETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASV  265 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~--------~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l  265 (490)
                      ++++|.++.+.++.+.+.....        ...+++++|+||||||||+|+++++..+.    ..+++++|..+..    
T Consensus        31 ~dv~G~~~~k~~l~~lv~~l~~~~~~~~lg~~ip~GvLL~GppGtGKTtLaraIa~~~~----~~~i~i~g~~~~~----  102 (499)
T 2dhr_A           31 KDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEAR----VPFITASGSDFVE----  102 (499)
T ss_dssp             TSSCSCHHHHHHHHHHHHHHHCGGGTTTTSCCCCSEEEEECSSSSSHHHHHHHHHHHTT----CCEEEEEGGGGTS----
T ss_pred             HHcCCcHHHHHHHHHHHHHhhchhhhhhccCCCCceEEEECCCCCCHHHHHHHHHHHhC----CCEEEEehhHHHH----
Confidence            7899999998888877654211        12356799999999999999999999864    6788998876532    


Q ss_pred             HHHHHHHhcCCCCCCcHHHHHHHHHHHHhcC--CCeEEEEEecCccccccC-----------HHHHHHhHhC-C-CCCCC
Q psy200          266 YETIVNELKLKPGGKSERHQLGAILKYFDTK--HKSILLILDEIDALESRK-----------QTILYTIFEW-P-SIPGS  330 (490)
Q Consensus       266 ~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~--~~~~vI~IDEid~l~~~~-----------~~~L~~l~~~-~-~~~~~  330 (490)
                                .+.+.....    +...+...  ..+++|||||||.+....           ...+..++.. . .....
T Consensus       103 ----------~~~g~~~~~----v~~lfq~a~~~~p~il~IDEId~l~~~r~~~~~~~~~e~~~~l~~LL~~Ldg~~~~~  168 (499)
T 2dhr_A          103 ----------MFVGVGAAR----VRDLFETAKRHAPCIVFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMDGFEKDT  168 (499)
T ss_dssp             ----------SCTTHHHHH----HHHHTTTSSSSSSCEEEEECGGGTCCCSSSSTTTSSHHHHHHHHHHHHHGGGCCSSC
T ss_pred             ----------hhhhhHHHH----HHHHHHHHHhcCCCEEEEehHHHHHHhhccCcCCCcHHHHHHHHHHHHHhcccccCc
Confidence                      122222222    23333322  347899999999986432           1233343322 1 12345


Q ss_pred             cEEEEEecCCCChhHhhhHHhhh--ccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCC-HHHHHHHHHHHHHhhCC
Q psy200          331 KLVLVGVANALDLTDRMLPRLQA--NVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFN-ASALQLLAGKVAAVSGD  407 (490)
Q Consensus       331 ~vilI~~tn~~~~~~~l~~~l~~--R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~-~~~i~~i~~~i~~~~Gd  407 (490)
                      .+++++++|..+   .+++.+.+  ||.   ..+.|++++.++..+||+.++...    .++ +..+..++.   .+.|+
T Consensus       169 ~viviAatn~p~---~LD~aLlr~gRfd---r~i~i~~Pd~~~R~~IL~~~~~~~----~l~~dv~l~~lA~---~t~G~  235 (499)
T 2dhr_A          169 AIVVMAATNRPD---ILDPALLRPGRFD---RQIAIDAPDVKGREQILRIHARGK----PLAEDVDLALLAK---RTPGF  235 (499)
T ss_dssp             CCEEEECCSCGG---GSCTTTSSTTSSC---CEEECCCCCHHHHHHHHHHTTSSS----CCCCSSTTHHHHT---TSCSC
T ss_pred             cEEEEEecCChh---hcCcccccccccc---eEEecCCCCHHHHHHHHHHHHhcC----CCChHHHHHHHHH---hcCCC
Confidence            678889998653   36666766  555   479999999999999998776543    233 233667776   78888


Q ss_pred             H-HHHHHHHHHHHHHHHhccccCCcccccCHHHHHHHHHHhccC
Q psy200          408 I-RKAIDITNHLIDLTYDNVKENGEVTGIGLKEVLGVISSVYCT  450 (490)
Q Consensus       408 ~-r~ai~ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~~~~~~~  450 (490)
                      . +.+.++|.+|+..|...+     ...|+++|+..|+..+...
T Consensus       236 ~gadL~~lv~~Aa~~A~~~~-----~~~It~~dl~~al~~v~~~  274 (499)
T 2dhr_A          236 VGADLENLLNEAALLAAREG-----RRKITMKDLEEAADRVMML  274 (499)
T ss_dssp             CHHHHHHHHHHHHHHHTTTC-----CSSCCSHHHHHHHHHHTTC
T ss_pred             CHHHHHHHHHHHHHHHHHhC-----CCccCHHHHHHHHHHHhcc
Confidence            7 788899999998888776     5689999999999998754

>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=99.72  E-value=2.3e-18  Score=186.49  Aligned_cols=226  Identities=17%  Similarity=0.234  Sum_probs=133.6

Q ss_pred             CCCCChHHHHHHHHHHHHhhhc---------cCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVN---------NETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAAS  264 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~---------~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~  264 (490)
                      +++.|.++.++.|.+.+...+.         ...++++|||||||||||++|++++++++    ..++.++++.+     
T Consensus       477 ~diggl~~~k~~l~e~v~~p~~~p~~f~~~g~~~~~gvLl~GPPGtGKT~lAkaiA~e~~----~~f~~v~~~~l-----  547 (806)
T 3cf2_A          477 EDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANECQ----ANFISIKGPEL-----  547 (806)
T ss_dssp             TTCCSCHHHHHHHTTTTTTTTTCSGGGSSSCCCCCSCCEEESSTTSSHHHHHHHHHHTTT----CEEEECCHHHH-----
T ss_pred             HHhCCHHHHHHHHHHHHHhhhhCHHHHHhcCCCCCceEEEecCCCCCchHHHHHHHHHhC----CceEEeccchh-----
Confidence            6788999999998887764332         12567899999999999999999999975    67777754432     


Q ss_pred             HHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccC-----------HHHHHHh---HhCCCCCCC
Q psy200          265 VYETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRK-----------QTILYTI---FEWPSIPGS  330 (490)
Q Consensus       265 l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~-----------~~~L~~l---~~~~~~~~~  330 (490)
                               -..+.|.++..+.+.|..+..  ..|+||||||||.+...+           ...+.++   ++- .....
T Consensus       548 ---------~s~~vGese~~vr~lF~~Ar~--~~P~IifiDEiDsl~~~R~~~~~~~~~~~~rv~~~lL~~mdg-~~~~~  615 (806)
T 3cf2_A          548 ---------LTMWFGESEANVREIFDKARQ--AAPCVLFFDELDSIAKARGGNIGDGGGAADRVINQILTEMDG-MSTKK  615 (806)
T ss_dssp             ---------HTTTCSSCHHHHHHHHHHHHT--TCSEEEECSCGGGCC--------------CHHHHHHHHHHHS-SCSSS
T ss_pred             ---------hccccchHHHHHHHHHHHHHH--cCCceeechhhhHHhhccCCCCCCCchHHHHHHHHHHHHHhC-CCCCC
Confidence                     237888899999998887765  468999999999997542           1122333   331 22456


Q ss_pred             cEEEEEecCCCChhHhhhHHhhh--ccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhC-C
Q psy200          331 KLVLVGVANALDLTDRMLPRLQA--NVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSG-D  407 (490)
Q Consensus       331 ~vilI~~tn~~~~~~~l~~~l~~--R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~G-d  407 (490)
                      .|+||++||+.   +.+++.+.+  ||.   ..|+|+.++.++..+||+.++.+..   .-.+..++.|++...+++| |
T Consensus       616 ~V~vi~aTN~p---~~lD~AllRpgRfd---~~i~v~lPd~~~R~~il~~~l~~~~---~~~~~dl~~la~~t~g~SGad  686 (806)
T 3cf2_A          616 NVFIIGATNRP---DIIDPAILRPGRLD---QLIYIPLPDEKSRVAILKANLRKSP---VAKDVDLEFLAKMTNGFSGAD  686 (806)
T ss_dssp             SEEEECC-CCS---SSSCHHHHSTTTSC---CEEEC-----CHHHHTTTTTSSCC-----CCC----------------C
T ss_pred             CEEEEEeCCCc---hhCCHhHcCCCcce---EEEEECCcCHHHHHHHHHHHhcCCC---CCCCCCHHHHHHhCCCCCHHH
Confidence            79999999965   456677766  777   5899999999999999988776541   1233447778876655555 5


Q ss_pred             HHHHHHHHHHHHHHHHhccccC--------------------CcccccCHHHHHHHHHHhccCcc
Q psy200          408 IRKAIDITNHLIDLTYDNVKEN--------------------GEVTGIGLKEVLGVISSVYCTSQ  452 (490)
Q Consensus       408 ~r~ai~ll~~a~~~a~~~~~~~--------------------~~~~~It~~~v~~a~~~~~~~~~  452 (490)
                      +.   ++|+.|...|.++....                    .....|+++||.+|+..+.++..
T Consensus       687 i~---~l~~~A~~~a~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~df~~al~~~~pSvs  748 (806)
T 3cf2_A          687 LT---EICQRACKLAIRESIESEIRRERERQTNPSAMEVEEDDPVPEIRRDHFEEAMRFARRSVS  748 (806)
T ss_dssp             HH---HHHHHHHHHHHHHHHC-----------------------CCC----CCTTTC--------
T ss_pred             HH---HHHHHHHHHHHHHHHHhhhhhhhhhccCccccccccccccCccCHHHHHHHHHhCCCCCC
Confidence            44   46667766665432110                    11346999999999999877644

>1ojl_A Transcriptional regulatory protein ZRAR; response regulator, two component system, AAA domain, NTRC family, DNA-binding; HET: ATP; 3.0A {Salmonella typhimurium}

Probab=99.72  E-value=2.2e-17  Score=161.56  Aligned_cols=215  Identities=17%  Similarity=0.235  Sum_probs=145.9

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHh
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNEL  273 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l  273 (490)
                      ++++|+...+..+.+.+....  ....+++|+|++|||||++|+++++... ..+..++.++|..... ..+...++...
T Consensus         2 ~~iig~s~~~~~~~~~~~~~a--~~~~~vLi~Ge~GtGKt~lAr~i~~~~~-~~~~~~v~v~~~~~~~-~l~~~~lfg~~   77 (304)
T 1ojl_A            2 SHMIGSSPAMQHLLNEIAMVA--PSDATVLIHGDSGTGKELVARALHACSA-RSDRPLVTLNCAALNE-SLLESELFGHE   77 (304)
T ss_dssp             -CCCCCSHHHHHHHHHHHHHC--STTSCEEEESCTTSCHHHHHHHHHHHSS-CSSSCCCEEECSSCCH-HHHHHHHTCCC
T ss_pred             CCcEECCHHHHHHHHHHHHHh--CCCCcEEEECCCCchHHHHHHHHHHhCc-ccCCCeEEEeCCCCCh-HHHHHHhcCcc
Confidence            468999999999999888743  4567899999999999999999988653 2345789999998732 22222222111


Q ss_pred             cCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCHHHHHHhHhCCCC--------CCCcEEEEEecCCCChhH
Q psy200          274 KLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPSI--------PGSKLVLVGVANALDLTD  345 (490)
Q Consensus       274 ~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~--------~~~~vilI~~tn~~~~~~  345 (490)
                      ...+.+... .....|..+ .    ..+||||||+.+....|..|+.+++....        ....+.+|++||.. +.+
T Consensus        78 ~g~~tg~~~-~~~g~~~~a-~----~g~L~LDEi~~l~~~~q~~Ll~~l~~~~~~~~g~~~~~~~~~riI~atn~~-l~~  150 (304)
T 1ojl_A           78 KGAFTGADK-RREGRFVEA-D----GGTLFLDEIGDISPLMQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRD-LAE  150 (304)
T ss_dssp             SSCCC---C-CCCCHHHHH-T----TSEEEEESCTTCCHHHHHHHHHHHHSSBCCBTTBCCCCBCCCEEEEEESSC-HHH
T ss_pred             ccccCchhh-hhcCHHHhc-C----CCEEEEeccccCCHHHHHHHHHHHhcCEeeecCCcccccCCeEEEEecCcc-HHH
Confidence            111111111 111122221 1    13899999999998888888887764321        13457888888853 222


Q ss_pred             -----hhhHHhhhccCCCCeeEEeCCCC--HHHHHHHHHHHHhcc----C-CCCCCCHHHHHHHHHHHHHhhCCHHHHHH
Q psy200          346 -----RMLPRLQANVTLQPTLMNFAPYS--REQILEIISQKLKQT----D-KFNMFNASALQLLAGKVAAVSGDIRKAID  413 (490)
Q Consensus       346 -----~l~~~l~~R~~~~~~~i~~~pls--~~e~~~il~~~l~~~----~-~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~  413 (490)
                           .+.+.+..|+..  ..+.++|+.  .+++..++.+++...    + ....+++++++.+..  +.|.||+|.+.+
T Consensus       151 ~v~~g~fr~~L~~Rl~~--~~i~lPpL~eR~edi~~l~~~~l~~~~~~~~~~~~~~s~~a~~~L~~--~~wpGnvReL~~  226 (304)
T 1ojl_A          151 EVSAGRFRQDLYYRLNV--VAIEMPSLRQRREDIPLLADHFLRRFAERNRKVVKGFTPQAMDLLIH--YDWPGNIRELEN  226 (304)
T ss_dssp             HHHHTSSCHHHHHHHSS--EEEECCCSGGGGGGHHHHHHHHHHHHHHHTTCCCCCBCHHHHHHHHH--CCCSSHHHHHHH
T ss_pred             HHHhCCcHHHHHhhcCe--eEEeccCHHHhHhhHHHHHHHHHHHHHHHhccCccCCCHHHHHHHHc--CCCCCCHHHHHH
Confidence                 245678888852  368899998  678887777766543    2 234689999999987  567999999999


Q ss_pred             HHHHHHHHHH
Q psy200          414 ITNHLIDLTY  423 (490)
Q Consensus       414 ll~~a~~~a~  423 (490)
                      ++++++..+.
T Consensus       227 ~l~~~~~~~~  236 (304)
T 1ojl_A          227 AIERAVVLLT  236 (304)
T ss_dssp             HHHHHHHHCC
T ss_pred             HHHHHHHhCC
Confidence            9999987654

>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=99.71  E-value=1.3e-16  Score=161.14  Aligned_cols=234  Identities=17%  Similarity=0.196  Sum_probs=150.4

Q ss_pred             CCCCChHHHHHHHHHHHHhhhc--------------------------cCCCCeEEEECCCCCcHHHHHHHHHHHhhhcC
Q psy200          194 CELPGREVQLEGIRQFLLGHVN--------------------------NETSGSMYISGPPGTGKSASLNLLVSRAEIKD  247 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~--------------------------~~~~~~ill~GppGtGKTtla~~l~~~l~~~~  247 (490)
                      +.++|+++.++.|..++...+.                          .....+++|+||||||||++|+++++.+.   
T Consensus        21 ~~viGq~~ak~~l~~~~~~~~~~~~~g~~~~~~~~~~~~~p~~~~~~~~~~~~~ill~Gp~GtGKT~la~~la~~l~---   97 (376)
T 1um8_A           21 NYVIGQEQAKKVFSVAVYNHYKRLSFKEKLKKQDNQDSNVELEHLEEVELSKSNILLIGPTGSGKTLMAQTLAKHLD---   97 (376)
T ss_dssp             TTCCSCHHHHHHHHHHHHHHHHHHHHHHHHHHHCSHHHHHHHHHHHHTTCCCCCEEEECCTTSSHHHHHHHHHHHTT---
T ss_pred             hHccCcHHHHHHHHHHHHHHHHHHHhhhhhhhccccccccccccccccccCCCCEEEECCCCCCHHHHHHHHHHHhC---
Confidence            7899999999999888732110                          12467899999999999999999999874   


Q ss_pred             CceEEEEeccCCCCHHHHHHHHHHHhcCCCCCCcHH-HHHHHHHHH---HhcCCCeEEEEEecCcccccc----------
Q psy200          248 AFKTIYINCNSVRNAASVYETIVNELKLKPGGKSER-HQLGAILKY---FDTKHKSILLILDEIDALESR----------  313 (490)
Q Consensus       248 ~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~~~s~~-~~~~~l~~~---l~~~~~~~vI~IDEid~l~~~----------  313 (490)
                       ..++.++|...... .            +.+.... .+...+...   +.. ....+|||||++.+...          
T Consensus        98 -~~~~~~~~~~~~~~-~------------~~g~~~~~~~~~~~~~~~~~~~~-~~~~vl~iDEi~~l~~~~~~~~~~~~~  162 (376)
T 1um8_A           98 -IPIAISDATSLTEA-G------------YVGEDVENILTRLLQASDWNVQK-AQKGIVFIDEIDKISRLSENRSITRDV  162 (376)
T ss_dssp             -CCEEEEEGGGCC---------------------CTHHHHHHHHHTTTCHHH-HTTSEEEEETGGGC-------------
T ss_pred             -CCEEEecchhhhhc-C------------cCCccHHHHHHHHHhhccchhhh-cCCeEEEEcCHHHHhhhcCCCceeccc
Confidence             67888888876321 1            1111111 122222111   111 12459999999999876          


Q ss_pred             ----CHHHHHHhHhCCC------------------CCCCcEEEEEecCCCChh---------------------------
Q psy200          314 ----KQTILYTIFEWPS------------------IPGSKLVLVGVANALDLT---------------------------  344 (490)
Q Consensus       314 ----~~~~L~~l~~~~~------------------~~~~~vilI~~tn~~~~~---------------------------  344 (490)
                          .++.|+.+++...                  ....++++|+++|..++.                           
T Consensus       163 ~~~~~~~~Ll~~le~~~~~~~~~~~~~~~~~~~~~i~t~n~~~I~~~~~~~l~~~l~~R~~~~~~g~~~~~~~~~~~~~~  242 (376)
T 1um8_A          163 SGEGVQQALLKIVEGSLVNIPPKGGRKHPEGNFIQIDTSDILFICAGAFDGLAEIIKKRTTQNVLGFTQEKMSKKEQEAI  242 (376)
T ss_dssp             -CHHHHHHHHHHHHCCEEC---------------CEECTTCEEEEEECCTTHHHHTTTSCSSCCCSCCCSSCCTTTTTTS
T ss_pred             chHHHHHHHHHHhhccceecccccccccCCcceEEEecCCeEEEecCCHHHHHHHHHHHhcccccCCCchhhhccchhHH
Confidence                5677888877321                  112456777777632111                           


Q ss_pred             -----------HhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHH----H-------HhccCCCCCCCHHHHHHHHHHHH
Q psy200          345 -----------DRMLPRLQANVTLQPTLMNFAPYSREQILEIISQ----K-------LKQTDKFNMFNASALQLLAGKVA  402 (490)
Q Consensus       345 -----------~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~----~-------l~~~~~~~~~~~~~i~~i~~~i~  402 (490)
                                 ..+.+.+.+||+   ..+.|+|++.+++..++..    .       +...+....+++++++.|++...
T Consensus       243 ~~~~~~~~l~~~~~~p~l~~R~~---~~i~~~~l~~~~l~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~l~~~~~  319 (376)
T 1um8_A          243 LHLVQTHDLVTYGLIPELIGRLP---VLSTLDSISLEAMVDILQKPKNALIKQYQQLFKMDEVDLIFEEEAIKEIAQLAL  319 (376)
T ss_dssp             GGGCCHHHHHHTTCCHHHHTTCC---EEEECCCCCHHHHHHHHHSSTTCHHHHHHHHHHTTTCEEEECHHHHHHHHHHHH
T ss_pred             HhhcCHHHHhhcCCChHHhcCCC---ceeeccCCCHHHHHHHHhhhHHHHHHHHHHHHhhcCceEEECHHHHHHHHHHhc
Confidence                       124577888887   4799999999999998862    1       21122345689999999998443


Q ss_pred             HhhCCHHHHHHHHHHHHHHHHhcccc-CCcccccCHHHHHHHHHHhc
Q psy200          403 AVSGDIRKAIDITNHLIDLTYDNVKE-NGEVTGIGLKEVLGVISSVY  448 (490)
Q Consensus       403 ~~~Gd~r~ai~ll~~a~~~a~~~~~~-~~~~~~It~~~v~~a~~~~~  448 (490)
                      ...||+|.+.+++++++..+..+... ......|+.++|..+...+.
T Consensus       320 ~~~~~~R~L~~~le~~~~~~~~~~~~~~~~~~~i~~~~v~~~~~~~~  366 (376)
T 1um8_A          320 ERKTGARGLRAIIEDFCLDIMFDLPKLKGSEVRITKDCVLKQAEPLI  366 (376)
T ss_dssp             HTTCTGGGHHHHHHHHHHHHHHTGGGGTTSEEEECHHHHTTSSCCEE
T ss_pred             ccccCcHHHHHHHHHHHHHHHhhccCCCCCEEEEeHHHhcCCCCcee
Confidence            34599999999999998765544311 11123689999887654433

>4fcw_A Chaperone protein CLPB; AAA domain; HET: ADP; 2.35A {Thermus thermophilus} PDB: 4fcv_A* 4fd2_A* 4fct_A*

Probab=99.71  E-value=9.4e-17  Score=157.61  Aligned_cols=218  Identities=14%  Similarity=0.192  Sum_probs=151.2

Q ss_pred             CCCCChHHHHHHHHHHHHhhhcc-----CCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVNN-----ETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYET  268 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~-----~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~  268 (490)
                      +.++|++..++.|...+......     .+..+++|+||+|||||++|+++++.+. .....+++++|........ ...
T Consensus        17 ~~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~ll~G~~GtGKt~la~~la~~~~-~~~~~~~~~~~~~~~~~~~-~~~   94 (311)
T 4fcw_A           17 KRVVGQDEAIRAVADAIRRARAGLKDPNRPIGSFLFLGPTGVGKTELAKTLAATLF-DTEEAMIRIDMTEYMEKHA-VSR   94 (311)
T ss_dssp             TTCCSCHHHHHHHHHHHHHHHHTCSCTTSCSEEEEEESCSSSSHHHHHHHHHHHHH-SCGGGEEEEEGGGCCSTTH-HHH
T ss_pred             hhcCCHHHHHHHHHHHHHHHhcCCCCCCCCceEEEEECCCCcCHHHHHHHHHHHHc-CCCcceEEeeccccccccc-HHH
Confidence            78999999999999988875321     1235899999999999999999999874 2234688999987754322 222


Q ss_pred             HHHHhcCC--CCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCHHHHHHhHhCCCCC--------CCcEEEEEec
Q psy200          269 IVNELKLK--PGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPSIP--------GSKLVLVGVA  338 (490)
Q Consensus       269 i~~~l~~~--~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~--------~~~vilI~~t  338 (490)
                      ++   +..  ..+....   ..+..++.. ....+|||||++.+....+..|+.+++.....        -.++++|+++
T Consensus        95 l~---g~~~~~~~~~~~---~~~~~~~~~-~~~~vl~lDEi~~l~~~~~~~Ll~~le~~~~~~~~~~~~~~~~~iiI~tt  167 (311)
T 4fcw_A           95 LI---GAPPGYVGYEEG---GQLTEAVRR-RPYSVILFDAIEKAHPDVFNILLQMLDDGRLTDSHGRTVDFRNTVIIMTS  167 (311)
T ss_dssp             HH---CCCTTSTTTTTC---CHHHHHHHH-CSSEEEEEETGGGSCHHHHHHHHHHHHHSEEECTTSCEEECTTEEEEEEE
T ss_pred             hc---CCCCcccccccc---chHHHHHHh-CCCeEEEEeChhhcCHHHHHHHHHHHhcCEEEcCCCCEEECCCcEEEEec
Confidence            21   111  1111110   123333332 23469999999999888888888887643211        1367788999


Q ss_pred             CCC---------------Ch--------hHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhcc-------CCCCC
Q psy200          339 NAL---------------DL--------TDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQT-------DKFNM  388 (490)
Q Consensus       339 n~~---------------~~--------~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~-------~~~~~  388 (490)
                      |..               ++        ...+.+.+.+||.   ..+.|.|++.+++..|+.+.+...       +....
T Consensus       168 n~~~~~i~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~R~~---~~~~~~p~~~~~~~~i~~~~l~~~~~~~~~~~~~~~  244 (311)
T 4fcw_A          168 NLGSPLILEGLQKGWPYERIRDEVFKVLQQHFRPEFLNRLD---EIVVFRPLTKEQIRQIVEIQMSYLRARLAEKRISLE  244 (311)
T ss_dssp             STTHHHHHTTTTSCCCSSTHHHHTHHHHHHHSCHHHHTTCS---EEEECCCCCHHHHHHHHHHHTHHHHHHHHTTTCEEE
T ss_pred             ccCHHHHHhhhcccccHHHHHHHHHHHHHHhCCHHHHhcCC---eEEEeCCCCHHHHHHHHHHHHHHHHHHHHhCCcEEE
Confidence            862               21        3355678889997   489999999999999998877653       22456


Q ss_pred             CCHHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHH
Q psy200          389 FNASALQLLAGKVAAVSGDIRKAIDITNHLIDLTY  423 (490)
Q Consensus       389 ~~~~~i~~i~~~i~~~~Gd~r~ai~ll~~a~~~a~  423 (490)
                      +++++++.+++......||+|.+.+++++++..+.
T Consensus       245 ~~~~~~~~l~~~~~~~~gn~R~L~~~i~~~~~~~~  279 (311)
T 4fcw_A          245 LTEAAKDFLAERGYDPVFGARPLRRVIQRELETPL  279 (311)
T ss_dssp             ECHHHHHHHHHHSCBTTTBTTTHHHHHHHHTHHHH
T ss_pred             eCHHHHHHHHHhCCCccCCchhHHHHHHHHHHHHH
Confidence            89999999997222227999999998888876544

>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=99.69  E-value=1.5e-16  Score=152.74  Aligned_cols=216  Identities=17%  Similarity=0.150  Sum_probs=139.5

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHh
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNEL  273 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l  273 (490)
                      +.++|++..+..+.+.+....  ....+++|+|++|||||++|+++++.+. ..+..+++++|.... ...+...++...
T Consensus         6 ~~~ig~~~~~~~~~~~~~~~~--~~~~~vll~G~~GtGKt~la~~i~~~~~-~~~~~~~~v~~~~~~-~~~~~~~l~g~~   81 (265)
T 2bjv_A            6 DNLLGEANSFLEVLEQVSHLA--PLDKPVLIIGERGTGKELIASRLHYLSS-RWQGPFISLNCAALN-ENLLDSELFGHE   81 (265)
T ss_dssp             ----CCCHHHHHHHHHHHHHT--TSCSCEEEECCTTSCHHHHHHHHHHTST-TTTSCEEEEEGGGSC-HHHHHHHHHCCC
T ss_pred             ccceeCCHHHHHHHHHHHHHh--CCCCCEEEECCCCCcHHHHHHHHHHhcC-ccCCCeEEEecCCCC-hhHHHHHhcCCc
Confidence            568999999999988887643  3457899999999999999999988764 234578999999873 222222222111


Q ss_pred             cCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCHHHHHHhHhCCC--------CCCCcEEEEEecCCC--Ch
Q psy200          274 KLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPS--------IPGSKLVLVGVANAL--DL  343 (490)
Q Consensus       274 ~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~--------~~~~~vilI~~tn~~--~~  343 (490)
                      ...+.+.... ....+..  .   ...+|||||++.+....|..|+.+++...        .....+.+|+++|..  ++
T Consensus        82 ~~~~~g~~~~-~~~~l~~--a---~~~~l~lDEi~~l~~~~q~~Ll~~l~~~~~~~~g~~~~~~~~~~iI~atn~~~~~~  155 (265)
T 2bjv_A           82 AGAFTGAQKR-HPGRFER--A---DGGTLFLDELATAPMMVQEKLLRVIEYGELERVGGSQPLQVNVRLVCATNADLPAM  155 (265)
T ss_dssp             ---------C-CCCHHHH--T---TTSEEEEESGGGSCHHHHHHHHHHHHHCEECCCCC--CEECCCEEEEEESSCHHHH
T ss_pred             cccccccccc-ccchhhh--c---CCcEEEEechHhcCHHHHHHHHHHHHhCCeecCCCcccccCCeEEEEecCcCHHHH
Confidence            1111111000 0011111  1   12499999999999888888888876321        112457788888853  11


Q ss_pred             h--HhhhHHhhhccCCCCeeEEeCCCCH--HHHHHHHHHHHhcc----CCC--CCCCHHHHHHHHHHHHHhhCCHHHHHH
Q psy200          344 T--DRMLPRLQANVTLQPTLMNFAPYSR--EQILEIISQKLKQT----DKF--NMFNASALQLLAGKVAAVSGDIRKAID  413 (490)
Q Consensus       344 ~--~~l~~~l~~R~~~~~~~i~~~pls~--~e~~~il~~~l~~~----~~~--~~~~~~~i~~i~~~i~~~~Gd~r~ai~  413 (490)
                      .  ..+.+.+.+||..  ..+.++|+..  +++..++.+++...    +..  ..+++++++.+..  +.|.||+|.+.+
T Consensus       156 ~~~~~~~~~L~~Rl~~--~~i~lp~L~~R~~di~~l~~~~l~~~~~~~~~~~~~~~~~~a~~~L~~--~~~~gn~reL~~  231 (265)
T 2bjv_A          156 VNEGTFRADLLDALAF--DVVQLPPLRERESDIMLMAEYFAIQMCREIKLPLFPGFTERARETLLN--YRWPGNIRELKN  231 (265)
T ss_dssp             HHHTSSCHHHHHHHCS--EEEECCCGGGCHHHHHHHHHHHHHHHHHHTTCSSCCCBCHHHHHHHHH--SCCTTHHHHHHH
T ss_pred             HHcCCccHHHHHhhcC--cEEeCCChhhhhHHHHHHHHHHHHHHHHHhCCCcccCcCHHHHHHHHh--CCCCCCHHHHHH
Confidence            1  1245788888853  3688999985  77777766655432    222  2689999999976  467899999999


Q ss_pred             HHHHHHHHHH
Q psy200          414 ITNHLIDLTY  423 (490)
Q Consensus       414 ll~~a~~~a~  423 (490)
                      ++++++..+.
T Consensus       232 ~l~~~~~~~~  241 (265)
T 2bjv_A          232 VVERSVYRHG  241 (265)
T ss_dssp             HHHHHHHHHC
T ss_pred             HHHHHHHhCC
Confidence            9999987664

>2x8a_A Nuclear valosin-containing protein-like; nuclear protein; 2.60A {Homo sapiens}

Probab=99.67  E-value=4.5e-15  Score=142.90  Aligned_cols=231  Identities=15%  Similarity=0.168  Sum_probs=141.3

Q ss_pred             CCCCChHHHHHHHHHHHHhhhc---------cCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVN---------NETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAAS  264 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~---------~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~  264 (490)
                      +++.|.++.++.|.+.+...+.         -..+++++|+||+|||||||+++++..+.    ..++++++....+   
T Consensus        10 ~di~g~~~~~~~l~~~i~~~~~~~~~l~~~~l~~~~GvlL~Gp~GtGKTtLakala~~~~----~~~i~i~g~~l~~---   82 (274)
T 2x8a_A           10 ADIGALEDIREELTMAILAPVRNPDQFKALGLVTPAGVLLAGPPGCGKTLLAKAVANESG----LNFISVKGPELLN---   82 (274)
T ss_dssp             --CCHHHHHHHHHHHHHTHHHHSHHHHHHTTCCCCSEEEEESSTTSCHHHHHHHHHHHTT----CEEEEEETTTTCS---
T ss_pred             HHhCCHHHHHHHHHHHHHHHhhCHHHHHHcCCCCCCeEEEECCCCCcHHHHHHHHHHHcC----CCEEEEEcHHHHh---
Confidence            6789999998888876543221         13445699999999999999999999875    4678888766532   


Q ss_pred             HHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccC--------HHHHHHh---HhCCCCCCCcEE
Q psy200          265 VYETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRK--------QTILYTI---FEWPSIPGSKLV  333 (490)
Q Consensus       265 l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~--------~~~L~~l---~~~~~~~~~~vi  333 (490)
                                 .+.+.....+...+..+..  ..++++|+||++.+....        ...+..+   ++- ......++
T Consensus        83 -----------~~~~~~~~~i~~vf~~a~~--~~p~i~~~Deid~~~~~r~~~~~~~~~~~~~~~l~~Lsg-g~~~~~~i  148 (274)
T 2x8a_A           83 -----------MYVGESERAVRQVFQRAKN--SAPCVIFFDEVDALCPRRSDRETGASVRVVNQLLTEMDG-LEARQQVF  148 (274)
T ss_dssp             -----------STTHHHHHHHHHHHHHHHH--TCSEEEEEETCTTTCC---------CTTHHHHHHHHHHT-CCSTTCEE
T ss_pred             -----------hhhhHHHHHHHHHHHHHHh--cCCCeEeeehhhhhhcccCCCcchHHHHHHHHHHHhhhc-ccccCCEE
Confidence                       1111222333334443322  457899999999875431        1112222   221 12345678


Q ss_pred             EEEecCCCChhHhhhHHhhh--ccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhC-CHHH
Q psy200          334 LVGVANALDLTDRMLPRLQA--NVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSG-DIRK  410 (490)
Q Consensus       334 lI~~tn~~~~~~~l~~~l~~--R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~G-d~r~  410 (490)
                      +++++|..   +.+++.+.+  ||.   ..|.++.++.++..+|++..+........-.+..++.++.... +.| ....
T Consensus       149 ~ia~tn~p---~~LD~al~r~gRfd---~~i~~~~P~~~~r~~il~~~~~~~~~~~~~~~~~~~~la~~~~-~~g~sgad  221 (274)
T 2x8a_A          149 IMAATNRP---DIIDPAILRPGRLD---KTLFVGLPPPADRLAILKTITKNGTKPPLDADVNLEAIAGDLR-CDCYTGAD  221 (274)
T ss_dssp             EEEEESCG---GGSCHHHHSTTSSC---EEEECCSCCHHHHHHHHHHHTTTTBTTBBCTTCCHHHHHTCSG-GGSCCHHH
T ss_pred             EEeecCCh---hhCCHhhcCcccCC---eEEEeCCcCHHHHHHHHHHHHhcccCCCCccccCHHHHHHhhc-cCCcCHHH
Confidence            88888854   445677765  776   5899999999999999998775421111112233556654111 123 3344


Q ss_pred             HHHHHHHHHHHHHhccccC------CcccccCHHHHHHHHHHhccCcc
Q psy200          411 AIDITNHLIDLTYDNVKEN------GEVTGIGLKEVLGVISSVYCTSQ  452 (490)
Q Consensus       411 ai~ll~~a~~~a~~~~~~~------~~~~~It~~~v~~a~~~~~~~~~  452 (490)
                      +.++|+.|...|.++....      .....|+.+||..|+..+.++..
T Consensus       222 l~~l~~~a~~~a~~~~~~~~~~~~~~~~~~i~~~df~~al~~~~ps~~  269 (274)
T 2x8a_A          222 LSALVREASICALRQEMARQKSGNEKGELKVSHKHFEEAFKKVRSSIS  269 (274)
T ss_dssp             HHHHHHHHHHHHHHHHC-----------CCBCHHHHHHHHTTCCCCC-
T ss_pred             HHHHHHHHHHHHHHHHHhhccccccccCCeecHHHHHHHHHHhcCCCC
Confidence            4567888877765532110      11347999999999998876544

>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=99.67  E-value=5.9e-16  Score=155.50  Aligned_cols=230  Identities=16%  Similarity=0.188  Sum_probs=152.0

Q ss_pred             CCCCChHHHHHHHHHHHHhhhc-----------cCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCH
Q psy200          194 CELPGREVQLEGIRQFLLGHVN-----------NETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNA  262 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~-----------~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~  262 (490)
                      +.++|++..++.|...+.....           .....+++|+||||||||++|+++++.+.    ..++.++|......
T Consensus        15 ~~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~~~~vll~GppGtGKT~la~~ia~~~~----~~~~~~~~~~l~~~   90 (363)
T 3hws_A           15 DYVIGQEQAKKVLAVAVYNHYKRLRNGDTSNGVELGKSNILLIGPTGSGKTLLAETLARLLD----VPFTMADATTLTEA   90 (363)
T ss_dssp             HHCCSCHHHHHHHHHHHHHHHHHHHTTSCSSSCCCCCCCEEEECCTTSSHHHHHHHHHHHTT----CCEEEEEHHHHTTC
T ss_pred             hhccCHHHHHHHHHHHHHHHHhhhccccccccccCCCCeEEEECCCCCCHHHHHHHHHHHcC----CCEEEechHHhccc
Confidence            5689999999999888843221           12567899999999999999999999874    67888988754321


Q ss_pred             HHHHHHHHHHhcCCCCCCc-HHHHHHHHHHH---HhcCCCeEEEEEecCcccccc--------------CHHHHHHhHhC
Q psy200          263 ASVYETIVNELKLKPGGKS-ERHQLGAILKY---FDTKHKSILLILDEIDALESR--------------KQTILYTIFEW  324 (490)
Q Consensus       263 ~~l~~~i~~~l~~~~~~~s-~~~~~~~l~~~---l~~~~~~~vI~IDEid~l~~~--------------~~~~L~~l~~~  324 (490)
                      . ++.            .. ...+...+..+   +.. ..+.||||||++.+...              .+..|+.+++-
T Consensus        91 ~-~~g------------~~~~~~~~~~~~~~~~~~~~-~~~~vl~lDEid~l~~~~~~~~~~~~~~~~~~~~~Ll~~leg  156 (363)
T 3hws_A           91 G-YVG------------EDVENIIQKLLQKCDYDVQK-AQRGIVYIDQIDKISRKSDNPSITRDVSGEGVQQALLKLIEG  156 (363)
T ss_dssp             H-HHH------------HHHTHHHHHHHHHTTTCHHH-HHHCEEEEECHHHHCCCSSCC---CHHHHHHHHHHHHHHHHC
T ss_pred             c-ccc------------ccHHHHHHHHHHHhhhhHHh-cCCcEEEEeChhhhcccccccccccccchHHHHHHHHHHhcC
Confidence            1 100            01 11112222211   000 13569999999999866              47778888771


Q ss_pred             C------------------CCCCCcEEEEEecCCCChhH-------------------------------------h---
Q psy200          325 P------------------SIPGSKLVLVGVANALDLTD-------------------------------------R---  346 (490)
Q Consensus       325 ~------------------~~~~~~vilI~~tn~~~~~~-------------------------------------~---  346 (490)
                      .                  .....++++|++++..++..                                     .   
T Consensus       157 ~~~~~~~~~~~~~~~~~~~~i~tsn~~~i~~g~~~~l~~~i~~~~~~~~~~gf~~~~~~~~~~~~~~~l~~~v~~~~l~~  236 (363)
T 3hws_A          157 TVAAVPPQGGRKHPQQEFLQVDTSKILFICGGAFAGLDKVISHRVETGSGIGFGATVKAKSDKASEGELLAQVEPEDLIK  236 (363)
T ss_dssp             C----------------CCCCCTTSSEEEEEECCTTHHHHHHHHHCCCC------------CCSCHHHHHHTCCHHHHHH
T ss_pred             ceeeccCccccccCCCceEEEECCCceEEecCCcHHHHHHHHHhhhccccCCccccccccccchhhHHHHHhCCHHHHHH
Confidence            1                  11334566666666432111                                     0   


Q ss_pred             --hhHHhhhccCCCCeeEEeCCCCHHHHHHHHHH----HH-------hccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHH
Q psy200          347 --MLPRLQANVTLQPTLMNFAPYSREQILEIISQ----KL-------KQTDKFNMFNASALQLLAGKVAAVSGDIRKAID  413 (490)
Q Consensus       347 --l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~----~l-------~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~  413 (490)
                        +.+.|.+||.   ..+.|.|++.+++.+|+..    .+       ...+....+++++++.|++..+.+.|+.|.+-+
T Consensus       237 ~~~~~~l~~R~~---~~~~~~pl~~~~~~~I~~~~~~~l~~~~~~~~~~~~~~l~~~~~a~~~L~~~~~~~~~gaR~L~~  313 (363)
T 3hws_A          237 FGLIPEFIGRLP---VVATLNELSEEALIQILKEPKNALTKQYQALFNLEGVDLEFRDEALDAIAKKAMARKTGARGLRS  313 (363)
T ss_dssp             HTCCHHHHTTCC---EEEECCCCCHHHHHHHHHSSTTCHHHHHHHHHHTTTCEEEECHHHHHHHHHHHHHTTCTTTTHHH
T ss_pred             cCCCHHHhcccC---eeeecCCCCHHHHHHHHHHHHHHHHHHHHHHHHhcCceEEECHHHHHHHHHhhcCCccCchHHHH
Confidence              4577888988   4788999999999888775    22       222234568999999999877788899999999


Q ss_pred             HHHHHHHHHHhccccC--CcccccCHHHHHHHH
Q psy200          414 ITNHLIDLTYDNVKEN--GEVTGIGLKEVLGVI  444 (490)
Q Consensus       414 ll~~a~~~a~~~~~~~--~~~~~It~~~v~~a~  444 (490)
                      ++++++..+..+....  .....|+.++|.+.+
T Consensus       314 ~ie~~~~~~l~~~~~~~~~~~~~I~~~~v~~~~  346 (363)
T 3hws_A          314 IVEAALLDTMYDLPSMEDVEKVVIDESVIDGQS  346 (363)
T ss_dssp             HHHHHHHHHHHSTTTCCCSEEEECHHHHTTCCS
T ss_pred             HHHHHHHHHHHhcccccCCceeEEcHHHHhCcC
Confidence            9999987766554221  112357777766544

>3pxg_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 3.65A {Bacillus subtilis}

Probab=99.66  E-value=1.5e-15  Score=157.50  Aligned_cols=214  Identities=17%  Similarity=0.172  Sum_probs=142.8

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhc------CCceEEEEeccCCCCHHHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIK------DAFKTIYINCNSVRNAASVYE  267 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~------~~~~~~~v~~~~~~~~~~l~~  267 (490)
                      +.++||+++++.+...|..    ...++++|+||||||||++++.+++.+...      .+..++.++|..         
T Consensus       180 d~iiGr~~~i~~l~~~l~r----~~~~~~LL~G~pG~GKT~la~~la~~l~~~~~p~~l~~~~~~~l~~~~---------  246 (468)
T 3pxg_A          180 DPVIGRSKEIQRVIEVLSR----RTKNNPVLIGEPGVGKTAIAEGLAQQIINNEVPEILRDKRVMTLDMGT---------  246 (468)
T ss_dssp             CCCCCCHHHHHHHHHHHHC----SSSCEEEEESCTTTTTHHHHHHHHHHHHSSCSCTTTSSCCEECC-------------
T ss_pred             CCccCcHHHHHHHHHHHhc----cCCCCeEEECCCCCCHHHHHHHHHHHHHhCCCChhhcCCeEEEeeCCc---------
Confidence            7899999999999998864    556789999999999999999999997421      245677777651         


Q ss_pred             HHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEEEecCCCChhH--
Q psy200          268 TIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVANALDLTD--  345 (490)
Q Consensus       268 ~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI~~tn~~~~~~--  345 (490)
                              .+.|.....+...+..+..  ..+.|||||    .....++.|.     .......+.+|++||..++..  
T Consensus       247 --------~~~g~~e~~~~~~~~~~~~--~~~~iLfiD----~~~~a~~~L~-----~~L~~g~v~vI~at~~~e~~~~~  307 (468)
T 3pxg_A          247 --------KYRGEFEDRLKKVMDEIRQ--AGNIILFID----AAIDASNILK-----PSLARGELQCIGATTLDEYRKYI  307 (468)
T ss_dssp             --------------CTTHHHHHHHHHT--CCCCEEEEC----C--------C-----CCTTSSSCEEEEECCTTTTHHHH
T ss_pred             --------cccchHHHHHHHHHHHHHh--cCCeEEEEe----CchhHHHHHH-----HhhcCCCEEEEecCCHHHHHHHh
Confidence                    1122222333444444333  346799999    1111223332     223455789999999766432  


Q ss_pred             hhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhcc--CCCCCCCHHHHHHHHHHHHHhhCC---HHHHHHHHHHHHH
Q psy200          346 RMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQT--DKFNMFNASALQLLAGKVAAVSGD---IRKAIDITNHLID  420 (490)
Q Consensus       346 ~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~--~~~~~~~~~~i~~i~~~i~~~~Gd---~r~ai~ll~~a~~  420 (490)
                      .+++.+.+||.    .+.|.+++.+++..||...+...  .....+++++++.+++....+.++   .+.+++++..|..
T Consensus       308 ~~~~al~~Rf~----~i~v~~p~~e~~~~iL~~~~~~~~~~~~~~i~~~al~~l~~~s~~~~~~~~lp~~ai~ll~~a~~  383 (468)
T 3pxg_A          308 EKDAALERRFQ----PIQVDQPSVDESIQILQGLRDRYEAHHRVSITDDAIEAAVKLSDRYISDRFLPDKAIDLIDEAGS  383 (468)
T ss_dssp             TTCSHHHHSEE----EEECCCCCHHHHHHHHHHTTTTSGGGSSCSCCHHHHHHHHHHHHHSSCCSCTTHHHHHHHHHHHH
T ss_pred             hcCHHHHHhCc----cceeCCCCHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhccCcCCcHHHHHHHHHHH
Confidence            35688999996    79999999999999999877653  134678999999999866666655   6689999999887


Q ss_pred             HHHhccccCCcccccCHHHHHHHHHHh
Q psy200          421 LTYDNVKENGEVTGIGLKEVLGVISSV  447 (490)
Q Consensus       421 ~a~~~~~~~~~~~~It~~~v~~a~~~~  447 (490)
                      .+.....    ..+..+..+...+..+
T Consensus       384 ~~~~~~~----~~p~~i~~l~~~i~~l  406 (468)
T 3pxg_A          384 KVRLRSF----TTPPNLKELEQKLDEV  406 (468)
T ss_dssp             HHHHHTT----SCCSSTHHHHHHHHHH
T ss_pred             HHHhccC----CCchHHHHHHHHHHHH
Confidence            6655442    2344455555555443

>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=99.66  E-value=1.8e-15  Score=144.17  Aligned_cols=213  Identities=16%  Similarity=0.184  Sum_probs=138.1

Q ss_pred             CCCCChHHHHHHHHHHHHhhh--------ccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHV--------NNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASV  265 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~--------~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l  265 (490)
                      ++++|.++.+.++.+.....-        .-....+++|+||+|+||||++++++..+.    ..++++++...      
T Consensus        16 ~~i~g~~~~~~~l~~l~~~~~~~~~~~~~~~~~~~g~ll~G~~G~GKTtl~~~i~~~~~----~~~i~~~~~~~------   85 (254)
T 1ixz_A           16 KDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEAR----VPFITASGSDF------   85 (254)
T ss_dssp             GGCCSCHHHHHHHHHHHHHHHCHHHHHHTTCCCCSEEEEECCTTSSHHHHHHHHHHHTT----CCEEEEEHHHH------
T ss_pred             HHhCCcHHHHHHHHHHHHHHHCHHHHHHcCCCCCCeEEEECCCCCCHHHHHHHHHHHhC----CCEEEeeHHHH------
Confidence            678898888777776554321        112345699999999999999999999864    45677765321      


Q ss_pred             HHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccC-----------HHHHHHhHhC--CCCCCCcE
Q psy200          266 YETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRK-----------QTILYTIFEW--PSIPGSKL  332 (490)
Q Consensus       266 ~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~-----------~~~L~~l~~~--~~~~~~~v  332 (490)
                      ..        ...+.....+...+..+.  ...+.++|+||+|.+....           ...+..++..  .......+
T Consensus        86 ~~--------~~~~~~~~~i~~~~~~~~--~~~~~i~~~Deid~l~~~~~~~~~~~~~~~~~~~~~ll~~l~g~~~~~~~  155 (254)
T 1ixz_A           86 VE--------MFVGVGAARVRDLFETAK--RHAPCIVFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMDGFEKDTAI  155 (254)
T ss_dssp             HH--------SCTTHHHHHHHHHHHHHT--TSSSEEEEEETHHHHHC---------CHHHHHHHHHHHHHHHTCCTTCCE
T ss_pred             HH--------HHhhHHHHHHHHHHHHHH--hcCCeEEEehhhhhhhcccCccccccchHHHHHHHHHHHHHhCCCCCCCE
Confidence            11        111122223333333322  1347899999999885331           1122222211  11234457


Q ss_pred             EEEEecCCCChhHhhhHHhhh--ccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCC-HHHHHHHHHHHHHhhCCH-
Q psy200          333 VLVGVANALDLTDRMLPRLQA--NVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFN-ASALQLLAGKVAAVSGDI-  408 (490)
Q Consensus       333 ilI~~tn~~~~~~~l~~~l~~--R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~-~~~i~~i~~~i~~~~Gd~-  408 (490)
                      ++++++|..   +.+++.+.+  ||.   ..+.|++++.++..+|++.++...    .+. +..+..++.   .+.|+. 
T Consensus       156 i~~a~t~~p---~~ld~~l~r~~rf~---~~i~i~~p~~~~r~~il~~~~~~~----~~~~~~~~~~la~---~~~G~~~  222 (254)
T 1ixz_A          156 VVMAATNRP---DILDPALLRPGRFD---RQIAIDAPDVKGREQILRIHARGK----PLAEDVDLALLAK---RTPGFVG  222 (254)
T ss_dssp             EEEEEESCG---GGSCGGGGSTTSSC---EEEECCSCCHHHHHHHHHHHHTTS----CBCTTCCHHHHHH---TCTTCCH
T ss_pred             EEEEccCCc---hhCCHHHcCCCcCC---eEEeeCCcCHHHHHHHHHHHHcCC----CCCcccCHHHHHH---HcCCCCH
Confidence            788888854   445677766  565   489999999999999998776543    122 233667776   677765 


Q ss_pred             HHHHHHHHHHHHHHHhccccCCcccccCHHHHHHHH
Q psy200          409 RKAIDITNHLIDLTYDNVKENGEVTGIGLKEVLGVI  444 (490)
Q Consensus       409 r~ai~ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~  444 (490)
                      +.+.++|++|...|..++     ...|+++++.+|+
T Consensus       223 ~dl~~~~~~a~~~a~~~~-----~~~I~~~dl~~a~  253 (254)
T 1ixz_A          223 ADLENLLNEAALLAAREG-----RRKITMKDLEEAA  253 (254)
T ss_dssp             HHHHHHHHHHHHHHHHTT-----CSSBCHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHhc-----CCCcCHHHHHHHh
Confidence            778889999999888776     5689999999875

>1iy2_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 3.20A {Thermus thermophilus} SCOP: c.37.1.20

Probab=99.66  E-value=2.2e-15  Score=145.62  Aligned_cols=213  Identities=17%  Similarity=0.191  Sum_probs=139.8

Q ss_pred             CCCCChHHHHHHHHHHHHhhhc--------cCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVN--------NETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASV  265 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~--------~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l  265 (490)
                      ++++|.++.++++.......-.        -....+++|+||+|+|||||+++++..+.    ..++++++..+      
T Consensus        40 ~~i~g~~~~~~~l~~l~~~~~~~~~l~~~~~~~~~gvll~Gp~GtGKTtl~~~i~~~~~----~~~i~~~~~~~------  109 (278)
T 1iy2_A           40 KDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEAR----VPFITASGSDF------  109 (278)
T ss_dssp             GGSSSCHHHHHHHHHHHHHHHCHHHHHHTTCCCCCEEEEECCTTSSHHHHHHHHHHHTT----CCEEEEEHHHH------
T ss_pred             HHhCChHHHHHHHHHHHHHHHCHHHHHHcCCCCCCeEEEECCCcChHHHHHHHHHHHcC----CCEEEecHHHH------
Confidence            6788988888877776543211        12345699999999999999999999874    55677765421      


Q ss_pred             HHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccC-----------HHHHHHhHh-CC-CCCCCcE
Q psy200          266 YETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRK-----------QTILYTIFE-WP-SIPGSKL  332 (490)
Q Consensus       266 ~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~-----------~~~L~~l~~-~~-~~~~~~v  332 (490)
                      ..        ...+.....+...+..+..  ..+.++|+||++.+....           ...+..++. +. ......+
T Consensus       110 ~~--------~~~~~~~~~i~~~~~~~~~--~~~~i~~iDeid~l~~~~~~~~~~~~~~~~~~~~~ll~~lsgg~~~~~~  179 (278)
T 1iy2_A          110 VE--------MFVGVGAARVRDLFETAKR--HAPCIVFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMDGFEKDTAI  179 (278)
T ss_dssp             HH--------STTTHHHHHHHHHHHHHHT--SCSEEEEEETHHHHHCC--------CHHHHHHHHHHHHHHTTCCTTCCE
T ss_pred             HH--------HHhhHHHHHHHHHHHHHHh--cCCcEEehhhhHhhhcccccccCCcchHHHHHHHHHHHHHhCCCCCCCE
Confidence            11        1111222233333443322  347899999999875321           223333332 11 1233457


Q ss_pred             EEEEecCCCChhHhhhHHhhh--ccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCC-HHHHHHHHHHHHHhhCCH-
Q psy200          333 VLVGVANALDLTDRMLPRLQA--NVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFN-ASALQLLAGKVAAVSGDI-  408 (490)
Q Consensus       333 ilI~~tn~~~~~~~l~~~l~~--R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~-~~~i~~i~~~i~~~~Gd~-  408 (490)
                      ++++++|..+   .+++.+.+  ||.   ..+.|.+++.++..+|+..++...    .+. +..+..++.   .+.|+. 
T Consensus       180 i~~a~t~~p~---~ld~~l~r~~rf~---~~i~i~~p~~~~r~~il~~~~~~~----~~~~~~~~~~la~---~~~G~~~  246 (278)
T 1iy2_A          180 VVMAATNRPD---ILDPALLRPGRFD---RQIAIDAPDVKGREQILRIHARGK----PLAEDVDLALLAK---RTPGFVG  246 (278)
T ss_dssp             EEEEEESCTT---SSCHHHHSTTSSC---CEEECCCCCHHHHHHHHHHHHTTS----CBCTTCCHHHHHH---TCTTCCH
T ss_pred             EEEEecCCch---hCCHhHcCCCcCC---eEEEeCCcCHHHHHHHHHHHHccC----CCCcccCHHHHHH---HcCCCCH
Confidence            8888888543   35666665  565   479999999999999999877543    222 223666765   677877 


Q ss_pred             HHHHHHHHHHHHHHHhccccCCcccccCHHHHHHHH
Q psy200          409 RKAIDITNHLIDLTYDNVKENGEVTGIGLKEVLGVI  444 (490)
Q Consensus       409 r~ai~ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~  444 (490)
                      +.+.++|++|...|..++     ...|+++|+.+|+
T Consensus       247 ~dl~~l~~~a~~~a~~~~-----~~~I~~~dl~~a~  277 (278)
T 1iy2_A          247 ADLENLLNEAALLAAREG-----RRKITMKDLEEAA  277 (278)
T ss_dssp             HHHHHHHHHHHHHHHHTT-----CCSBCHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHhC-----CCCcCHHHHHHHh
Confidence            667789999998888776     5689999999875

>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=99.66  E-value=2.5e-15  Score=149.93  Aligned_cols=240  Identities=19%  Similarity=0.200  Sum_probs=147.1

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhc---CCceEEEEeccCCCCHHHHHHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIK---DAFKTIYINCNSVRNAASVYETIV  270 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~---~~~~~~~v~~~~~~~~~~l~~~i~  270 (490)
                      ++++|+++.++.+...+.    ....++++|+||||||||++|+++++.+...   ....   ++|..... ......+.
T Consensus        24 ~~i~G~~~~~~~l~~~~~----~~~~~~vLl~G~~GtGKT~la~~la~~~~~~~~~~~~~---~~~~~~~~-~~~~~~~~   95 (350)
T 1g8p_A           24 SAIVGQEDMKLALLLTAV----DPGIGGVLVFGDRGTGKSTAVRALAALLPEIEAVEGCP---VSSPNVEM-IPDWATVL   95 (350)
T ss_dssp             GGSCSCHHHHHHHHHHHH----CGGGCCEEEECCGGGCTTHHHHHHHHHSCCEEEETTCT---TCCSSGGG-SCTTCCCS
T ss_pred             hhccChHHHHHHHHHHhh----CCCCceEEEECCCCccHHHHHHHHHHhCcccccccccc---cccccccc-ccchhhhh
Confidence            568999886655433332    2334579999999999999999999987410   0000   12221100 00000000


Q ss_pred             HHhcC---------CCCCCcHHHHHHH--HHHHHhcC-----------CCeEEEEEecCccccccCHHHHHHhHhCC---
Q psy200          271 NELKL---------KPGGKSERHQLGA--ILKYFDTK-----------HKSILLILDEIDALESRKQTILYTIFEWP---  325 (490)
Q Consensus       271 ~~l~~---------~~~~~s~~~~~~~--l~~~l~~~-----------~~~~vI~IDEid~l~~~~~~~L~~l~~~~---  325 (490)
                       .+..         ...+.+...+...  +...+..+           ....+|||||++.+....++.|+.+++..   
T Consensus        96 -~~~~~~~~~~~~~~~~~~~~~~l~g~~~~~~~~~~~~~~~~~g~~~~a~~~vl~iDEi~~l~~~~~~~Ll~~le~~~~~  174 (350)
T 1g8p_A           96 -STNVIRKPTPVVDLPLGVSEDRVVGALDIERAISKGEKAFEPGLLARANRGYLYIDECNLLEDHIVDLLLDVAQSGENV  174 (350)
T ss_dssp             -CCCEEEECCCEEEECTTCCHHHHHCEECHHHHHHHCGGGEECCHHHHHTTEEEEETTGGGSCHHHHHHHHHHHHHSEEE
T ss_pred             -ccccccCCCcccccCCCcchhhheeechhhhhhcCCceeecCceeeecCCCEEEEeChhhCCHHHHHHHHHHHhcCceE
Confidence             0000         0001111111100  00000000           12459999999999988888888877632   


Q ss_pred             --CCC-----CCcEEEEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCC-HHHHHHHHHHHHh----------------
Q psy200          326 --SIP-----GSKLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYS-REQILEIISQKLK----------------  381 (490)
Q Consensus       326 --~~~-----~~~vilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls-~~e~~~il~~~l~----------------  381 (490)
                        ...     ..++++|+++|..+  ..+.+.+.+||+.   .+.+.+++ .++..+|+.+++.                
T Consensus       175 ~~~~g~~~~~~~~~~li~~~n~~~--~~l~~~L~~R~~~---~~~l~~~~~~~~~~~il~~~~~~~~~~~~~~~~~~~~~  249 (350)
T 1g8p_A          175 VERDGLSIRHPARFVLVGSGNPEE--GDLRPQLLDRFGL---SVEVLSPRDVETRVEVIRRRDTYDADPKAFLEEWRPKD  249 (350)
T ss_dssp             ECCTTCCEEEECCEEEEEEECSCS--CCCCHHHHTTCSE---EEECCCCCSHHHHHHHHHHHHHHHHCHHHHHHHHHHHH
T ss_pred             EEecceEEeeCCceEEEEEeCCCC--CCCCHHHHhhcce---EEEcCCCCcHHHHHHHHHHHHhcccCchhhccccccch
Confidence              111     23789999998532  3567889999973   69999995 5555577655211                


Q ss_pred             -----------ccCCCCCCCHHHHHHHHHHHHHhhC-CHHHHHHHHHHHHHHHHhccccCCcccccCHHHHHHHHHHhcc
Q psy200          382 -----------QTDKFNMFNASALQLLAGKVAAVSG-DIRKAIDITNHLIDLTYDNVKENGEVTGIGLKEVLGVISSVYC  449 (490)
Q Consensus       382 -----------~~~~~~~~~~~~i~~i~~~i~~~~G-d~r~ai~ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~~~~~~  449 (490)
                                 .......+++++++.|++......+ ++|.++++|+.|...|..++     ...|+.+|+..++..+..
T Consensus       250 ~~~~~~i~~~~~~~~~~~ls~~~~~~l~~~~~~~~~~~~R~~~~ll~~a~~~A~~~~-----~~~v~~~~v~~a~~~~l~  324 (350)
T 1g8p_A          250 MDIRNQILEARERLPKVEAPNTALYDCAALCIALGSDGLRGELTLLRSARALAALEG-----ATAVGRDHLKRVATMALS  324 (350)
T ss_dssp             HHHHHHHHHHHHHGGGCBCCHHHHHHHHHHHHHSSSCSHHHHHHHHHHHHHHHHHTT-----CSBCCHHHHHHHHHHHHG
T ss_pred             HHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHhCCCCccHHHHHHHHHHHHHHHcC-----CCcCCHHHHHHHHHHHHh
Confidence                       1112346899999999985444444 78999999999999998887     568999999999999887


Q ss_pred             Ccc
Q psy200          450 TSQ  452 (490)
Q Consensus       450 ~~~  452 (490)
                      ...
T Consensus       325 ~r~  327 (350)
T 1g8p_A          325 HRL  327 (350)
T ss_dssp             GGC
T ss_pred             hcc
Confidence            665

>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=99.63  E-value=1.2e-14  Score=159.82  Aligned_cols=234  Identities=17%  Similarity=0.173  Sum_probs=156.0

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhc------CCceEEEEeccCCCCHHHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIK------DAFKTIYINCNSVRNAASVYE  267 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~------~~~~~~~v~~~~~~~~~~l~~  267 (490)
                      ++++||+++++.+.+.|..    ....+++|+||||||||++++.+++.+...      .+..++.+++.....      
T Consensus       186 d~~iGr~~~i~~l~~~l~~----~~~~~vlL~G~~GtGKT~la~~la~~l~~~~v~~~~~~~~~~~~~~~~l~~------  255 (758)
T 1r6b_X          186 DPLIGREKELERAIQVLCR----RRKNNPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYSLDIGSLLA------  255 (758)
T ss_dssp             CCCCSCHHHHHHHHHHHTS----SSSCEEEEECCTTSSHHHHHHHHHHHHHHTCSCGGGTTCEEEECCCC---C------
T ss_pred             CCccCCHHHHHHHHHHHhc----cCCCCeEEEcCCCCCHHHHHHHHHHHHHhCCCChhhcCCEEEEEcHHHHhc------
Confidence            8899999999999998854    467889999999999999999999987422      134555555443311      


Q ss_pred             HHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCcccccc-----CHHHHHHhHhCCCCCCCcEEEEEecCCCC
Q psy200          268 TIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESR-----KQTILYTIFEWPSIPGSKLVLVGVANALD  342 (490)
Q Consensus       268 ~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~-----~~~~L~~l~~~~~~~~~~vilI~~tn~~~  342 (490)
                            +..+.+.....+...+... .. .++.+|||||+|.+...     ....+..++. .......+.+|++++..+
T Consensus       256 ------~~~~~g~~e~~l~~~~~~~-~~-~~~~iL~IDEi~~l~~~~~~~~~~~~~~~~L~-~~l~~~~~~~I~at~~~~  326 (758)
T 1r6b_X          256 ------GTKYRGDFEKRFKALLKQL-EQ-DTNSILFIDEIHTIIGAGAASGGQVDAANLIK-PLLSSGKIRVIGSTTYQE  326 (758)
T ss_dssp             ------CCCCSSCHHHHHHHHHHHH-SS-SSCEEEEETTTTTTTTSCCSSSCHHHHHHHHS-SCSSSCCCEEEEEECHHH
T ss_pred             ------cccccchHHHHHHHHHHHH-Hh-cCCeEEEEechHHHhhcCCCCcchHHHHHHHH-HHHhCCCeEEEEEeCchH
Confidence                  1123334344444444433 22 34689999999999532     1222223332 122345788888888433


Q ss_pred             hhHh--hhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhcc--CCCCCCCHHHHHHHHHHHHHhhCC---HHHHHHHH
Q psy200          343 LTDR--MLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQT--DKFNMFNASALQLLAGKVAAVSGD---IRKAIDIT  415 (490)
Q Consensus       343 ~~~~--l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~--~~~~~~~~~~i~~i~~~i~~~~Gd---~r~ai~ll  415 (490)
                      +...  +++++.+||.    .+.|.+++.+++.++|...+...  .....+++++++.++....++.++   ...+++++
T Consensus       327 ~~~~~~~d~aL~~Rf~----~i~v~~p~~~e~~~il~~l~~~~~~~~~v~~~~~al~~~~~~s~~~i~~~~lp~~~i~ll  402 (758)
T 1r6b_X          327 FSNIFEKDRALARRFQ----KIDITEPSIEETVQIINGLKPKYEAHHDVRYTAKAVRAAVELAVKYINDRHLPDKAIDVI  402 (758)
T ss_dssp             HHCCCCCTTSSGGGEE----EEECCCCCHHHHHHHHHHHHHHHHHHHTCCCCHHHHHHHHHHHHHHCTTSCTTHHHHHHH
T ss_pred             HhhhhhcCHHHHhCce----EEEcCCCCHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhhhcccccCchHHHHHH
Confidence            2222  3467888986    79999999999999998776542  124568999999998866555443   45788899


Q ss_pred             HHHHHHHHhccccCCcccccCHHHHHHHHHHhccCc
Q psy200          416 NHLIDLTYDNVKENGEVTGIGLKEVLGVISSVYCTS  451 (490)
Q Consensus       416 ~~a~~~a~~~~~~~~~~~~It~~~v~~a~~~~~~~~  451 (490)
                      ..|...+...... .....|+.++|..++..+.+.+
T Consensus       403 d~a~~~~~~~~~~-~~~~~v~~~di~~~~~~~~~ip  437 (758)
T 1r6b_X          403 DEAGARARLMPVS-KRKKTVNVADIESVVARIARIP  437 (758)
T ss_dssp             HHHHHHHHHSSSC-CCCCSCCHHHHHHHHHHHSCCC
T ss_pred             HHHHHHHhccccc-ccCCccCHHHHHHHHHHhcCCC
Confidence            8887766552100 0135799999999999887544

>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=99.62  E-value=2.2e-14  Score=142.25  Aligned_cols=196  Identities=13%  Similarity=0.126  Sum_probs=128.1

Q ss_pred             hHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHH---hcC
Q psy200          199 REVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNE---LKL  275 (490)
Q Consensus       199 re~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~---l~~  275 (490)
                      +++.++.+...+..   +..++.++|+||+|+|||++++.+++.+.......  ...|..+.+...+...-.-+   +..
T Consensus         7 ~~~~~~~l~~~i~~---~~~~~a~L~~G~~G~GKt~~a~~la~~l~~~~~~~--~~~c~~c~~c~~~~~~~~~d~~~~~~   81 (334)
T 1a5t_A            7 LRPDFEKLVASYQA---GRGHHALLIQALPGMGDDALIYALSRYLLCQQPQG--HKSCGHCRGCQLMQAGTHPDYYTLAP   81 (334)
T ss_dssp             GHHHHHHHHHHHHT---TCCCSEEEEECCTTSCHHHHHHHHHHHHTCSSCBT--TBCCSCSHHHHHHHHTCCTTEEEECC
T ss_pred             hHHHHHHHHHHHHc---CCcceeEEEECCCCchHHHHHHHHHHHHhCCCCCC--CCCCCCCHHHHHHhcCCCCCEEEEec
Confidence            44555666666642   33456799999999999999999999986322100  01122111111100000000   000


Q ss_pred             C--CCCCcHHHHHHHHHHHHhc--CCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEEEecCCCChhHhhhHHh
Q psy200          276 K--PGGKSERHQLGAILKYFDT--KHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVANALDLTDRMLPRL  351 (490)
Q Consensus       276 ~--~~~~s~~~~~~~l~~~l~~--~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI~~tn~~~~~~~l~~~l  351 (490)
                      .  ....+.+.+++.+..+...  .++..|+||||+|.|....++.|...++.   ....+++|.+++.   .+.+.+.+
T Consensus        82 ~~~~~~~~i~~ir~l~~~~~~~~~~~~~kvviIdead~l~~~a~naLLk~lEe---p~~~~~~Il~t~~---~~~l~~ti  155 (334)
T 1a5t_A           82 EKGKNTLGVDAVREVTEKLNEHARLGGAKVVWVTDAALLTDAAANALLKTLEE---PPAETWFFLATRE---PERLLATL  155 (334)
T ss_dssp             CTTCSSBCHHHHHHHHHHTTSCCTTSSCEEEEESCGGGBCHHHHHHHHHHHTS---CCTTEEEEEEESC---GGGSCHHH
T ss_pred             cccCCCCCHHHHHHHHHHHhhccccCCcEEEEECchhhcCHHHHHHHHHHhcC---CCCCeEEEEEeCC---hHhCcHHH
Confidence            0  1123445555544432221  24578999999999988888888888774   3446777777763   46788999


Q ss_pred             hhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHHHHHHHH
Q psy200          352 QANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITNHLI  419 (490)
Q Consensus       352 ~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll~~a~  419 (490)
                      ++||.    .+.|.+++.+++.+++.+++       .+++++++.+++   ...|+++.++++++.+.
T Consensus       156 ~SRc~----~~~~~~~~~~~~~~~L~~~~-------~~~~~~~~~l~~---~s~G~~r~a~~~l~~~~  209 (334)
T 1a5t_A          156 RSRCR----LHYLAPPPEQYAVTWLSREV-------TMSQDALLAALR---LSAGSPGAALALFQGDN  209 (334)
T ss_dssp             HTTSE----EEECCCCCHHHHHHHHHHHC-------CCCHHHHHHHHH---HTTTCHHHHHHTTSSHH
T ss_pred             hhcce----eeeCCCCCHHHHHHHHHHhc-------CCCHHHHHHHHH---HcCCCHHHHHHHhccch
Confidence            99995    89999999999999998864       368899888887   67899999998876654

>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=99.62  E-value=5.4e-15  Score=164.36  Aligned_cols=206  Identities=18%  Similarity=0.207  Sum_probs=137.8

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhc------CCceEEEEeccCCCCHHHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIK------DAFKTIYINCNSVRNAASVYE  267 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~------~~~~~~~v~~~~~~~~~~l~~  267 (490)
                      ++++||++++..+.++|..    ...++++|+||||||||++++.+++.+...      .+..+++++|.....      
T Consensus       170 d~viGr~~~i~~l~~~l~~----~~~~~vlL~G~pG~GKT~la~~la~~l~~~~~p~~l~~~~~~~l~~~~l~~------  239 (854)
T 1qvr_A          170 DPVIGRDEEIRRVIQILLR----RTKNNPVLIGEPGVGKTAIVEGLAQRIVKGDVPEGLKGKRIVSLQMGSLLA------  239 (854)
T ss_dssp             CCCCSCHHHHHHHHHHHHC----SSCCCCEEEECTTSCHHHHHHHHHHHHHHTCSCTTSTTCEEEEECC-----------
T ss_pred             cccCCcHHHHHHHHHHHhc----CCCCceEEEcCCCCCHHHHHHHHHHHHhcCCCchhhcCCeEEEeehHHhhc------
Confidence            8899999999999998853    556789999999999999999999988431      256888898865422      


Q ss_pred             HHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccC--------HHHHHHhHhCCCCCCCcEEEEEecC
Q psy200          268 TIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRK--------QTILYTIFEWPSIPGSKLVLVGVAN  339 (490)
Q Consensus       268 ~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~--------~~~L~~l~~~~~~~~~~vilI~~tn  339 (490)
                            +..+.+.....+...+..+.. .++++||||||+|.+....        .+.|..+++     ...+.+|+++|
T Consensus       240 ------g~~~~g~~~~~l~~~~~~~~~-~~~~~iL~IDEi~~l~~~~~~~g~~~~~~~L~~~l~-----~~~i~~I~at~  307 (854)
T 1qvr_A          240 ------GAKYRGEFEERLKAVIQEVVQ-SQGEVILFIDELHTVVGAGKAEGAVDAGNMLKPALA-----RGELRLIGATT  307 (854)
T ss_dssp             ------------CHHHHHHHHHHHHHT-TCSSEEEEECCC-------------------HHHHH-----TTCCCEEEEEC
T ss_pred             ------cCccchHHHHHHHHHHHHHHh-cCCCeEEEEecHHHHhccCCccchHHHHHHHHHHHh-----CCCeEEEEecC
Confidence                  112233334444445444333 3468999999999997332        233444443     24577888887


Q ss_pred             CCChhH-hhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhcc--CCCCCCCHHHHHHHHHHHHHhhCC---HHHHHH
Q psy200          340 ALDLTD-RMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQT--DKFNMFNASALQLLAGKVAAVSGD---IRKAID  413 (490)
Q Consensus       340 ~~~~~~-~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~--~~~~~~~~~~i~~i~~~i~~~~Gd---~r~ai~  413 (490)
                      ..++.. .+++.+.+||.    .+.|++++.+++..+++..+...  .....++++++..+++...++.++   ...+++
T Consensus       308 ~~~~~~~~~d~aL~rRf~----~i~l~~p~~~e~~~iL~~~~~~~~~~~~~~i~~~al~~~~~ls~r~i~~~~lp~kai~  383 (854)
T 1qvr_A          308 LDEYREIEKDPALERRFQ----PVYVDEPTVEETISILRGLKEKYEVHHGVRISDSAIIAAATLSHRYITERRLPDKAID  383 (854)
T ss_dssp             HHHHHHHTTCTTTCSCCC----CEEECCCCHHHHHHHHHHHHHHHHHHTTCEECHHHHHHHHHHHHHHCCSSCTHHHHHH
T ss_pred             chHHhhhccCHHHHhCCc----eEEeCCCCHHHHHHHHHhhhhhhhhhcCCCCCHHHHHHHHHHHhhhcccccChHHHHH
Confidence            433211 23678889996    69999999999999998766533  134568999999999877666555   788999


Q ss_pred             HHHHHHHHHHhc
Q psy200          414 ITNHLIDLTYDN  425 (490)
Q Consensus       414 ll~~a~~~a~~~  425 (490)
                      ++..|...+...
T Consensus       384 lldea~a~~~~~  395 (854)
T 1qvr_A          384 LIDEAAARLRMA  395 (854)
T ss_dssp             HHHHHHHHHHHT
T ss_pred             HHHHHHHHHHhh
Confidence            999988776654

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=99.61  E-value=3.5e-15  Score=164.02  Aligned_cols=206  Identities=16%  Similarity=0.170  Sum_probs=148.7

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccC-----CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNE-----TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYET  268 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~-----~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~  268 (490)
                      ..++|++..++.|...+.....+.     +.++++|+||+|||||++|+++++.+. ..+..+++++|+.+...      
T Consensus       491 ~~viGq~~a~~~l~~~i~~~~~~~~~~~~p~~~~Ll~Gp~GtGKT~lA~ala~~l~-~~~~~~i~i~~s~~~~~------  563 (758)
T 3pxi_A          491 SRVIGQDEAVVAVAKAVRRARAGLKDPKRPIGSFIFLGPTGVGKTELARALAESIF-GDEESMIRIDMSEYMEK------  563 (758)
T ss_dssp             TTSCSCHHHHHHHHHHHHHHTTTCSCTTSCSEEEEEESCTTSSHHHHHHHHHHHHH-SCTTCEEEEEGGGGCSS------
T ss_pred             CcCcChHHHHHHHHHHHHHHHcccCCCCCCceEEEEECCCCCCHHHHHHHHHHHhc-CCCcceEEEechhcccc------
Confidence            789999999999999888653221     123699999999999999999999873 34567899999877431      


Q ss_pred             HHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCHHHHHHhHhCCCC--------CCCcEEEEEecCC
Q psy200          269 IVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPSI--------PGSKLVLVGVANA  340 (490)
Q Consensus       269 i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~--------~~~~vilI~~tn~  340 (490)
                              .. .+..    .+..++.. ....|||||||+.+....++.|+++++....        ...++++|+++|.
T Consensus       564 --------~~-~~~~----~l~~~~~~-~~~~vl~lDEi~~~~~~~~~~Ll~~le~g~~~~~~g~~~~~~~~~iI~ttn~  629 (758)
T 3pxi_A          564 --------HS-TSGG----QLTEKVRR-KPYSVVLLDAIEKAHPDVFNILLQVLEDGRLTDSKGRTVDFRNTILIMTSNV  629 (758)
T ss_dssp             --------CC-CC-------CHHHHHH-CSSSEEEEECGGGSCHHHHHHHHHHHHHSBCC-----CCBCTTCEEEEEESS
T ss_pred             --------cc-cccc----hhhHHHHh-CCCeEEEEeCccccCHHHHHHHHHHhccCeEEcCCCCEeccCCeEEEEeCCC
Confidence                    11 1111    12222322 2345999999999988888888888875321        2346788999983


Q ss_pred             CC---------hhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhcc-------CCCCCCCHHHHHHHHHHHHHh
Q psy200          341 LD---------LTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQT-------DKFNMFNASALQLLAGKVAAV  404 (490)
Q Consensus       341 ~~---------~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~-------~~~~~~~~~~i~~i~~~i~~~  404 (490)
                      ..         +...+.+.+.+||.   ..+.|.|++.+++..|+...+...       +....+++++++.|++..+.+
T Consensus       630 ~~~~~~~~~~~~~~~f~p~l~~Rl~---~~i~~~~l~~~~~~~i~~~~l~~~~~~~~~~~~~~~~~~~a~~~l~~~~~~~  706 (758)
T 3pxi_A          630 GASEKDKVMGELKRAFRPEFINRID---EIIVFHSLEKKHLTEIVSLMSDQLTKRLKEQDLSIELTDAAKAKVAEEGVDL  706 (758)
T ss_dssp             STTCCHHHHHHHHHHSCHHHHTTSS---EEEECC--CHHHHHHHHHHHHHHHHHHHHTTTCEEEECHHHHHHHHGGGCCT
T ss_pred             ChhhHHHHHHHHHhhCCHHHHhhCC---eEEecCCCCHHHHHHHHHHHHHHHHHHHHhCCCeEEECHHHHHHHHHhCCCC
Confidence            21         12335688999996   489999999999999988877553       234568999999998866778


Q ss_pred             hCCHHHHHHHHHHHHHHHH
Q psy200          405 SGDIRKAIDITNHLIDLTY  423 (490)
Q Consensus       405 ~Gd~r~ai~ll~~a~~~a~  423 (490)
                      .||+|.+-+++++++....
T Consensus       707 ~~~~R~L~~~i~~~v~~~l  725 (758)
T 3pxi_A          707 EYGARPLRRAIQKHVEDRL  725 (758)
T ss_dssp             TTTTTTHHHHHHHHTHHHH
T ss_pred             CCCChHHHHHHHHHHHHHH
Confidence            9999998888888765543

>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=99.61  E-value=4.3e-15  Score=156.59  Aligned_cols=233  Identities=18%  Similarity=0.212  Sum_probs=143.7

Q ss_pred             CCCCChHHHHHHHHHHHHhhh--ccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHV--NNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVN  271 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~--~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~  271 (490)
                      ++++|.++....+.+++.-..  ....+.+++|+||||||||+++++++..+.    ..+..++|........+..... 
T Consensus        81 ~di~G~~~vk~~i~~~~~l~~~~~~~~g~~vll~Gp~GtGKTtlar~ia~~l~----~~~~~i~~~~~~~~~~~~g~~~-  155 (543)
T 3m6a_A           81 EEHHGLEKVKERILEYLAVQKLTKSLKGPILCLAGPPGVGKTSLAKSIAKSLG----RKFVRISLGGVRDESEIRGHRR-  155 (543)
T ss_dssp             HHCSSCHHHHHHHHHHHHHHHHSSSCCSCEEEEESSSSSSHHHHHHHHHHHHT----CEEEEECCCC-------------
T ss_pred             HHhccHHHHHHHHHHHHHHHHhcccCCCCEEEEECCCCCCHHHHHHHHHHhcC----CCeEEEEecccchhhhhhhHHH-
Confidence            678999998888876554221  122567899999999999999999999875    5678888877544332221111 


Q ss_pred             HhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCH----HHHHHhHhCCCC------------CCCcEEEE
Q psy200          272 ELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQ----TILYTIFEWPSI------------PGSKLVLV  335 (490)
Q Consensus       272 ~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~----~~L~~l~~~~~~------------~~~~vilI  335 (490)
                          .+.+.....+...|..+.  ...+ +|||||++.+....+    +.|+.+++....            ....+++|
T Consensus       156 ----~~ig~~~~~~~~~~~~a~--~~~~-vl~lDEid~l~~~~~~~~~~~LL~~ld~~~~~~~~~~~~~~~~~~~~v~iI  228 (543)
T 3m6a_A          156 ----TYVGAMPGRIIQGMKKAG--KLNP-VFLLDEIDKMSSDFRGDPSSAMLEVLDPEQNSSFSDHYIEETFDLSKVLFI  228 (543)
T ss_dssp             ------------CHHHHHHTTC--SSSE-EEEEEESSSCC---------CCGGGTCTTTTTBCCCSSSCCCCBCSSCEEE
T ss_pred             ----HHhccCchHHHHHHHHhh--ccCC-EEEEhhhhhhhhhhccCHHHHHHHHHhhhhcceeecccCCeeecccceEEE
Confidence                111222222222222211  1233 999999999987633    455555432111            11578999


Q ss_pred             EecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhc-----cCC---CCCCCHHHHHHHHHHHHHhhCC
Q psy200          336 GVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQ-----TDK---FNMFNASALQLLAGKVAAVSGD  407 (490)
Q Consensus       336 ~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~-----~~~---~~~~~~~~i~~i~~~i~~~~Gd  407 (490)
                      +++|..   +.+.+.+.+||.    .+.|.+|+.++...|+..++..     .+.   ...++++++..+++ .+.+.|+
T Consensus       229 ~ttN~~---~~l~~aL~~R~~----vi~~~~~~~~e~~~Il~~~l~~~~~~~~~~~~~~i~i~~~~l~~l~~-~~~~~~~  300 (543)
T 3m6a_A          229 ATANNL---ATIPGPLRDRME----IINIAGYTEIEKLEIVKDHLLPKQIKEHGLKKSNLQLRDQAILDIIR-YYTREAG  300 (543)
T ss_dssp             EECSST---TTSCHHHHHHEE----EEECCCCCHHHHHHHHHHTHHHHHHHHTTCCGGGCEECHHHHHHHHH-HHCCCSS
T ss_pred             eccCcc---ccCCHHHHhhcc----eeeeCCCCHHHHHHHHHHHHHHHHHHHcCCCcccccCCHHHHHHHHH-hCChhhc
Confidence            999954   466788999995    7999999999999998876622     111   34578999999876 3345588


Q ss_pred             HHHHHHHHHHHHHHHHhccc-cCCcccccCHHHHHHHHHH
Q psy200          408 IRKAIDITNHLIDLTYDNVK-ENGEVTGIGLKEVLGVISS  446 (490)
Q Consensus       408 ~r~ai~ll~~a~~~a~~~~~-~~~~~~~It~~~v~~a~~~  446 (490)
                      +|.+-+.++.++..+....- .+.....|+.+++.+++..
T Consensus       301 vR~L~~~i~~~~~~aa~~~~~~~~~~~~It~~~l~~~Lg~  340 (543)
T 3m6a_A          301 VRSLERQLAAICRKAAKAIVAEERKRITVTEKNLQDFIGK  340 (543)
T ss_dssp             SHHHHHHHHHHHHHHHHHHHTTCCSCCEECTTTTHHHHCS
T ss_pred             hhHHHHHHHHHHHHHHHHHHhcCCcceecCHHHHHHHhCC
Confidence            99887777666655433210 0111457999999988854

>2qen_A Walker-type ATPase; unknown function; HET: ADP; 2.25A {Pyrococcus abyssi}

Probab=99.61  E-value=2.6e-14  Score=142.15  Aligned_cols=196  Identities=12%  Similarity=0.196  Sum_probs=126.3

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCC------CHHHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVR------NAASVYE  267 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~------~~~~l~~  267 (490)
                      +.|+||+++++.|..++..      ++.++|+|++|+|||+|++.+++..      .+++++|....      +...++.
T Consensus        12 ~~~~gR~~el~~L~~~l~~------~~~v~i~G~~G~GKT~Ll~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~   79 (350)
T 2qen_A           12 EDIFDREEESRKLEESLEN------YPLTLLLGIRRVGKSSLLRAFLNER------PGILIDCRELYAERGHITREELIK   79 (350)
T ss_dssp             GGSCSCHHHHHHHHHHHHH------CSEEEEECCTTSSHHHHHHHHHHHS------SEEEEEHHHHHHTTTCBCHHHHHH
T ss_pred             HhcCChHHHHHHHHHHHhc------CCeEEEECCCcCCHHHHHHHHHHHc------CcEEEEeecccccccCCCHHHHHH
Confidence            5799999999999998864      2799999999999999999999875      26888876543      5566777


Q ss_pred             HHHHHhcC-------------------CCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccc----cCH---HHHHHh
Q psy200          268 TIVNELKL-------------------KPGGKSERHQLGAILKYFDTKHKSILLILDEIDALES----RKQ---TILYTI  321 (490)
Q Consensus       268 ~i~~~l~~-------------------~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~----~~~---~~L~~l  321 (490)
                      .+...+..                   ........++.+.+.+.....+ +++|||||+|++..    ...   ..|..+
T Consensus        80 ~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~-~~vlvlDe~~~~~~~~~~~~~~~~~~L~~~  158 (350)
T 2qen_A           80 ELQSTISPFQKFQSKFKISLNLKFLTLEPRKLSLREVFRELNDLGEELG-EFIVAFDEAQYLRFYGSRGGKELLALFAYA  158 (350)
T ss_dssp             HHHHHSCSHHHHHHHHTCCCCCGGGTSCGGGCCHHHHHHHHHHHHHHHS-CEEEEEETGGGGGGBTTTTTHHHHHHHHHH
T ss_pred             HHHHHHHHHHhHhhhceeEEEecceeeccccchHHHHHHHHHHHHhccC-CEEEEEeCHHHHhccCccchhhHHHHHHHH
Confidence            77665532                   0001234555555555444323 89999999999975    222   333344


Q ss_pred             HhCCCCCCCcEEEEEecCCCChhHhh------hHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHH
Q psy200          322 FEWPSIPGSKLVLVGVANALDLTDRM------LPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQ  395 (490)
Q Consensus       322 ~~~~~~~~~~vilI~~tn~~~~~~~l------~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~  395 (490)
                      ++..  .  ++.+|.++....+...+      ...+..|+.   ..+.+.|++.+|..+++...+...+  ..++++.+.
T Consensus       159 ~~~~--~--~~~~il~g~~~~~l~~~l~~~~~~~~l~~~~~---~~i~l~pl~~~e~~~~l~~~~~~~~--~~~~~~~~~  229 (350)
T 2qen_A          159 YDSL--P--NLKIILTGSEVGLLHDFLKITDYESPLYGRIA---GEVLVKPFDKDTSVEFLKRGFREVN--LDVPENEIE  229 (350)
T ss_dssp             HHHC--T--TEEEEEEESSHHHHHHHHCTTCTTSTTTTCCC---EEEECCCCCHHHHHHHHHHHHHTTT--CCCCHHHHH
T ss_pred             HHhc--C--CeEEEEECCcHHHHHHHHhhcCCCCccccCcc---ceeeCCCCCHHHHHHHHHHHHHHcC--CCCCHHHHH
Confidence            3322  2  34444444321111221      112222322   4799999999999999998776542  346788777


Q ss_pred             HHHHHHHHhhCCHHHHHHHH
Q psy200          396 LLAGKVAAVSGDIRKAIDIT  415 (490)
Q Consensus       396 ~i~~~i~~~~Gd~r~ai~ll  415 (490)
                      .+++    .+|+.+.++..+
T Consensus       230 ~i~~----~tgG~P~~l~~~  245 (350)
T 2qen_A          230 EAVE----LLDGIPGWLVVF  245 (350)
T ss_dssp             HHHH----HHTTCHHHHHHH
T ss_pred             HHHH----HhCCCHHHHHHH
Confidence            7765    555555566544

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20

Probab=99.60  E-value=2.3e-15  Score=136.01  Aligned_cols=157  Identities=18%  Similarity=0.249  Sum_probs=105.2

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhc------CCceEEEEeccCCCCHHHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIK------DAFKTIYINCNSVRNAASVYE  267 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~------~~~~~~~v~~~~~~~~~~l~~  267 (490)
                      ++++|++++++.+..++..    ....+++|+|++|+|||++++.+++.+...      .+..+++++|.....      
T Consensus        22 ~~~~g~~~~~~~l~~~l~~----~~~~~~ll~G~~G~GKT~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------   91 (195)
T 1jbk_A           22 DPVIGRDEEIRRTIQVLQR----RTKNNPVLIGEPGVGKTAIVEGLAQRIINGEVPEGLKGRRVLALDMGALVA------   91 (195)
T ss_dssp             CCCCSCHHHHHHHHHHHTS----SSSCEEEEECCTTSCHHHHHHHHHHHHHHTCSCGGGTTCEEEEECHHHHHT------
T ss_pred             cccccchHHHHHHHHHHhc----CCCCceEEECCCCCCHHHHHHHHHHHHHhCCCchhhcCCcEEEeeHHHHhc------
Confidence            7899999999999888853    556789999999999999999999987531      245778887643210      


Q ss_pred             HHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCcccccc--------CHHHHHHhHhCCCCCCCcEEEEEecC
Q psy200          268 TIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESR--------KQTILYTIFEWPSIPGSKLVLVGVAN  339 (490)
Q Consensus       268 ~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~--------~~~~L~~l~~~~~~~~~~vilI~~tn  339 (490)
                            +....+.....+...+.. +...+++.||||||+|.+...        .++.+..+++.     .++.+|++++
T Consensus        92 ------~~~~~~~~~~~~~~~~~~-~~~~~~~~vl~iDe~~~l~~~~~~~~~~~~~~~l~~~~~~-----~~~~~i~~~~  159 (195)
T 1jbk_A           92 ------GAKYRGEFEERLKGVLND-LAKQEGNVILFIDELHTMVGAGKADGAMDAGNMLKPALAR-----GELHCVGATT  159 (195)
T ss_dssp             ------TTCSHHHHHHHHHHHHHH-HHHSTTTEEEEEETGGGGTT------CCCCHHHHHHHHHT-----TSCCEEEEEC
T ss_pred             ------cCCccccHHHHHHHHHHH-HhhcCCCeEEEEeCHHHHhccCcccchHHHHHHHHHhhcc-----CCeEEEEeCC
Confidence                  001111111122222222 223456789999999999632        25666665542     3566777777


Q ss_pred             CCChhH--hhhHHhhhccCCCCeeEEeCCCCHHHHHHHH
Q psy200          340 ALDLTD--RMLPRLQANVTLQPTLMNFAPYSREQILEII  376 (490)
Q Consensus       340 ~~~~~~--~l~~~l~~R~~~~~~~i~~~pls~~e~~~il  376 (490)
                      ..++..  .+.+.+.+||.    .+.|.+++.+++.++|
T Consensus       160 ~~~~~~~~~~~~~l~~r~~----~i~~~~p~~~~~~~il  194 (195)
T 1jbk_A          160 LDEYRQYIEKDAALERRFQ----KVFVAEPSVEDTIAIL  194 (195)
T ss_dssp             HHHHHHHTTTCHHHHTTEE----EEECCCCCHHHHHTTC
T ss_pred             HHHHHHHHhcCHHHHHHhc----eeecCCCCHHHHHHHh
Confidence            432221  34688999986    6999999999988765

>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=99.57  E-value=1.2e-14  Score=160.05  Aligned_cols=215  Identities=18%  Similarity=0.207  Sum_probs=147.5

Q ss_pred             CCCCChHHHHHHHHHHHHhhhcc-----CCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVNN-----ETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYET  268 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~-----~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~  268 (490)
                      ..++|++..++.|...+.....+     .+.++++|+||+|||||++|+++++.+.    ..++.++|+.+.....+   
T Consensus       458 ~~v~g~~~~~~~l~~~i~~~~~g~~~~~~p~~~~ll~G~~GtGKT~la~~la~~l~----~~~~~i~~s~~~~~~~~---  530 (758)
T 1r6b_X          458 MLVFGQDKAIEALTEAIKMARAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSKALG----IELLRFDMSEYMERHTV---  530 (758)
T ss_dssp             TTSCSCHHHHHHHHHHHHHHHTTCSCTTSCSEEEEEECSTTSSHHHHHHHHHHHHT----CEEEEEEGGGCSSSSCC---
T ss_pred             hhccCHHHHHHHHHHHHHHHhcccCCCCCCceEEEEECCCCCcHHHHHHHHHHHhc----CCEEEEechhhcchhhH---
Confidence            78999999999998888754321     1334799999999999999999999884    67899999877432100   


Q ss_pred             HHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCHHHHHHhHhCCCCC--------CCcEEEEEecCC
Q psy200          269 IVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPSIP--------GSKLVLVGVANA  340 (490)
Q Consensus       269 i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~--------~~~vilI~~tn~  340 (490)
                        ..+.+...|.........+...+.. ....|||||||+.+....++.|+++++.....        -.+++||+++|.
T Consensus       531 --~~l~g~~~g~~g~~~~~~l~~~~~~-~~~~vl~lDEi~~~~~~~~~~Ll~~le~~~~~~~~g~~~~~~~~~iI~tsN~  607 (758)
T 1r6b_X          531 --SRLIGAPPGYVGFDQGGLLTDAVIK-HPHAVLLLDEIEKAHPDVFNILLQVMDNGTLTDNNGRKADFRNVVLVMTTNA  607 (758)
T ss_dssp             --SSSCCCCSCSHHHHHTTHHHHHHHH-CSSEEEEEETGGGSCHHHHHHHHHHHHHSEEEETTTEEEECTTEEEEEEECS
T ss_pred             --hhhcCCCCCCcCccccchHHHHHHh-CCCcEEEEeCccccCHHHHHHHHHHhcCcEEEcCCCCEEecCCeEEEEecCc
Confidence              0011111111111111223333433 33679999999999887888888888743210        146789999985


Q ss_pred             CC----------------------hhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhcc-------CCCCCCCH
Q psy200          341 LD----------------------LTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQT-------DKFNMFNA  391 (490)
Q Consensus       341 ~~----------------------~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~-------~~~~~~~~  391 (490)
                      ..                      +...+.+.+.+||.   ..+.|+|++.+++..|+..++...       +....+++
T Consensus       608 ~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~l~~R~~---~~i~~~~l~~~~~~~i~~~~l~~~~~~~~~~~~~~~~~~  684 (758)
T 1r6b_X          608 GVRETERKSIGLIHQDNSTDAMEEIKKIFTPEFRNRLD---NIIWFDHLSTDVIHQVVDKFIVELQVQLDQKGVSLEVSQ  684 (758)
T ss_dssp             SCC-----------------CHHHHHHHSCHHHHTTCS---EEEECCCCCHHHHHHHHHHHHHHHHHHHHHTTEEEEECH
T ss_pred             chhhhhhcccCccccchHHHHHHHHHHhcCHHHHhhCC---cceeeCCCCHHHHHHHHHHHHHHHHHHHHHCCcEEEeCH
Confidence            21                      11256788999997   479999999999999999887632       11246899


Q ss_pred             HHHHHHHHHHHHhhCCHHHHHHHHHHHHHH
Q psy200          392 SALQLLAGKVAAVSGDIRKAIDITNHLIDL  421 (490)
Q Consensus       392 ~~i~~i~~~i~~~~Gd~r~ai~ll~~a~~~  421 (490)
                      ++++.|++......+++|.+.+++++++..
T Consensus       685 ~a~~~l~~~~~~~~~g~R~l~~~i~~~~~~  714 (758)
T 1r6b_X          685 EARNWLAEKGYDRAMGARPMARVIQDNLKK  714 (758)
T ss_dssp             HHHHHHHHHHCBTTTBTTTHHHHHHHHHTH
T ss_pred             HHHHHHHHhCCCcCCCchHHHHHHHHHHHH
Confidence            999999983333344588888888877653

>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=99.55  E-value=1.7e-13  Score=139.07  Aligned_cols=148  Identities=16%  Similarity=0.236  Sum_probs=98.6

Q ss_pred             eEEEEEecCcccccc------------CHHHHHHhHhCCC-------CCCCcEEEEEecCC-CChhHhhhHHhhhccCCC
Q psy200          299 SILLILDEIDALESR------------KQTILYTIFEWPS-------IPGSKLVLVGVANA-LDLTDRMLPRLQANVTLQ  358 (490)
Q Consensus       299 ~~vI~IDEid~l~~~------------~~~~L~~l~~~~~-------~~~~~vilI~~tn~-~~~~~~l~~~l~~R~~~~  358 (490)
                      ..+|++||||.+...            -|+.|+.+++-..       ....+++|||+... ...+..+.+.|.+||.  
T Consensus       251 ~~il~~DEidki~~~~~~~~~D~s~egvq~aLL~~le~~~~~~~~~~~d~~~ilfI~~gaf~~~~~~dlipel~~R~~--  328 (444)
T 1g41_A          251 NGIVFIDEIDKICKKGEYSGADVSREGVQRDLLPLVEGSTVSTKHGMVKTDHILFIASGAFQVARPSDLIPELQGRLP--  328 (444)
T ss_dssp             HCEEEEETGGGGSCCSSCSSSHHHHHHHHHHHHHHHHCCEEEETTEEEECTTCEEEEEECCSSCCGGGSCHHHHTTCC--
T ss_pred             CCeeeHHHHHHHhhccCCCCCCchHHHHHHHHHHHhcccccccccceecCCcEEEEeccccccCChhhcchHHhcccc--
Confidence            348999999999754            1457777776321       23567888888720 1112235688999997  


Q ss_pred             CeeEEeCCCCHHHHHHHHH-----------HHHhccCCCCCCCHHHHHHHHHHHHH-----hhCCHHHHHHHHHHHHHHH
Q psy200          359 PTLMNFAPYSREQILEIIS-----------QKLKQTDKFNMFNASALQLLAGKVAA-----VSGDIRKAIDITNHLIDLT  422 (490)
Q Consensus       359 ~~~i~~~pls~~e~~~il~-----------~~l~~~~~~~~~~~~~i~~i~~~i~~-----~~Gd~r~ai~ll~~a~~~a  422 (490)
                       .++.|++|+.++...|+.           ..+...+....|++++++.|++....     ..++.|.+-++++.++..+
T Consensus       329 -i~i~l~~lt~~e~~~Il~~~~~~l~~q~~~~~~~~~~~l~~~~~al~~i~~~a~~~~~~t~~~GaR~L~~~ie~~~~~~  407 (444)
T 1g41_A          329 -IRVELTALSAADFERILTEPHASLTEQYKALMATEGVNIAFTTDAVKKIAEAAFRVNEKTENIGARRLHTVMERLMDKI  407 (444)
T ss_dssp             -EEEECCCCCHHHHHHHHHSSTTCHHHHHHHHHHTTTCEEEECHHHHHHHHHHHHHHHHHSCCCGGGHHHHHHHHHHHHH
T ss_pred             -eeeeCCCCCHHHHHHHHHHHHHhHHHHHHHHhcccCceEEECHHHHHHHHHHHHHhccCCccCCchHHHHHHHHHHHHH
Confidence             369999999999999983           12222345667999999999986543     3578888877777766543


Q ss_pred             Hhcccc-CCcccccCHHHHHHHHHHhcc
Q psy200          423 YDNVKE-NGEVTGIGLKEVLGVISSVYC  449 (490)
Q Consensus       423 ~~~~~~-~~~~~~It~~~v~~a~~~~~~  449 (490)
                      ..+... ....-.|+.+.|...+.....
T Consensus       408 ~~~~~~~~~~~~~i~~~~v~~~l~~~~~  435 (444)
T 1g41_A          408 SFSASDMNGQTVNIDAAYVADALGEVVE  435 (444)
T ss_dssp             HHHGGGCTTCEEEECHHHHHHHHTTTTT
T ss_pred             HhhccccCCCeEEEeHHHHHHhcCcccc
Confidence            332111 111346999999887766543

>3t15_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic; photosynthesis, rubisco activase, AAA+ protein; 2.95A {Nicotiana tabacum} PDB: 3zw6_A

Probab=99.54  E-value=3.5e-14  Score=138.13  Aligned_cols=157  Identities=15%  Similarity=0.200  Sum_probs=97.1

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHH--h
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYF--D  294 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l--~  294 (490)
                      ..+.+++|+||||||||++|++++++++    ..+++++|..+.              ..+.|.....+...|..+.  .
T Consensus        34 ~~p~~lLl~GppGtGKT~la~aiA~~l~----~~~i~v~~~~l~--------------~~~~g~~~~~i~~~f~~a~~~~   95 (293)
T 3t15_A           34 KVPLILGIWGGKGQGKSFQCELVFRKMG----INPIMMSAGELE--------------SGNAGEPAKLIRQRYREAAEII   95 (293)
T ss_dssp             CCCSEEEEEECTTSCHHHHHHHHHHHHT----CCCEEEEHHHHH--------------CC---HHHHHHHHHHHHHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHhC----CCEEEEeHHHhh--------------hccCchhHHHHHHHHHHHHHHH
Confidence            3567899999999999999999999985    677888875432              1233344445555555442  1


Q ss_pred             cCCCeEEEEEecCccccccC-------------HHHHHHhHhCC----------CCCCCcEEEEEecCCCChhHhhhHHh
Q psy200          295 TKHKSILLILDEIDALESRK-------------QTILYTIFEWP----------SIPGSKLVLVGVANALDLTDRMLPRL  351 (490)
Q Consensus       295 ~~~~~~vI~IDEid~l~~~~-------------~~~L~~l~~~~----------~~~~~~vilI~~tn~~~~~~~l~~~l  351 (490)
                      ....++||||||||.+....             +..|..+++-.          .....++++|++||..+   .+++.+
T Consensus        96 ~~~~~~vl~iDEiD~~~~~~~~~~~~~~~~~~v~~~Ll~~ld~~~~~~~~~~~~~~~~~~v~vI~ttN~~~---~ld~al  172 (293)
T 3t15_A           96 RKGNMCCLFINDLDAGAGRMGGTTQYTVNNQMVNATLMNIADNPTNVQLPGMYNKQENARVPIIVTGNDFS---TLYAPL  172 (293)
T ss_dssp             TTSSCCCEEEECCC--------------CHHHHHHHHHHHHHCCC-----------CCCCCCEEEECSSCC---C--CHH
T ss_pred             hcCCCeEEEEechhhhcCCCCCCccccchHHHHHHHHHHHhccccccccccccccccCCCcEEEEecCCcc---cCCHHH
Confidence            23568999999999987632             14555555411          12356799999999654   334444


Q ss_pred             h--hccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhC
Q psy200          352 Q--ANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSG  406 (490)
Q Consensus       352 ~--~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~G  406 (490)
                      .  .||.   ..+.  .++.++..+|++..+...    .++.+.+..+..   ...|
T Consensus       173 ~R~~R~d---~~i~--~P~~~~r~~Il~~~~~~~----~~~~~~l~~~~~---~~~~  217 (293)
T 3t15_A          173 IRDGRME---KFYW--APTREDRIGVCTGIFRTD----NVPAEDVVKIVD---NFPG  217 (293)
T ss_dssp             HHHHHEE---EEEE--CCCHHHHHHHHHHHHGGG----CCCHHHHHHHHH---HSCS
T ss_pred             hCCCCCc---eeEe--CcCHHHHHHHHHHhccCC----CCCHHHHHHHhC---CCCc
Confidence            4  3664   2343  349999999999887654    355555555554   5555

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=99.54  E-value=9.3e-14  Score=152.68  Aligned_cols=196  Identities=16%  Similarity=0.149  Sum_probs=132.3

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhc------CCceEEEEeccCCCCHHHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIK------DAFKTIYINCNSVRNAASVYE  267 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~------~~~~~~~v~~~~~~~~~~l~~  267 (490)
                      +.++|++++++.+..+|..    ....+++|+||||||||++|+.+++.+...      .+..++.+++           
T Consensus       180 d~iiG~~~~i~~l~~~l~~----~~~~~vLL~G~pGtGKT~la~~la~~l~~~~~p~~l~~~~~~~~~~-----------  244 (758)
T 3pxi_A          180 DPVIGRSKEIQRVIEVLSR----RTKNNPVLIGEPGVGKTAIAEGLAQQIINNEVPEILRDKRVMTLDM-----------  244 (758)
T ss_dssp             CCCCCCHHHHHHHHHHHHC----SSSCEEEEESCTTTTTHHHHHHHHHHHHSSCSCTTTSSCCEECC-------------
T ss_pred             CCccCchHHHHHHHHHHhC----CCCCCeEEECCCCCCHHHHHHHHHHHHhcCCCChhhcCCeEEEecc-----------
Confidence            7899999999999998864    566789999999999999999999997421      1345666655           


Q ss_pred             HHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEEEecCCCChhH--
Q psy200          268 TIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVANALDLTD--  345 (490)
Q Consensus       268 ~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI~~tn~~~~~~--  345 (490)
                            +..+.|.....+...+..+..  ..+.|||||    .....++.|     ........+.+|++||..++..  
T Consensus       245 ------g~~~~G~~e~~l~~~~~~~~~--~~~~iLfiD----~~~~~~~~L-----~~~l~~~~v~~I~at~~~~~~~~~  307 (758)
T 3pxi_A          245 ------GTKYRGEFEDRLKKVMDEIRQ--AGNIILFID----AAIDASNIL-----KPSLARGELQCIGATTLDEYRKYI  307 (758)
T ss_dssp             --------------CTTHHHHHHHHHT--CCCCEEEEC----C-------------CCCTTSSSCEEEEECCTTTTHHHH
T ss_pred             ------cccccchHHHHHHHHHHHHHh--cCCEEEEEc----CchhHHHHH-----HHHHhcCCEEEEeCCChHHHHHHh
Confidence                  112233333444555554443  457799999    111123333     2233456789999999766432  


Q ss_pred             hhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhcc--CCCCCCCHHHHHHHHHHHHHhhC---CHHHHHHHHHHHHH
Q psy200          346 RMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQT--DKFNMFNASALQLLAGKVAAVSG---DIRKAIDITNHLID  420 (490)
Q Consensus       346 ~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~--~~~~~~~~~~i~~i~~~i~~~~G---d~r~ai~ll~~a~~  420 (490)
                      .+++.+.+||.    .+.|.+++.+++..|+...+...  .....+++++++.+++....+-+   -...+++++..|..
T Consensus       308 ~~d~al~rRf~----~i~v~~p~~~~~~~il~~~~~~~~~~~~~~i~~~al~~~~~~s~~~i~~~~~p~~ai~ll~~a~~  383 (758)
T 3pxi_A          308 EKDAALERRFQ----PIQVDQPSVDESIQILQGLRDRYEAHHRVSITDDAIEAAVKLSDRYISDRFLPDKAIDLIDEAGS  383 (758)
T ss_dssp             TTCSHHHHSEE----EEECCCCCHHHHHHHHHHTTTTSGGGSSCSCCHHHHHHHHHHHHHSSCCSCTTHHHHHHHHHHHH
T ss_pred             hccHHHHhhCc----EEEeCCCCHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhcccccCcCCcHHHHHHHHHHH
Confidence            45788999995    79999999999999999776553  13456899999999886555433   35678888888876


Q ss_pred             HHHhc
Q psy200          421 LTYDN  425 (490)
Q Consensus       421 ~a~~~  425 (490)
                      .+...
T Consensus       384 ~~~~~  388 (758)
T 3pxi_A          384 KVRLR  388 (758)
T ss_dssp             HHHHH
T ss_pred             HHHhh
Confidence            65543

>3nbx_X ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structure, rossman fold, hydro; HET: ADP; 2.91A {Escherichia coli}

Probab=99.53  E-value=6.6e-14  Score=145.07  Aligned_cols=228  Identities=14%  Similarity=0.087  Sum_probs=146.9

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHh
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNEL  273 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l  273 (490)
                      ..++|+++.++.+...+..      +.+++|+||||||||++|+++++.+.  ....+.+++|.- .++.+++.      
T Consensus        22 ~~ivGq~~~i~~l~~al~~------~~~VLL~GpPGtGKT~LAraLa~~l~--~~~~f~~~~~~~-~t~~dL~G------   86 (500)
T 3nbx_X           22 KGLYERSHAIRLCLLAALS------GESVFLLGPPGIAKSLIARRLKFAFQ--NARAFEYLMTRF-STPEEVFG------   86 (500)
T ss_dssp             TTCSSCHHHHHHHHHHHHH------TCEEEEECCSSSSHHHHHHHGGGGBS--SCCEEEEECCTT-CCHHHHHC------
T ss_pred             hhhHHHHHHHHHHHHHHhc------CCeeEeecCchHHHHHHHHHHHHHHh--hhhHHHHHHHhc-CCHHHhcC------
Confidence            7899999999888777753      56999999999999999999998874  223556666653 24433322      


Q ss_pred             cCCCCCCcHHHHHHHHHHHHhcC-CCeEEEEEecCccccccCHHHHHHhHhCCC--------CCCCcEEEEEecCCCChh
Q psy200          274 KLKPGGKSERHQLGAILKYFDTK-HKSILLILDEIDALESRKQTILYTIFEWPS--------IPGSKLVLVGVANALDLT  344 (490)
Q Consensus       274 ~~~~~~~s~~~~~~~l~~~l~~~-~~~~vI~IDEid~l~~~~~~~L~~l~~~~~--------~~~~~vilI~~tn~~~~~  344 (490)
                        ...+..... ...+..+..+. ..+.|||||||+.+....+..|+.+++...        ..+.++ +|++||...-.
T Consensus        87 --~~~~~~~~~-~g~~~~~~~g~l~~~~IL~IDEI~r~~~~~q~~LL~~lee~~v~i~G~~~~~~~~~-iI~ATN~lpe~  162 (500)
T 3nbx_X           87 --PLSIQALKD-EGRYERLTSGYLPEAEIVFLDEIWKAGPAILNTLLTAINERQFRNGAHVEKIPMRL-LVAASNELPEA  162 (500)
T ss_dssp             --CBC-----------CBCCTTSGGGCSEEEEESGGGCCHHHHHHHHHHHHSSEEECSSSEEECCCCE-EEEEESSCCCT
T ss_pred             --cccHHHHhh-chhHHhhhccCCCcceeeeHHhHhhhcHHHHHHHHHHHHHHhccCCCCcCCcchhh-hhhccccCCCc
Confidence              111000000 00111000100 024599999999998888888888876321        112334 56677754222


Q ss_pred             HhhhHHhhhccCCCCeeEEeCCCCH-HHHHHHHHHHHhcc---------------------CCCCCCCHHHHHHHHHHHH
Q psy200          345 DRMLPRLQANVTLQPTLMNFAPYSR-EQILEIISQKLKQT---------------------DKFNMFNASALQLLAGKVA  402 (490)
Q Consensus       345 ~~l~~~l~~R~~~~~~~i~~~pls~-~e~~~il~~~l~~~---------------------~~~~~~~~~~i~~i~~~i~  402 (490)
                      ..+.+.+.+||.   ..+.+++++. ++...|+..+....                     -....+++++++.+++.+.
T Consensus       163 ~~~~~aLldRF~---~~i~v~~p~~~ee~~~IL~~~~~~~~~~~~~~~~~~~e~l~~~~~~~~~v~v~d~v~e~i~~l~~  239 (500)
T 3nbx_X          163 DSSLEALYDRML---IRLWLDKVQDKANFRSMLTSQQDENDNPVPDALQVTDEEYERWQKEIGEITLPDHVFELIFMLRQ  239 (500)
T ss_dssp             TCTTHHHHTTCC---EEEECCSCCCHHHHHHHHTCCCCTTSCCSCTTTSBCHHHHHHHHHHHTTCBCCHHHHHHHHHHHH
T ss_pred             cccHHHHHHHHH---HHHHHHHhhhhhhHHHHHhcccccCCCCCCccceecHHHHHHHHhcCCcccCchHHHHHHHHHHH
Confidence            334568888986   3789999986 66777776543211                     0134578888888887553


Q ss_pred             H-------hhCCHHHHHHHHHHHHHHHHhccccCCcccccCHHHHHHHHHHhcc
Q psy200          403 A-------VSGDIRKAIDITNHLIDLTYDNVKENGEVTGIGLKEVLGVISSVYC  449 (490)
Q Consensus       403 ~-------~~Gd~r~ai~ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~~~~~~  449 (490)
                      .       ...+.|.++.++..|...|...+     ...|+.+|+. ++..+..
T Consensus       240 ~lr~~r~~~~iS~R~~~~llr~A~A~A~l~g-----r~~Vt~eDv~-~a~~vL~  287 (500)
T 3nbx_X          240 QLDKLPDAPYVSDRRWKKAIRLLQASAFFSG-----RSAVAPVDLI-LLKDCLW  287 (500)
T ss_dssp             HHHHCSSSCCCCHHHHHHHHHHHHHHHHHTT-----CSBCCGGGGG-GGGGTSC
T ss_pred             HhhcCCCCCccchhHHHHHHHHHHHHHhhcC-----CccccchHHH-HHHhhhh
Confidence            2       13478999999999988999988     6688888888 5544443

>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=99.53  E-value=3.4e-14  Score=157.95  Aligned_cols=220  Identities=15%  Similarity=0.194  Sum_probs=147.5

Q ss_pred             CCCCChHHHHHHHHHHHHhhhcc-----CCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVNN-----ETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYET  268 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~-----~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~  268 (490)
                      ..++|++..++.|...+.....+     .+..+++|+||+|||||++|+++++.+. ..+..+++++|..+..... ...
T Consensus       558 ~~viG~~~a~~~l~~~i~~~~~g~~~~~~p~~~vLl~Gp~GtGKT~lA~~la~~~~-~~~~~~i~i~~~~~~~~~~-~s~  635 (854)
T 1qvr_A          558 KRVVGQDEAIRAVADAIRRARAGLKDPNRPIGSFLFLGPTGVGKTELAKTLAATLF-DTEEAMIRIDMTEYMEKHA-VSR  635 (854)
T ss_dssp             HHSCSCHHHHHHHHHHHHHHGGGCSCSSSCSEEEEEBSCSSSSHHHHHHHHHHHHH-SSGGGEEEECTTTCCSSGG-GGG
T ss_pred             cccCCcHHHHHHHHHHHHHHhcccCCCCCCceEEEEECCCCCCHHHHHHHHHHHhc-CCCCcEEEEechhccchhH-HHH
Confidence            46899999999999988765332     1225899999999999999999999874 2245789999988754211 111


Q ss_pred             HHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCHHHHHHhHhCCCCC--------CCcEEEEEecCC
Q psy200          269 IVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPSIP--------GSKLVLVGVANA  340 (490)
Q Consensus       269 i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~--------~~~vilI~~tn~  340 (490)
                      ++..- ..+.|...   ...+..++.. ....+||||||+.+....++.|+++++.....        -.++++|+++|.
T Consensus       636 l~g~~-~~~~G~~~---~g~l~~~~~~-~~~~vl~lDEi~~l~~~~~~~Ll~~l~~~~~~~~~g~~vd~~~~iiI~tsn~  710 (854)
T 1qvr_A          636 LIGAP-PGYVGYEE---GGQLTEAVRR-RPYSVILFDEIEKAHPDVFNILLQILDDGRLTDSHGRTVDFRNTVIILTSNL  710 (854)
T ss_dssp             C------------------CHHHHHHH-CSSEEEEESSGGGSCHHHHHHHHHHHTTTEECCSSSCCEECTTEEEEEECCT
T ss_pred             HcCCC-CCCcCccc---cchHHHHHHh-CCCeEEEEecccccCHHHHHHHHHHhccCceECCCCCEeccCCeEEEEecCc
Confidence            10000 00111111   1122333332 23569999999999888888888888744211        136788999985


Q ss_pred             C-----C----------hh--------HhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhcc-------CCCCCCC
Q psy200          341 L-----D----------LT--------DRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQT-------DKFNMFN  390 (490)
Q Consensus       341 ~-----~----------~~--------~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~-------~~~~~~~  390 (490)
                      -     +          +.        ..+.+.|.+||.   ..+.|.|++.+++..|+.+++...       +....++
T Consensus       711 ~~~~~~~~~~~~~~~~~l~~~v~~~~~~~f~~~l~~Rl~---~~i~~~pl~~edi~~i~~~~l~~~~~~~~~~~~~~~~~  787 (854)
T 1qvr_A          711 GSPLILEGLQKGWPYERIRDEVFKVLQQHFRPEFLNRLD---EIVVFRPLTKEQIRQIVEIQLSYLRARLAEKRISLELT  787 (854)
T ss_dssp             THHHHHHHHHTTCCHHHHHHHHHHHHHTTSCHHHHHTCS---BCCBCCCCCHHHHHHHHHHHHHHHHHHHHTTTCEEEEC
T ss_pred             ChHHHhhhcccccchHHHHHHHHHHHHhhCCHHHHHhcC---eEEeCCCCCHHHHHHHHHHHHHHHHHHHHhCCceEEEC
Confidence            1     1          11        123467888887   378899999999999998877642       1134689


Q ss_pred             HHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHH
Q psy200          391 ASALQLLAGKVAAVSGDIRKAIDITNHLIDLTY  423 (490)
Q Consensus       391 ~~~i~~i~~~i~~~~Gd~r~ai~ll~~a~~~a~  423 (490)
                      +++++.|++......||+|.+.+++++++..+.
T Consensus       788 ~~a~~~L~~~~~~~~gn~R~L~~~i~~~~~~~~  820 (854)
T 1qvr_A          788 EAAKDFLAERGYDPVFGARPLRRVIQRELETPL  820 (854)
T ss_dssp             HHHHHHHHHHHCBTTTBTSTHHHHHHHHTHHHH
T ss_pred             HHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHH
Confidence            999999998433337999999999988876554

>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=99.49  E-value=5.2e-13  Score=130.19  Aligned_cols=172  Identities=13%  Similarity=0.084  Sum_probs=120.1

Q ss_pred             ChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhc--CCceEEEEeccCCCCHHHHHHHHHHHhcC
Q psy200          198 GREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIK--DAFKTIYINCNSVRNAASVYETIVNELKL  275 (490)
Q Consensus       198 gre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~--~~~~~~~v~~~~~~~~~~l~~~i~~~l~~  275 (490)
                      |+++.++.|...+..    +..++++|+||+|+|||++++++++.+...  ....+++++....                
T Consensus         1 g~~~~~~~L~~~i~~----~~~~~~Lf~Gp~G~GKtt~a~~la~~~~~~~~~~~d~~~l~~~~~----------------   60 (305)
T 2gno_A            1 GAKDQLETLKRIIEK----SEGISILINGEDLSYPREVSLELPEYVEKFPPKASDVLEIDPEGE----------------   60 (305)
T ss_dssp             ---CHHHHHHHHHHT----CSSEEEEEECSSSSHHHHHHHHHHHHHHTSCCCTTTEEEECCSSS----------------
T ss_pred             ChHHHHHHHHHHHHC----CCCcEEEEECCCCCCHHHHHHHHHHhCchhhccCCCEEEEcCCcC----------------
Confidence            566777777777764    447789999999999999999999865311  1335566654321                


Q ss_pred             CCCCCcHHHHHHHHHHHHhc--CCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEEEecCCCChhHhhhHHhhh
Q psy200          276 KPGGKSERHQLGAILKYFDT--KHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVANALDLTDRMLPRLQA  353 (490)
Q Consensus       276 ~~~~~s~~~~~~~l~~~l~~--~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI~~tn~~~~~~~l~~~l~~  353 (490)
                         ..+.+.+++.+..+...  .++..|+||||+|.|....++.|...++.+   ....++|.+|+.   ..++.+.+++
T Consensus        61 ---~~~id~ir~li~~~~~~p~~~~~kvviIdead~lt~~a~naLLk~LEep---~~~t~fIl~t~~---~~kl~~tI~S  131 (305)
T 2gno_A           61 ---NIGIDDIRTIKDFLNYSPELYTRKYVIVHDCERMTQQAANAFLKALEEP---PEYAVIVLNTRR---WHYLLPTIKS  131 (305)
T ss_dssp             ---CBCHHHHHHHHHHHTSCCSSSSSEEEEETTGGGBCHHHHHHTHHHHHSC---CTTEEEEEEESC---GGGSCHHHHT
T ss_pred             ---CCCHHHHHHHHHHHhhccccCCceEEEeccHHHhCHHHHHHHHHHHhCC---CCCeEEEEEECC---hHhChHHHHc
Confidence               12344455544333221  245679999999999988888898888743   345666666653   4678899999


Q ss_pred             ccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHHHHHHH
Q psy200          354 NVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITNHL  418 (490)
Q Consensus       354 R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll~~a  418 (490)
                      |      .+.|.+++.+++.+++.+.+.       ++++++.       ...|+++.++++++..
T Consensus       132 R------~~~f~~l~~~~i~~~L~~~~~-------i~~~~~~-------~~~g~~~~al~~l~~~  176 (305)
T 2gno_A          132 R------VFRVVVNVPKEFRDLVKEKIG-------DLWEELP-------LLERDFKTALEAYKLG  176 (305)
T ss_dssp             T------SEEEECCCCHHHHHHHHHHHT-------THHHHCG-------GGGTCHHHHHHHHHHH
T ss_pred             e------eEeCCCCCHHHHHHHHHHHhC-------CCHHHHH-------HHCCCHHHHHHHHHHH
Confidence            8      399999999999999998871       4555552       3589999999887643

>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural genomics, structural genomics consortium, SGC, unknown function; 1.70A {Plasmodium falciparum}

Probab=99.49  E-value=2.6e-14  Score=128.60  Aligned_cols=149  Identities=17%  Similarity=0.216  Sum_probs=96.5

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhc------CCceEEEEeccCCCCHHHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIK------DAFKTIYINCNSVRNAASVYE  267 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~------~~~~~~~v~~~~~~~~~~l~~  267 (490)
                      ++++|++++++.+.+++..    ....+++|+||+|+|||++++.+++.+...      .+..++++++...      ..
T Consensus        22 ~~~~g~~~~~~~l~~~l~~----~~~~~vll~G~~G~GKT~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~   91 (187)
T 2p65_A           22 DPVIGRDTEIRRAIQILSR----RTKNNPILLGDPGVGKTAIVEGLAIKIVQGDVPDSLKGRKLVSLDLSSL------IA   91 (187)
T ss_dssp             CCCCSCHHHHHHHHHHHTS----SSSCEEEEESCGGGCHHHHHHHHHHHHHTTCSCTTTTTCEEEEECHHHH------HH
T ss_pred             chhhcchHHHHHHHHHHhC----CCCCceEEECCCCCCHHHHHHHHHHHHHhcCCcchhcCCeEEEEeHHHh------hc
Confidence            7899999999999888853    557789999999999999999999987421      2456777765322      10


Q ss_pred             HHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCcccc---------ccCHHHHHHhHhCCCCCCCcEEEEEec
Q psy200          268 TIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALE---------SRKQTILYTIFEWPSIPGSKLVLVGVA  338 (490)
Q Consensus       268 ~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~---------~~~~~~L~~l~~~~~~~~~~vilI~~t  338 (490)
                          .  ....+.....+...+.. +...+++.+|||||+|.+.         ....+.|..+++     ...+++|+++
T Consensus        92 ----~--~~~~~~~~~~~~~~~~~-~~~~~~~~vl~iDe~~~l~~~~~~~~~~~~~~~~l~~~~~-----~~~~~ii~~~  159 (187)
T 2p65_A           92 ----G--AKYRGDFEERLKSILKE-VQDAEGQVVMFIDEIHTVVGAGAVAEGALDAGNILKPMLA-----RGELRCIGAT  159 (187)
T ss_dssp             ----H--CCSHHHHHHHHHHHHHH-HHHTTTSEEEEETTGGGGSSSSSSCTTSCCTHHHHHHHHH-----TTCSCEEEEE
T ss_pred             ----C--CCchhHHHHHHHHHHHH-HHhcCCceEEEEeCHHHhcccccccccchHHHHHHHHHHh-----cCCeeEEEec
Confidence                0  01111111122223332 3333567899999999997         222345555544     2457788888


Q ss_pred             CCCChh--HhhhHHhhhccCCCCeeEEeCCCC
Q psy200          339 NALDLT--DRMLPRLQANVTLQPTLMNFAPYS  368 (490)
Q Consensus       339 n~~~~~--~~l~~~l~~R~~~~~~~i~~~pls  368 (490)
                      |..++.  ..+++.+.+||.    .+.+.+++
T Consensus       160 ~~~~~~~~~~~~~~l~~R~~----~i~i~~p~  187 (187)
T 2p65_A          160 TVSEYRQFIEKDKALERRFQ----QILVEQPS  187 (187)
T ss_dssp             CHHHHHHHTTTCHHHHHHEE----EEECCSCC
T ss_pred             CHHHHHHHHhccHHHHHhcC----cccCCCCC
Confidence            743321  235788999996    68887764

>1ny5_A Transcriptional regulator (NTRC family); AAA+ ATPase, sigma54 activator, bacterial transcription, DIM transcription; HET: ADP; 2.40A {Aquifex aeolicus} SCOP: c.23.1.1 c.37.1.20 PDB: 1ny6_A* 3m0e_A* 1zy2_A*

Probab=99.46  E-value=5.4e-13  Score=134.81  Aligned_cols=227  Identities=17%  Similarity=0.168  Sum_probs=153.0

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHh
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNEL  273 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l  273 (490)
                      ..++|....+.++.+.+...  ......++|+|++||||+++++.++.... ...-+++.+||..+. ...+-.+++..-
T Consensus       137 ~~~ig~s~~m~~l~~~i~~~--a~~~~~vli~Ge~GtGK~~lAr~ih~~s~-r~~~~fv~v~~~~~~-~~~~~~elfg~~  212 (387)
T 1ny5_A          137 EEYVFESPKMKEILEKIKKI--SCAECPVLITGESGVGKEVVARLIHKLSD-RSKEPFVALNVASIP-RDIFEAELFGYE  212 (387)
T ss_dssp             CCCCCCSHHHHHHHHHHHHH--TTCCSCEEEECSTTSSHHHHHHHHHHHST-TTTSCEEEEETTTSC-HHHHHHHHHCBC
T ss_pred             hhhhhccHHhhHHHHHHHHh--cCCCCCeEEecCCCcCHHHHHHHHHHhcC-CCCCCeEEEecCCCC-HHHHHHHhcCCC
Confidence            46888888888888888763  34567789999999999999999976543 334578999999873 333334443332


Q ss_pred             cCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCHHHHHHhHhCCCC--------CCCcEEEEEecCCCChhH
Q psy200          274 KLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPSI--------PGSKLVLVGVANALDLTD  345 (490)
Q Consensus       274 ~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~--------~~~~vilI~~tn~~~~~~  345 (490)
                      .+.+.|.... ....|..+  . +  -+||||||+.|....|..|.++++....        ....+.+|++||.. +..
T Consensus       213 ~g~~tga~~~-~~g~~~~a--~-~--gtlfldei~~l~~~~q~~Ll~~l~~~~~~~~g~~~~~~~~~rii~at~~~-l~~  285 (387)
T 1ny5_A          213 KGAFTGAVSS-KEGFFELA--D-G--GTLFLDEIGELSLEAQAKLLRVIESGKFYRLGGRKEIEVNVRILAATNRN-IKE  285 (387)
T ss_dssp             TTSSTTCCSC-BCCHHHHT--T-T--SEEEEESGGGCCHHHHHHHHHHHHHSEECCBTCCSBEECCCEEEEEESSC-HHH
T ss_pred             CCCCCCcccc-cCCceeeC--C-C--cEEEEcChhhCCHHHHHHHHHHHhcCcEEeCCCCceeeccEEEEEeCCCC-HHH
Confidence            2223222111 11122221  1 1  2999999999999889888888764311        12466788888842 222


Q ss_pred             -----hhhHHhhhccCCCCeeEEeCCCC--HHHHHHHHHHHHhcc----CCC-CCCCHHHHHHHHHHHHHhhCCHHHHHH
Q psy200          346 -----RMLPRLQANVTLQPTLMNFAPYS--REQILEIISQKLKQT----DKF-NMFNASALQLLAGKVAAVSGDIRKAID  413 (490)
Q Consensus       346 -----~l~~~l~~R~~~~~~~i~~~pls--~~e~~~il~~~l~~~----~~~-~~~~~~~i~~i~~~i~~~~Gd~r~ai~  413 (490)
                           .+.+.+..|+..  ..|.++|+.  .+++..++.+++...    +.. ..+++++++.+..  +.|.||+|++.+
T Consensus       286 ~~~~g~fr~dl~~rl~~--~~i~lPpLreR~~Di~~l~~~~l~~~~~~~~~~~~~~~~~a~~~l~~--~~wpGNvreL~~  361 (387)
T 1ny5_A          286 LVKEGKFREDLYYRLGV--IEIEIPPLRERKEDIIPLANHFLKKFSRKYAKEVEGFTKSAQELLLS--YPWYGNVRELKN  361 (387)
T ss_dssp             HHHTTSSCHHHHHHHTT--EEEECCCGGGCHHHHHHHHHHHHHHHHHHTTCCCCEECHHHHHHHHH--SCCTTHHHHHHH
T ss_pred             HHHcCCccHHHHHhhcC--CeecCCcchhccccHHHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHh--CCCCcHHHHHHH
Confidence                 234556666653  368889987  478887777766543    222 3489999999987  789999999999


Q ss_pred             HHHHHHHHHHhccccCCcccccCHHHHHHH
Q psy200          414 ITNHLIDLTYDNVKENGEVTGIGLKEVLGV  443 (490)
Q Consensus       414 ll~~a~~~a~~~~~~~~~~~~It~~~v~~a  443 (490)
                      ++++|+..+.  +      ..|+.+++-..
T Consensus       362 ~i~~~~~~~~--~------~~i~~~~l~~~  383 (387)
T 1ny5_A          362 VIERAVLFSE--G------KFIDRGELSCL  383 (387)
T ss_dssp             HHHHHHHHCC--S------SEECHHHHHHH
T ss_pred             HHHHHHHhCC--C------CcCcHHHCcHh
Confidence            9999987663  2      36888887543

>3k1j_A LON protease, ATP-dependent protease LON; ATP-binding, nucleotide-binding, Pro hydrolase; HET: ADP PE8; 2.00A {Thermococcus onnurineus}

Probab=99.45  E-value=2.2e-13  Score=145.68  Aligned_cols=239  Identities=18%  Similarity=0.211  Sum_probs=150.6

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCC------------
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRN------------  261 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~------------  261 (490)
                      ++++|++..++.+...+..      +.+++|+||+||||||+++.++..+... .+..+.+.+.....            
T Consensus        41 ~~i~G~~~~l~~l~~~i~~------g~~vll~Gp~GtGKTtlar~ia~~l~~~-~~~~~~~~~~~~~~~~p~i~~~p~g~  113 (604)
T 3k1j_A           41 DQVIGQEHAVEVIKTAANQ------KRHVLLIGEPGTGKSMLGQAMAELLPTE-TLEDILVFPNPEDENMPRIKTVPACQ  113 (604)
T ss_dssp             HHCCSCHHHHHHHHHHHHT------TCCEEEECCTTSSHHHHHHHHHHTSCCS-SCEEEEEECCTTCTTSCEEEEEETTH
T ss_pred             ceEECchhhHhhccccccC------CCEEEEEeCCCCCHHHHHHHHhccCCcc-cCCeEEEeCCcccccCCcEEEEecch
Confidence            7899999999888887753      4699999999999999999999977421 22333343322210            


Q ss_pred             HHHHHHHHHHHhc----------------C-------C----------CCCCcHHHHHHHHH------------------
Q psy200          262 AASVYETIVNELK----------------L-------K----------PGGKSERHQLGAIL------------------  290 (490)
Q Consensus       262 ~~~l~~~i~~~l~----------------~-------~----------~~~~s~~~~~~~l~------------------  290 (490)
                      ...+...+.....                .       .          ........++..+.                  
T Consensus       114 ~~~~~e~~~~~~~~~~~~r~~~~~~~~~~~~~nl~v~~~~~~~~~~v~~~~~~~~~L~G~~~~~~~~~g~~~~g~~~~i~  193 (604)
T 3k1j_A          114 GRRIVEKYREKAKSQESVKSSNMRLKSTVLVPKLLVDNCGRTKAPFIDATGAHAGALLGDVRHDPFQSGGLGTPAHERVE  193 (604)
T ss_dssp             HHHHHHHHHHHHHHHTCC-----------CCCEEEECCTTCSSCCEEECTTCCHHHHHCEECCCCC----CCCCGGGGEE
T ss_pred             HHHHHHHHHHhhccchhhhhhcccccccccccceeeccccCCCCCEEEcCCCCHHhcCceEEechhhcCCcccccccccc
Confidence            1122221111000                0       0          00111111111000                  


Q ss_pred             -HHHhcCCCeEEEEEecCccccccCHHHHHHhHhCCC------------------CCCCcEEEEEecCCCChhHhhhHHh
Q psy200          291 -KYFDTKHKSILLILDEIDALESRKQTILYTIFEWPS------------------IPGSKLVLVGVANALDLTDRMLPRL  351 (490)
Q Consensus       291 -~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~------------------~~~~~vilI~~tn~~~~~~~l~~~l  351 (490)
                       ..+.. ...-+|||||++.|....++.|+.+++...                  ....++.||+++|.. ....+.+.|
T Consensus       194 ~g~~~~-a~~gvL~LDEi~~l~~~~q~~Ll~~Le~~~~~~~g~~~~~~~~~l~~~~~p~~~~vI~atn~~-~~~~l~~~l  271 (604)
T 3k1j_A          194 PGMIHR-AHKGVLFIDEIATLSLKMQQSLLTAMQEKKFPITGQSEMSSGAMVRTEPVPCDFVLVAAGNLD-TVDKMHPAL  271 (604)
T ss_dssp             CCHHHH-TTTSEEEETTGGGSCHHHHHHHHHHHHHSEECCBCSCTTSGGGGCBCSCEECCCEEEEEECHH-HHHHSCHHH
T ss_pred             Cceeee-cCCCEEEEechhhCCHHHHHHHHHHHHcCcEEecccccccccccCCCCccceeEEEEEecCHH-HHhhcCHHH
Confidence             00000 122399999999998778888888776321                  112467899999853 335678899


Q ss_pred             hhccCCCCeeEEeCCC---CHHHHHHHHHHHHhcc---CCCCCCCHHHHHHHHHHHHHhhC-------CHHHHHHHHHHH
Q psy200          352 QANVTLQPTLMNFAPY---SREQILEIISQKLKQT---DKFNMFNASALQLLAGKVAAVSG-------DIRKAIDITNHL  418 (490)
Q Consensus       352 ~~R~~~~~~~i~~~pl---s~~e~~~il~~~l~~~---~~~~~~~~~~i~~i~~~i~~~~G-------d~r~ai~ll~~a  418 (490)
                      ++||......+.|+..   ..+.+..++.......   +....+++++++.|.+....+.|       +.|.+.++++.|
T Consensus       272 ~~R~~v~~i~i~l~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~ls~eAl~~Li~~~~r~~g~r~~l~~~~R~l~~llr~A  351 (604)
T 3k1j_A          272 RSRIRGYGYEVYMRTTMPDTIENRRKLVQFVAQEVKRDGKIPHFTKEAVEEIVREAQKRAGRKGHLTLRLRDLGGIVRAA  351 (604)
T ss_dssp             HHHHHHHSEEEECCSEEECCHHHHHHHHHHHHHHHHHHCSSCCBBHHHHHHHHHHHHHTTCSTTEEECCHHHHHHHHHHH
T ss_pred             HHHhhccceEeeccccccCCHHHHHHHHHHHHHHHhhccCcccCCHHHHHHHHHHHhhhhccccccccCHHHHHHHHHHH
Confidence            9998421114565533   4555666664443322   23457899999999986666677       599999999999


Q ss_pred             HHHHHhccccCCcccccCHHHHHHHHHH
Q psy200          419 IDLTYDNVKENGEVTGIGLKEVLGVISS  446 (490)
Q Consensus       419 ~~~a~~~~~~~~~~~~It~~~v~~a~~~  446 (490)
                      ..+|..++     ...|+.+|+.+|+..
T Consensus       352 ~~~A~~~~-----~~~I~~edv~~A~~~  374 (604)
T 3k1j_A          352 GDIAVKKG-----KKYVEREDVIEAVKM  374 (604)
T ss_dssp             HHHHHHTT-----CSSBCHHHHHHHHHH
T ss_pred             HHHHHhcC-----cccccHHHHHHHHHh
Confidence            99998887     678999999999954

>3dzd_A Transcriptional regulator (NTRC family); sigma43 activator, AAA+ ATPase, response regulator, transcriptional activator, ATP-binding; HET: ADP; 2.40A {Aquifex aeolicus} PDB: 1zit_A 2jrl_A

Probab=99.44  E-value=3.6e-13  Score=135.10  Aligned_cols=214  Identities=18%  Similarity=0.259  Sum_probs=145.1

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHh
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNEL  273 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l  273 (490)
                      ..++|......++...+...  ......++|+|++||||+++++.++.......  .++.+||..+.. ..+..+++..-
T Consensus       129 ~~~ig~s~~~~~~~~~~~~~--a~~~~~vli~GesGtGKe~lAr~ih~~s~r~~--~fv~vnc~~~~~-~~~~~~lfg~~  203 (368)
T 3dzd_A          129 IEFVGEHPKILEIKRLIPKI--AKSKAPVLITGESGTGKEIVARLIHRYSGRKG--AFVDLNCASIPQ-ELAESELFGHE  203 (368)
T ss_dssp             CCCCCCSHHHHHHHHHHHHH--HTSCSCEEEECCTTSSHHHHHHHHHHHHCCCS--CEEEEESSSSCT-TTHHHHHHEEC
T ss_pred             ccccccchHHHHHHhhhhhh--hccchhheEEeCCCchHHHHHHHHHHhccccC--CcEEEEcccCCh-HHHHHHhcCcc
Confidence            45788888888887777653  24456799999999999999999977654222  389999998743 23333343332


Q ss_pred             cCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCHHHHHHhHhCCCC--------CCCcEEEEEecCCCChhH
Q psy200          274 KLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPSI--------PGSKLVLVGVANALDLTD  345 (490)
Q Consensus       274 ~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~--------~~~~vilI~~tn~~~~~~  345 (490)
                      .+.+.|.... ....+..  ..+|   +||||||+.|....|..|..+++....        ....+.+|++||.. +..
T Consensus       204 ~g~~tga~~~-~~g~~~~--a~~g---tlfldei~~l~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~rii~at~~~-l~~  276 (368)
T 3dzd_A          204 KGAFTGALTR-KKGKLEL--ADQG---TLFLDEVGELDQRVQAKLLRVLETGSFTRLGGNQKIEVDIRVISATNKN-LEE  276 (368)
T ss_dssp             SCSSSSCCCC-EECHHHH--TTTS---EEEEETGGGSCHHHHHHHHHHHHHSEECCBTCCCBEECCCEEEEEESSC-HHH
T ss_pred             ccccCCcccc-cCChHhh--cCCC---eEEecChhhCCHHHHHHHHHHHHhCCcccCCCCcceeeeeEEEEecCCC-HHH
Confidence            2333322111 1112222  1222   899999999999999999888764311        12356788888842 332


Q ss_pred             h-----hhHHhhhccCCCCeeEEeCCCCH--HHHHHHHHHHHhcc----C-CCCCCCHHHHHHHHHHHHHhhCCHHHHHH
Q psy200          346 R-----MLPRLQANVTLQPTLMNFAPYSR--EQILEIISQKLKQT----D-KFNMFNASALQLLAGKVAAVSGDIRKAID  413 (490)
Q Consensus       346 ~-----l~~~l~~R~~~~~~~i~~~pls~--~e~~~il~~~l~~~----~-~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~  413 (490)
                      .     +.+.+..|+..  ..|.++|+..  +++..++.+.+.+.    + ....+++++++.+..  +.|.||+|++.+
T Consensus       277 ~v~~g~fr~dL~~rl~~--~~i~lPpLreR~~Di~~l~~~~l~~~~~~~~~~~~~~~~~a~~~L~~--~~wpGNvreL~n  352 (368)
T 3dzd_A          277 EIKKGNFREDLYYRLSV--FQIYLPPLRERGKDVILLAEYFLKKFAKEYKKNCFELSEETKEYLMK--QEWKGNVRELKN  352 (368)
T ss_dssp             HHHTTSSCHHHHHHHTS--EEEECCCGGGSTTHHHHHHHHHHHHHHHHTTCCCCCBCHHHHHHHHT--CCCTTHHHHHHH
T ss_pred             HHHcCCccHHHHHHhCC--eEEeCCChhhchhhHHHHHHHHHHHHHHHcCCCCCCcCHHHHHHHHh--CCCCcHHHHHHH
Confidence            2     33467777763  3688999987  78888777766543    2 224689999999987  788999999999


Q ss_pred             HHHHHHHHHH
Q psy200          414 ITNHLIDLTY  423 (490)
Q Consensus       414 ll~~a~~~a~  423 (490)
                      ++++++.++.
T Consensus       353 ~i~~~~~~~~  362 (368)
T 3dzd_A          353 LIERAVILCE  362 (368)
T ss_dssp             HHHHHHHTCC
T ss_pred             HHHHHHHhCC
Confidence            9999987653

>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=99.42  E-value=7.2e-12  Score=124.61  Aligned_cols=192  Identities=16%  Similarity=0.229  Sum_probs=115.1

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCC-----CCHHHHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSV-----RNAASVYET  268 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~-----~~~~~l~~~  268 (490)
                      +.|+||+++++.|.. +..       +.++|+|++|+|||+|++.+++.+.    ..++|++|...     .+...++..
T Consensus        13 ~~~~gR~~el~~L~~-l~~-------~~v~i~G~~G~GKT~L~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~   80 (357)
T 2fna_A           13 KDFFDREKEIEKLKG-LRA-------PITLVLGLRRTGKSSIIKIGINELN----LPYIYLDLRKFEERNYISYKDFLLE   80 (357)
T ss_dssp             GGSCCCHHHHHHHHH-TCS-------SEEEEEESTTSSHHHHHHHHHHHHT----CCEEEEEGGGGTTCSCCCHHHHHHH
T ss_pred             HHhcChHHHHHHHHH-hcC-------CcEEEECCCCCCHHHHHHHHHHhcC----CCEEEEEchhhccccCCCHHHHHHH
Confidence            679999999999888 642       5999999999999999999998874    24678887653     355666665


Q ss_pred             HHHHhcC--------------------CC----------CCCcHHHHHHHHHHHHhcCCCeEEEEEecCcccccc----C
Q psy200          269 IVNELKL--------------------KP----------GGKSERHQLGAILKYFDTKHKSILLILDEIDALESR----K  314 (490)
Q Consensus       269 i~~~l~~--------------------~~----------~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~----~  314 (490)
                      +...+..                    ..          .......+.+.+.+   ...++++|||||+|++...    .
T Consensus        81 l~~~l~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~---~~~~~~vlvlDe~~~~~~~~~~~~  157 (357)
T 2fna_A           81 LQKEINKLVKRLPSLLKALKNIQGIVIMGNEIKFNWNRKDRLSFANLLESFEQ---ASKDNVIIVLDEAQELVKLRGVNL  157 (357)
T ss_dssp             HHHHHHHHHHHCTTHHHHTTTSTTEEECSSSEEEC-----CCCHHHHHHHHHH---TCSSCEEEEEETGGGGGGCTTCCC
T ss_pred             HHHHHHHHhhhhhHHHHHhcccceEEecceEEEeccCCcchhhHHHHHHHHHh---cCCCCeEEEEECHHHhhccCchhH
Confidence            5544310                    00          01123333333322   1113899999999998752    2


Q ss_pred             HHHHHHhHhCCCCCCCcEEEEEecCCCChhHhh------hHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCC
Q psy200          315 QTILYTIFEWPSIPGSKLVLVGVANALDLTDRM------LPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNM  388 (490)
Q Consensus       315 ~~~L~~l~~~~~~~~~~vilI~~tn~~~~~~~l------~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~  388 (490)
                      ...|..+.+..  .  ++.+|.++........+      ...+..|+.   ..+.+.|++.++..+++...+...+.  .
T Consensus       158 ~~~l~~~~~~~--~--~~~~i~~g~~~~~l~~~l~~~~~~~~l~~r~~---~~i~l~~l~~~e~~~~l~~~~~~~~~--~  228 (357)
T 2fna_A          158 LPALAYAYDNL--K--RIKFIMSGSEMGLLYDYLRVEDPESPLFGRAF---STVELKPFSREEAIEFLRRGFQEADI--D  228 (357)
T ss_dssp             HHHHHHHHHHC--T--TEEEEEEESSHHHHHHHTTTTCTTSTTTTCCC---EEEEECCCCHHHHHHHHHHHHHHHTC--C
T ss_pred             HHHHHHHHHcC--C--CeEEEEEcCchHHHHHHHhccCCCCccccCcc---ceeecCCCCHHHHHHHHHHHHHHcCC--C
Confidence            34555554422  2  34444444422211221      012333322   47999999999999999987754321  1


Q ss_pred             CCHHHHHHHHHHHHHhhCCHHHHHHHH
Q psy200          389 FNASALQLLAGKVAAVSGDIRKAIDIT  415 (490)
Q Consensus       389 ~~~~~i~~i~~~i~~~~Gd~r~ai~ll  415 (490)
                      .++.  ..+++    .+|+.+.++..+
T Consensus       229 ~~~~--~~i~~----~t~G~P~~l~~~  249 (357)
T 2fna_A          229 FKDY--EVVYE----KIGGIPGWLTYF  249 (357)
T ss_dssp             CCCH--HHHHH----HHCSCHHHHHHH
T ss_pred             CCcH--HHHHH----HhCCCHHHHHHH
Confidence            2222  44443    555555555543

>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural genomics, center for structural genomics; 2.80A {Escherichia coli}

Probab=99.41  E-value=2.7e-13  Score=117.55  Aligned_cols=138  Identities=20%  Similarity=0.238  Sum_probs=92.2

Q ss_pred             CCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhc
Q psy200          195 ELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELK  274 (490)
Q Consensus       195 ~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~  274 (490)
                      +++|+...+.++.+.+...  .....+++|+||+|||||++|+++++... ..+..++ ++|......            
T Consensus         2 ~iiG~s~~~~~~~~~~~~~--a~~~~~vll~G~~GtGKt~lA~~i~~~~~-~~~~~~v-~~~~~~~~~------------   65 (145)
T 3n70_A            2 ELIGRSEWINQYRRRLQQL--SETDIAVWLYGAPGTGRMTGARYLHQFGR-NAQGEFV-YRELTPDNA------------   65 (145)
T ss_dssp             --CCSSHHHHHHHHHHHHH--TTCCSCEEEESSTTSSHHHHHHHHHHSST-TTTSCCE-EEECCTTTS------------
T ss_pred             CceeCCHHHHHHHHHHHHH--hCCCCCEEEECCCCCCHHHHHHHHHHhCC-ccCCCEE-EECCCCCcc------------
Confidence            5899999999999988764  34567899999999999999999988653 2234667 998876432            


Q ss_pred             CCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEEEecCCCChhH-----hhhH
Q psy200          275 LKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVANALDLTD-----RMLP  349 (490)
Q Consensus       275 ~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI~~tn~~~~~~-----~l~~  349 (490)
                              ......+..+ .    ..+|||||++.+....|..|+.++..   ....+.+|+++|.. +.+     .+.+
T Consensus        66 --------~~~~~~~~~a-~----~g~l~ldei~~l~~~~q~~Ll~~l~~---~~~~~~~I~~t~~~-~~~~~~~~~~~~  128 (145)
T 3n70_A           66 --------PQLNDFIALA-Q----GGTLVLSHPEHLTREQQYHLVQLQSQ---EHRPFRLIGIGDTS-LVELAASNHIIA  128 (145)
T ss_dssp             --------SCHHHHHHHH-T----TSCEEEECGGGSCHHHHHHHHHHHHS---SSCSSCEEEEESSC-HHHHHHHSCCCH
T ss_pred             --------hhhhcHHHHc-C----CcEEEEcChHHCCHHHHHHHHHHHhh---cCCCEEEEEECCcC-HHHHHHcCCCCH
Confidence                    1122222222 1    23899999999998888888887743   23456677778742 111     2344


Q ss_pred             HhhhccCCCCeeEEeCCC
Q psy200          350 RLQANVTLQPTLMNFAPY  367 (490)
Q Consensus       350 ~l~~R~~~~~~~i~~~pl  367 (490)
                      .+..|+..  ..|.++|+
T Consensus       129 ~L~~rl~~--~~i~lPpL  144 (145)
T 3n70_A          129 ELYYCFAM--TQIACLPL  144 (145)
T ss_dssp             HHHHHHHH--HEEECCCC
T ss_pred             HHHHHhcC--CEEeCCCC
Confidence            55555532  25777776

>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=99.40  E-value=1e-11  Score=131.39  Aligned_cols=195  Identities=11%  Similarity=0.142  Sum_probs=129.1

Q ss_pred             CChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHH--hhhcCCc-eEEEEeccCCC--CHHHHHHHHHH
Q psy200          197 PGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSR--AEIKDAF-KTIYINCNSVR--NAASVYETIVN  271 (490)
Q Consensus       197 vgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~--l~~~~~~-~~~~v~~~~~~--~~~~l~~~i~~  271 (490)
                      +||++++++|.++|... .....+.+.|+|++|+||||||+.+++.  ......| ..+|++.....  +...++..|+.
T Consensus       131 ~GR~~~~~~l~~~L~~~-~~~~~~vv~I~G~gGvGKTtLA~~v~~~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~~~il~  209 (549)
T 2a5y_B          131 YIREYHVDRVIKKLDEM-CDLDSFFLFLHGRAGSGKSVIASQALSKSDQLIGINYDSIVWLKDSGTAPKSTFDLFTDILL  209 (549)
T ss_dssp             CCCHHHHHHHHHHHHHH-TTSSSEEEEEECSTTSSHHHHHHHHHHHCSSTBTTTBSEEEEEECCCCSTTHHHHHHHHHHH
T ss_pred             CCchHHHHHHHHHHhcc-cCCCceEEEEEcCCCCCHHHHHHHHHHhhhHHHhccCCcEEEEEECCCCCCCHHHHHHHHHH
Confidence            59999999999999652 1234578899999999999999999972  2223556 56777766653  57788999999


Q ss_pred             HhcCCCC--------CCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEEEecCCCCh
Q psy200          272 ELKLKPG--------GKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVANALDL  343 (490)
Q Consensus       272 ~l~~~~~--------~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI~~tn~~~~  343 (490)
                      .++....        ......+...+.+.+.. +++++||||++|....     + .   |....+++|++  +|.....
T Consensus       210 ~l~~~~~~~~~~~~~~~~~~~l~~~l~~~L~~-~kr~LlVLDdv~~~~~-----~-~---~~~~~gs~ilv--TTR~~~v  277 (549)
T 2a5y_B          210 MLKSEDDLLNFPSVEHVTSVVLKRMICNALID-RPNTLFVFDDVVQEET-----I-R---WAQELRLRCLV--TTRDVEI  277 (549)
T ss_dssp             HHTTTSCCTTCCCCTTCCHHHHHHHHHHHHTT-STTEEEEEEEECCHHH-----H-H---HHHHTTCEEEE--EESBGGG
T ss_pred             HHhcCcccccccccccccHHHHHHHHHHHHcC-CCcEEEEEECCCCchh-----h-c---ccccCCCEEEE--EcCCHHH
Confidence            9875421        12344556677777763 2389999999999532     1 1   11114444444  3432111


Q ss_pred             hHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHHHHHH
Q psy200          344 TDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITNH  417 (490)
Q Consensus       344 ~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll~~  417 (490)
                      .        ..++.....+.+.+++.++.+++|.++....   .  .+..+..+++.+...||+++.||.++..
T Consensus       278 ~--------~~~~~~~~~~~l~~L~~~ea~~Lf~~~a~~~---~--~~~~~~~~~~~I~~~c~GlPLAl~~~g~  338 (549)
T 2a5y_B          278 S--------NAASQTCEFIEVTSLEIDECYDFLEAYGMPM---P--VGEKEEDVLNKTIELSSGNPATLMMFFK  338 (549)
T ss_dssp             G--------GGCCSCEEEEECCCCCHHHHHHHHHHTSCCC---C----CHHHHHHHHHHHHHTTCHHHHHHHHT
T ss_pred             H--------HHcCCCCeEEECCCCCHHHHHHHHHHHhcCC---C--CchhHHHHHHHHHHHhCCChHHHHHHHH
Confidence            1        1111111369999999999999999874322   1  1244566677777899999999987743

>3co5_A Putative two-component system transcriptional RES regulator; structural genomics, APC89341.1; 2.40A {Neisseria gonorrhoeae}

Probab=99.38  E-value=6e-13  Score=115.10  Aligned_cols=137  Identities=8%  Similarity=0.097  Sum_probs=91.3

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHh
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNEL  273 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l  273 (490)
                      -+++|++..++++.+.+....  ....+++|+|++|||||++|+++++...     .+++++|.....  .+        
T Consensus         4 ~~~iG~s~~~~~l~~~~~~~~--~~~~~vll~G~~GtGKt~lA~~i~~~~~-----~~~~~~~~~~~~--~~--------   66 (143)
T 3co5_A            4 FDKLGNSAAIQEMNREVEAAA--KRTSPVFLTGEAGSPFETVARYFHKNGT-----PWVSPARVEYLI--DM--------   66 (143)
T ss_dssp             ----CCCHHHHHHHHHHHHHH--TCSSCEEEEEETTCCHHHHHGGGCCTTS-----CEECCSSTTHHH--HC--------
T ss_pred             cCceeCCHHHHHHHHHHHHHh--CCCCcEEEECCCCccHHHHHHHHHHhCC-----CeEEechhhCCh--Hh--------
Confidence            468999999999999988654  4567899999999999999999987642     678888875311  00        


Q ss_pred             cCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEEEecCCC--ChhHhhhHHh
Q psy200          274 KLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVANAL--DLTDRMLPRL  351 (490)
Q Consensus       274 ~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI~~tn~~--~~~~~l~~~l  351 (490)
                                 ....+..  .   ...+|||||++.+....|..|+.+++...  ...+.+|+++|..  ++...+.+.+
T Consensus        67 -----------~~~~~~~--a---~~~~l~lDei~~l~~~~q~~Ll~~l~~~~--~~~~~iI~~tn~~~~~~~~~~~~~L  128 (143)
T 3co5_A           67 -----------PMELLQK--A---EGGVLYVGDIAQYSRNIQTGITFIIGKAE--RCRVRVIASCSYAAGSDGISCEEKL  128 (143)
T ss_dssp             -----------HHHHHHH--T---TTSEEEEEECTTCCHHHHHHHHHHHHHHT--TTTCEEEEEEEECTTTC--CHHHHH
T ss_pred             -----------hhhHHHh--C---CCCeEEEeChHHCCHHHHHHHHHHHHhCC--CCCEEEEEecCCCHHHHHhCccHHH
Confidence                       1112221  1   12389999999999888888888776432  3456677777632  2211166777


Q ss_pred             hhccCCCCeeEEeCCC
Q psy200          352 QANVTLQPTLMNFAPY  367 (490)
Q Consensus       352 ~~R~~~~~~~i~~~pl  367 (490)
                      ..|+..  ..|.++|+
T Consensus       129 ~~rl~~--~~i~lPpL  142 (143)
T 3co5_A          129 AGLFSE--SVVRIPPL  142 (143)
T ss_dssp             HHHSSS--EEEEECCC
T ss_pred             HHHhcC--cEEeCCCC
Confidence            777653  36788876

>3f9v_A Minichromosome maintenance protein MCM; replicative helicase, DNA replication, MCM complex, AAA+ Pro ATP-binding, DNA-binding, helicase; 4.35A {Sulfolobus solfataricus}

Probab=99.33  E-value=8.5e-13  Score=140.31  Aligned_cols=237  Identities=14%  Similarity=0.123  Sum_probs=143.6

Q ss_pred             cchHHHhhcCCCCCCChHHHHHHHHHHHHhhhccCC-----------CCeEEEECCCCCcHHHHHHHHHHHhhhcCCceE
Q psy200          183 KPKVEEKAKDSCELPGREVQLEGIRQFLLGHVNNET-----------SGSMYISGPPGTGKSASLNLLVSRAEIKDAFKT  251 (490)
Q Consensus       183 ~~~~~~~~l~~~~lvgre~~~~~l~~~L~~~~~~~~-----------~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~  251 (490)
                      .|......+. ..++|++..+..+...+    .++.           ..+++|+||||||||++|+++++.+.     ..
T Consensus       285 ~~~~l~~~l~-~~I~G~e~vk~al~~~l----~~g~~~~~~~~~~r~~~~vLL~GppGtGKT~LAr~la~~~~-----r~  354 (595)
T 3f9v_A          285 IRDRIISSIA-PSIYGHWELKEALALAL----FGGVPKVLEDTRIRGDIHILIIGDPGTAKSQMLQFISRVAP-----RA  354 (595)
T ss_dssp             GGGTHHHHTS-STTSCCHHHHHHHTTTT----TCCCCEETTTTEECCSCCEEEEESSCCTHHHHHHSSSTTCS-----CE
T ss_pred             HHHHHHHhhc-chhcChHHHHHHHHHHH----hCCCcccccCCCcCCCcceEEECCCchHHHHHHHHHHHhCC-----Cc
Confidence            3443333344 78999998766554333    2221           12899999999999999999988763     11


Q ss_pred             EEEeccCCCCHHHHHHHHH-HHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCHHHHHHhHhCCCC---
Q psy200          252 IYINCNSVRNAASVYETIV-NELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPSI---  327 (490)
Q Consensus       252 ~~v~~~~~~~~~~l~~~i~-~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~---  327 (490)
                      .+..... .+...+...+. ..+...+. ...    ..+..  ..   ..+||||||+.+....+..|...++....   
T Consensus       355 ~~~~~~~-~~~~~l~~~~~~~~~~g~~~-~~~----G~l~~--A~---~gil~IDEid~l~~~~q~~Ll~~le~~~i~i~  423 (595)
T 3f9v_A          355 VYTTGKG-STAAGLTAAVVREKGTGEYY-LEA----GALVL--AD---GGIAVIDEIDKMRDEDRVAIHEAMEQQTVSIA  423 (595)
T ss_dssp             ECCCTTC-STTTTSEEECSSGGGTSSCS-EEE----CHHHH--HS---SSEECCTTTTCCCSHHHHHHHHHHHSSSEEEE
T ss_pred             eecCCCc-cccccccceeeecccccccc-ccC----CeeEe--cC---CCcEEeehhhhCCHhHhhhhHHHHhCCEEEEe
Confidence            1111000 00000000000 00000000 000    01111  11   23999999999998888999888874321   


Q ss_pred             -------CCCcEEEEEecCCCChhH----------hhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccC------
Q psy200          328 -------PGSKLVLVGVANALDLTD----------RMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTD------  384 (490)
Q Consensus       328 -------~~~~vilI~~tn~~~~~~----------~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~------  384 (490)
                             .+.++.+|+++|...-..          .+.+.+.+||++   .+.+.++...+...++.+.+....      
T Consensus       424 ~~g~~~~~~~~~~vIaatNp~~G~~~~~~~~~~ni~l~~aLl~RFDl---~~~~~~~~~~e~~~i~~~il~~~~~~~~~~  500 (595)
T 3f9v_A          424 KAGIVAKLNARAAVIAAGNPKFGRYISERPVSDNINLPPTILSRFDL---IFILKDQPGEQDRELANYILDVHSGKSTKN  500 (595)
T ss_dssp             SSSSEEEECCCCEEEEEECCTTCCSCTTSCSCTTTCSCSSSGGGCSC---CEEECCTTHHHHHHHHHHHHTTTCCCSSSS
T ss_pred             cCCcEEEecCceEEEEEcCCcCCccCcccCchhccCCCHHHHhhCeE---EEEeCCCCCHHHHHHHHHHHHHhhcccccc
Confidence                   135778999999652111          556788899975   455666655555555555554321      


Q ss_pred             -----------------CCCCCCHHHHHHHHHHHH------------HhhCCHHHHHHHHHHHHHHHHhccccCCccccc
Q psy200          385 -----------------KFNMFNASALQLLAGKVA------------AVSGDIRKAIDITNHLIDLTYDNVKENGEVTGI  435 (490)
Q Consensus       385 -----------------~~~~~~~~~i~~i~~~i~------------~~~Gd~r~ai~ll~~a~~~a~~~~~~~~~~~~I  435 (490)
                                       ....+++++.+.|.+.+.            .+.++.|.+.++++.|...|...+     ...|
T Consensus       501 ~l~~~~l~~~i~~ar~~~~p~ls~ea~~~l~~~y~~lR~~~~~~~~~~~~~s~R~l~~lirla~a~A~l~~-----~~~V  575 (595)
T 3f9v_A          501 IIDIDTLRKYIAYARKYVTPKITSEAKNLITDFFVEMRKKSSETPDSPILITPRQLEALIRISEAYAKMAL-----KAEV  575 (595)
T ss_dssp             TTCCTTTHHHHHHHHHHHCCCCCCCTHHHHHHHHTTSSCSCCBCSSSCBCSSTTTTTHHHHHHHHHHHTTS-----SCCS
T ss_pred             CCCHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHhhccCCCccccccHHHHHHHHHHHHHHHHHhC-----cCCC
Confidence                             012466666777776433            257889999999999999999988     7799


Q ss_pred             CHHHHHHHHHHhc
Q psy200          436 GLKEVLGVISSVY  448 (490)
Q Consensus       436 t~~~v~~a~~~~~  448 (490)
                      +.+|+..|+.-+.
T Consensus       576 ~~~dv~~Ai~l~~  588 (595)
T 3f9v_A          576 TREDAERAINIMR  588 (595)
T ss_dssp             SHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHH
Confidence            9999999987554

>1jr3_D DNA polymerase III, delta subunit; processivity, processivity clamp, clamp loader, AAA+ ATPase, transferase; HET: DNA; 2.70A {Escherichia coli} SCOP: a.80.1.1 c.37.1.20 PDB: 1jqj_C* 1xxh_A* 1xxi_A* 3glf_A* 3glg_A* 3glh_A* 3gli_A*

Probab=99.22  E-value=5.1e-10  Score=111.16  Aligned_cols=189  Identities=13%  Similarity=0.036  Sum_probs=132.5

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHhhhcC--CceEEEEeccCCCCHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHh
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRAEIKD--AFKTIYINCNSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFD  294 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l~~~~--~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~  294 (490)
                      .-.+..+|+|+.|.||++.++.+++.+....  .+.++.++.  .                    ....++.+.+...--
T Consensus        16 ~~~~~yl~~G~e~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~--~--------------------~~~~~l~~~~~~~pl   73 (343)
T 1jr3_D           16 GLRAAYLLLGNDPLLLQESQDAVRQVAAAQGFEEHHTFSIDP--N--------------------TDWNAIFSLCQAMSL   73 (343)
T ss_dssp             CCCSEEEEEESCHHHHHHHHHHHHHHHHHHTCCEEEEEECCT--T--------------------CCHHHHHHHHHHHHH
T ss_pred             CCCcEEEEECCcHHHHHHHHHHHHHHHHhCCCCeeEEEEecC--C--------------------CCHHHHHHHhcCcCC
Confidence            4577899999999999999999999875322  112222221  1                    223334333322111


Q ss_pred             cCCCeEEEEEecCcc-ccccCHHHHHHhHhCCCCCCCcEEEEEecCCCC---hhHhhhHHhhhccCCCCeeEEeCCCCHH
Q psy200          295 TKHKSILLILDEIDA-LESRKQTILYTIFEWPSIPGSKLVLVGVANALD---LTDRMLPRLQANVTLQPTLMNFAPYSRE  370 (490)
Q Consensus       295 ~~~~~~vI~IDEid~-l~~~~~~~L~~l~~~~~~~~~~vilI~~tn~~~---~~~~l~~~l~~R~~~~~~~i~~~pls~~  370 (490)
                       .+...||+|||++. +....++.|..+++.+   ....++|.+++..+   -...+.+.+.+||.    .+.|.+++..
T Consensus        74 -f~~~kvvii~~~~~kl~~~~~~aLl~~le~p---~~~~~~il~~~~~~~~~~~~k~~~~i~sr~~----~~~~~~l~~~  145 (343)
T 1jr3_D           74 -FASRQTLLLLLPENGPNAAINEQLLTLTGLL---HDDLLLIVRGNKLSKAQENAAWFTALANRSV----QVTCQTPEQA  145 (343)
T ss_dssp             -CCSCEEEEEECCSSCCCTTHHHHHHHHHTTC---BTTEEEEEEESCCCTTTTTSHHHHHHTTTCE----EEEECCCCTT
T ss_pred             -ccCCeEEEEECCCCCCChHHHHHHHHHHhcC---CCCeEEEEEcCCCChhhHhhHHHHHHHhCce----EEEeeCCCHH
Confidence             24466999999999 8877788888887643   22344443443322   13467788899985    8999999999


Q ss_pred             HHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHhccccCCcccccCHHHHHHHHHHhc
Q psy200          371 QILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITNHLIDLTYDNVKENGEVTGIGLKEVLGVISSVY  448 (490)
Q Consensus       371 e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~~~~~  448 (490)
                      ++..++..++...  ...+++++++.+++   ...||++.+++.|+.....+. .       ..|+.++|...+....
T Consensus       146 ~l~~~l~~~~~~~--g~~i~~~a~~~l~~---~~~gdl~~~~~elekl~l~~~-~-------~~It~e~V~~~~~~~~  210 (343)
T 1jr3_D          146 QLPRWVAARAKQL--NLELDDAANQVLCY---CYEGNLLALAQALERLSLLWP-D-------GKLTLPRVEQAVNDAA  210 (343)
T ss_dssp             HHHHHHHHHHHHT--TCEECHHHHHHHHH---SSTTCHHHHHHHHHHHHHHCT-T-------CEECHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHc--CCCCCHHHHHHHHH---HhchHHHHHHHHHHHHHHhcC-C-------CCCCHHHHHHHHhhhh
Confidence            9999999999887  45689999999997   678999999999998876541 2       3688888877766543

>1z6t_A APAF-1, apoptotic protease activating factor 1; caspase activation, ADP, nucleotide binding, CARD, apoptosis; HET: ADP; 2.21A {Homo sapiens}

Probab=99.21  E-value=1.3e-10  Score=124.12  Aligned_cols=194  Identities=15%  Similarity=0.140  Sum_probs=120.6

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhh-cCCc--eEEEEeccCCCCHHHHHHH--
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEI-KDAF--KTIYINCNSVRNAASVYET--  268 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~-~~~~--~~~~v~~~~~~~~~~l~~~--  268 (490)
                      ..|+||+.+++.|.++|...  .+..+.++|+|++|+|||+||..+++.... ...|  .++|+++... +...++..  
T Consensus       124 ~~~vGR~~~l~~L~~~L~~~--~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~~~~f~~~v~wv~~~~~-~~~~~~~~l~  200 (591)
T 1z6t_A          124 VVFVTRKKLVNAIQQKLSKL--KGEPGWVTIHGMAGCGKSVLAAEAVRDHSLLEGCFPGGVHWVSVGKQ-DKSGLLMKLQ  200 (591)
T ss_dssp             SSCCCCHHHHHHHHHHHTTS--TTSCEEEEEECCTTSSHHHHHHHHHCCHHHHHHHCTTCEEEEEEESC-CHHHHHHHHH
T ss_pred             CeecccHHHHHHHHHHHhcc--cCCCceEEEEcCCCCCHHHHHHHHHhchhHHHhhCCCceEEEECCCC-chHHHHHHHH
Confidence            67999999999999998642  345678999999999999999999865321 1223  4677777655 33334333  


Q ss_pred             -HHHHhcC-----CCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEEEecCCCC
Q psy200          269 -IVNELKL-----KPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVANALD  342 (490)
Q Consensus       269 -i~~~l~~-----~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI~~tn~~~  342 (490)
                       ++..++.     .........+...+...+....++++|||||+|..     ..+    ++. ..++  .+|.+|....
T Consensus       201 ~l~~~l~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~LLVLDdv~~~-----~~l----~~l-~~~~--~ilvTsR~~~  268 (591)
T 1z6t_A          201 NLCTRLDQDESFSQRLPLNIEEAKDRLRILMLRKHPRSLLILDDVWDS-----WVL----KAF-DSQC--QILLTTRDKS  268 (591)
T ss_dssp             HHHHHHCSSCCSCSSCCCSHHHHHHHHHHHHHHTCTTCEEEEEEECCH-----HHH----HTT-CSSC--EEEEEESCGG
T ss_pred             HHHHHhccccccccCCCCCHHHHHHHHHHHHccCCCCeEEEEeCCCCH-----HHH----HHh-cCCC--eEEEECCCcH
Confidence             3445542     12234566677777777766557899999999873     222    222 2333  3443443221


Q ss_pred             hhHhhhHHhhhccCCCCeeEEe---CCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHHHHHHHH
Q psy200          343 LTDRMLPRLQANVTLQPTLMNF---APYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITNHLI  419 (490)
Q Consensus       343 ~~~~l~~~l~~R~~~~~~~i~~---~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll~~a~  419 (490)
                      ....    +.   +   ..+.+   .+++.++..++|...+...  .... ++....|+    ..+|+.+.+|.++...+
T Consensus       269 ~~~~----~~---~---~~~~v~~l~~L~~~ea~~L~~~~~~~~--~~~~-~~~~~~i~----~~~~G~PLal~~~a~~l  331 (591)
T 1z6t_A          269 VTDS----VM---G---PKYVVPVESSLGKEKGLEILSLFVNMK--KADL-PEQAHSII----KECKGSPLVVSLIGALL  331 (591)
T ss_dssp             GGTT----CC---S---CEEEEECCSSCCHHHHHHHHHHHHTSC--GGGS-CTHHHHHH----HHHTTCHHHHHHHHHHH
T ss_pred             HHHh----cC---C---CceEeecCCCCCHHHHHHHHHHHhCCC--cccc-cHHHHHHH----HHhCCCcHHHHHHHHHH
Confidence            1111    00   1   12333   5899999999999887542  1111 23344454    47899999988765543

>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=99.12  E-value=2.3e-10  Score=102.63  Aligned_cols=126  Identities=15%  Similarity=0.180  Sum_probs=72.7

Q ss_pred             CCCCC----hHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHH
Q psy200          194 CELPG----REVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETI  269 (490)
Q Consensus       194 ~~lvg----re~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i  269 (490)
                      +++++    +++.++.+..++... ....+..++|+||+|+|||||+++++..+....+..+++++      ..+++..+
T Consensus        10 ~~~~~~~~~~~~~~~~~~~~~~~~-~~~~g~~~~l~G~~G~GKTtL~~~i~~~~~~~~g~~~~~~~------~~~~~~~~   82 (180)
T 3ec2_A           10 DTYHPKNVSQNRALLTIRVFVHNF-NPEEGKGLTFVGSPGVGKTHLAVATLKAIYEKKGIRGYFFD------TKDLIFRL   82 (180)
T ss_dssp             SSCCCCSHHHHHHHHHHHHHHHSC-CGGGCCEEEECCSSSSSHHHHHHHHHHHHHHHSCCCCCEEE------HHHHHHHH
T ss_pred             ccccCCCHHHHHHHHHHHHHHHhc-cccCCCEEEEECCCCCCHHHHHHHHHHHHHHHcCCeEEEEE------HHHHHHHH
Confidence            45554    445556666666542 22347889999999999999999999988533445555654      33444444


Q ss_pred             HHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCcc--ccccCHHHHHHhHhCCCCCCCcEEEEEecC
Q psy200          270 VNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDA--LESRKQTILYTIFEWPSIPGSKLVLVGVAN  339 (490)
Q Consensus       270 ~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~--l~~~~~~~L~~l~~~~~~~~~~vilI~~tn  339 (490)
                      ...+.....    ..   .+. .+.   ++.+|||||++.  +....+..++.+++.....+  ..+|.++|
T Consensus        83 ~~~~~~~~~----~~---~~~-~~~---~~~llilDE~~~~~~~~~~~~~l~~ll~~~~~~~--~~ii~tsn  141 (180)
T 3ec2_A           83 KHLMDEGKD----TK---FLK-TVL---NSPVLVLDDLGSERLSDWQRELISYIITYRYNNL--KSTIITTN  141 (180)
T ss_dssp             HHHHHHTCC----SH---HHH-HHH---TCSEEEEETCSSSCCCHHHHHHHHHHHHHHHHTT--CEEEEECC
T ss_pred             HHHhcCchH----HH---HHH-Hhc---CCCEEEEeCCCCCcCCHHHHHHHHHHHHHHHHcC--CCEEEEcC
Confidence            433322111    11   111 222   355999999984  34445566767665332122  33444566

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A*

Probab=99.10  E-value=1.9e-09  Score=118.25  Aligned_cols=191  Identities=15%  Similarity=0.150  Sum_probs=118.3

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCc--eEEEEeccCCCCHHHHHHHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAF--KTIYINCNSVRNAASVYETIVN  271 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~--~~~~v~~~~~~~~~~l~~~i~~  271 (490)
                      ...+||+.++++|.++|..   ....+.+.|+|++|+||||||+.+++.......|  .++|++.....+...++..|..
T Consensus       128 k~~VGRe~eLeeL~elL~~---~d~~RVV~IvGmGGIGKTTLAk~Vy~d~rV~~~Fd~gV~WVsVs~~~d~~~IL~~Ll~  204 (1221)
T 1vt4_I          128 KYNVSRLQPYLKLRQALLE---LRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQK  204 (1221)
T ss_dssp             CSCCCCHHHHHHHHHHHHH---CCSSCEEEECCSTTSSHHHHHHHHHHHCHHHHHHSSCEEEEECCCSSSHHHHHHHHHH
T ss_pred             CCCCCcHHHHHHHHHHHhc---cCCCeEEEEEcCCCccHHHHHHHHHHhhHHHHhCCCcEEEEEeCCCCCHHHHHHHHHH
Confidence            4459999999999999974   2346789999999999999999998753222334  4788888877777777777766


Q ss_pred             HhcC---CC---CC--C----cHHHHHHHHHHHHh-cCCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEEEec
Q psy200          272 ELKL---KP---GG--K----SERHQLGAILKYFD-TKHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVA  338 (490)
Q Consensus       272 ~l~~---~~---~~--~----s~~~~~~~l~~~l~-~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI~~t  338 (490)
                      .++.   ..   .+  .    ....+.+.+...+. ..+++++|||||+|..     +.+..+ .    .+++|++  +|
T Consensus       205 lL~~i~~~~~~~~d~~~~ip~~leeL~e~Lr~lL~~l~~KRvLLVLDDVwd~-----eqLe~f-~----pGSRILV--TT  272 (1221)
T 1vt4_I          205 LLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNA-----KAWNAF-N----LSCKILL--TT  272 (1221)
T ss_dssp             HHHHHCSSSTTTSCCCSSHHHHHHHHHHHHHHHHHHSTTSSCEEEEESCCCH-----HHHHHH-H----SSCCEEE--EC
T ss_pred             HHhhcCcccccccccccCCCCCHHHHHHHHHHHHHhhcCCCEEEEEeCcChH-----HHHHhh-C----CCeEEEE--ec
Confidence            5432   11   11  0    22334455555552 2467899999999992     333222 2    4455554  34


Q ss_pred             CCCChhHhhhHHhhhccCCCCeeEEeC----CCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHHH
Q psy200          339 NALDLTDRMLPRLQANVTLQPTLMNFA----PYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDI  414 (490)
Q Consensus       339 n~~~~~~~l~~~l~~R~~~~~~~i~~~----pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~l  414 (490)
                      . ......   .+.....   ..+.+.    +++.+|.+++|...+...      ..+..    .   ..||+++.+|.+
T Consensus       273 R-d~~Va~---~l~g~~v---y~LeL~d~dL~LS~eEA~eLF~~~~g~~------~eeL~----~---eICgGLPLALkL  332 (1221)
T 1vt4_I          273 R-FKQVTD---FLSAATT---THISLDHHSMTLTPDEVKSLLLKYLDCR------PQDLP----R---EVLTTNPRRLSI  332 (1221)
T ss_dssp             S-CSHHHH---HHHHHSS---CEEEECSSSSCCCHHHHHHHHHHHHCCC------TTTHH----H---HHCCCCHHHHHH
T ss_pred             c-ChHHHH---hcCCCeE---EEecCccccCCcCHHHHHHHHHHHcCCC------HHHHH----H---HHhCCCHHHHHH
Confidence            3 222221   1111101   145555    899999999999885321      11111    1   238899999887


Q ss_pred             HHHHH
Q psy200          415 TNHLI  419 (490)
Q Consensus       415 l~~a~  419 (490)
                      +...+
T Consensus       333 aGs~L  337 (1221)
T 1vt4_I          333 IAESI  337 (1221)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            65543

>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=99.09  E-value=1.8e-09  Score=124.70  Aligned_cols=197  Identities=17%  Similarity=0.142  Sum_probs=126.5

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhh-cCCc--eEEEEeccCCCCH--HHHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEI-KDAF--KTIYINCNSVRNA--ASVYET  268 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~-~~~~--~~~~v~~~~~~~~--~~l~~~  268 (490)
                      ..|+||++++++|.++|..  .....+.+.|+|++|+|||+||+.+++.... ...|  .++|++.......  ...+..
T Consensus       124 ~~~vgR~~~~~~l~~~l~~--~~~~~~~v~i~G~gG~GKTtLa~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~  201 (1249)
T 3sfz_A          124 VIFVTRKKLVHAIQQKLWK--LNGEPGWVTIYGMAGCGKSVLAAEAVRDHSLLEGCFSGGVHWVSIGKQDKSGLLMKLQN  201 (1249)
T ss_dssp             SSCCCCHHHHHHHHHHHHT--TTTSCEEEEEECSTTSSHHHHHHHHTCCHHHHTTTSTTCEEEEECCSCCHHHHHHHHHH
T ss_pred             ceeccHHHHHHHHHHHHhh--ccCCCCEEEEEeCCCCCHHHHHHHHhcChhHHHhhCCCeEEEEEECCcCchHHHHHHHH
Confidence            6799999999999999964  2345678889999999999999999876432 2223  4668877664322  233566


Q ss_pred             HHHHhcCCC-----CCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEEEecCCCCh
Q psy200          269 IVNELKLKP-----GGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVANALDL  343 (490)
Q Consensus       269 i~~~l~~~~-----~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI~~tn~~~~  343 (490)
                      ++..+....     .......+.+.+...+...+++++||||++|...     .+..     ...+++  ||.+|....+
T Consensus       202 ~~~~l~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~LlvlDd~~~~~-----~~~~-----~~~~~~--ilvTtR~~~~  269 (1249)
T 3sfz_A          202 LCMRLDQEESFSQRLPLNIEEAKDRLRVLMLRKHPRSLLILDDVWDPW-----VLKA-----FDNQCQ--ILLTTRDKSV  269 (1249)
T ss_dssp             HHHHHTTTCTTCSSCCSSHHHHHHHHHHHTSSSSCSCEEEEESCCCHH-----HHTT-----TCSSCE--EEEEESSTTT
T ss_pred             HHHHhhhhcccccCCCCCHHHHHHHHHHHHhccCCCEEEEEecCCCHH-----HHHh-----hcCCCE--EEEEcCCHHH
Confidence            666665432     2345677777777777655568999999999742     2211     123443  3334432222


Q ss_pred             hHhhhHHhhhccCCCCeeEEeCC-CCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHHHHHHHH
Q psy200          344 TDRMLPRLQANVTLQPTLMNFAP-YSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITNHLI  419 (490)
Q Consensus       344 ~~~l~~~l~~R~~~~~~~i~~~p-ls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll~~a~  419 (490)
                      ...        +......+.+.+ ++.++..++|..+....  ...+. +....|    ...||+++.||.++...+
T Consensus       270 ~~~--------~~~~~~~~~~~~~l~~~~a~~l~~~~~~~~--~~~~~-~~~~~i----~~~~~glPLal~~~~~~l  331 (1249)
T 3sfz_A          270 TDS--------VMGPKHVVPVESGLGREKGLEILSLFVNMK--KEDLP-AEAHSI----IKECKGSPLVVSLIGALL  331 (1249)
T ss_dssp             TTT--------CCSCBCCEECCSSCCHHHHHHHHHHHHTSC--STTCC-THHHHH----HHHTTTCHHHHHHHHHHH
T ss_pred             HHh--------hcCCceEEEecCCCCHHHHHHHHHHhhCCC--hhhCc-HHHHHH----HHHhCCCHHHHHHHHHHh
Confidence            111        111113688886 99999999999877443  12222 233444    458999999998765544

>3f8t_A Predicted ATPase involved in replication control, CDC46/MCM family; helicase, MCM homolog, DNA replication, ATP-binding, DNA-binding; 1.90A {Methanopyrus kandleri AV19}

Probab=98.97  E-value=4.8e-09  Score=105.85  Aligned_cols=236  Identities=13%  Similarity=0.069  Sum_probs=141.6

Q ss_pred             cchHHHhhcCCCCCCChHHHHHHHHHHHHhhh-ccCCCCeEEEECCCCCcHHHHHHHH-HHHhhhcCCceEEEEeccCCC
Q psy200          183 KPKVEEKAKDSCELPGREVQLEGIRQFLLGHV-NNETSGSMYISGPPGTGKSASLNLL-VSRAEIKDAFKTIYINCNSVR  260 (490)
Q Consensus       183 ~~~~~~~~l~~~~lvgre~~~~~l~~~L~~~~-~~~~~~~ill~GppGtGKTtla~~l-~~~l~~~~~~~~~~v~~~~~~  260 (490)
                      .|......+. . ++|++..+..|.-.|.... +....-++||.|+||+ ||++++++ ++.+.     +.+|.... ..
T Consensus       204 ~~~~l~~sIa-p-I~G~e~vK~aLll~L~GG~~k~rgdihVLL~G~PGt-KS~Lar~i~~~i~p-----R~~ft~g~-~s  274 (506)
T 3f8t_A          204 PLTTFARAIA-P-LPGAEEVGKMLALQLFSCVGKNSERLHVLLAGYPVV-CSEILHHVLDHLAP-----RGVYVDLR-RT  274 (506)
T ss_dssp             HHHHHHHHHC-C-STTCHHHHHHHHHHHTTCCSSGGGCCCEEEESCHHH-HHHHHHHHHHHTCS-----SEEEEEGG-GC
T ss_pred             HHHHHHHHhc-c-cCCCHHHHHHHHHHHcCCccccCCceeEEEECCCCh-HHHHHHHHHHHhCC-----CeEEecCC-CC
Confidence            3444444444 5 9999987666555553200 0001228999999999 99999999 55432     23444322 12


Q ss_pred             CHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCHHHHHHhHhCCC------CCCCcEEE
Q psy200          261 NAASVYETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPS------IPGSKLVL  334 (490)
Q Consensus       261 ~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~------~~~~~vil  334 (490)
                      +...+...    +... .| ..-+ ...+.  +..+|   +++||||+.+....|..|.+.|+...      .-+.++.|
T Consensus       275 s~~gLt~s----~r~~-tG-~~~~-~G~l~--LAdgG---vl~lDEIn~~~~~~qsaLlEaMEe~~VtI~G~~lparf~V  342 (506)
T 3f8t_A          275 ELTDLTAV----LKED-RG-WALR-AGAAV--LADGG---ILAVDHLEGAPEPHRWALMEAMDKGTVTVDGIALNARCAV  342 (506)
T ss_dssp             CHHHHSEE----EEES-SS-EEEE-ECHHH--HTTTS---EEEEECCTTCCHHHHHHHHHHHHHSEEEETTEEEECCCEE
T ss_pred             CccCceEE----EEcC-CC-cccC-CCeeE--EcCCC---eeehHhhhhCCHHHHHHHHHHHhCCcEEECCEEcCCCeEE
Confidence            22222111    1111 11 0000 00111  22222   99999999999999999998876432      12457899


Q ss_pred             EEecCCCChhH--------hhhHHhhhccCCCCeeEEe--------------CCCCHHHHHHHHHHHHhccCCCCCCCHH
Q psy200          335 VGVANALDLTD--------RMLPRLQANVTLQPTLMNF--------------APYSREQILEIISQKLKQTDKFNMFNAS  392 (490)
Q Consensus       335 I~~tn~~~~~~--------~l~~~l~~R~~~~~~~i~~--------------~pls~~e~~~il~~~l~~~~~~~~~~~~  392 (490)
                      |+++|..+..+        .+-+.+.+||++   .+.+              ..++.+++.+++.. ++.......++++
T Consensus       343 IAA~NP~~~yd~~~s~~~~~Lp~alLDRFDL---i~i~~d~pd~e~d~e~~~~~ls~e~L~~yi~~-ar~~~~~p~ls~e  418 (506)
T 3f8t_A          343 LAAINPGEQWPSDPPIARIDLDQDFLSHFDL---IAFLGVDPRPGEPEEQDTEVPSYTLLRRYLLY-AIREHPAPELTEE  418 (506)
T ss_dssp             EEEECCCC--CCSCGGGGCCSCHHHHTTCSE---EEETTC--------------CCHHHHHHHHHH-HHHHCSCCEECHH
T ss_pred             EEEeCcccccCCCCCccccCCChHHhhheee---EEEecCCCChhHhhcccCCCCCHHHHHHHHHH-HHhcCCCceeCHH
Confidence            99999765211        455788899974   2221              23445556665553 2311124668898


Q ss_pred             HHHHHHHHHHHh---------------hCCHHHHHHHHHHHHHHHHhccccCCcccccCHHHHHHHHHHhc
Q psy200          393 ALQLLAGKVAAV---------------SGDIRKAIDITNHLIDLTYDNVKENGEVTGIGLKEVLGVISSVY  448 (490)
Q Consensus       393 ~i~~i~~~i~~~---------------~Gd~r~ai~ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~~~~~  448 (490)
                      +.+.|.+.+...               .-..|.++.+++.|-..|..++     ...|+.+|+..|+.-+.
T Consensus       419 a~~yI~~~y~~tR~~~~~~~~~~~~~~giSpR~leaLiRlA~A~A~L~g-----R~~V~~eDV~~Ai~L~~  484 (506)
T 3f8t_A          419 ARKRLEHWYETRREEVEERLGMGLPTLPVTRRQLESVERLAKAHARMRL-----SDDVEPEDVDIAAELVD  484 (506)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTTCCCCCCCHHHHHHHHHHHHHHHHHTT-----CSEECHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCcccccccccccccccHHHHHHHHHHHHHHHHHcC-----cCCCCHHHHHHHHHHHH
Confidence            888877654322               1247888889999999999999     78999999999987654

>2kjq_A DNAA-related protein; solution structure, NESG, structural genomics, PSI-2, protei structure initiative; NMR {Neisseria meningitidis serogroup B}

Probab=98.96  E-value=6.1e-10  Score=96.69  Aligned_cols=106  Identities=21%  Similarity=0.303  Sum_probs=70.1

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCC
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFDTKH  297 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~  297 (490)
                      .+..++|+|++|+|||+|+++++..+.. .+..++++++......                            ..+   .
T Consensus        35 ~g~~~~l~G~~G~GKTtL~~~i~~~~~~-~g~~~~~~~~~~~~~~----------------------------~~~---~   82 (149)
T 2kjq_A           35 HGQFIYVWGEEGAGKSHLLQAWVAQALE-AGKNAAYIDAASMPLT----------------------------DAA---F   82 (149)
T ss_dssp             CCSEEEEESSSTTTTCHHHHHHHHHHHT-TTCCEEEEETTTSCCC----------------------------GGG---G
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHHHh-cCCcEEEEcHHHhhHH----------------------------HHH---h
Confidence            5678999999999999999999998753 3456788877655321                            011   2


Q ss_pred             CeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEEEecC-CCChhHhhhHHhhhccCC
Q psy200          298 KSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVAN-ALDLTDRMLPRLQANVTL  357 (490)
Q Consensus       298 ~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI~~tn-~~~~~~~l~~~l~~R~~~  357 (490)
                      ++.+|||||++.+....++.|+.+++.....+..++++ +++ .......+ +++.+|+..
T Consensus        83 ~~~lLilDE~~~~~~~~~~~l~~li~~~~~~g~~~iii-ts~~~p~~l~~~-~~L~SRl~~  141 (149)
T 2kjq_A           83 EAEYLAVDQVEKLGNEEQALLFSIFNRFRNSGKGFLLL-GSEYTPQQLVIR-EDLRTRMAY  141 (149)
T ss_dssp             GCSEEEEESTTCCCSHHHHHHHHHHHHHHHHTCCEEEE-EESSCTTTSSCC-HHHHHHGGG
T ss_pred             CCCEEEEeCccccChHHHHHHHHHHHHHHHcCCcEEEE-ECCCCHHHcccc-HHHHHHHhc
Confidence            35599999999987666777888766432223332333 344 22222223 788888864

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426}

Probab=98.91  E-value=1.5e-09  Score=99.06  Aligned_cols=100  Identities=13%  Similarity=0.252  Sum_probs=57.9

Q ss_pred             CCCCChH----HHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHH
Q psy200          194 CELPGRE----VQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETI  269 (490)
Q Consensus       194 ~~lvgre----~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i  269 (490)
                      +++++..    ..++.+..++........+.+++|+|++|+|||++++++++.+.. .+..+++++|.      .++..+
T Consensus        25 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~G~~GtGKT~la~~i~~~~~~-~~~~~~~~~~~------~~~~~~   97 (202)
T 2w58_A           25 SDVDLNDDGRIKAIRFAERFVAEYEPGKKMKGLYLHGSFGVGKTYLLAAIANELAK-RNVSSLIVYVP------ELFREL   97 (202)
T ss_dssp             TSSCCSSHHHHHHHHHHHHHHHHCCSSCCCCEEEEECSTTSSHHHHHHHHHHHHHT-TTCCEEEEEHH------HHHHHH
T ss_pred             hhccCCChhHHHHHHHHHHHHHHhhhccCCCeEEEECCCCCCHHHHHHHHHHHHHH-cCCeEEEEEhH------HHHHHH
Confidence            4555432    345555566654211112379999999999999999999998852 34577788664      334443


Q ss_pred             HHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCcccc
Q psy200          270 VNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALE  311 (490)
Q Consensus       270 ~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~  311 (490)
                      ...+..    .....+.+.    +..   ..+|||||++...
T Consensus        98 ~~~~~~----~~~~~~~~~----~~~---~~~lilDei~~~~  128 (202)
T 2w58_A           98 KHSLQD----QTMNEKLDY----IKK---VPVLMLDDLGAEA  128 (202)
T ss_dssp             HHC-------CCCHHHHHH----HHH---SSEEEEEEECCC-
T ss_pred             HHHhcc----chHHHHHHH----hcC---CCEEEEcCCCCCc
Confidence            332211    112222222    222   2399999997753

>4akg_A Glutathione S-transferase class-MU 26 kDa isozyme heavy chain cytoplasmic; motor protein, AAA+ protein, ASCE protein, P-loop ntpase; HET: ATP ADP; 3.30A {Schistosoma japonicum} PDB: 4ai6_A* 4akh_A* 4aki_A* 3qmz_A

Probab=98.85  E-value=1.4e-08  Score=122.37  Aligned_cols=162  Identities=17%  Similarity=0.259  Sum_probs=106.4

Q ss_pred             HHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCCC--CC
Q psy200          202 QLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKP--GG  279 (490)
Q Consensus       202 ~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~--~~  279 (490)
                      ...+...++..++..  +++++|+||||||||++|+.++...   .++.++.++++...+...+...+-..+....  .|
T Consensus      1252 DT~R~~~ll~~~l~~--~~~vLL~GPpGtGKT~la~~~l~~~---~~~~~~~infsa~ts~~~~~~~i~~~~~~~~~~~g 1326 (2695)
T 4akg_A         1252 DTIKHEKIFYDLLNS--KRGIILCGPPGSGKTMIMNNALRNS---SLYDVVGINFSKDTTTEHILSALHRHTNYVTTSKG 1326 (2695)
T ss_dssp             HHHHHHHHHHHHHHH--TCEEEEECSTTSSHHHHHHHHHHSC---SSCEEEEEECCTTCCHHHHHHHHHHHBCCEEETTT
T ss_pred             chHHHHHHHHHHHHC--CCeEEEECCCCCCHHHHHHHHHhcC---CCCceEEEEeecCCCHHHHHHHHHHHhhhccccCC
Confidence            333445555554433  5799999999999999997776654   4578889999887666554443333221100  00


Q ss_pred             CcHHHHHHHHHHHHh--cCCCeEEEEEecCcccccc------CHHHHHHhHhCCCC---C-C-----CcEEEEEecCCCC
Q psy200          280 KSERHQLGAILKYFD--TKHKSILLILDEIDALESR------KQTILYTIFEWPSI---P-G-----SKLVLVGVANALD  342 (490)
Q Consensus       280 ~s~~~~~~~l~~~l~--~~~~~~vI~IDEid~l~~~------~~~~L~~l~~~~~~---~-~-----~~vilI~~tn~~~  342 (490)
                      .           .+.  ..++++||||||++.....      ..+.|.++++....   . .     .++.+||++|+..
T Consensus      1327 ~-----------~~~P~~~gk~~VlFiDEinmp~~d~yg~q~~lelLRq~le~gg~yd~~~~~~~~~~~i~lIaA~Npp~ 1395 (2695)
T 4akg_A         1327 L-----------TLLPKSDIKNLVLFCDEINLPKLDKYGSQNVVLFLRQLMEKQGFWKTPENKWVTIERIHIVGACNPPT 1395 (2695)
T ss_dssp             E-----------EEEEBSSSSCEEEEEETTTCSCCCSSSCCHHHHHHHHHHHTSSEECTTTCCEEEEESEEEEEEECCTT
T ss_pred             c-----------cccCCCCCceEEEEecccccccccccCchhHHHHHHHHHhcCCEEEcCCCcEEEecCEEEEEecCCCc
Confidence            0           000  1356789999998765433      25677888764311   1 1     3578999999652


Q ss_pred             --hhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhcc
Q psy200          343 --LTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQT  383 (490)
Q Consensus       343 --~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~  383 (490)
                        -...+.+++.+||.    .+.++.++.+++..|+...+...
T Consensus      1396 ~gGR~~l~~rllRrf~----vi~i~~P~~~~l~~I~~~il~~~ 1434 (2695)
T 4akg_A         1396 DPGRIPMSERFTRHAA----ILYLGYPSGKSLSQIYEIYYKAI 1434 (2695)
T ss_dssp             STTCCCCCHHHHTTEE----EEECCCCTTTHHHHHHHHHHHHH
T ss_pred             cCCCccCChhhhheee----EEEeCCCCHHHHHHHHHHHHHHH
Confidence              11345778888985    89999999999999998887654

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3}

Probab=98.56  E-value=5.7e-08  Score=94.74  Aligned_cols=57  Identities=19%  Similarity=0.246  Sum_probs=40.2

Q ss_pred             HHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEecc
Q psy200          200 EVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCN  257 (490)
Q Consensus       200 e~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~  257 (490)
                      ...++.+..|+...- .....+++|+||+|+|||+|+.++++.+....+..++++++.
T Consensus       134 ~~~~~~~~~~i~~~~-~~~~~~lll~G~~GtGKT~La~aia~~~~~~~g~~v~~~~~~  190 (308)
T 2qgz_A          134 MEAFSAILDFVEQYP-SAEQKGLYLYGDMGIGKSYLLAAMAHELSEKKGVSTTLLHFP  190 (308)
T ss_dssp             HHHHHHHHHHHHHCS-CSSCCEEEEECSTTSSHHHHHHHHHHHHHHHSCCCEEEEEHH
T ss_pred             HHHHHHHHHHHHhcc-ccCCceEEEECCCCCCHHHHHHHHHHHHHHhcCCcEEEEEHH
Confidence            345555566665421 113679999999999999999999998752345677777654

>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=98.35  E-value=4.7e-06  Score=78.52  Aligned_cols=132  Identities=12%  Similarity=0.170  Sum_probs=76.4

Q ss_pred             HHHHHHhhhccC--CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCCCCCCcHH
Q psy200          206 IRQFLLGHVNNE--TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKPGGKSER  283 (490)
Q Consensus       206 l~~~L~~~~~~~--~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~~~s~~  283 (490)
                      +..+|..++...  +.++++|+||||||||+++.++++.+.    . ...++....                .+      
T Consensus        89 ~~~~l~~~l~~~~~~~n~~~l~GppgtGKt~~a~ala~~~~----l-~G~vn~~~~----------------~f------  141 (267)
T 1u0j_A           89 AASVFLGWATKKFGKRNTIWLFGPATTGKTNIAEAIAHTVP----F-YGCVNWTNE----------------NF------  141 (267)
T ss_dssp             HHHHHHHHHTTCSTTCCEEEEECSTTSSHHHHHHHHHHHSS----C-EEECCTTCS----------------SC------
T ss_pred             HHHHHHHHHhCCCCCCcEEEEECCCCCCHHHHHHHHHhhhc----c-cceeecccc----------------cc------
Confidence            344455554443  346899999999999999999998753    1 111121100                00      


Q ss_pred             HHHHHHHHHHhcCCCeEEEEEecCccccccCHHHHHHhHhCC------------CCCCCcEEEEEecCCCChh-------
Q psy200          284 HQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWP------------SIPGSKLVLVGVANALDLT-------  344 (490)
Q Consensus       284 ~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~------------~~~~~~vilI~~tn~~~~~-------  344 (490)
                              .+.......|++.||.... ...+..+..+++-.            +....+  +|.++|..-..       
T Consensus       142 --------~l~~~~~k~i~l~Ee~~~~-~d~~~~lr~i~~G~~~~id~K~k~~~~v~~tP--vIitsN~~i~~~~~g~~~  210 (267)
T 1u0j_A          142 --------PFNDCVDKMVIWWEEGKMT-AKVVESAKAILGGSKVRVDQKCKSSAQIDPTP--VIVTSNTNMCAVIDGNST  210 (267)
T ss_dssp             --------TTGGGSSCSEEEECSCCEE-TTTHHHHHHHHTTCCEEC------CCEECCCC--EEEEESSCTTCEEETTEE
T ss_pred             --------ccccccccEEEEeccccch-hHHHHHHHHHhCCCcEEEecCcCCcccccCCC--EEEEecCCcccccccCcc
Confidence                    0111122346666666554 45556677776511            112233  44456631000       


Q ss_pred             -HhhhHHhhhccCCCCeeEEeC--------CCCHHHHHHHHHHH
Q psy200          345 -DRMLPRLQANVTLQPTLMNFA--------PYSREQILEIISQK  379 (490)
Q Consensus       345 -~~l~~~l~~R~~~~~~~i~~~--------pls~~e~~~il~~~  379 (490)
                       +...+.|++|+.    .+.|.        +++.++...+|...
T Consensus       211 s~~~~~~L~sR~~----~f~F~~~~p~~~~~lt~~~~~~f~~w~  250 (267)
T 1u0j_A          211 TFEHQQPLQDRMF----KFELTRRLDHDFGKVTKQEVKDFFRWA  250 (267)
T ss_dssp             ECTTHHHHHTTEE----EEECCSCCCTTSCCCCHHHHHHHHHHH
T ss_pred             chhhhHHHhhhEE----EEECCCcCCcccCCCCHHHHHHHHHHH
Confidence             234567999985    79998        89999999999843

>3vkg_A Dynein heavy chain, cytoplasmic; AAA+ protein, molecular motor, microtubles, motor protein; HET: ADP SPM; 2.81A {Dictyostelium discoideum} PDB: 3vkh_A*

Probab=98.34  E-value=2e-06  Score=104.74  Aligned_cols=158  Identities=16%  Similarity=0.210  Sum_probs=104.2

Q ss_pred             HHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCCCC---CCc
Q psy200          205 GIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKPG---GKS  281 (490)
Q Consensus       205 ~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~---~~s  281 (490)
                      +...++..++.  .+++++|+||+|||||+++..++..+   .++.++.+|++...+...+...+-..+.....   |.-
T Consensus      1292 R~~~ll~~ll~--~~~pvLL~GptGtGKT~li~~~L~~l---~~~~~~~infS~~Tta~~l~~~~e~~~e~~~~~~~G~~ 1366 (3245)
T 3vkg_A         1292 RHVDVLHAWLS--EHRPLILCGPPGSGKTMTLTSTLRAF---PDFEVVSLNFSSATTPELLLKTFDHHCEYKRTPSGETV 1366 (3245)
T ss_dssp             HHHHHHHHHHH--TTCCCEEESSTTSSHHHHHHHHGGGC---TTEEEEEECCCTTCCHHHHHHHHHHHEEEEECTTSCEE
T ss_pred             HHHHHHHHHHH--CCCcEEEECCCCCCHHHHHHHHHHhC---CCCceEEEEeeCCCCHHHHHHHHhhcceEEeccCCCcc
Confidence            44445554443  36789999999999999987766554   45678899999887777666655333321110   000


Q ss_pred             HHHHHHHHHHHHh--cCCCeEEEEEecCcccccc------CHHHHHHhHhCCC--C-------CCCcEEEEEecCCCC--
Q psy200          282 ERHQLGAILKYFD--TKHKSILLILDEIDALESR------KQTILYTIFEWPS--I-------PGSKLVLVGVANALD--  342 (490)
Q Consensus       282 ~~~~~~~l~~~l~--~~~~~~vI~IDEid~l~~~------~~~~L~~l~~~~~--~-------~~~~vilI~~tn~~~--  342 (490)
                                 +.  ..|+.+||||||++.-...      ..+.|.++++...  .       .-..+.+|+++|...  
T Consensus      1367 -----------~~p~~~Gk~~VlFiDDiNmp~~D~yGtQ~~ielLrqlld~~g~yd~~~~~~~~i~d~~~vaamnPp~~g 1435 (3245)
T 3vkg_A         1367 -----------LRPTQLGKWLVVFCDEINLPSTDKYGTQRVITFIRQMVEKGGFWRTSDHTWIKLDKIQFVGACNPPTDA 1435 (3245)
T ss_dssp             -----------EEESSTTCEEEEEETTTTCCCCCTTSCCHHHHHHHHHHHHSEEEETTTTEEEEESSEEEEEEECCTTST
T ss_pred             -----------cCCCcCCceEEEEecccCCCCccccccccHHHHHHHHHHcCCeEECCCCeEEEecCeEEEEEcCCCCCC
Confidence                       00  1267899999999864432      2467777765321  0       123567888888542  


Q ss_pred             hhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhc
Q psy200          343 LTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQ  382 (490)
Q Consensus       343 ~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~  382 (490)
                      -...+.+++.+||.    .+.++.++.+++..|+...+..
T Consensus      1436 Gr~~l~~Rf~r~F~----vi~i~~ps~esL~~If~til~~ 1471 (3245)
T 3vkg_A         1436 GRVQLTHRFLRHAP----ILLVDFPSTSSLTQIYGTFNRA 1471 (3245)
T ss_dssp             TCCCCCHHHHTTCC----EEECCCCCHHHHHHHHHHHHHH
T ss_pred             CCccCCHHHHhhce----EEEeCCCCHHHHHHHHHHHHHH
Confidence            22345678889996    7999999999999998766543

>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=98.26  E-value=8.6e-07  Score=91.40  Aligned_cols=142  Identities=14%  Similarity=0.131  Sum_probs=69.4

Q ss_pred             cCCCCcchHHHhhcCCCCCC-ChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEec
Q psy200          178 LFSEDKPKVEEKAKDSCELP-GREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINC  256 (490)
Q Consensus       178 ~~~~~~~~~~~~~l~~~~lv-gre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~  256 (490)
                      .+|..+|.+...    +.|- ++.+.+..+..++..    + .+.++|.|++|||||+++.+++..+.......++.+ +
T Consensus        12 ~~~~~~~~p~~~----~~Ln~~Q~~av~~~~~~i~~----~-~~~~li~G~aGTGKT~ll~~~~~~l~~~~~~~il~~-a   81 (459)
T 3upu_A           12 SGLVPRGSHMTF----DDLTEGQKNAFNIVMKAIKE----K-KHHVTINGPAGTGATTLTKFIIEALISTGETGIILA-A   81 (459)
T ss_dssp             ---------CCS----SCCCHHHHHHHHHHHHHHHS----S-SCEEEEECCTTSCHHHHHHHHHHHHHHTTCCCEEEE-E
T ss_pred             CCCccccCCCcc----ccCCHHHHHHHHHHHHHHhc----C-CCEEEEEeCCCCCHHHHHHHHHHHHHhcCCceEEEe-c
Confidence            367778887655    5554 455555555555542    2 349999999999999999999998864333233333 2


Q ss_pred             cCCCCHHHHHHHHHHHhcCCCCCCcHHHHHHHH----------H-HHHhcCCCeEEEEEecCccccccCHHHHHHhHhCC
Q psy200          257 NSVRNAASVYETIVNELKLKPGGKSERHQLGAI----------L-KYFDTKHKSILLILDEIDALESRKQTILYTIFEWP  325 (490)
Q Consensus       257 ~~~~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l----------~-~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~  325 (490)
                      ...    .....+...++..  ..+...+....          . .......+..+|||||++.+.......|..++.  
T Consensus        82 ~T~----~Aa~~l~~~~~~~--~~T~h~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iiiDE~~~~~~~~~~~l~~~~~--  153 (459)
T 3upu_A           82 PTH----AAKKILSKLSGKE--ASTIHSILKINPVTYEENVLFEQKEVPDLAKCRVLICDEVSMYDRKLFKILLSTIP--  153 (459)
T ss_dssp             SSH----HHHHHHHHHHSSC--EEEHHHHHTEEEEECSSCEEEEECSCCCCSSCSEEEESCGGGCCHHHHHHHHHHSC--
T ss_pred             CcH----HHHHHHHhhhccc--hhhHHHHhccCcccccccchhcccccccccCCCEEEEECchhCCHHHHHHHHHhcc--
Confidence            221    1111111112110  01111111000          0 000011235699999999987544444443332  


Q ss_pred             CCCCCcEEEEEecC
Q psy200          326 SIPGSKLVLVGVAN  339 (490)
Q Consensus       326 ~~~~~~vilI~~tn  339 (490)
                        .+.+++++|-.+
T Consensus       154 --~~~~~~~vGD~~  165 (459)
T 3upu_A          154 --PWCTIIGIGDNK  165 (459)
T ss_dssp             --TTCEEEEEECTT
T ss_pred             --CCCEEEEECCHH
Confidence              566788887665

>2r2a_A Uncharacterized protein; zonular occludens toxin, structural genomics, APC84050.2, PS protein structure initiative; HET: MSE; 1.82A {Neisseria meningitidis MC58}

Probab=98.24  E-value=2.6e-06  Score=77.29  Aligned_cols=136  Identities=13%  Similarity=0.182  Sum_probs=66.1

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHhhh----cCC-ceEEEEeccCCCCHHHH-HHHHHHHhcCCCC-CCcHHHHHHHHHH
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRAEI----KDA-FKTIYINCNSVRNAASV-YETIVNELKLKPG-GKSERHQLGAILK  291 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l~~----~~~-~~~~~v~~~~~~~~~~l-~~~i~~~l~~~~~-~~s~~~~~~~l~~  291 (490)
                      ....+|+|+||+|||+++...+.....    ..+ ..+.+.++..+...... ... ...+..... ........+.+. 
T Consensus         5 ~mi~l~tG~pGsGKT~~a~~~~~~~~~~~~~~~g~r~v~~~~~~gL~~~~~~~~~~-k~~~~~~~~~~~~~~~~~~~~~-   82 (199)
T 2r2a_A            5 AEICLITGTPGSGKTLKMVSMMANDEMFKPDENGIRRKVFTNIKGLKIPHTYIETD-AKKLPKSTDEQLSAHDMYEWIK-   82 (199)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHCGGGSCCTTSCCCCEEECCTTBCSCCEEEECC-TTTCSSCCSSCEEGGGHHHHTT-
T ss_pred             eeEEEEEeCCCCCHHHHHHHHHHHHHhhcccccCceEEEEecCCCccccccccchh-hhhccccCcccccHHHHHHHhh-
Confidence            347889999999999999876554321    223 34445555543210000 000 000000000 001122222110 


Q ss_pred             HHhcCCCeEEEEEecCccccccC---H--HHHHHhHhCCCCCCCcEEEEEecCCCChhHhhhHHhhhccCCCCeeEEeCC
Q psy200          292 YFDTKHKSILLILDEIDALESRK---Q--TILYTIFEWPSIPGSKLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAP  366 (490)
Q Consensus       292 ~l~~~~~~~vI~IDEid~l~~~~---~--~~L~~l~~~~~~~~~~vilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~p  366 (490)
                       .. .++..||||||+|.+....   .  ..+...++.....+..+  |.+++.   ...+...++.|+..   .+++.+
T Consensus        83 -~~-~~~~~vliIDEAq~l~~~~~~~~e~~rll~~l~~~r~~~~~i--il~tq~---~~~l~~~lr~ri~~---~~~l~~  152 (199)
T 2r2a_A           83 -KP-ENIGSIVIVDEAQDVWPARSAGSKIPENVQWLNTHRHQGIDI--FVLTQG---PKLLDQNLRTLVRK---HYHIAS  152 (199)
T ss_dssp             -SG-GGTTCEEEETTGGGTSBCCCTTCCCCHHHHGGGGTTTTTCEE--EEEESC---GGGBCHHHHTTEEE---EEEEEE
T ss_pred             -cc-ccCceEEEEEChhhhccCccccchhHHHHHHHHhcCcCCeEE--EEECCC---HHHHhHHHHHHhhe---EEEEcC
Confidence             11 2457799999999995322   1  12333444333333344  444543   45566678888873   566665

>1tue_A Replication protein E1; helicase, replication, E1E2 complex, AAA+ protein; 2.10A {Human papillomavirus type 18} SCOP: c.37.1.20

Probab=98.23  E-value=1.1e-06  Score=79.13  Aligned_cols=45  Identities=22%  Similarity=0.259  Sum_probs=33.3

Q ss_pred             CChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          197 PGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       197 vgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      +.-..-+..+..++..   -...++++|+||||||||+++.++++.+.
T Consensus        39 ~~~~~f~~~l~~~~~~---iPkkn~ili~GPPGtGKTt~a~ala~~l~   83 (212)
T 1tue_A           39 IEFITFLGALKSFLKG---TPKKNCLVFCGPANTGKSYFGMSFIHFIQ   83 (212)
T ss_dssp             CCHHHHHHHHHHHHHT---CTTCSEEEEESCGGGCHHHHHHHHHHHHT
T ss_pred             cCHHHHHHHHHHHHhc---CCcccEEEEECCCCCCHHHHHHHHHHHhC
Confidence            3444456666666653   12346799999999999999999999874

>4akg_A Glutathione S-transferase class-MU 26 kDa isozyme heavy chain cytoplasmic; motor protein, AAA+ protein, ASCE protein, P-loop ntpase; HET: ATP ADP; 3.30A {Schistosoma japonicum} PDB: 4ai6_A* 4akh_A* 4aki_A* 3qmz_A

Probab=98.17  E-value=6.7e-05  Score=91.05  Aligned_cols=130  Identities=13%  Similarity=0.118  Sum_probs=84.6

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCC
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFDTKHK  298 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~  298 (490)
                      ..+.++.||+|||||++++.+++.++    ..++.+||....+..+                    +...|..+...+  
T Consensus       645 ~~~~~l~GpaGtGKTe~vk~LA~~lg----~~~v~~nc~e~ld~~~--------------------lg~~~~g~~~~G--  698 (2695)
T 4akg_A          645 KYGGCFFGPAGTGKTETVKAFGQNLG----RVVVVFNCDDSFDYQV--------------------LSRLLVGITQIG--  698 (2695)
T ss_dssp             TCEEEEECCTTSCHHHHHHHHHHTTT----CCCEEEETTSSCCHHH--------------------HHHHHHHHHHHT--
T ss_pred             CCCCcccCCCCCCcHHHHHHHHHHhC----CcEEEEECCCCCChhH--------------------hhHHHHHHHhcC--
Confidence            46788999999999999999999986    5678889998755433                    334444444432  


Q ss_pred             eEEEEEecCccccccCHHHHHHh-------HhCCC----------CCCCcEEEEEecCCC-ChhHhhhHHhhhccCCCCe
Q psy200          299 SILLILDEIDALESRKQTILYTI-------FEWPS----------IPGSKLVLVGVANAL-DLTDRMLPRLQANVTLQPT  360 (490)
Q Consensus       299 ~~vI~IDEid~l~~~~~~~L~~l-------~~~~~----------~~~~~vilI~~tn~~-~~~~~l~~~l~~R~~~~~~  360 (490)
                       ..+++|||+.+.......+...       +....          ..+..+.++.+.|.- .-...+-+.++.||.    
T Consensus       699 -aw~~~DE~nr~~~evLs~l~~~l~~i~~al~~~~~~i~~~g~~i~l~~~~~vfiT~NPgy~g~~eLP~~Lk~~Fr----  773 (2695)
T 4akg_A          699 -AWGCFDEFNRLDEKVLSAVSANIQQIQNGLQVGKSHITLLEEETPLSPHTAVFITLNPGYNGRSELPENLKKSFR----  773 (2695)
T ss_dssp             -CEEEEETTTSSCHHHHHHHHHHHHHHHHHHHHTCSEEECSSSEEECCTTCEEEEEECCCSSSSCCCCHHHHTTEE----
T ss_pred             -CEeeehhhhhcChHHHHHHHHHHHHHHHHHHcCCcEEeeCCcEEecCCCceEEEEeCCCccCcccccHHHHhheE----
Confidence             4899999999977654444221       11000          012344555566631 011223346777884    


Q ss_pred             eEEeCCCCHHHHHHHHHHH
Q psy200          361 LMNFAPYSREQILEIISQK  379 (490)
Q Consensus       361 ~i~~~pls~~e~~~il~~~  379 (490)
                      .+.+..++.+.+.+++...
T Consensus       774 ~v~m~~Pd~~~i~ei~l~s  792 (2695)
T 4akg_A          774 EFSMKSPQSGTIAEMILQI  792 (2695)
T ss_dssp             EEECCCCCHHHHHHHHHHH
T ss_pred             EEEeeCCCHHHHHHHHHHh
Confidence            7999999999988886544

>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=98.00  E-value=3.2e-06  Score=77.95  Aligned_cols=112  Identities=18%  Similarity=0.194  Sum_probs=61.4

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCCCCC---CcHHHHHHHHHHHH
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKPGG---KSERHQLGAILKYF  293 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~~---~s~~~~~~~l~~~l  293 (490)
                      ..+..++++|++|+||||++..++..+... +..++.+..... + . ....++..++.....   ....++.+.+.+..
T Consensus        10 ~~G~i~litG~mGsGKTT~ll~~~~r~~~~-g~kVli~~~~~d-~-r-~~~~i~srlG~~~~~~~~~~~~~i~~~i~~~~   85 (223)
T 2b8t_A           10 KIGWIEFITGPMFAGKTAELIRRLHRLEYA-DVKYLVFKPKID-T-R-SIRNIQSRTGTSLPSVEVESAPEILNYIMSNS   85 (223)
T ss_dssp             -CCEEEEEECSTTSCHHHHHHHHHHHHHHT-TCCEEEEEECCC-G-G-GCSSCCCCCCCSSCCEEESSTHHHHHHHHSTT
T ss_pred             CCcEEEEEECCCCCcHHHHHHHHHHHHHhc-CCEEEEEEeccC-c-h-HHHHHHHhcCCCccccccCCHHHHHHHHHHHh
Confidence            356788899999999999999888887532 334555533221 1 1 111223333322211   12233433333222


Q ss_pred             hcCCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEEEe
Q psy200          294 DTKHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGV  337 (490)
Q Consensus       294 ~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI~~  337 (490)
                      . .+++-+|+|||++.+.....+.+..+.+    .+..++++|.
T Consensus        86 ~-~~~~dvViIDEaQ~l~~~~ve~l~~L~~----~gi~Vil~Gl  124 (223)
T 2b8t_A           86 F-NDETKVIGIDEVQFFDDRICEVANILAE----NGFVVIISGL  124 (223)
T ss_dssp             S-CTTCCEEEECSGGGSCTHHHHHHHHHHH----TTCEEEEECC
T ss_pred             h-CCCCCEEEEecCccCcHHHHHHHHHHHh----CCCeEEEEec
Confidence            2 2446799999999986543344444443    2456666655

>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=97.94  E-value=7.8e-05  Score=69.28  Aligned_cols=94  Identities=19%  Similarity=0.191  Sum_probs=56.3

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcC-----CceEEEEeccCCCCHHHHHHHHHHHhcCCC----------CCCcH
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKD-----AFKTIYINCNSVRNAASVYETIVNELKLKP----------GGKSE  282 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~-----~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~----------~~~s~  282 (490)
                      .+..++|+|++|+||||++..++.......     ...++|++.........+. .++..++...          ...+.
T Consensus        23 ~G~~~~i~G~~GsGKTtl~~~l~~~~~~~~~~g~~~~~~~~i~~~~~~~~~~~~-~~~~~~g~~~~~~~~~~~~~~~~~~  101 (243)
T 1n0w_A           23 TGSITEMFGEFRTGKTQICHTLAVTCQLPIDRGGGEGKAMYIDTEGTFRPERLL-AVAERYGLSGSDVLDNVAYARAFNT  101 (243)
T ss_dssp             TTSEEEEECCTTSSHHHHHHHHHHHTTSCGGGTCCSSEEEEEESSSCCCHHHHH-HHHHHTTCCHHHHHHTEEEEECCSH
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHHHhCchhcCCCCCeEEEEECCCCcCHHHHH-HHHHHcCCCHHHHhhCeEEEecCCH
Confidence            567899999999999999999998643211     3578888876643333332 2333333211          11223


Q ss_pred             HHHHH---HHHHHHhcCCCeEEEEEecCcccccc
Q psy200          283 RHQLG---AILKYFDTKHKSILLILDEIDALESR  313 (490)
Q Consensus       283 ~~~~~---~l~~~l~~~~~~~vI~IDEid~l~~~  313 (490)
                      .+...   .+.+.+.. .++.+|||||+..+...
T Consensus       102 ~~~~~~~~~~~~~~~~-~~~~lliiD~~~~~~~~  134 (243)
T 1n0w_A          102 DHQTQLLYQASAMMVE-SRYALLIVDSATALYRT  134 (243)
T ss_dssp             HHHHHHHHHHHHHHHH-SCEEEEEEETSSGGGC-
T ss_pred             HHHHHHHHHHHHHHhc-CCceEEEEeCchHHHHH
Confidence            33222   23333433 45889999999988643

>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=97.92  E-value=3.4e-05  Score=70.61  Aligned_cols=88  Identities=17%  Similarity=0.169  Sum_probs=52.5

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhc-----------C--CCCCCcHHH
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELK-----------L--KPGGKSERH  284 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~-----------~--~~~~~s~~~  284 (490)
                      .+..++|+|++|+||||++..++.  .  .+..++|++.....+...+.. +...++           .  .........
T Consensus        19 ~G~~~~i~G~~GsGKTtl~~~l~~--~--~~~~v~~i~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   93 (220)
T 2cvh_A           19 PGVLTQVYGPYASGKTTLALQTGL--L--SGKKVAYVDTEGGFSPERLVQ-MAETRGLNPEEALSRFILFTPSDFKEQRR   93 (220)
T ss_dssp             TTSEEEEECSTTSSHHHHHHHHHH--H--HCSEEEEEESSCCCCHHHHHH-HHHTTTCCHHHHHHHEEEECCTTTSHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHH--H--cCCcEEEEECCCCCCHHHHHH-HHHhcCCChHHHhhcEEEEecCCHHHHHH
Confidence            567899999999999999999988  2  345778887765334443332 222221           1  111111122


Q ss_pred             HHHHHHHHHhcCCCeEEEEEecCccccc
Q psy200          285 QLGAILKYFDTKHKSILLILDEIDALES  312 (490)
Q Consensus       285 ~~~~l~~~l~~~~~~~vI~IDEid~l~~  312 (490)
                      ....+.. +... ++.+|||||+..+..
T Consensus        94 ~~~~~~~-l~~~-~~~lliiD~~~~~l~  119 (220)
T 2cvh_A           94 VIGSLKK-TVDS-NFALVVVDSITAHYR  119 (220)
T ss_dssp             HHHHHHH-HCCT-TEEEEEEECCCCCTT
T ss_pred             HHHHHHH-Hhhc-CCCEEEEcCcHHHhh
Confidence            2332222 2222 588999999998853

>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=97.87  E-value=0.00015  Score=64.43  Aligned_cols=24  Identities=33%  Similarity=0.654  Sum_probs=21.8

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHhh
Q psy200          221 SMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      .+.|+||+|+|||||++.++..+.
T Consensus         2 ~i~l~G~nGsGKTTLl~~l~g~l~   25 (178)
T 1ye8_A            2 KIIITGEPGVGKTTLVKKIVERLG   25 (178)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHG
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhC
Confidence            578999999999999999998874

>2w0m_A SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus solfataricus P2}

Probab=97.81  E-value=9.8e-05  Score=67.99  Aligned_cols=89  Identities=15%  Similarity=0.182  Sum_probs=54.0

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCCC--------------------
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKP--------------------  277 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~--------------------  277 (490)
                      .+..++|+|++|+||||+++.++..+... ...+++++...  ....+...+. .++...                    
T Consensus        22 ~G~~~~i~G~~GsGKTtl~~~l~~~~~~~-~~~v~~~~~~~--~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~   97 (235)
T 2w0m_A           22 QGFFIALTGEPGTGKTIFSLHFIAKGLRD-GDPCIYVTTEE--SRDSIIRQAK-QFNWDFEEYIEKKLIIIDALMKEKED   97 (235)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHHHHHHHH-TCCEEEEESSS--CHHHHHHHHH-HTTCCCGGGBTTTEEEEECCC----C
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHHHHHHC-CCeEEEEEccc--CHHHHHHHHH-HhcchHHHHhhCCEEEEeccccccCc
Confidence            46788999999999999999999766422 23566665433  3344433322 332110                    


Q ss_pred             ----CCCcHHHHHHHHHHHHhcCCCeE--EEEEecCcccc
Q psy200          278 ----GGKSERHQLGAILKYFDTKHKSI--LLILDEIDALE  311 (490)
Q Consensus       278 ----~~~s~~~~~~~l~~~l~~~~~~~--vI~IDEid~l~  311 (490)
                          ...+..++...+...+.. .++-  +|||||+..+.
T Consensus        98 ~~~~~~~~~~~~~~~~~~~~~~-~~~~~~llilDe~~~~~  136 (235)
T 2w0m_A           98 QWSLVNLTPEELVNKVIEAKQK-LGYGKARLVIDSVSALF  136 (235)
T ss_dssp             TTBCSSCCHHHHHHHHHHHHHH-HCSSCEEEEEETGGGGS
T ss_pred             eeeecCCCHHHHHHHHHHHHHh-hCCCceEEEEECchHhh
Confidence                011345555555554433 2355  99999999875

>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=97.80  E-value=4.3e-05  Score=73.80  Aligned_cols=75  Identities=12%  Similarity=0.136  Sum_probs=45.4

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCC
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFDTKH  297 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~  297 (490)
                      .+..++|+||||+|||+|+.+++...+  ....++.+......+             . .. ...+...+.+.+.+.+.+
T Consensus       122 ~gsviLI~GpPGsGKTtLAlqlA~~~G--~~VlyIs~~~eE~v~-------------~-~~-~~le~~l~~i~~~l~~~~  184 (331)
T 2vhj_A          122 ASGMVIVTGKGNSGKTPLVHALGEALG--GKDKYATVRFGEPLS-------------G-YN-TDFNVFVDDIARAMLQHR  184 (331)
T ss_dssp             ESEEEEEECSCSSSHHHHHHHHHHHHH--TTSCCEEEEBSCSST-------------T-CB-CCHHHHHHHHHHHHHHCS
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHhCC--CCEEEEEecchhhhh-------------h-hh-cCHHHHHHHHHHHHhhCC
Confidence            345679999999999999999998722  222233331121100             0 00 234555555555555433


Q ss_pred             CeEEEEEecCccccc
Q psy200          298 KSILLILDEIDALES  312 (490)
Q Consensus       298 ~~~vI~IDEid~l~~  312 (490)
                         +||||+++.+..
T Consensus       185 ---LLVIDsI~aL~~  196 (331)
T 2vhj_A          185 ---VIVIDSLKNVIG  196 (331)
T ss_dssp             ---EEEEECCTTTC-
T ss_pred             ---EEEEeccccccc
Confidence               999999999854

>2orw_A Thymidine kinase; TMTK, TP4A, transferase; HET: 4TA; 1.50A {Thermotoga maritima} PDB: 2qpo_A 2qq0_A* 2qqe_A*

Probab=97.78  E-value=7.3e-06  Score=73.38  Aligned_cols=111  Identities=14%  Similarity=0.142  Sum_probs=54.2

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCC
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFDTKHK  298 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~  298 (490)
                      +..++|+|++|+||||++..++..+.. .+..++.+..... + ......+...++............+.+ +.+.  +.
T Consensus         3 g~i~vi~G~~gsGKTT~ll~~~~~~~~-~g~~v~~~~~~~d-~-r~~~~~i~s~~g~~~~~~~~~~~~~~~-~~~~--~~   76 (184)
T 2orw_A            3 GKLTVITGPMYSGKTTELLSFVEIYKL-GKKKVAVFKPKID-S-RYHSTMIVSHSGNGVEAHVIERPEEMR-KYIE--ED   76 (184)
T ss_dssp             CCEEEEEESTTSSHHHHHHHHHHHHHH-TTCEEEEEEEC-------CCCEECC----CEECEEESSGGGGG-GGCC--TT
T ss_pred             cEEEEEECCCCCCHHHHHHHHHHHHHH-CCCeEEEEeeccc-c-ccCcccEEecCCCceeeEEECCHHHHH-HHhc--CC
Confidence            457889999999999999767666532 2344444432211 0 000000000001000000000111111 1111  24


Q ss_pred             eEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEEEecC
Q psy200          299 SILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVAN  339 (490)
Q Consensus       299 ~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI~~tn  339 (490)
                      .-+|||||+|.+.....+.|..+.+.    +..+++.|.+.
T Consensus        77 ~dvviIDE~Q~~~~~~~~~l~~l~~~----~~~Vi~~Gl~~  113 (184)
T 2orw_A           77 TRGVFIDEVQFFNPSLFEVVKDLLDR----GIDVFCAGLDL  113 (184)
T ss_dssp             EEEEEECCGGGSCTTHHHHHHHHHHT----TCEEEEEEESB
T ss_pred             CCEEEEECcccCCHHHHHHHHHHHHC----CCCEEEEeecc
Confidence            67999999999865555566555552    45666666653

>2z43_A DNA repair and recombination protein RADA; archaea, filament, DNA binding, molecular SWI RECA, DMC1; HET: DNA; 1.93A {Sulfolobus solfataricus} PDB: 2bke_A* 2dfl_A* 2zub_A* 2zuc_A* 2zud_A*

Probab=97.70  E-value=0.00013  Score=71.40  Aligned_cols=94  Identities=14%  Similarity=0.173  Sum_probs=59.2

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcC-----CceEEEEeccCCCCHHHHHHHHHHHhcCCC----------CCCcH
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKD-----AFKTIYINCNSVRNAASVYETIVNELKLKP----------GGKSE  282 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~-----~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~----------~~~s~  282 (490)
                      .+..++|+|++|+|||+++..++.......     +..++|++.....+...+. .++..++...          ...+.
T Consensus       106 ~G~i~~i~G~~GsGKT~la~~la~~~~~~~~~gg~~~~vlyi~~e~~~~~~~l~-~~~~~~g~~~~~~~~~l~~~~~~~~  184 (324)
T 2z43_A          106 TRTMTEFFGEFGSGKTQLCHQLSVNVQLPPEKGGLSGKAVYIDTEGTFRWERIE-NMAKALGLDIDNVMNNIYYIRAINT  184 (324)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSCEEEEEESSSCCCHHHHH-HHHHHTTCCHHHHHHTEEEEECCSH
T ss_pred             CCcEEEEECCCCCCHhHHHHHHHHHHhcccccCCCCCeEEEEECCCCCCHHHHH-HHHHHhCCCHHHHhccEEEEeCCCH
Confidence            567899999999999999999998754221     4578898876643444443 2334443211          01122


Q ss_pred             H---HHHHHHHHHHhcCCCeEEEEEecCccccc
Q psy200          283 R---HQLGAILKYFDTKHKSILLILDEIDALES  312 (490)
Q Consensus       283 ~---~~~~~l~~~l~~~~~~~vI~IDEid~l~~  312 (490)
                      .   .+...+...+....++.+||||.+..+..
T Consensus       185 ~~~~~~l~~l~~~~~~~~~~~lvVIDsl~~l~~  217 (324)
T 2z43_A          185 DHQIAIVDDLQELVSKDPSIKLIVVDSVTSHFR  217 (324)
T ss_dssp             HHHHHHHHHHHHHHHHCTTEEEEEETTTTHHHH
T ss_pred             HHHHHHHHHHHHHHHhccCCCEEEEeCcHHHhh
Confidence            2   23344444444435688999999999853

>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=97.68  E-value=0.00021  Score=70.43  Aligned_cols=88  Identities=14%  Similarity=0.155  Sum_probs=58.9

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCCC------CCCcHHHHHHHHHH
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKP------GGKSERHQLGAILK  291 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~------~~~s~~~~~~~l~~  291 (490)
                      .+..++|+||+|+|||||+..++..+.. .+..++|++........     .+..++...      ...+..++...+..
T Consensus        60 ~G~i~~I~GppGsGKSTLal~la~~~~~-~gg~VlyId~E~s~~~~-----ra~rlgv~~~~l~i~~~~~~e~~l~~~~~  133 (356)
T 3hr8_A           60 RGRIVEIFGQESSGKTTLALHAIAEAQK-MGGVAAFIDAEHALDPV-----YAKNLGVDLKSLLISQPDHGEQALEIVDE  133 (356)
T ss_dssp             TTEEEEEEESTTSSHHHHHHHHHHHHHH-TTCCEEEEESSCCCCHH-----HHHHHTCCGGGCEEECCSSHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHHh-cCCeEEEEecccccchH-----HHHHcCCchhhhhhhhccCHHHHHHHHHH
Confidence            4668999999999999999999988753 23467888776554432     333343321      12345566665555


Q ss_pred             HHhcCCCeEEEEEecCccccc
Q psy200          292 YFDTKHKSILLILDEIDALES  312 (490)
Q Consensus       292 ~l~~~~~~~vI~IDEid~l~~  312 (490)
                      .+.. ..+.+||||.+..+..
T Consensus       134 l~~~-~~~dlvVIDSi~~l~~  153 (356)
T 3hr8_A          134 LVRS-GVVDLIVVDSVAALVP  153 (356)
T ss_dssp             HHHT-SCCSEEEEECTTTCCC
T ss_pred             Hhhh-cCCCeEEehHhhhhcC
Confidence            4443 4567999999998874

>1w4r_A Thymidine kinase; type II, human, cytosolic, phosphorylation, transferase; HET: TTP; 1.83A {Homo sapiens} PDB: 1xbt_A* 2wvj_A* 2j87_A*

Probab=97.68  E-value=2.3e-05  Score=70.05  Aligned_cols=107  Identities=15%  Similarity=0.109  Sum_probs=58.5

Q ss_pred             CCCCeEEEECCCCCcHH-HHHHHHHHHhhhcCCceEEEEeccCC-CCHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHh
Q psy200          217 ETSGSMYISGPPGTGKS-ASLNLLVSRAEIKDAFKTIYINCNSV-RNAASVYETIVNELKLKPGGKSERHQLGAILKYFD  294 (490)
Q Consensus       217 ~~~~~ill~GppGtGKT-tla~~l~~~l~~~~~~~~~~v~~~~~-~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~  294 (490)
                      ..+...+|||+.|+||| .|++++.+...  .+..++++...-. +....+...+-........ ....++.+.    ..
T Consensus        18 ~~g~l~fiyG~MgsGKTt~Ll~~i~n~~~--~~~kvl~~kp~~D~R~~~~i~S~~g~~~~A~~~-~~~~d~~~~----~~   90 (195)
T 1w4r_A           18 TRGQIQVILGPMFSGKSTELMRRVRRFQI--AQYKCLVIKYAKDTRYSSSFCTHDRNTMEALPA-CLLRDVAQE----AL   90 (195)
T ss_dssp             -CCEEEEEEECTTSCHHHHHHHHHHHHHH--TTCCEEEEEETTCCCGGGSCCHHHHHHSEEEEE-SSGGGGHHH----HH
T ss_pred             CceEEEEEECCCCCcHHHHHHHHHHHHHH--cCCeEEEEccccCccchhhhhhccCCcccceec-CCHHHHHHh----cc
Confidence            35678999999999999 88888877654  3456666653311 1112233333222111000 112223322    21


Q ss_pred             cCCCeEEEEEecCccccccCHHH-HHHhHhCCCCCCCcEEEEEecC
Q psy200          295 TKHKSILLILDEIDALESRKQTI-LYTIFEWPSIPGSKLVLVGVAN  339 (490)
Q Consensus       295 ~~~~~~vI~IDEid~l~~~~~~~-L~~l~~~~~~~~~~vilI~~tn  339 (490)
                         ..-+|+|||+|.+ .. +.. +..+.+    .+.+|++.|...
T Consensus        91 ---~~DvIlIDEaQFf-k~-~ve~~~~L~~----~gk~VI~~GL~~  127 (195)
T 1w4r_A           91 ---GVAVIGIDEGQFF-PD-IVEFCEAMAN----AGKTVIVAALDG  127 (195)
T ss_dssp             ---TCSEEEESSGGGC-TT-HHHHHHHHHH----TTCEEEEEEESB
T ss_pred             ---CCCEEEEEchhhh-HH-HHHHHHHHHH----CCCeEEEEeccc
Confidence               1349999999999 43 433 333332    455777766654

>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=97.68  E-value=0.00023  Score=70.17  Aligned_cols=94  Identities=20%  Similarity=0.205  Sum_probs=58.6

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhc-----CCceEEEEeccCCCCHHHHHHHHHHHhcCC-------------CCC
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIK-----DAFKTIYINCNSVRNAASVYETIVNELKLK-------------PGG  279 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~-----~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~-------------~~~  279 (490)
                      .+..++|+|++|+|||+++..++......     .+..++|++.....+...+.. ++..++..             ...
T Consensus       121 ~G~i~~I~G~~GsGKTtla~~la~~~~~~~~~gg~~~~vlyi~~E~~~~~~~l~~-~~~~~g~~~~~~l~~l~~~~~~~~  199 (343)
T 1v5w_A          121 SMAITEAFGEFRTGKTQLSHTLCVTAQLPGAGGYPGGKIIFIDTENTFRPDRLRD-IADRFNVDHDAVLDNVLYARAYTS  199 (343)
T ss_dssp             SSEEEEEECCTTCTHHHHHHHHHHHTTSCBTTTBCCCEEEEEESSSCCCHHHHHH-HHHHTTCCHHHHHHTEEEEECCST
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHhcccccCCCCCeEEEEECCCCCCHHHHHH-HHHHcCCCHHHHHhceeEeecCCH
Confidence            45678999999999999999999875321     245788998766444444432 23333321             111


Q ss_pred             CcHHHHHHHHHHHHhcC-CCeEEEEEecCccccc
Q psy200          280 KSERHQLGAILKYFDTK-HKSILLILDEIDALES  312 (490)
Q Consensus       280 ~s~~~~~~~l~~~l~~~-~~~~vI~IDEid~l~~  312 (490)
                      ....++...+...+... .+..+||||.+..+..
T Consensus       200 e~~~~ll~~l~~~i~~~~~~~~lvVIDsl~~l~~  233 (343)
T 1v5w_A          200 EHQMELLDYVAAKFHEEAGIFKLLIIDSIMALFR  233 (343)
T ss_dssp             THHHHHHHHHHHHHHHSCSSEEEEEEETSGGGHH
T ss_pred             HHHHHHHHHHHHHHHhcCCCccEEEEechHHHHH
Confidence            22223333444444442 5678999999998863

>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=97.66  E-value=0.00047  Score=68.35  Aligned_cols=88  Identities=17%  Similarity=0.246  Sum_probs=58.7

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCCC------CCCcHHHHHHHHHH
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKP------GGKSERHQLGAILK  291 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~------~~~s~~~~~~~l~~  291 (490)
                      .+..++|+|+||+|||+++..++..+.. .+..++|++.......  ++   +..++...      ...+.+++.+.+..
T Consensus        73 ~G~li~I~G~pGsGKTtlal~la~~~~~-~g~~vlyi~~E~s~~~--~~---a~~~g~d~~~l~i~~~~~~e~~l~~l~~  146 (366)
T 1xp8_A           73 RGRITEIYGPESGGKTTLALAIVAQAQK-AGGTCAFIDAEHALDP--VY---ARALGVNTDELLVSQPDNGEQALEIMEL  146 (366)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHHHH-TTCCEEEEESSCCCCH--HH---HHHTTCCGGGCEEECCSSHHHHHHHHHH
T ss_pred             CCcEEEEEcCCCCChHHHHHHHHHHHHH-CCCeEEEEECCCChhH--HH---HHHcCCCHHHceeecCCcHHHHHHHHHH
Confidence            5678999999999999999999887643 2357888887654332  21   33333221      11345666666655


Q ss_pred             HHhcCCCeEEEEEecCccccc
Q psy200          292 YFDTKHKSILLILDEIDALES  312 (490)
Q Consensus       292 ~l~~~~~~~vI~IDEid~l~~  312 (490)
                      .... +...+||||.+..+..
T Consensus       147 l~~~-~~~~lVVIDsl~~l~~  166 (366)
T 1xp8_A          147 LVRS-GAIDVVVVDSVAALTP  166 (366)
T ss_dssp             HHTT-TCCSEEEEECTTTCCC
T ss_pred             HHhc-CCCCEEEEeChHHhcc
Confidence            5443 4567999999999873

>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=97.64  E-value=0.00017  Score=71.15  Aligned_cols=87  Identities=15%  Similarity=0.200  Sum_probs=57.0

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCCC------CCCcHHHHHHHHHH
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKP------GGKSERHQLGAILK  291 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~------~~~s~~~~~~~l~~  291 (490)
                      .+..++|+|++|+|||||+..++..+.. .+..++|++........     ....++...      ...+..++.+.+..
T Consensus        60 ~G~iv~I~G~pGsGKTtLal~la~~~~~-~g~~vlyi~~E~~~~~~-----~a~~lG~~~~~l~i~~~~~~e~~l~~~~~  133 (349)
T 2zr9_A           60 RGRVIEIYGPESSGKTTVALHAVANAQA-AGGIAAFIDAEHALDPE-----YAKKLGVDTDSLLVSQPDTGEQALEIADM  133 (349)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHHHH-TTCCEEEEESSCCCCHH-----HHHHTTCCGGGCEEECCSSHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHh-CCCeEEEEECCCCcCHH-----HHHHcCCCHHHeEEecCCCHHHHHHHHHH
Confidence            5678999999999999999999877642 34467888766543322     233343221      11235555555544


Q ss_pred             HHhcCCCeEEEEEecCcccc
Q psy200          292 YFDTKHKSILLILDEIDALE  311 (490)
Q Consensus       292 ~l~~~~~~~vI~IDEid~l~  311 (490)
                      ... ..++.+||||++..+.
T Consensus       134 l~~-~~~~~lIVIDsl~~l~  152 (349)
T 2zr9_A          134 LVR-SGALDIIVIDSVAALV  152 (349)
T ss_dssp             HHT-TTCCSEEEEECGGGCC
T ss_pred             HHh-cCCCCEEEEcChHhhc
Confidence            443 3457799999999987

>3e1s_A Exodeoxyribonuclease V, subunit RECD; alpha and beta protein, ATP-binding, nucleotide-binding, HYD; 2.20A {Deinococcus radiodurans} PDB: 3gp8_A 3gpl_A*

Probab=97.64  E-value=0.00022  Score=75.22  Aligned_cols=109  Identities=20%  Similarity=0.294  Sum_probs=58.7

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCCCCCCcHHHHHHH----HHHHHh
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKPGGKSERHQLGA----ILKYFD  294 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~~~s~~~~~~~----l~~~l~  294 (490)
                      .+.++|+|+||||||+++..++..+.. .+..++.+ ++.....    ..+...++..  ..+...+...    +.....
T Consensus       204 ~~~~~I~G~pGTGKTt~i~~l~~~l~~-~g~~Vl~~-ApT~~Aa----~~L~e~~~~~--a~Tih~ll~~~~~~~~~~~~  275 (574)
T 3e1s_A          204 HRLVVLTGGPGTGKSTTTKAVADLAES-LGLEVGLC-APTGKAA----RRLGEVTGRT--ASTVHRLLGYGPQGFRHNHL  275 (574)
T ss_dssp             CSEEEEECCTTSCHHHHHHHHHHHHHH-TTCCEEEE-ESSHHHH----HHHHHHHTSC--EEEHHHHTTEETTEESCSSS
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHHHHh-cCCeEEEe-cCcHHHH----HHhHhhhccc--HHHHHHHHcCCcchhhhhhc
Confidence            578999999999999999999987753 23444433 3322111    1222222111  0111111100    000000


Q ss_pred             cCCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEEEecC
Q psy200          295 TKHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVAN  339 (490)
Q Consensus       295 ~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI~~tn  339 (490)
                      .....-+|||||++.+..   ..+..++.... .+.+++++|-.+
T Consensus       276 ~~~~~dvlIIDEasml~~---~~~~~Ll~~~~-~~~~lilvGD~~  316 (574)
T 3e1s_A          276 EPAPYDLLIVDEVSMMGD---ALMLSLLAAVP-PGARVLLVGDTD  316 (574)
T ss_dssp             SCCSCSEEEECCGGGCCH---HHHHHHHTTSC-TTCEEEEEECTT
T ss_pred             ccccCCEEEEcCccCCCH---HHHHHHHHhCc-CCCEEEEEeccc
Confidence            112345999999999864   34444554332 567889988775

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=97.62  E-value=0.00015  Score=85.46  Aligned_cols=88  Identities=14%  Similarity=0.194  Sum_probs=57.7

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCCC------CCCcHHHHHHHHHH
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKP------GGKSERHQLGAILK  291 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~------~~~s~~~~~~~l~~  291 (490)
                      .+.+++|+||||||||+||.+++.+... .+..++|+++........     +..++.+.      .-...+++...+..
T Consensus      1426 ~g~~vll~GppGtGKT~LA~ala~ea~~-~G~~v~Fi~~e~~~~~l~-----a~~~G~dl~~l~v~~~~~~E~~l~~~~~ 1499 (2050)
T 3cmu_A         1426 MGRIVEIYGPESSGKTTLTLQVIAAAQR-EGKTCAFIDAEHALDPIY-----ARKLGVDIDNLLCSQPDTGEQALEICDA 1499 (2050)
T ss_dssp             TTSEEEEECCTTSSHHHHHHHHHHHHHT-TTCCEEEECTTSCCCHHH-----HHHTTCCTTTCEEECCSSHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHH-cCCcEEEEEcccccCHHH-----HHHcCCCchhceeecCChHHHHHHHHHH
Confidence            5679999999999999999999887652 345788887766544333     33333210      01123344444444


Q ss_pred             HHhcCCCeEEEEEecCccccc
Q psy200          292 YFDTKHKSILLILDEIDALES  312 (490)
Q Consensus       292 ~l~~~~~~~vI~IDEid~l~~  312 (490)
                      ..+. .++.+|||||++.+..
T Consensus      1500 lvr~-~~~~lVVIDsi~al~p 1519 (2050)
T 3cmu_A         1500 LARS-GAVDVIVVDSVAALTP 1519 (2050)
T ss_dssp             HHHH-TCCSEEEESCGGGCCC
T ss_pred             HHhc-CCCCEEEEcChhHhcc
Confidence            4433 5688999999987654

>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=97.61  E-value=0.00095  Score=67.47  Aligned_cols=237  Identities=14%  Similarity=0.125  Sum_probs=111.1

Q ss_pred             hHHHHHHHHHHHHhhhcc---------CCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCC-HHHHHHH
Q psy200          199 REVQLEGIRQFLLGHVNN---------ETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRN-AASVYET  268 (490)
Q Consensus       199 re~~~~~l~~~L~~~~~~---------~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~-~~~l~~~  268 (490)
                      .+..++.+.+.|...+..         ..+..++|+|++|+||||++..++..+.. .+..+..++|..... ..+.+..
T Consensus        68 ~~~v~~~v~~eL~~~L~~~~~~~~~~~~~~~vI~lvG~~GsGKTTt~~kLA~~l~~-~G~kVllv~~D~~r~~a~eqL~~  146 (433)
T 3kl4_A           68 KEWFISIVYDELSKLFGGDKEPNVNPTKLPFIIMLVGVQGSGKTTTAGKLAYFYKK-RGYKVGLVAADVYRPAAYDQLLQ  146 (433)
T ss_dssp             HHHHHHHHHHHHHHHHCSSSCCCCSCCSSSEEEEECCCTTSCHHHHHHHHHHHHHH-TTCCEEEEEECCSCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhcCccccccccccCCCeEEEEECCCCCCHHHHHHHHHHHHHH-cCCeEEEEecCccchhHHHHHHH
Confidence            344445555555543332         13568889999999999999999998863 355677777665532 2223334


Q ss_pred             HHHHhcCCC----CCCcHHHHH-HHHHHHHhcCCCeEEEEEecCcccc--ccC--HHHHHHhHhCCCCCCCcEEEEEec-
Q psy200          269 IVNELKLKP----GGKSERHQL-GAILKYFDTKHKSILLILDEIDALE--SRK--QTILYTIFEWPSIPGSKLVLVGVA-  338 (490)
Q Consensus       269 i~~~l~~~~----~~~s~~~~~-~~l~~~l~~~~~~~vI~IDEid~l~--~~~--~~~L~~l~~~~~~~~~~vilI~~t-  338 (490)
                      +...++.+.    .+.....+. ..+..+..  ...-+||||....+.  ...  ...+..+....  ....++++..+ 
T Consensus       147 ~~~~~gv~~~~~~~~~dp~~i~~~al~~a~~--~~~DvvIIDTaGr~~~~~d~~lm~el~~i~~~~--~pd~vlLVlDa~  222 (433)
T 3kl4_A          147 LGNQIGVQVYGEPNNQNPIEIAKKGVDIFVK--NKMDIIIVDTAGRHGYGEETKLLEEMKEMYDVL--KPDDVILVIDAS  222 (433)
T ss_dssp             HHHTTTCCEECCTTCSCHHHHHHHHHHHTTT--TTCSEEEEEECCCSSSCCTTHHHHHHHHHHHHH--CCSEEEEEEEGG
T ss_pred             HHHhcCCceeeccccCCHHHHHHHHHHHHHh--cCCCEEEEECCCCccccCCHHHHHHHHHHHHhh--CCcceEEEEeCc
Confidence            444444321    112222222 22222221  245699999998765  222  12222222221  12244444333 


Q ss_pred             CCCChhHhhhHHhhhccCCCCeeEEeCCCCHH----HHHHHHHHHHhcc------CCC----CCCCHH-HHHHHHHHHHH
Q psy200          339 NALDLTDRMLPRLQANVTLQPTLMNFAPYSRE----QILEIISQKLKQT------DKF----NMFNAS-ALQLLAGKVAA  403 (490)
Q Consensus       339 n~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~----e~~~il~~~l~~~------~~~----~~~~~~-~i~~i~~~i~~  403 (490)
                      +..+.. .+...+...+..  ..+.+..++.+    ....+... ...-      +..    ..+.++ .+..|.     
T Consensus       223 ~gq~a~-~~a~~f~~~~~~--~gVIlTKlD~~a~~G~als~~~~-~g~Pi~fig~Ge~v~dL~~f~p~~~~~~ll-----  293 (433)
T 3kl4_A          223 IGQKAY-DLASRFHQASPI--GSVIITKMDGTAKGGGALSAVVA-TGATIKFIGTGEKIDELETFNAKRFVSRIL-----  293 (433)
T ss_dssp             GGGGGH-HHHHHHHHHCSS--EEEEEECGGGCSCHHHHHHHHHH-HTCEEEEEECCSSSSCEEECCHHHHHHHHH-----
T ss_pred             cchHHH-HHHHHHhcccCC--cEEEEecccccccchHHHHHHHH-HCCCEEEEECCCChHhCccCCHHHHHHHhc-----
Confidence            221211 222334433332  45777777642    23333332 1110      111    123442 223332     


Q ss_pred             hhCCHHHHHHHHHHHHHHHHhccc-cCCccc--ccCHHHHHHHHHHhcc
Q psy200          404 VSGDIRKAIDITNHLIDLTYDNVK-ENGEVT--GIGLKEVLGVISSVYC  449 (490)
Q Consensus       404 ~~Gd~r~ai~ll~~a~~~a~~~~~-~~~~~~--~It~~~v~~a~~~~~~  449 (490)
                      ..||+-.++.-++.++.....+.. +.....  ..+.+|+...+..+..
T Consensus       294 g~gd~~~l~e~~~~~~~~~~~~~~~~k~~~g~~~f~~~d~~~q~~~~~k  342 (433)
T 3kl4_A          294 GMGDIESILEKVKGLEEYDKIQKKMEDVMEGKGKLTLRDVYAQIIALRK  342 (433)
T ss_dssp             CSSHHHHHHHHHHHC-------------------CCHHHHHHHHHHHHH
T ss_pred             CCchHHHHHHHHHHhhhHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHh
Confidence            357777666555444322210000 000123  7999999998888753

>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=97.60  E-value=0.0033  Score=63.53  Aligned_cols=233  Identities=12%  Similarity=0.116  Sum_probs=116.4

Q ss_pred             HHHHHHHHHHHHhhhcc--------CCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCH-HHHHHHHH
Q psy200          200 EVQLEGIRQFLLGHVNN--------ETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNA-ASVYETIV  270 (490)
Q Consensus       200 e~~~~~l~~~L~~~~~~--------~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~-~~l~~~i~  270 (490)
                      +..++.|.+.|...+..        ..+..++|+|++|+||||++..++..+.. .+..++.+.|...... .+.+..+.
T Consensus        73 ~~v~~~l~~eL~~~L~~~~~~~~~~~~p~vIlivG~~G~GKTTt~~kLA~~l~~-~G~kVllv~~D~~R~aa~eqL~~~~  151 (443)
T 3dm5_A           73 EHIIKIVYEELTKFLGTEAKPIEIKEKPTILLMVGIQGSGKTTTVAKLARYFQK-RGYKVGVVCSDTWRPGAYHQLRQLL  151 (443)
T ss_dssp             HHHHHHHHHHHHHHTTSSCCCCCCCSSSEEEEEECCTTSSHHHHHHHHHHHHHT-TTCCEEEEECCCSSTHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhcCcccccccCCCCeEEEEECcCCCCHHHHHHHHHHHHHH-CCCeEEEEeCCCcchhHHHHHHHHH
Confidence            44445555555544321        23568899999999999999999998863 3567777877766543 23333444


Q ss_pred             HHhcCC----CCCCcHHHH-HHHHHHHHhcCCCeEEEEEecCccccccC--HHHHHHhHhCCCCCCCcEEEEE-ecCCCC
Q psy200          271 NELKLK----PGGKSERHQ-LGAILKYFDTKHKSILLILDEIDALESRK--QTILYTIFEWPSIPGSKLVLVG-VANALD  342 (490)
Q Consensus       271 ~~l~~~----~~~~s~~~~-~~~l~~~l~~~~~~~vI~IDEid~l~~~~--~~~L~~l~~~~~~~~~~vilI~-~tn~~~  342 (490)
                      ...+.+    ..+.....+ .+.+..+..  ...-+||||....+....  ...+..+..... . ..+++|. ++...+
T Consensus       152 ~~~gvpv~~~~~~~dp~~i~~~al~~a~~--~~~DvVIIDTaGrl~~d~~lm~el~~i~~~~~-p-d~vlLVvDA~~gq~  227 (443)
T 3dm5_A          152 DRYHIEVFGNPQEKDAIKLAKEGVDYFKS--KGVDIIIVDTAGRHKEDKALIEEMKQISNVIH-P-HEVILVIDGTIGQQ  227 (443)
T ss_dssp             GGGTCEEECCTTCCCHHHHHHHHHHHHHH--TTCSEEEEECCCCSSCCHHHHHHHHHHHHHHC-C-SEEEEEEEGGGGGG
T ss_pred             HhcCCcEEecCCCCCHHHHHHHHHHHHHh--CCCCEEEEECCCcccchHHHHHHHHHHHHhhc-C-ceEEEEEeCCCchh
Confidence            444331    122233333 344444333  224599999998765331  112222222111 2 2344443 332222


Q ss_pred             hhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhcc---------CC----CCCCCHHHHHHHHHHHHHhhCCHH
Q psy200          343 LTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQT---------DK----FNMFNASALQLLAGKVAAVSGDIR  409 (490)
Q Consensus       343 ~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~---------~~----~~~~~~~~i~~i~~~i~~~~Gd~r  409 (490)
                      ... ....+...+.+  ..+.++.++.......+.......         +.    -..|+++   .++..+ -.-||+-
T Consensus       228 a~~-~a~~f~~~~~i--~gVIlTKlD~~~~gG~~ls~~~~~g~PI~fig~Ge~vddL~~f~~~---~~~~~l-lg~gd~~  300 (443)
T 3dm5_A          228 AYN-QALAFKEATPI--GSIIVTKLDGSAKGGGALSAVAATGAPIKFIGTGEKIDDIEPFDPP---RFVSRL-LGLGDIQ  300 (443)
T ss_dssp             HHH-HHHHHHHSCTT--EEEEEECCSSCSSHHHHHHHHHTTCCCEEEEECSSSTTCEEECCHH---HHHHHH-TTTTCHH
T ss_pred             HHH-HHHHHHhhCCC--eEEEEECCCCcccccHHHHHHHHHCCCEEEEEcCCChHHhhhCCHH---HHHHHH-cCCCcHH
Confidence            111 12334333332  357777776432222222221111         11    1123443   222211 2468888


Q ss_pred             HHHHHHHHHHH-------HHHhccccCCcccccCHHHHHHHHHHhcc
Q psy200          410 KAIDITNHLID-------LTYDNVKENGEVTGIGLKEVLGVISSVYC  449 (490)
Q Consensus       410 ~ai~ll~~a~~-------~a~~~~~~~~~~~~It~~~v~~a~~~~~~  449 (490)
                      .++.-.+.++.       ++..-.     ....|.+|+..-+..+..
T Consensus       301 ~l~e~~~~~~~~~~~~~~~~~k~~-----~~~f~l~d~~~q~~~~~k  342 (443)
T 3dm5_A          301 GLLEKFKELEKEVEIKEEDIERFL-----RGKFTLKDMYAQLEAMRK  342 (443)
T ss_dssp             HHHHHHHHHHTTHHHHHHHHHHHH-----TTCCCHHHHHHHHHHHHT
T ss_pred             HHHHHHHHhhhhhHHHHHHHHHHh-----hCCcCHHHHHHHHHHHHh
Confidence            77765544432       221111     346999999998888654

>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=97.58  E-value=0.00031  Score=67.60  Aligned_cols=40  Identities=13%  Similarity=0.013  Sum_probs=30.9

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEec
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINC  256 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~  256 (490)
                      ..+..++|.|++|+|||||++.++..+....+..+++++.
T Consensus        33 ~~G~~~~i~G~~G~GKTTl~~~ia~~~~~~~G~~v~~~~~   72 (296)
T 1cr0_A           33 RGGEVIMVTSGSGMGKSTFVRQQALQWGTAMGKKVGLAML   72 (296)
T ss_dssp             CTTCEEEEEESTTSSHHHHHHHHHHHHHHTSCCCEEEEES
T ss_pred             CCCeEEEEEeCCCCCHHHHHHHHHHHHHHHcCCeEEEEeC
Confidence            4567899999999999999999998876443435566654

>2r6a_A DNAB helicase, replicative helicase; replication, DNAB; 2.90A {Geobacillus stearothermophilus} PDB: 2r6c_A 2r6d_A 2r6e_A 2vyf_A 2vye_A

Probab=97.58  E-value=0.00045  Score=70.82  Aligned_cols=92  Identities=9%  Similarity=0.086  Sum_probs=59.2

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHH-hcC---------------------
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNE-LKL---------------------  275 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~-l~~---------------------  275 (490)
                      .+..++|.|+||+|||+++..++..+....+..+++++...  +...+...+... ++.                     
T Consensus       202 ~G~liiI~G~pG~GKTtl~l~ia~~~~~~~g~~Vl~~s~E~--s~~~l~~r~~~~~~~~~~~~l~~g~l~~~~~~~~~~a  279 (454)
T 2r6a_A          202 RSDLIIVAARPSVGKTAFALNIAQNVATKTNENVAIFSLEM--SAQQLVMRMLCAEGNINAQNLRTGKLTPEDWGKLTMA  279 (454)
T ss_dssp             TTCEEEEECCTTSCHHHHHHHHHHHHHHHSSCCEEEEESSS--CHHHHHHHHHHHHHTCCHHHHHTSCCCHHHHHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHHHHhCCCcEEEEECCC--CHHHHHHHHHHHHcCCCHHHHhcCCCCHHHHHHHHHH
Confidence            55689999999999999999999887643445677776432  344444443211 110                     


Q ss_pred             ------------CCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccc
Q psy200          276 ------------KPGGKSERHQLGAILKYFDTKHKSILLILDEIDALES  312 (490)
Q Consensus       276 ------------~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~  312 (490)
                                  ...+.+..++...+...... .++-+||||+++.+..
T Consensus       280 ~~~l~~~~l~i~d~~~~s~~~i~~~~~~l~~~-~~~~livID~l~~~~~  327 (454)
T 2r6a_A          280 MGSLSNAGIYIDDTPSIRVSDIRAKCRRLKQE-SGLGMIVIDYLQLIQG  327 (454)
T ss_dssp             HHHHHSSCEEEECCTTCCHHHHHHHHHHHHTT-TCCCEEEEECGGGSCC
T ss_pred             HHHHhcCCEEEECCCCCCHHHHHHHHHHHHHH-cCCCEEEEccHHHhcc
Confidence                        11123556666555554433 3477999999999874

>2dr3_A UPF0273 protein PH0284; RECA superfamily ATPase, hexamer, structural genomics; HET: ADP; 2.00A {Pyrococcus horikoshii}

Probab=97.54  E-value=0.00063  Score=63.11  Aligned_cols=89  Identities=15%  Similarity=0.212  Sum_probs=54.2

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCC----------------C----
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLK----------------P----  277 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~----------------~----  277 (490)
                      .+..++|+|++|+|||+++..++..+.. .+..++|++...  +...+...+. .++..                +    
T Consensus        22 ~G~~~~i~G~~GsGKTtl~~~~~~~~~~-~~~~v~~~~~e~--~~~~~~~~~~-~~g~~~~~~~~~~~l~~~~~~~~~~~   97 (247)
T 2dr3_A           22 ERNVVLLSGGPGTGKTIFSQQFLWNGLK-MGEPGIYVALEE--HPVQVRQNMA-QFGWDVKPYEEKGMFAMVDAFTAGIG   97 (247)
T ss_dssp             TTCEEEEEECTTSSHHHHHHHHHHHHHH-TTCCEEEEESSS--CHHHHHHHHH-TTTCCCHHHHHHTSEEEEECSTTTTC
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHHh-cCCeEEEEEccC--CHHHHHHHHH-HcCCCHHHHhhCCcEEEEecchhhcc
Confidence            4668999999999999998888776542 344677776543  3344433321 11110                0    


Q ss_pred             -----------CCCcHHHHHHHHHHHHhcCCCeEEEEEecCcccc
Q psy200          278 -----------GGKSERHQLGAILKYFDTKHKSILLILDEIDALE  311 (490)
Q Consensus       278 -----------~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~  311 (490)
                                 ...+..++...+.+.+.. .++.+|+||++..+.
T Consensus        98 ~~~~~~~~~~~~~~~~~~~~~~i~~~~~~-~~~~~vviD~~~~l~  141 (247)
T 2dr3_A           98 KSKEYEKYIVHDLTDIREFIEVLRQAIRD-INAKRVVVDSVTTLY  141 (247)
T ss_dssp             C--CCCSCBCSCCSSHHHHHHHHHHHHHH-HTCCEEEEETSGGGT
T ss_pred             cccccccccccCccCHHHHHHHHHHHHHH-hCCCEEEECCchHhh
Confidence                       012334445555555543 235699999999986

>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=97.54  E-value=0.0003  Score=70.57  Aligned_cols=93  Identities=24%  Similarity=0.300  Sum_probs=54.6

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhc-----CCceEEEEeccCCCCHHHHHHHHHHHhcCCC----------CCCcH
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIK-----DAFKTIYINCNSVRNAASVYETIVNELKLKP----------GGKSE  282 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~-----~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~----------~~~s~  282 (490)
                      .+..+.|+|++|+|||||+..++-.....     ....++|++.........+ ..+...++...          .....
T Consensus       177 ~Gei~~I~G~sGsGKTTLl~~la~~~~~p~~~Gg~~~~viyid~E~~~~~~rl-~~~a~~~gl~~~~vleni~~~~~~~~  255 (400)
T 3lda_A          177 TGSITELFGEFRTGKSQLCHTLAVTCQIPLDIGGGEGKCLYIDTEGTFRPVRL-VSIAQRFGLDPDDALNNVAYARAYNA  255 (400)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSSEEEEEESSSCCCHHHH-HHHHHHTTCCHHHHHHTEEEEECCSH
T ss_pred             CCcEEEEEcCCCCChHHHHHHHHHHhccCcccCCCCCcEEEEeCCCccCHHHH-HHHHHHcCCChHhHhhcEEEeccCCh
Confidence            56789999999999999999876444321     1346888887654333332 23444443210          01122


Q ss_pred             HHH---HHHHHHHHhcCCCeEEEEEecCccccc
Q psy200          283 RHQ---LGAILKYFDTKHKSILLILDEIDALES  312 (490)
Q Consensus       283 ~~~---~~~l~~~l~~~~~~~vI~IDEid~l~~  312 (490)
                      ...   ...+...+.. .++.+|+||++..+..
T Consensus       256 ~~~~~~l~~~~~~l~~-~~~~llVIDs~t~~~~  287 (400)
T 3lda_A          256 DHQLRLLDAAAQMMSE-SRFSLIVVDSVMALYR  287 (400)
T ss_dssp             HHHHHHHHHHHHHHHH-SCEEEEEEETGGGGCC
T ss_pred             HHHHHHHHHHHHHHHh-cCCceEEecchhhhCc
Confidence            222   2222333333 4688999999988764

>2q6t_A DNAB replication FORK helicase; hydrolase; 2.90A {Thermus aquaticus}

Probab=97.52  E-value=0.00069  Score=69.21  Aligned_cols=93  Identities=13%  Similarity=0.117  Sum_probs=61.3

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhc-C---------------------
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELK-L---------------------  275 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~-~---------------------  275 (490)
                      .+..++|.|+||+|||+++..++.......+.+++|++.-.  +...+...++.... .                     
T Consensus       199 ~G~l~ii~G~pg~GKT~lal~ia~~~a~~~g~~vl~~slE~--~~~~l~~R~~~~~~~i~~~~l~~g~l~~~~~~~~~~a  276 (444)
T 2q6t_A          199 PGSLNIIAARPAMGKTAFALTIAQNAALKEGVGVGIYSLEM--PAAQLTLRMMCSEARIDMNRVRLGQLTDRDFSRLVDV  276 (444)
T ss_dssp             TTCEEEEEECTTSCHHHHHHHHHHHHHHTTCCCEEEEESSS--CHHHHHHHHHHHHTTCCTTTCCGGGCCHHHHHHHHHH
T ss_pred             CCcEEEEEeCCCCCHHHHHHHHHHHHHHhCCCeEEEEECCC--CHHHHHHHHHHHHcCCCHHHHhCCCCCHHHHHHHHHH
Confidence            56689999999999999999999887644455777776532  45555555432211 0                     


Q ss_pred             ------------CCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCcccccc
Q psy200          276 ------------KPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESR  313 (490)
Q Consensus       276 ------------~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~  313 (490)
                                  ...+.+..++...+.+..... ++-+||||.++.+...
T Consensus       277 ~~~l~~~~l~i~d~~~~s~~~l~~~~~~l~~~~-~~~lIvID~l~~~~~~  325 (444)
T 2q6t_A          277 ASRLSEAPIYIDDTPDLTLMEVRARARRLVSQN-QVGLIIIDYLQLMSGP  325 (444)
T ss_dssp             HHHHHTSCEEEECCTTCBHHHHHHHHHHHHHHS-CCCEEEEECGGGCBCC
T ss_pred             HHHHhcCCEEEECCCCCCHHHHHHHHHHHHHHc-CCCEEEEcChhhcCCC
Confidence                        112235566666666555443 4679999999998643

>2fz4_A DNA repair protein RAD25; RECA-like domain, DNA damage recognition domain, DNA binding; HET: DNA; 2.40A {Archaeoglobus fulgidus} SCOP: c.37.1.19

Probab=97.50  E-value=0.00094  Score=62.05  Aligned_cols=103  Identities=18%  Similarity=0.261  Sum_probs=55.6

Q ss_pred             CChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcC-
Q psy200          197 PGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKL-  275 (490)
Q Consensus       197 vgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~-  275 (490)
                      .-+..+.+.+..++.       .+.++|+||+|+|||.++..++..+.    ..++++. +.    ..+..++...+.. 
T Consensus        93 ~l~~~Q~~ai~~~~~-------~~~~ll~~~tG~GKT~~a~~~~~~~~----~~~liv~-P~----~~L~~q~~~~~~~~  156 (237)
T 2fz4_A           93 SLRDYQEKALERWLV-------DKRGCIVLPTGSGKTHVAMAAINELS----TPTLIVV-PT----LALAEQWKERLGIF  156 (237)
T ss_dssp             CCCHHHHHHHHHHTT-------TSEEEEEESSSTTHHHHHHHHHHHSC----SCEEEEE-SS----HHHHHHHHHHHGGG
T ss_pred             CcCHHHHHHHHHHHh-------CCCEEEEeCCCCCHHHHHHHHHHHcC----CCEEEEe-CC----HHHHHHHHHHHHhC
Confidence            334455555555442       23589999999999999998887752    3444442 21    2233333333221 


Q ss_pred             --C-C---CC----------CcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCHHHH
Q psy200          276 --K-P---GG----------KSERHQLGAILKYFDTKHKSILLILDEIDALESRKQTIL  318 (490)
Q Consensus       276 --~-~---~~----------~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L  318 (490)
                        . .   .+          .+.+.+...+.. +.  .+..+|||||+|.+.......+
T Consensus       157 ~~~~v~~~~g~~~~~~~i~v~T~~~l~~~~~~-~~--~~~~llIiDEaH~l~~~~~~~i  212 (237)
T 2fz4_A          157 GEEYVGEFSGRIKELKPLTVSTYDSAYVNAEK-LG--NRFMLLIFDEVHHLPAESYVQI  212 (237)
T ss_dssp             CGGGEEEESSSCBCCCSEEEEEHHHHHHTHHH-HT--TTCSEEEEECSSCCCTTTHHHH
T ss_pred             CCCeEEEEeCCCCCcCCEEEEeHHHHHhhHHH-hc--ccCCEEEEECCccCCChHHHHH
Confidence              1 0   00          012233322221 21  2355999999999976654443

>4a1f_A DNAB helicase, replicative DNA helicase; hydrolase, DNA replication, ATPase; HET: FLC; 2.50A {Helicobacter pylori}

Probab=97.45  E-value=0.00088  Score=65.50  Aligned_cols=121  Identities=12%  Similarity=0.054  Sum_probs=75.9

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhc----------------------
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELK----------------------  274 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~----------------------  274 (490)
                      .++..++|.|+||+|||+++..++..+.. .+..+++++.-  .+..++...++....                      
T Consensus        44 ~~G~LiiIaG~pG~GKTt~al~ia~~~a~-~g~~Vl~fSlE--ms~~ql~~Rlls~~~~v~~~~l~~g~Ls~~e~~~l~~  120 (338)
T 4a1f_A           44 NKGSLVIIGARPSMGKTSLMMNMVLSALN-DDRGVAVFSLE--MSAEQLALRALSDLTSINMHDLESGRLDDDQWENLAK  120 (338)
T ss_dssp             CTTCEEEEEECTTSCHHHHHHHHHHHHHH-TTCEEEEEESS--SCHHHHHHHHHHHHHCCCHHHHHHTCCCHHHHHHHHH
T ss_pred             CCCcEEEEEeCCCCCHHHHHHHHHHHHHH-cCCeEEEEeCC--CCHHHHHHHHHHHhhCCCHHHHhcCCCCHHHHHHHHH
Confidence            35678999999999999999999988754 44567777543  255555555433210                      


Q ss_pred             ------------CCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccC---------HHHHHHhHhCCCCCCCcEE
Q psy200          275 ------------LKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRK---------QTILYTIFEWPSIPGSKLV  333 (490)
Q Consensus       275 ------------~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~---------~~~L~~l~~~~~~~~~~vi  333 (490)
                                  ....+.+..++...+.......++.-+||||-++.|....         .+....|..+....+..|+
T Consensus       121 a~~~l~~~~l~I~d~~~~si~~i~~~ir~l~~~~gg~~lIVIDyLqlm~~~~~~~~r~~ei~~isr~LK~lAkel~vpVi  200 (338)
T 4a1f_A          121 CFDHLSQKKLFFYDKSYVRIEQIRLQLRKLKSQHKELGIAFIDYLQLMSGSKATKERHEQIAEISRELKTLARELEIPII  200 (338)
T ss_dssp             HHHHHHHSCEEEECCTTCCHHHHHHHHHHHHHHCTTEEEEEEEEEECCCTHHHHHHCCCCHHHHHHHHHHHHHHHTSCEE
T ss_pred             HHHHHhcCCeEEeCCCCCcHHHHHHHHHHHHHhcCCCCEEEEechHHhcCCCCCCChHHHHHHHHHHHHHHHHHcCCeEE
Confidence                        0123346677777777665554368899999999986421         1222233222233456777


Q ss_pred             EEEecCC
Q psy200          334 LVGVANA  340 (490)
Q Consensus       334 lI~~tn~  340 (490)
                      +++-.|+
T Consensus       201 ~lsQl~R  207 (338)
T 4a1f_A          201 ALVQLNR  207 (338)
T ss_dssp             EEEECCG
T ss_pred             EEEecCc
Confidence            7776653

>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=97.44  E-value=0.00045  Score=68.28  Aligned_cols=88  Identities=15%  Similarity=0.231  Sum_probs=57.4

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCCC------CCCcHHHHHHHHHH
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKP------GGKSERHQLGAILK  291 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~------~~~s~~~~~~~l~~  291 (490)
                      .+..++|+|+||+|||+++..++..+.. .+..++|++.....+..  +   +..++...      ...+..++.+.+..
T Consensus        62 ~G~ii~I~G~pGsGKTtLal~la~~~~~-~g~~vlyid~E~s~~~~--~---a~~~g~~~~~l~i~~~~~~e~~~~~~~~  135 (356)
T 1u94_A           62 MGRIVEIYGPESSGKTTLTLQVIAAAQR-EGKTCAFIDAEHALDPI--Y---ARKLGVDIDNLLCSQPDTGEQALEICDA  135 (356)
T ss_dssp             TTSEEEEECSTTSSHHHHHHHHHHHHHH-TTCCEEEEESSCCCCHH--H---HHHTTCCGGGCEEECCSSHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHH-CCCeEEEEeCCCCccHH--H---HHHcCCChhheeeeCCCCHHHHHHHHHH
Confidence            5678999999999999999999887653 33478888875543322  1   23333211      11234555555554


Q ss_pred             HHhcCCCeEEEEEecCccccc
Q psy200          292 YFDTKHKSILLILDEIDALES  312 (490)
Q Consensus       292 ~l~~~~~~~vI~IDEid~l~~  312 (490)
                      .... ....+||||.+..+..
T Consensus       136 l~~~-~~~~lVVIDsl~~l~~  155 (356)
T 1u94_A          136 LARS-GAVDVIVVDSVAALTP  155 (356)
T ss_dssp             HHHH-TCCSEEEEECGGGCCC
T ss_pred             HHhc-cCCCEEEEcCHHHhcc
Confidence            4433 3466999999999874

>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=97.43  E-value=0.00026  Score=65.03  Aligned_cols=42  Identities=19%  Similarity=0.225  Sum_probs=31.3

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhc-----CCceEEEEeccCC
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIK-----DAFKTIYINCNSV  259 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~-----~~~~~~~v~~~~~  259 (490)
                      .+..+.|+||+|+|||||++.++..+...     ..-..++++....
T Consensus        24 ~G~~~~l~G~nGsGKSTll~~l~g~~~~~~~~g~~~~~~i~~~~~~~   70 (231)
T 4a74_A           24 TQAITEVFGEFGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWIDTENT   70 (231)
T ss_dssp             SSEEEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSCEEEEEESSSC
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHhcccccCCCCCEEEEEECCCC
Confidence            46688999999999999999998865321     1235778876553

>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=97.42  E-value=0.00049  Score=69.87  Aligned_cols=97  Identities=14%  Similarity=0.240  Sum_probs=58.2

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCC-CHHHHHHHHHHHhcC-------CCCCCcH--HH---
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVR-NAASVYETIVNELKL-------KPGGKSE--RH---  284 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~-~~~~l~~~i~~~l~~-------~~~~~s~--~~---  284 (490)
                      .++.++|+|++|+|||+|++.++...........+++.+.... ...+++.++...=..       .....+.  ..   
T Consensus       150 kGq~~~i~G~sGvGKTtL~~~l~~~~~~~~~~i~V~~~iGerttev~el~~~l~~~~~l~~tvvv~~~~~d~pg~r~~~~  229 (473)
T 1sky_E          150 KGGKIGLFGGAGVGKTVLIQELIHNIAQEHGGISVFAGVGERTREGNDLYHEMKDSGVISKTAMVFGQMNEPPGARMRVA  229 (473)
T ss_dssp             TTCEEEEECCSSSCHHHHHHHHHHHHHHHTCCCEEEEEESSCHHHHHHHHHHHHHTSGGGGEEEEEECTTSCHHHHHHHH
T ss_pred             cCCEEEEECCCCCCccHHHHHHHhhhhhccCcEEEEeeeccCchHHHHHHHHhhhcCCcceeEEEEEcCCCCHHHHHHHH
Confidence            4668999999999999999999887654333334566555543 234555555332000       0110111  11   


Q ss_pred             -HHHHHHHHHhc-CCCeEEEEEecCccccccC
Q psy200          285 -QLGAILKYFDT-KHKSILLILDEIDALESRK  314 (490)
Q Consensus       285 -~~~~l~~~l~~-~~~~~vI~IDEid~l~~~~  314 (490)
                       ..-.+.+++.. .++.++||+|++.++....
T Consensus       230 ~~~ltiAEyFrd~~G~~VLl~~D~itR~a~A~  261 (473)
T 1sky_E          230 LTGLTMAEYFRDEQGQDGLLFIDNIFRFTQAG  261 (473)
T ss_dssp             HHHHHHHHHHHHHSCCEEEEEEECTHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCCcEEEEeccHHHHHHHH
Confidence             01134455555 6889999999999987543

>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=97.41  E-value=0.00035  Score=68.95  Aligned_cols=94  Identities=15%  Similarity=0.148  Sum_probs=54.9

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcC-----CceEEEEeccCCCCHHHHHHHHHHHhcCC-------------CCC
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKD-----AFKTIYINCNSVRNAASVYETIVNELKLK-------------PGG  279 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~-----~~~~~~v~~~~~~~~~~l~~~i~~~l~~~-------------~~~  279 (490)
                      .+..+.|+|++|+|||||++.++..+...+     +-.++|++.........+ ..+...++..             +..
T Consensus       130 ~G~i~~I~G~~GsGKTTL~~~l~~~~~~~~~~Gg~~G~vi~i~~e~~~~~~~i-~~i~q~~~~~~~~v~~ni~~~~~~~~  208 (349)
T 1pzn_A          130 TQAITEVFGEFGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWIDTENTFRPERI-REIAQNRGLDPDEVLKHIYVARAFNS  208 (349)
T ss_dssp             SSEEEEEEESTTSSHHHHHHHHHHHTTSCGGGTSCSCEEEEEESSSCCCHHHH-HHHHHTTTCCHHHHGGGEEEEECCSH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHhccchhcCCCCCeEEEEeCCCCCCHHHH-HHHHHHcCCCHHHHhhCEEEEecCCh
Confidence            567888999999999999999998763211     125688887554322222 2233322211             000


Q ss_pred             CcHHHHHHHHHHHHhcC----CCeEEEEEecCccccc
Q psy200          280 KSERHQLGAILKYFDTK----HKSILLILDEIDALES  312 (490)
Q Consensus       280 ~s~~~~~~~l~~~l~~~----~~~~vI~IDEid~l~~  312 (490)
                      .....+...+...+...    .++-+|||||+-.+..
T Consensus       209 ~~~~~~l~~~~~~~~~lS~G~~~~~llIlDs~ta~ld  245 (349)
T 1pzn_A          209 NHQMLLVQQAEDKIKELLNTDRPVKLLIVDSLTSHFR  245 (349)
T ss_dssp             HHHHHHHHHHHHHHHHSSSSSSCEEEEEEETSSTTHH
T ss_pred             HHHHHHHHHHHHHHHHhccccCCCCEEEEeCchHhhh
Confidence            11122333333334321    4688999999998853

>1w36_D RECD, exodeoxyribonuclease V alpha chain; recombination, helicase, hydrolase, DNA repair; HET: DNA; 3.1A {Escherichia coli} SCOP: c.37.1.19 c.37.1.19 PDB: 3k70_D*

Probab=97.39  E-value=0.0002  Score=76.23  Aligned_cols=26  Identities=35%  Similarity=0.483  Sum_probs=23.3

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      .+.++|+|+|||||||++..+...+.
T Consensus       164 ~~~~vi~G~pGTGKTt~l~~ll~~l~  189 (608)
T 1w36_D          164 RRISVISGGPGTGKTTTVAKLLAALI  189 (608)
T ss_dssp             BSEEEEECCTTSTHHHHHHHHHHHHH
T ss_pred             CCCEEEEeCCCCCHHHHHHHHHHHHH
Confidence            57899999999999999999888775

>2i3b_A HCR-ntpase, human cancer-related ntpase; AAA, rossmann, hydrolase; NMR {Homo sapiens} SCOP: c.37.1.11

Probab=97.38  E-value=1.9e-05  Score=70.94  Aligned_cols=25  Identities=24%  Similarity=0.612  Sum_probs=22.5

Q ss_pred             CeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          220 GSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       220 ~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      ..+.|+|++|+||||+++.++..+.
T Consensus         2 ~~i~i~G~nG~GKTTll~~l~g~~~   26 (189)
T 2i3b_A            2 RHVFLTGPPGVGKTTLIHKASEVLK   26 (189)
T ss_dssp             CCEEEESCCSSCHHHHHHHHHHHHH
T ss_pred             CEEEEECCCCChHHHHHHHHHhhcc
Confidence            4688999999999999999999875

>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=97.36  E-value=0.00092  Score=64.28  Aligned_cols=88  Identities=15%  Similarity=0.187  Sum_probs=57.6

Q ss_pred             CeEEEECCCCCcHHHHHHHHHHHhhhc-CCceEEEEeccCCCCHHHHHHHHHHHhcCCCC------CCcHHHH-HHHHHH
Q psy200          220 GSMYISGPPGTGKSASLNLLVSRAEIK-DAFKTIYINCNSVRNAASVYETIVNELKLKPG------GKSERHQ-LGAILK  291 (490)
Q Consensus       220 ~~ill~GppGtGKTtla~~l~~~l~~~-~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~------~~s~~~~-~~~l~~  291 (490)
                      +.++|+||||+|||+|+-.++..+... .+-.++|++........     .+..|+....      ..+.+++ .+.+..
T Consensus        29 GiteI~G~pGsGKTtL~Lq~~~~~~~~g~g~~vlyId~E~s~~~~-----ra~~lGvd~d~llv~~~~~~E~~~l~i~~~  103 (333)
T 3io5_A           29 GLLILAGPSKSFKSNFGLTMVSSYMRQYPDAVCLFYDSEFGITPA-----YLRSMGVDPERVIHTPVQSLEQLRIDMVNQ  103 (333)
T ss_dssp             EEEEEEESSSSSHHHHHHHHHHHHHHHCTTCEEEEEESSCCCCHH-----HHHHTTCCGGGEEEEECSBHHHHHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHhcCCCceEEEEeccchhhHH-----HHHHhCCCHHHeEEEcCCCHHHHHHHHHHH
Confidence            368899999999999998888776533 24578999876654432     2455554211      1244555 443333


Q ss_pred             HH-hcCCCeEEEEEecCccccc
Q psy200          292 YF-DTKHKSILLILDEIDALES  312 (490)
Q Consensus       292 ~l-~~~~~~~vI~IDEid~l~~  312 (490)
                      .- -..+++.+||||-|..|..
T Consensus       104 l~~i~~~~~~lvVIDSI~aL~~  125 (333)
T 3io5_A          104 LDAIERGEKVVVFIDSLGNLAS  125 (333)
T ss_dssp             HHTCCTTCCEEEEEECSTTCBC
T ss_pred             HHHhhccCceEEEEeccccccc
Confidence            20 2336789999999999973

>3bh0_A DNAB-like replicative helicase; ATPase, replication; 2.35A {Bacillus phage SPP1}

Probab=97.36  E-value=0.0019  Score=62.65  Aligned_cols=92  Identities=11%  Similarity=0.056  Sum_probs=59.3

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhc---------------C------
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELK---------------L------  275 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~---------------~------  275 (490)
                      ..+..++|.|+||+|||+++..++...... +..++|++.-  .+...+...+.....               .      
T Consensus        66 ~~G~l~li~G~pG~GKTtl~l~ia~~~a~~-g~~vl~~slE--~s~~~l~~R~~~~~~~i~~~~l~~~~~~l~~~~~~~l  142 (315)
T 3bh0_A           66 KRRNFVLIAARPSMGKTAFALKQAKNMSDN-DDVVNLHSLE--MGKKENIKRLIVTAGSINAQKIKAARRDFASEDWGKL  142 (315)
T ss_dssp             CTTCEEEEECCTTSSHHHHHHHHHHHHHTT-TCEEEEEESS--SCHHHHHHHHHHHHTTCCHHHHHSCHHHHCSSCHHHH
T ss_pred             CCCcEEEEEeCCCCCHHHHHHHHHHHHHHc-CCeEEEEECC--CCHHHHHHHHHHHHcCCCHHHHhcCCCCCCHHHHHHH
Confidence            356789999999999999999998776532 2577777654  255555544443210               0      


Q ss_pred             ---------------CCCCCcHHHHHHHHHHHHhcCCCeE--EEEEecCccccc
Q psy200          276 ---------------KPGGKSERHQLGAILKYFDTKHKSI--LLILDEIDALES  312 (490)
Q Consensus       276 ---------------~~~~~s~~~~~~~l~~~l~~~~~~~--vI~IDEid~l~~  312 (490)
                                     ...+.+..++...+.+..... +.-  +||||-++.+..
T Consensus       143 ~~a~~~l~~~~i~i~d~~~~~~~~i~~~i~~l~~~~-~~~~~lVVID~l~~l~~  195 (315)
T 3bh0_A          143 SMAIGEISNSNINIFDKAGQSVNYIWSKTRQTKRKN-PGKRVIVMIDYLQLLEP  195 (315)
T ss_dssp             HHHHHHHHTSCEEEECCSCCBHHHHHHHHHHHHHTS-SSCCEEEEEECGGGSBC
T ss_pred             HHHHHHHhCCCEEEECCCCCCHHHHHHHHHHHHHhc-CCCCeEEEEeCchhcCC
Confidence                           112245666666666654432 344  999999998863

>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=97.33  E-value=0.0025  Score=59.38  Aligned_cols=28  Identities=25%  Similarity=0.360  Sum_probs=24.5

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      ..+..|+|+|++|+||||+++.+++.++
T Consensus        27 ~~~~~I~l~G~~GsGKsT~a~~L~~~~g   54 (243)
T 3tlx_A           27 KPDGRYIFLGAPGSGKGTQSLNLKKSHC   54 (243)
T ss_dssp             SCCEEEEEECCTTSSHHHHHHHHHHHHC
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHHhC
Confidence            3567899999999999999999998864

>3llm_A ATP-dependent RNA helicase A; alpha-beta-alpha, structural genomics, structural genomics consortium, SGC, activator, ATP-binding, DNA-binding; HET: ADP; 2.80A {Homo sapiens}

Probab=97.31  E-value=0.0014  Score=60.70  Aligned_cols=115  Identities=18%  Similarity=0.189  Sum_probs=58.0

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHh-hhcC---CceEEEEeccCCCCHHHHHHHHHHHhcCCC----------------C
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRA-EIKD---AFKTIYINCNSVRNAASVYETIVNELKLKP----------------G  278 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l-~~~~---~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~----------------~  278 (490)
                      +..++|.|+.|+|||+++..++-.. ....   ...++++. ........+...+...++...                .
T Consensus        76 g~~~~i~g~TGsGKTt~~~~~~~~~~~~~~~~~~~~~l~~~-p~~~la~q~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~  154 (235)
T 3llm_A           76 NSVVIIRGATGCGKTTQVPQFILDDFIQNDRAAECNIVVTQ-PRRISAVSVAERVAFERGEEPGKSCGYSVRFESILPRP  154 (235)
T ss_dssp             CSEEEEECCTTSSHHHHHHHHHHHHHHHTTCGGGCEEEEEE-SSHHHHHHHHHHHHHTTTCCTTSSEEEEETTEEECCCS
T ss_pred             CCEEEEEeCCCCCcHHhHHHHHhcchhhcCCCCceEEEEec-cchHHHHHHHHHHHHHhccccCceEEEeechhhccCCC
Confidence            5689999999999998776654432 1111   22444442 211122233444444433210                0


Q ss_pred             C-----CcHHHHHHHHHHHHhcCCCeEEEEEecCccc-cccC-H-HHHHHhHhCCCCCCCcEEEEEecC
Q psy200          279 G-----KSERHQLGAILKYFDTKHKSILLILDEIDAL-ESRK-Q-TILYTIFEWPSIPGSKLVLVGVAN  339 (490)
Q Consensus       279 ~-----~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l-~~~~-~-~~L~~l~~~~~~~~~~vilI~~tn  339 (490)
                      +     .+...+.+.+..   .-....+|||||+|.+ ...+ . ..+..++...  ...+++++.+|-
T Consensus       155 ~~~Ivv~Tpg~l~~~l~~---~l~~~~~lVlDEah~~~~~~~~~~~~l~~i~~~~--~~~~~il~SAT~  218 (235)
T 3llm_A          155 HASIMFCTVGVLLRKLEA---GIRGISHVIVDEIHERDINTDFLLVVLRDVVQAY--PEVRIVLMSATI  218 (235)
T ss_dssp             SSEEEEEEHHHHHHHHHH---CCTTCCEEEECCTTSCCHHHHHHHHHHHHHHHHC--TTSEEEEEECSS
T ss_pred             CCeEEEECHHHHHHHHHh---hhcCCcEEEEECCccCCcchHHHHHHHHHHHhhC--CCCeEEEEecCC
Confidence            0     133444444433   2234569999999985 2211 1 2333343322  345677776663

>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=97.30  E-value=0.0015  Score=59.26  Aligned_cols=24  Identities=29%  Similarity=0.551  Sum_probs=21.6

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHhh
Q psy200          221 SMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      .|+|.||||+||+|.++.+++.++
T Consensus         2 ~Iil~GpPGsGKgTqa~~La~~~g   25 (206)
T 3sr0_A            2 ILVFLGPPGAGKGTQAKRLAKEKG   25 (206)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHC
Confidence            478899999999999999999864

>2i1q_A DNA repair and recombination protein RADA; ATPase, recombinase, ATP complex, calcium stimulation, RECA, DMC1; HET: DNA ANP; 1.90A {Methanococcus voltae} SCOP: a.60.4.1 c.37.1.11 PDB: 1xu4_A* 2b21_A* 2fpk_A* 2fpl_A* 2fpm_A* 1t4g_A* 3fyh_A* 2f1j_A* 2f1i_A* 2f1h_A* 3ntu_A* 3ewa_A* 3ew9_A* 3etl_A* 4dc9_A* 2gdj_A*

Probab=97.29  E-value=0.00082  Score=65.50  Aligned_cols=94  Identities=11%  Similarity=0.167  Sum_probs=57.9

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhc-----------CC----ceEEEEeccCCCCHHHHHHHHHHHhcCCC-----
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIK-----------DA----FKTIYINCNSVRNAASVYETIVNELKLKP-----  277 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~-----------~~----~~~~~v~~~~~~~~~~l~~~i~~~l~~~~-----  277 (490)
                      .+..++|+|+||+|||+++..++......           .+    ..++|++.....+...+.. ++..++...     
T Consensus        97 ~g~i~~i~G~~gsGKT~la~~la~~~~l~~~~~~~~~~~~~gg~~~~~v~yi~~e~~~~~~~l~~-~~~~~g~~~~~~~~  175 (322)
T 2i1q_A           97 SQSVTEFAGVFGSGKTQIMHQSCVNLQNPEFLFYDEEAVSKGEVAQPKAVYIDTEGTFRPERIMQ-MAEHAGIDGQTVLD  175 (322)
T ss_dssp             TTEEEEEEESTTSSHHHHHHHHHHHTTCGGGEECCTTTSCTTTTSSEEEEEEESSSCCCHHHHHH-HHHHHTCCHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHhccccccccccccccCCCCCceEEEEECCCCCCHHHHHH-HHHHcCCCHHHHhc
Confidence            46688999999999999999998764211           11    5788888766434554432 233333211     


Q ss_pred             -----CCCcHHH---HHHHHHHHHhcCCCeEEEEEecCccccc
Q psy200          278 -----GGKSERH---QLGAILKYFDTKHKSILLILDEIDALES  312 (490)
Q Consensus       278 -----~~~s~~~---~~~~l~~~l~~~~~~~vI~IDEid~l~~  312 (490)
                           ...+..+   +.+.+...+....+..+||||.+..+..
T Consensus       176 ~l~~~~~~~~~~~~~~l~~l~~~~~~~~~~~lvVIDsl~~l~~  218 (322)
T 2i1q_A          176 NTFVARAYNSDMQMLFAEKIEDLIQEGNNIKLVVIDSLTSTFR  218 (322)
T ss_dssp             TEEEEECSSHHHHHHHHHTHHHHHHTTCEEEEEEEECSSHHHH
T ss_pred             CEEEEeCCCHHHHHHHHHHHHHHHhhccCccEEEEECcHHHHH
Confidence                 0112222   3334444444435678999999998853

>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=97.28  E-value=0.0042  Score=59.70  Aligned_cols=89  Identities=17%  Similarity=0.174  Sum_probs=54.2

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCC-CHHHHHHHHHHHhcCCCC-CCcHHHHHHHHHHHHhc
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVR-NAASVYETIVNELKLKPG-GKSERHQLGAILKYFDT  295 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~-~~~~l~~~i~~~l~~~~~-~~s~~~~~~~l~~~l~~  295 (490)
                      .+..++|+|++|+||||++..++..+....+..+..+.+.... ...+.+..+...++.... ......+...+..+   
T Consensus       104 ~g~vi~lvG~~GsGKTTl~~~LA~~l~~~~G~~V~lv~~D~~r~~a~eqL~~~~~~~gl~~~~~~~~~~l~~al~~~---  180 (296)
T 2px0_A          104 HSKYIVLFGSTGAGKTTTLAKLAAISMLEKHKKIAFITTDTYRIAAVEQLKTYAELLQAPLEVCYTKEEFQQAKELF---  180 (296)
T ss_dssp             CSSEEEEEESTTSSHHHHHHHHHHHHHHTTCCCEEEEECCCSSTTHHHHHHHHHTTTTCCCCBCSSHHHHHHHHHHG---
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHHHhcCCEEEEEecCcccchHHHHHHHHHHhcCCCeEecCCHHHHHHHHHHh---
Confidence            4678999999999999999999998864345566777665543 223334443333333221 12334444444322   


Q ss_pred             CCCeEEEEEecCccc
Q psy200          296 KHKSILLILDEIDAL  310 (490)
Q Consensus       296 ~~~~~vI~IDEid~l  310 (490)
                       ..+-+||||-....
T Consensus       181 -~~~dlvIiDT~G~~  194 (296)
T 2px0_A          181 -SEYDHVFVDTAGRN  194 (296)
T ss_dssp             -GGSSEEEEECCCCC
T ss_pred             -cCCCEEEEeCCCCC
Confidence             33569999966554

>3umf_A Adenylate kinase; rossmann fold, transferase; 2.05A {Schistosoma mansoni}

Probab=97.27  E-value=0.0047  Score=56.41  Aligned_cols=28  Identities=25%  Similarity=0.538  Sum_probs=24.8

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      ..++.|+|.||||+||+|.++.+++.++
T Consensus        27 ~k~kiI~llGpPGsGKgTqa~~L~~~~g   54 (217)
T 3umf_A           27 AKAKVIFVLGGPGSGKGTQCEKLVQKFH   54 (217)
T ss_dssp             TSCEEEEEECCTTCCHHHHHHHHHHHHC
T ss_pred             cCCcEEEEECCCCCCHHHHHHHHHHHHC
Confidence            3567899999999999999999999864

>3cmw_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 2.80A {Escherichia coli} PDB: 3cmt_A* 3cmx_A* 3cmv_A*

Probab=97.27  E-value=0.00043  Score=80.59  Aligned_cols=87  Identities=15%  Similarity=0.189  Sum_probs=56.2

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCC---CCCC----cHHHHHHHHHH
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLK---PGGK----SERHQLGAILK  291 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~---~~~~----s~~~~~~~l~~  291 (490)
                      ++.++||||||||||+++.+++.+.... +-..+||.+....  .+++.   ..|+..   +.+.    ++..+...+..
T Consensus      1082 g~~~l~~G~~g~GKT~la~~~~~~~~~~-g~~~~fi~~~~~~--~~~~~---~~~G~d~~~~~~~~~~~~e~~l~~~~~~ 1155 (1706)
T 3cmw_A         1082 GRIVEIYGPESSGKTTLTLQVIAAAQRE-GKTCAFIDAEHAL--DPIYA---RKLGVDIDNLLCSQPDTGEQALEICDAL 1155 (1706)
T ss_dssp             TSEEEEECSTTSSHHHHHHHHHHHHHHT-TCCEEEECTTSCC--CHHHH---HHTTCCGGGCEEECCSSHHHHHHHHHHH
T ss_pred             CCEEEEEcCCCCChHHHHHHHHHHhhhc-CCceeEEEcccch--HHHHH---HHhCCCHHHHhhccccchHHHHHHHHHH
Confidence            4559999999999999999999887543 4567888765533  23332   344431   2222    44445333332


Q ss_pred             HHhcCCCeEEEEEecCcccccc
Q psy200          292 YFDTKHKSILLILDEIDALESR  313 (490)
Q Consensus       292 ~l~~~~~~~vI~IDEid~l~~~  313 (490)
                      +  +...+++||+|+++.|...
T Consensus      1156 a--r~~~~~~i~~d~~~al~~~ 1175 (1706)
T 3cmw_A         1156 A--RSGAVDVIVVDSVAALTPK 1175 (1706)
T ss_dssp             H--HHTCCSEEEESCGGGCCCH
T ss_pred             H--HhcCCeEEEeCchHhcCcc
Confidence            2  2256899999999977655

>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=97.21  E-value=0.0052  Score=54.66  Aligned_cols=24  Identities=46%  Similarity=0.657  Sum_probs=21.9

Q ss_pred             CeEEEECCCCCcHHHHHHHHHHHh
Q psy200          220 GSMYISGPPGTGKSASLNLLVSRA  243 (490)
Q Consensus       220 ~~ill~GppGtGKTtla~~l~~~l  243 (490)
                      +.|+|+||+|+|||||++.+....
T Consensus         2 RpIVi~GPSG~GK~Tl~~~L~~~~   25 (186)
T 1ex7_A            2 RPIVISGPSGTGKSTLLKKLFAEY   25 (186)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHC
T ss_pred             CEEEEECCCCCCHHHHHHHHHHhC
Confidence            578999999999999999998875

>2j9r_A Thymidine kinase; TK1, DNK, lasso, transferase, ATP-binding, deoxyribonucleoside kinase, DNA synthesis, phosphate accept nucleotide-binding; HET: THM; 2.7A {Bacillus anthracis} PDB: 2ja1_A*

Probab=97.18  E-value=0.00033  Score=63.60  Aligned_cols=107  Identities=17%  Similarity=0.195  Sum_probs=52.0

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCCCC--C-CcHHHHHHHHHHHHh
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKPG--G-KSERHQLGAILKYFD  294 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~--~-~s~~~~~~~l~~~l~  294 (490)
                      .+...+++|+.|+||||.+-.++..+.. .+..++.+..... + ..-...+...++....  . ....++.+.    +.
T Consensus        27 ~G~l~vitG~MgsGKTT~lL~~a~r~~~-~g~kVli~k~~~d-~-R~ge~~i~s~~g~~~~a~~~~~~~~~~~~----~~   99 (214)
T 2j9r_A           27 NGWIEVICGSMFSGKSEELIRRVRRTQF-AKQHAIVFKPCID-N-RYSEEDVVSHNGLKVKAVPVSASKDIFKH----IT   99 (214)
T ss_dssp             SCEEEEEECSTTSCHHHHHHHHHHHHHH-TTCCEEEEECC-------------------CCEEECSSGGGGGGG----CC
T ss_pred             CCEEEEEECCCCCcHHHHHHHHHHHHHH-CCCEEEEEEeccC-C-cchHHHHHhhcCCeeEEeecCCHHHHHHH----Hh
Confidence            4567779999999999988888877642 3345555542221 1 1111123333322111  0 111111111    11


Q ss_pred             cCCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEEEe
Q psy200          295 TKHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGV  337 (490)
Q Consensus       295 ~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI~~  337 (490)
                        +..-+|+|||++.+....-+.+..+.+    .+..|++.|.
T Consensus       100 --~~~dvViIDEaQF~~~~~V~~l~~l~~----~~~~Vi~~Gl  136 (214)
T 2j9r_A          100 --EEMDVIAIDEVQFFDGDIVEVVQVLAN----RGYRVIVAGL  136 (214)
T ss_dssp             --SSCCEEEECCGGGSCTTHHHHHHHHHH----TTCEEEEEEC
T ss_pred             --cCCCEEEEECcccCCHHHHHHHHHHhh----CCCEEEEEec
Confidence              234599999999986554444544433    2445555554

>1xx6_A Thymidine kinase; NESG, northeast structural genomics consortium, protein STRU initiative, PSI, structural genomics, DNA synthesis; HET: ADP; 2.00A {Clostridium acetobutylicum} SCOP: c.37.1.24 g.39.1.14

Probab=97.18  E-value=0.00013  Score=65.51  Aligned_cols=109  Identities=26%  Similarity=0.347  Sum_probs=54.6

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCCCC--C-CcHHHHHHHHHHHH
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKPG--G-KSERHQLGAILKYF  293 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~--~-~s~~~~~~~l~~~l  293 (490)
                      ..+...+++|+.|+||||.+-.+++.+.. .+..++.+..... +... ...+...++....  . ....++.+    .+
T Consensus         6 ~~g~i~v~~G~mgsGKTT~ll~~a~r~~~-~g~kV~v~k~~~d-~r~~-~~~i~s~~g~~~~a~~~~~~~~i~~----~~   78 (191)
T 1xx6_A            6 DHGWVEVIVGPMYSGKSEELIRRIRRAKI-AKQKIQVFKPEID-NRYS-KEDVVSHMGEKEQAVAIKNSREILK----YF   78 (191)
T ss_dssp             TCCEEEEEECSTTSSHHHHHHHHHHHHHH-TTCCEEEEEEC---------CEEECTTSCEEECEEESSSTHHHH----HC
T ss_pred             CCCEEEEEECCCCCcHHHHHHHHHHHHHH-CCCEEEEEEeccC-ccch-HHHHHhhcCCceeeEeeCCHHHHHH----HH
Confidence            34568889999999999999888888742 2334444432111 1000 0111112221100  0 01112221    12


Q ss_pred             hcCCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEEEec
Q psy200          294 DTKHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVA  338 (490)
Q Consensus       294 ~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI~~t  338 (490)
                      .  +..-+|+|||++.+.....+.+..+.+    .+..|++.|..
T Consensus        79 ~--~~~dvViIDEaqfl~~~~v~~l~~l~~----~~~~Vi~~Gl~  117 (191)
T 1xx6_A           79 E--EDTEVIAIDEVQFFDDEIVEIVNKIAE----SGRRVICAGLD  117 (191)
T ss_dssp             C--TTCSEEEECSGGGSCTHHHHHHHHHHH----TTCEEEEEECS
T ss_pred             h--ccCCEEEEECCCCCCHHHHHHHHHHHh----CCCEEEEEecc
Confidence            1  124599999999986543444444433    24566666553

>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=97.17  E-value=0.0011  Score=63.20  Aligned_cols=27  Identities=22%  Similarity=0.223  Sum_probs=24.0

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      .+..++|+|++|+|||||+..++..+.
T Consensus        29 ~G~i~~i~G~~GsGKTtl~~~l~~~~~   55 (279)
T 1nlf_A           29 AGTVGALVSPGGAGKSMLALQLAAQIA   55 (279)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHHH
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHHHHh
Confidence            467899999999999999999998665

>2zts_A Putative uncharacterized protein PH0186; KAIC like protein, ATP-binding, nucleotide-binding, ATP- binding protein; HET: ADP; 2.07A {Pyrococcus horikoshii}

Probab=97.15  E-value=0.0011  Score=61.67  Aligned_cols=49  Identities=12%  Similarity=0.261  Sum_probs=32.8

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHH
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYET  268 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~  268 (490)
                      .+..++|+|+||+|||+++..++.+.....+..+++++...  +...+...
T Consensus        29 ~G~l~~i~G~pG~GKT~l~l~~~~~~~~~~~~~v~~~s~E~--~~~~~~~~   77 (251)
T 2zts_A           29 EGTTVLLTGGTGTGKTTFAAQFIYKGAEEYGEPGVFVTLEE--RARDLRRE   77 (251)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHHHHHHHHHCCCEEEEESSS--CHHHHHHH
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHHHHHhcCCCceeecccC--CHHHHHHH
Confidence            56789999999999999998877654323334566665432  44555443

>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=97.13  E-value=0.00049  Score=67.84  Aligned_cols=95  Identities=16%  Similarity=0.170  Sum_probs=57.7

Q ss_pred             ccCCCCeEEEECCCCCcHHHHHHHHHHHhhh-cCCceEEEEeccCCCCHHHHHHHHHHHhcC-----CCCCCcHHHH---
Q psy200          215 NNETSGSMYISGPPGTGKSASLNLLVSRAEI-KDAFKTIYINCNSVRNAASVYETIVNELKL-----KPGGKSERHQ---  285 (490)
Q Consensus       215 ~~~~~~~ill~GppGtGKTtla~~l~~~l~~-~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~-----~~~~~s~~~~---  285 (490)
                      .-..+..++|+|++|+|||+|++.+++.+.. .+++.++++-+..-  ..+ ...+.+.+..     .........+   
T Consensus       170 pi~rGQr~~IvG~sG~GKTtLl~~Iar~i~~~~~~v~~I~~lIGER--~~E-v~~~~~~~~~~vV~atadep~~~r~~~a  246 (422)
T 3ice_A          170 PIGRGQRGLIVAPPKAGKTMLLQNIAQSIAYNHPDCVLMVLLIDER--PEE-VTEMQRLVKGEVVASTFDEPASRHVQVA  246 (422)
T ss_dssp             CCBTTCEEEEECCSSSSHHHHHHHHHHHHHHHCTTSEEEEEEESSC--HHH-HHHHHTTCSSEEEEECTTSCHHHHHHHH
T ss_pred             eecCCcEEEEecCCCCChhHHHHHHHHHHhhcCCCeeEEEEEecCC--hHH-HHHHHHHhCeEEEEeCCCCCHHHHHHHH
Confidence            3457889999999999999999999887753 35666666655432  111 2222333311     1111111111   


Q ss_pred             --HHHHHHHHhcCCCeEEEEEecCccccc
Q psy200          286 --LGAILKYFDTKHKSILLILDEIDALES  312 (490)
Q Consensus       286 --~~~l~~~l~~~~~~~vI~IDEid~l~~  312 (490)
                        .-.+.+++...++.++||+|++-++..
T Consensus       247 ~~alt~AEyfrd~G~dVLil~DslTR~A~  275 (422)
T 3ice_A          247 EMVIEKAKRLVEHKKDVIILLDSITRLAR  275 (422)
T ss_dssp             HHHHHHHHHHHHTSCEEEEEEECHHHHHH
T ss_pred             HHHHHHHHHHHhcCCCEEEEEeCchHHHH
Confidence              112334455568899999999988764

>3bgw_A DNAB-like replicative helicase; ATPase, replication; 3.91A {Bacillus phage SPP1}

Probab=97.11  E-value=0.003  Score=64.35  Aligned_cols=91  Identities=11%  Similarity=0.056  Sum_probs=58.7

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHh---------------cC-------
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNEL---------------KL-------  275 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l---------------~~-------  275 (490)
                      ++..++|.|+||+|||+++..++...... +..+++++.-.  +..++...+....               ..       
T Consensus       196 ~G~liiIaG~pG~GKTtlal~ia~~~a~~-g~~vl~fSlEm--s~~ql~~R~~~~~~~i~~~~l~~g~~~l~~~~~~~l~  272 (444)
T 3bgw_A          196 RRNFVLIAARPSMGKTAFALKQAKNMSDN-DDVVNLHSLEM--GKKENIKRLIVTAGSINAQKIKAARRDFASEDWGKLS  272 (444)
T ss_dssp             SSCEEEEEECSSSSHHHHHHHHHHHHHHT-TCEEEEECSSS--CTTHHHHHHHHHHSCCCHHHHHHTGGGTCCSCHHHHH
T ss_pred             CCcEEEEEeCCCCChHHHHHHHHHHHHHc-CCEEEEEECCC--CHHHHHHHHHHHHcCCCHHHHhcccCCCCHHHHHHHH
Confidence            55689999999999999999999887543 56777776543  3333333332211               00       


Q ss_pred             --------------CCCCCcHHHHHHHHHHHHhcCCCeE--EEEEecCccccc
Q psy200          276 --------------KPGGKSERHQLGAILKYFDTKHKSI--LLILDEIDALES  312 (490)
Q Consensus       276 --------------~~~~~s~~~~~~~l~~~l~~~~~~~--vI~IDEid~l~~  312 (490)
                                    ...+.+..++...+.+..... +.-  +||||-++.+..
T Consensus       273 ~a~~~l~~~~l~i~d~~~~s~~~i~~~ir~l~~~~-~~~~~lIVID~Lq~~~~  324 (444)
T 3bgw_A          273 MAIGEISNSNINIFDKAGQSVNYIWSKTRQTKRKN-PGKRVIVMIDYLQLLEP  324 (444)
T ss_dssp             HHHHHHHTSCEEEECCSSCBHHHHHHHHHHHHHHS-CSSCEEEEEECSTTSBC
T ss_pred             HHHHHHhcCCEEEECCCCCCHHHHHHHHHHHHHHh-CCCCeEEEEecHHhccC
Confidence                          112345666776666655442 345  999999998863

>3e2i_A Thymidine kinase; Zn-binding, ATP-binding, DNA synthesis, nucleotide-B transferase; HET: MSE; 2.01A {Staphylococcus aureus}

Probab=97.09  E-value=0.00026  Score=64.22  Aligned_cols=109  Identities=13%  Similarity=0.087  Sum_probs=54.0

Q ss_pred             CCCCeEEEECCCCCcHHH-HHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCCCCCC---cHHHHHHHHHHH
Q psy200          217 ETSGSMYISGPPGTGKSA-SLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKPGGK---SERHQLGAILKY  292 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTt-la~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~~~---s~~~~~~~l~~~  292 (490)
                      ..+...+|+|+.|+|||| |++.+.+...  .+..++.+...-. + ..-...+...++......   ...++.+.    
T Consensus        26 ~~G~I~vitG~M~sGKTT~Llr~~~r~~~--~g~kvli~kp~~D-~-R~~~~~I~Sr~G~~~~a~~v~~~~di~~~----   97 (219)
T 3e2i_A           26 HSGWIECITGSMFSGKSEELIRRLRRGIY--AKQKVVVFKPAID-D-RYHKEKVVSHNGNAIEAINISKASEIMTH----   97 (219)
T ss_dssp             -CCEEEEEEECTTSCHHHHHHHHHHHHHH--TTCCEEEEEEC-------------CBTTBCCEEEEESSGGGGGGS----
T ss_pred             CCceEEEEECCCCCCHHHHHHHHHHHHHH--cCCceEEEEeccC-C-cchhhhHHHhcCCceeeEEeCCHHHHHHH----
Confidence            356788899999999999 5566544332  2333333322211 1 111122333333221111   11222221    


Q ss_pred             HhcCCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEEEecC
Q psy200          293 FDTKHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVAN  339 (490)
Q Consensus       293 l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI~~tn  339 (490)
                      +  ..+..+|+|||+|.+....-+.+..+.+    .+.+|++.|...
T Consensus        98 i--~~~~dvV~IDEaQFf~~~~v~~l~~la~----~gi~Vi~~GLd~  138 (219)
T 3e2i_A           98 D--LTNVDVIGIDEVQFFDDEIVSIVEKLSA----DGHRVIVAGLDM  138 (219)
T ss_dssp             C--CTTCSEEEECCGGGSCTHHHHHHHHHHH----TTCEEEEEEESB
T ss_pred             H--hcCCCEEEEechhcCCHHHHHHHHHHHH----CCCEEEEeeccc
Confidence            1  1345699999999998654455555543    355666666654

>2iut_A DNA translocase FTSK; nucleotide-binding, chromosome partition, ATP-binding, DNA- cell division, DNA translocation, KOPS, membrane; HET: DNA SAP; 2.25A {Pseudomonas aeruginosa} PDB: 2iuu_A*

Probab=97.08  E-value=0.015  Score=60.38  Aligned_cols=73  Identities=16%  Similarity=0.234  Sum_probs=47.1

Q ss_pred             eEEEEEecCccccccC----HHHHHHhHhCCCCCCCcEEEEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHH
Q psy200          299 SILLILDEIDALESRK----QTILYTIFEWPSIPGSKLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILE  374 (490)
Q Consensus       299 ~~vI~IDEid~l~~~~----~~~L~~l~~~~~~~~~~vilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~  374 (490)
                      +++|||||++.+....    .+.|..+....  ....|.+|.+|.+.. .+.+...++..|.   .+|.|.--+..+...
T Consensus       344 ~ivvVIDE~~~L~~~~~~~~~~~L~~Iar~G--Ra~GIhLIlaTQRPs-~d~I~~~Iran~~---~RI~lrv~s~~Dsr~  417 (574)
T 2iut_A          344 TIVVVVDEFADMMMIVGKKVEELIARIAQKA--RAAGIHLILATQRPS-VDVITGLIKANIP---TRIAFQVSSKIDSRT  417 (574)
T ss_dssp             EEEEEESCCTTHHHHTCHHHHHHHHHHHHHC--TTTTEEEEEEESCCC-TTTSCHHHHHTCC---EEEEECCSCHHHHHH
T ss_pred             cEEEEEeCHHHHhhhhhHHHHHHHHHHHHHH--hhCCeEEEEEecCcc-cccccHHHHhhhc---cEEEEEcCCHHHHHH
Confidence            5899999999886432    23455555544  344566666676443 1233445666666   478899889988887


Q ss_pred             HHH
Q psy200          375 IIS  377 (490)
Q Consensus       375 il~  377 (490)
                      +|-
T Consensus       418 ILd  420 (574)
T 2iut_A          418 ILD  420 (574)
T ss_dssp             HHS
T ss_pred             hcC
Confidence            774

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=97.07  E-value=0.0016  Score=76.96  Aligned_cols=89  Identities=16%  Similarity=0.250  Sum_probs=56.8

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCCCCCC-----cHHHHHHHHHHH
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKPGGK-----SERHQLGAILKY  292 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~~~-----s~~~~~~~l~~~  292 (490)
                      .+.+++|+|++|||||+++.+++.+... .+..++|+.+......  ++   ...++......     ...+....+.+.
T Consensus      1080 ~g~~vll~G~~GtGKT~la~~~~~ea~k-~Ge~~~Fit~ee~~~~--L~---a~~~G~dl~~l~~~~pd~~e~~~~i~~~ 1153 (2050)
T 3cmu_A         1080 MGRIVEIYGPESSGKTTLTLQVIAAAQR-EGKTCAFIDAEHALDP--IY---ARKLGVDIDNLLCSQPDTGEQALEICDA 1153 (2050)
T ss_dssp             TTSEEEEECCTTSSHHHHHHHHHHHHHT-TTCCEEEECTTSCCCH--HH---HHHTTCCTTTCEEECCSSHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHHH-cCCeEEEEEccccHHH--HH---HHHcCCChhHheeecCcchHHHHHHHHH
Confidence            5678999999999999999999987653 3667889987765433  22   23333221100     011222233333


Q ss_pred             HhcCCCeEEEEEecCccccc
Q psy200          293 FDTKHKSILLILDEIDALES  312 (490)
Q Consensus       293 l~~~~~~~vI~IDEid~l~~  312 (490)
                      +.+..++.+||||++..+..
T Consensus      1154 l~~~~~~dlvVIDsl~~L~~ 1173 (2050)
T 3cmu_A         1154 LARSGAVDVIVVDSVAALTP 1173 (2050)
T ss_dssp             HHHHTCCSEEEESCGGGCCC
T ss_pred             HHHhCCCCEEEECCcccccc
Confidence            43345688999999999843

>1q57_A DNA primase/helicase; dntpase, DNA replication, transferase; HET: DNA; 3.45A {Enterobacteria phage T7} SCOP: c.37.1.11 e.13.1.2

Probab=97.06  E-value=0.0032  Score=65.33  Aligned_cols=92  Identities=11%  Similarity=0.052  Sum_probs=58.5

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHh-cCC--------------------
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNEL-KLK--------------------  276 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l-~~~--------------------  276 (490)
                      .+..++|.|+||+|||+++..++..+....+..+++++.-.  +..++...++... +..                    
T Consensus       241 ~G~l~li~G~pG~GKT~lal~~a~~~a~~~g~~vl~~s~E~--s~~~l~~r~~~~~~~~~~~~~~~~~~g~l~~~~~~~~  318 (503)
T 1q57_A          241 GGEVIMVTSGSGMVMSTFVRQQALQWGTAMGKKVGLAMLEE--SVEETAEDLIGLHNRVRLRQSDSLKREIIENGKFDQW  318 (503)
T ss_dssp             TTCEEEEEESSCHHHHHHHHHHHHHHTTTSCCCEEEEESSS--CHHHHHHHHHHHHTTSCCTTCHHHHHHHHHTSHHHHH
T ss_pred             CCeEEEEeecCCCCchHHHHHHHHHHHHhcCCcEEEEeccC--CHHHHHHHHHHHHcCCChhhccccccCCCCHHHHHHH
Confidence            46689999999999999999999887643345677776533  4555554443221 110                    


Q ss_pred             --------------C-CCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccc
Q psy200          277 --------------P-GGKSERHQLGAILKYFDTKHKSILLILDEIDALES  312 (490)
Q Consensus       277 --------------~-~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~  312 (490)
                                    . ...+..++...+...... .++-+||||-++.+..
T Consensus       319 ~~~~~~~~~l~i~~~~~~~~~~~i~~~i~~~~~~-~~~~lvVID~l~~l~~  368 (503)
T 1q57_A          319 FDELFGNDTFHLYDSFAEAETDRLLAKLAYMRSG-LGCDVIILDHISIVVS  368 (503)
T ss_dssp             HHHHHTTTCEEEECCC---CHHHHHHHHHHHHHT-TCCSEEEEECTTCCCS
T ss_pred             HHHHhccCCEEEECCCCCCCHHHHHHHHHHHHHh-cCCCEEEEccchhcCC
Confidence                          0 113455666666555444 3466999999998753

>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=97.06  E-value=0.0034  Score=60.57  Aligned_cols=90  Identities=16%  Similarity=0.184  Sum_probs=53.1

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCH-HHHHHHHHHHhcCC----CCCCcHHH-HHHHHHH
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNA-ASVYETIVNELKLK----PGGKSERH-QLGAILK  291 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~-~~l~~~i~~~l~~~----~~~~s~~~-~~~~l~~  291 (490)
                      .+..++|+|++|+||||++..++..+... +..+..+++...... .+-+..+...++..    ..+..... ..+.+..
T Consensus       103 ~~~vi~ivG~~GsGKTTl~~~LA~~l~~~-g~kV~lv~~D~~r~~a~eqL~~~~~~~gl~~~~~~s~~~~~~v~~~al~~  181 (306)
T 1vma_A          103 PPFVIMVVGVNGTGKTTSCGKLAKMFVDE-GKSVVLAAADTFRAAAIEQLKIWGERVGATVISHSEGADPAAVAFDAVAH  181 (306)
T ss_dssp             SCEEEEEECCTTSSHHHHHHHHHHHHHHT-TCCEEEEEECTTCHHHHHHHHHHHHHHTCEEECCSTTCCHHHHHHHHHHH
T ss_pred             CCeEEEEEcCCCChHHHHHHHHHHHHHhc-CCEEEEEccccccHHHHHHHHHHHHHcCCcEEecCCccCHHHHHHHHHHH
Confidence            45678899999999999999999888632 345666665544321 11223344444331    11222222 2334444


Q ss_pred             HHhcCCCeEEEEEecCccc
Q psy200          292 YFDTKHKSILLILDEIDAL  310 (490)
Q Consensus       292 ~l~~~~~~~vI~IDEid~l  310 (490)
                      ++.  ..+-+||||+...+
T Consensus       182 a~~--~~~dvvIiDtpg~~  198 (306)
T 1vma_A          182 ALA--RNKDVVIIDTAGRL  198 (306)
T ss_dssp             HHH--TTCSEEEEEECCCC
T ss_pred             HHh--cCCCEEEEECCCch
Confidence            443  33559999999864

>3vkg_A Dynein heavy chain, cytoplasmic; AAA+ protein, molecular motor, microtubles, motor protein; HET: ADP SPM; 2.81A {Dictyostelium discoideum} PDB: 3vkh_A*

Probab=97.05  E-value=0.018  Score=70.92  Aligned_cols=159  Identities=19%  Similarity=0.191  Sum_probs=90.3

Q ss_pred             CCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhc
Q psy200          195 ELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELK  274 (490)
Q Consensus       195 ~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~  274 (490)
                      +||--++.+++|..+-+-  -..+.+++||+|.+|+||++|++.++.-.    ++.++.+......+..+          
T Consensus      1624 ~LVlF~daleHv~RI~RI--L~qp~GhaLLVGvgGSGkqSLtrLAa~i~----~~~vfqi~i~k~Y~~~~---------- 1687 (3245)
T 3vkg_A         1624 PLVLFNEVLDHILRIDRV--FRQPQGHALLIGVSGGGKSVLSRFVAWMN----GLSIYTIKVNNNYKSSD---------- 1687 (3245)
T ss_dssp             CCCCCHHHHHHHHHHHHH--HTSTTCCEEEEESTTSSHHHHHHHHHHHT----TCEEECCC----CCHHH----------
T ss_pred             eEEeHHHHHHHHHHHHHH--HccCCCCeEEecCCCCcHHHHHHHHHHHh----CCeeEEEeeeCCCCHHH----------
Confidence            466667777776665432  34567899999999999999999887764    46777666554433333          


Q ss_pred             CCCCCCcHHHHHHHHHHHHh---cCCCeEEEEEecCccccccC-------------------------------------
Q psy200          275 LKPGGKSERHQLGAILKYFD---TKHKSILLILDEIDALESRK-------------------------------------  314 (490)
Q Consensus       275 ~~~~~~s~~~~~~~l~~~l~---~~~~~~vI~IDEid~l~~~~-------------------------------------  314 (490)
                                +.+.|...+.   -.+++++++++|-+-....-                                     
T Consensus      1688 ----------f~eDLk~l~~~aG~~~~~~vFL~tD~qi~~e~FLE~IN~lL~sGEVP~LF~~dE~~~i~~~~r~~a~~~g 1757 (3245)
T 3vkg_A         1688 ----------FDDDLRMLLKRAGCKEEKICFIFDESNVLESSFLERMNTLLAGGEVPGLFEGEEFTALMHACKETAQRNG 1757 (3245)
T ss_dssp             ----------HHHHHHHHHHHHHTSCCCEEEEEEGGGCSSTHHHHHHHHHHHHSCCTTSSCTTTHHHHHHHHHHHHHHTT
T ss_pred             ----------HHHHHHHHHHHHhcCCCCEEEEEeccccccHHHHHHHHHHhccCCccccCCHHHHHHHHHHHHHHHHhcC
Confidence                      3333333221   12455566665544322110                                     


Q ss_pred             -----HHHHHHhHhCCCCCCCcEEEEEecCCCChhH--hhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhcc
Q psy200          315 -----QTILYTIFEWPSIPGSKLVLVGVANALDLTD--RMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQT  383 (490)
Q Consensus       315 -----~~~L~~l~~~~~~~~~~vilI~~tn~~~~~~--~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~  383 (490)
                           .+.++.+|-..-..+-+|+++.......+..  +..|.|..+|.    +--|.+++.+.+..+-.+.+...
T Consensus      1758 ~~~dt~~~l~~~Fi~rvr~NLHvVL~mSPvg~~fR~R~r~fPaLvncct----IDWf~~Wp~eAL~~Va~~fl~~~ 1829 (3245)
T 3vkg_A         1758 LILDSEEELYKYFTSQVRRNLHVVFTMNPASPDFHNRSATSPALFNRCV----LDWFGEWSPEALFQVGSEFTRNL 1829 (3245)
T ss_dssp             CCCCCHHHHHHHHHHHHTTTCCEEEEECTTSTTTTC----CTHHHHHSE----EEEEESCCHHHHHHHHHHHTTTS
T ss_pred             CCCCCHHHHHHHHHHHHHHcCEEEEEECCCCHHHHHHHHHChHHhhCce----eeecCCCCHHHHHHHHHHHHhhc
Confidence                 1112222111111345566655443222322  34688888885    78899999999988888777653

>1qde_A EIF4A, translation initiation factor 4A; DEAD box protein family, gene regulation; 2.00A {Saccharomyces cerevisiae} SCOP: c.37.1.19 PDB: 1qva_A

Probab=97.03  E-value=0.0022  Score=58.63  Aligned_cols=35  Identities=17%  Similarity=0.293  Sum_probs=22.6

Q ss_pred             CeEEEECCCCCcHHHH-HHHHHHHhhhc-CCceEEEE
Q psy200          220 GSMYISGPPGTGKSAS-LNLLVSRAEIK-DAFKTIYI  254 (490)
Q Consensus       220 ~~ill~GppGtGKTtl-a~~l~~~l~~~-~~~~~~~v  254 (490)
                      +.+++.+|+|+|||.. +-.+++.+... ....++++
T Consensus        52 ~~~lv~~pTGsGKT~~~~~~~l~~l~~~~~~~~~lil   88 (224)
T 1qde_A           52 HDVLAQAQSGTGKTGTFSIAALQRIDTSVKAPQALML   88 (224)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHHCCTTCCSCCEEEE
T ss_pred             CCEEEECCCCCcHHHHHHHHHHHHHhccCCCceEEEE
Confidence            5799999999999987 44455554322 22344544

>3be4_A Adenylate kinase; malaria, cryptosporidium parvum nonprotein inhibitors, nucleotide-binding, transferase; HET: AP5; 1.60A {Cryptosporidium parvum iowa II}

Probab=96.98  E-value=0.0033  Score=57.38  Aligned_cols=26  Identities=19%  Similarity=0.466  Sum_probs=23.4

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      +..|+|.|++|+||||+++.+++.++
T Consensus         5 ~~~I~l~G~~GsGKsT~a~~La~~l~   30 (217)
T 3be4_A            5 KHNLILIGAPGSGKGTQCEFIKKEYG   30 (217)
T ss_dssp             CCEEEEEECTTSSHHHHHHHHHHHHC
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHHhC
Confidence            45789999999999999999999874

>2ga8_A Hypothetical 39.9 kDa protein; YFR007W, YFH7, unknown function; HET: CME; 1.77A {Saccharomyces cerevisiae} PDB: 2gaa_A*

Probab=96.96  E-value=0.001  Score=65.05  Aligned_cols=48  Identities=19%  Similarity=0.281  Sum_probs=38.6

Q ss_pred             CChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          197 PGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       197 vgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      +..++.++.+...+...+..+....++|+|++|+||||+++.++..+.
T Consensus         2 ~~~~~L~~~il~~l~~~i~~g~~~~i~l~G~~G~GKTTl~~~la~~l~   49 (359)
T 2ga8_A            2 VDTHKLADDVLQLLDNRIEDNYRVCVILVGSPGSGKSTIAEELCQIIN   49 (359)
T ss_dssp             CCHHHHHHHHHHHHHHTTTTCSCEEEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             ccHHHHHHHHHHHHHHHhccCCeeEEEEECCCCCcHHHHHHHHHHHhC
Confidence            455666777777777666656666799999999999999999999875

>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=96.95  E-value=0.00072  Score=59.43  Aligned_cols=26  Identities=23%  Similarity=0.300  Sum_probs=23.5

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      +..++|+|++|+||||+++.+++.+.
T Consensus         3 ~~~i~l~G~~GsGKST~a~~La~~l~   28 (178)
T 1qhx_A            3 TRMIILNGGSSAGKSGIVRCLQSVLP   28 (178)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHSS
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHhcC
Confidence            45789999999999999999999875

>3cmw_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 2.80A {Escherichia coli} PDB: 3cmt_A* 3cmx_A* 3cmv_A*

Probab=96.93  E-value=0.0023  Score=74.63  Aligned_cols=87  Identities=15%  Similarity=0.258  Sum_probs=59.8

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCC------CCCCcHHHHHHHHHH
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLK------PGGKSERHQLGAILK  291 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~------~~~~s~~~~~~~l~~  291 (490)
                      ++..++|+|+||+|||+|+..++..+.. .+..++|++.......  ++   +..++..      ....+..++.+.+..
T Consensus       731 ~G~lVlI~G~PG~GKTtLal~lA~~aa~-~g~~VlyiS~Ees~~q--l~---A~~lGvd~~~L~i~~~~~leei~~~l~~  804 (1706)
T 3cmw_A          731 MGRIVEIYGPESSGKTTLTLQVIAAAQR-EGKTCAFIDAEHALDP--IY---ARKLGVDIDNLLCSQPDTGEQALEICDA  804 (1706)
T ss_dssp             TTSEEEEECSTTSSHHHHHHHHHHHHHH-TTCCEEEECTTSCCCH--HH---HHHTTCCGGGCEEECCSSHHHHHHHHHH
T ss_pred             CCceEEEECCCCCCcHHHHHHHHHHHHH-cCCCeEEEeccchHHH--HH---HHHcCCChhheEEecCCcHHHHHHHHHH
Confidence            5568999999999999999999988753 3346788876654332  22   3444421      112355666666665


Q ss_pred             HHhcCCCeEEEEEecCcccc
Q psy200          292 YFDTKHKSILLILDEIDALE  311 (490)
Q Consensus       292 ~l~~~~~~~vI~IDEid~l~  311 (490)
                      .... .++.+||||.++.+.
T Consensus       805 lv~~-~~~~lVVIDsLq~l~  823 (1706)
T 3cmw_A          805 LARS-GAVDVIVVDSVAALT  823 (1706)
T ss_dssp             HHHH-TCCSEEEESCSTTCC
T ss_pred             HHHc-cCCCEEEEechhhhc
Confidence            5544 457799999999987

>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=96.89  E-value=0.00094  Score=59.70  Aligned_cols=118  Identities=9%  Similarity=0.016  Sum_probs=62.2

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCC---CCHHHHHHHHHHH---hcC--CCCCCc----HHHH
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSV---RNAASVYETIVNE---LKL--KPGGKS----ERHQ  285 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~---~~~~~l~~~i~~~---l~~--~~~~~s----~~~~  285 (490)
                      ..+.++|++.+|.||||+|-.++-... ..++++..+.....   .....++..+.-.   ++.  .+....    ....
T Consensus        27 ~~g~i~v~tG~GkGKTTaA~GlalRA~-g~G~rV~~vQF~Kg~~~~gE~~~l~~L~v~~~~~g~gf~~~~~~~~~~~~~a  105 (196)
T 1g5t_A           27 ERGIIIVFTGNGKGKTTAAFGTAARAV-GHGKNVGVVQFIKGTWPNGERNLLEPHGVEFQVMATGFTWETQNREADTAAC  105 (196)
T ss_dssp             CCCCEEEEESSSSCHHHHHHHHHHHHH-HTTCCEEEEESSCCSSCCHHHHHHGGGTCEEEECCTTCCCCGGGHHHHHHHH
T ss_pred             cCceEEEECCCCCCHHHHHHHHHHHHH-HCCCeEEEEEeeCCCCCccHHHHHHhCCcEEEEcccccccCCCCcHHHHHHH
Confidence            356888999999999999999887764 34566666643321   1233444443100   011  111111    1222


Q ss_pred             HHHHHHHHhc--CCCeEEEEEecCcccccc---CHHHHHHhHhCCCCCCCcEEEEEecC
Q psy200          286 LGAILKYFDT--KHKSILLILDEIDALESR---KQTILYTIFEWPSIPGSKLVLVGVAN  339 (490)
Q Consensus       286 ~~~l~~~l~~--~~~~~vI~IDEid~l~~~---~~~~L~~l~~~~~~~~~~vilI~~tn  339 (490)
                      ...+..+.+.  .++.-+|||||+-.....   ..+.++.++.   ......-+|.+++
T Consensus       106 ~~~l~~a~~~l~~~~yDlvILDEi~~al~~g~l~~~ev~~~l~---~Rp~~~~vIlTGr  161 (196)
T 1g5t_A          106 MAVWQHGKRMLADPLLDMVVLDELTYMVAYDYLPLEEVISALN---ARPGHQTVIITGR  161 (196)
T ss_dssp             HHHHHHHHHHTTCTTCSEEEEETHHHHHHTTSSCHHHHHHHHH---TSCTTCEEEEECS
T ss_pred             HHHHHHHHHHHhcCCCCEEEEeCCCccccCCCCCHHHHHHHHH---hCcCCCEEEEECC
Confidence            3333333332  256779999999654222   3445555554   2333455555555

>2r8r_A Sensor protein; KDPD, PFAM02702, MCSG, structural genomics, protein structure initiative, midwest center for structural genomics, kinase; 2.30A {Pseudomonas syringae PV}

Probab=96.87  E-value=0.0031  Score=57.64  Aligned_cols=39  Identities=10%  Similarity=0.172  Sum_probs=29.6

Q ss_pred             CeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCC
Q psy200          220 GSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSV  259 (490)
Q Consensus       220 ~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~  259 (490)
                      -.+++.|++|+||||++-.++..+.. .++.++.+.+...
T Consensus         7 l~I~~~~kgGvGKTt~a~~la~~l~~-~G~~V~v~d~D~q   45 (228)
T 2r8r_A            7 LKVFLGAAPGVGKTYAMLQAAHAQLR-QGVRVMAGVVETH   45 (228)
T ss_dssp             EEEEEESSTTSSHHHHHHHHHHHHHH-TTCCEEEEECCCT
T ss_pred             EEEEEECCCCCcHHHHHHHHHHHHHH-CCCCEEEEEeCCC
Confidence            46899999999999999999988753 3456666655443

>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=96.87  E-value=0.0036  Score=58.93  Aligned_cols=35  Identities=23%  Similarity=0.292  Sum_probs=26.8

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEE
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYI  254 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v  254 (490)
                      +..|+|.|+||+||||+++.+++.+.. .++.++.+
T Consensus         4 ~~lIvl~G~pGSGKSTla~~La~~L~~-~g~~~i~~   38 (260)
T 3a4m_A            4 IMLIILTGLPGVGKSTFSKNLAKILSK-NNIDVIVL   38 (260)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHHH-TTCCEEEE
T ss_pred             CEEEEEEcCCCCCHHHHHHHHHHHHHh-CCCEEEEE
Confidence            457899999999999999999988541 23445544

>2gxq_A Heat resistant RNA dependent ATPase; RNA helicase, atomic resolution, AMP complex, ribosome biogenesis, thermophilic, hydrolase; HET: AMP; 1.20A {Thermus thermophilus HB27} PDB: 2gxs_A* 2gxu_A 3mwj_A 3mwk_A* 3mwl_A* 3nbf_A* 3nej_A

Probab=96.87  E-value=0.004  Score=55.97  Aligned_cols=25  Identities=20%  Similarity=0.280  Sum_probs=18.6

Q ss_pred             CCeEEEECCCCCcHHHHH-HHHHHHh
Q psy200          219 SGSMYISGPPGTGKSASL-NLLVSRA  243 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla-~~l~~~l  243 (490)
                      ++.+++.+|+|+|||..+ -.+...+
T Consensus        38 ~~~~li~~~TGsGKT~~~~~~~~~~l   63 (207)
T 2gxq_A           38 GKDLIGQARTGTGKTLAFALPIAERL   63 (207)
T ss_dssp             TCCEEEECCTTSCHHHHHHHHHHHHC
T ss_pred             CCCEEEECCCCChHHHHHHHHHHHHH
Confidence            357999999999999874 3444444

>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=96.86  E-value=0.0075  Score=54.69  Aligned_cols=24  Identities=25%  Similarity=0.480  Sum_probs=21.5

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHhh
Q psy200          221 SMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      .|+|+|++|+||||+++.+++.++
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~~~   25 (216)
T 3dl0_A            2 NLVLMGLPGAGKGTQGERIVEKYG   25 (216)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHSS
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhC
Confidence            478999999999999999998864

>1hv8_A Putative ATP-dependent RNA helicase MJ0669; RNA-binding protein, ATPase, RNA binding protein; 3.00A {Methanocaldococcus jannaschii} SCOP: c.37.1.19 c.37.1.19

Probab=96.78  E-value=0.0052  Score=60.23  Aligned_cols=36  Identities=17%  Similarity=0.313  Sum_probs=23.7

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHh-hhcCCceEEEE
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRA-EIKDAFKTIYI  254 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l-~~~~~~~~~~v  254 (490)
                      .+.+++.+|+|+|||..+-..+-.+ .......++++
T Consensus        44 ~~~~l~~~~TGsGKT~~~~~~~~~~~~~~~~~~~lil   80 (367)
T 1hv8_A           44 EYNIVAQARTGSGKTASFAIPLIELVNENNGIEAIIL   80 (367)
T ss_dssp             CSEEEEECCSSSSHHHHHHHHHHHHSCSSSSCCEEEE
T ss_pred             CCCEEEECCCCChHHHHHHHHHHHHhcccCCCcEEEE
Confidence            3689999999999999866554443 22223445555

>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=96.78  E-value=0.0027  Score=64.33  Aligned_cols=88  Identities=18%  Similarity=0.280  Sum_probs=50.7

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCH-HHHHHHHHHHhcCCC-----CCCcHHH-HHHHHHH
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNA-ASVYETIVNELKLKP-----GGKSERH-QLGAILK  291 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~-~~l~~~i~~~l~~~~-----~~~s~~~-~~~~l~~  291 (490)
                      +..++|+|++|+||||++..++..+... +..++.+++...... .+.+..+....+...     .+..... +...+..
T Consensus        99 ~~vI~ivG~~GvGKTTla~~La~~l~~~-G~kVllv~~D~~r~~a~~qL~~~~~~~gv~v~~~~~~~~dp~~i~~~~l~~  177 (432)
T 2v3c_C           99 QNVILLVGIQGSGKTTTAAKLARYIQKR-GLKPALIAADTYRPAAYEQLKQLAEKIHVPIYGDETRTKSPVDIVKEGMEK  177 (432)
T ss_dssp             CCCEEEECCSSSSTTHHHHHHHHHHHHH-HCCEEEECCSCCCTTGGGSSHHHHHHSSCCEECCSSSCCSSSTTHHHHHHT
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHc-CCeEEEEeccccCchHHHHHHHhhhccCcceEecCCCCCCHHHHHHHHHHH
Confidence            4689999999999999999999987532 456777776554321 111222333332211     1111111 1222222


Q ss_pred             HHhcCCCeEEEEEecCcccc
Q psy200          292 YFDTKHKSILLILDEIDALE  311 (490)
Q Consensus       292 ~l~~~~~~~vI~IDEid~l~  311 (490)
                      +    ...-+||||....+.
T Consensus       178 ~----~~~D~vIIDT~G~~~  193 (432)
T 2v3c_C          178 F----KKADVLIIDTAGRHK  193 (432)
T ss_dssp             T----SSCSEEEEECCCSCS
T ss_pred             h----hCCCEEEEcCCCCcc
Confidence            2    334589999998875

>3trf_A Shikimate kinase, SK; amino acid biosynthesis, transferase; 2.60A {Coxiella burnetii}

Probab=96.74  E-value=0.0011  Score=58.81  Aligned_cols=26  Identities=23%  Similarity=0.363  Sum_probs=23.7

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      ...|+|+|++|+||||+++.+++.++
T Consensus         5 ~~~i~l~G~~GsGKst~a~~La~~l~   30 (185)
T 3trf_A            5 LTNIYLIGLMGAGKTSVGSQLAKLTK   30 (185)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHHHHC
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHhC
Confidence            56899999999999999999999875

>3vaa_A Shikimate kinase, SK; structural genomics, center for structural genomics of infec diseases, csgid, metal binding, transferase; 1.70A {Bacteroides thetaiotaomicron}

Probab=96.72  E-value=0.0012  Score=59.39  Aligned_cols=27  Identities=15%  Similarity=0.313  Sum_probs=24.5

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      .+..++|+|++|+||||+++.+++.++
T Consensus        24 ~~~~i~l~G~~GsGKsTl~~~La~~l~   50 (199)
T 3vaa_A           24 AMVRIFLTGYMGAGKTTLGKAFARKLN   50 (199)
T ss_dssp             CCCEEEEECCTTSCHHHHHHHHHHHHT
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHHHcC
Confidence            467899999999999999999999875

>1vec_A ATP-dependent RNA helicase P54; DEAD-box protein, RNA binding protein; HET: TLA; 2.01A {Homo sapiens} SCOP: c.37.1.19

Probab=96.70  E-value=0.0039  Score=56.04  Aligned_cols=40  Identities=23%  Similarity=0.307  Sum_probs=24.1

Q ss_pred             CeEEEEEecCccccccC-HHHHHHhHhCCCCCCCcEEEEEec
Q psy200          298 KSILLILDEIDALESRK-QTILYTIFEWPSIPGSKLVLVGVA  338 (490)
Q Consensus       298 ~~~vI~IDEid~l~~~~-~~~L~~l~~~~~~~~~~vilI~~t  338 (490)
                      +..+|||||+|.+.... ...+..++.... ...+++++.+|
T Consensus       146 ~~~~lViDEah~~~~~~~~~~l~~i~~~~~-~~~~~l~~SAT  186 (206)
T 1vec_A          146 HVQMIVLDEADKLLSQDFVQIMEDIILTLP-KNRQILLYSAT  186 (206)
T ss_dssp             TCCEEEEETHHHHTSTTTHHHHHHHHHHSC-TTCEEEEEESC
T ss_pred             cCCEEEEEChHHhHhhCcHHHHHHHHHhCC-ccceEEEEEee
Confidence            45699999999987543 344444443321 24566666555

>1tev_A UMP-CMP kinase; ploop, NMP binding region, LID region, conformational changes, transferase; 2.10A {Homo sapiens} SCOP: c.37.1.1

Probab=96.70  E-value=0.0031  Score=55.94  Aligned_cols=26  Identities=23%  Similarity=0.457  Sum_probs=23.1

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      +..|+|.|++|+||||+++.+++.++
T Consensus         3 ~~~I~l~G~~GsGKsT~a~~L~~~~~   28 (196)
T 1tev_A            3 PLVVFVLGGPGAGKGTQCARIVEKYG   28 (196)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHC
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHHhC
Confidence            45789999999999999999998874

>4eun_A Thermoresistant glucokinase; putative sugar kinase, enzyme function initiative, EFI, STRU genomics, transferase; 1.60A {Janibacter SP}

Probab=96.68  E-value=0.0011  Score=59.75  Aligned_cols=38  Identities=13%  Similarity=0.294  Sum_probs=28.6

Q ss_pred             cCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCC
Q psy200          216 NETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSV  259 (490)
Q Consensus       216 ~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~  259 (490)
                      ...+..++|.|++|+||||+++.++..++      .++++....
T Consensus        26 ~~~g~~i~l~G~~GsGKSTl~~~L~~~~g------~~~i~~d~~   63 (200)
T 4eun_A           26 GEPTRHVVVMGVSGSGKTTIAHGVADETG------LEFAEADAF   63 (200)
T ss_dssp             --CCCEEEEECCTTSCHHHHHHHHHHHHC------CEEEEGGGG
T ss_pred             CCCCcEEEEECCCCCCHHHHHHHHHHhhC------CeEEccccc
Confidence            34677899999999999999999998763      345555444

>1gvn_B Zeta; postsegregational killing system, plasmid; 1.95A {Streptococcus pyogenes} SCOP: c.37.1.21 PDB: 3q8x_B*

Probab=96.68  E-value=0.0012  Score=63.14  Aligned_cols=26  Identities=19%  Similarity=0.523  Sum_probs=23.4

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHh
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRA  243 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l  243 (490)
                      .+..++|.|++|+||||+++.+++.+
T Consensus        32 ~~~livl~G~sGsGKSTla~~L~~~~   57 (287)
T 1gvn_B           32 SPTAFLLGGQPGSGKTSLRSAIFEET   57 (287)
T ss_dssp             SCEEEEEECCTTSCTHHHHHHHHHHT
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHh
Confidence            45678999999999999999999876

>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=96.67  E-value=0.0016  Score=58.58  Aligned_cols=38  Identities=16%  Similarity=0.231  Sum_probs=29.8

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEe
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYIN  255 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~  255 (490)
                      ..+..++|.|++|+||||+++.++..+. ..+...++++
T Consensus        23 ~~g~~i~l~G~sGsGKSTl~~~La~~l~-~~G~~~~~~d   60 (200)
T 3uie_A           23 QKGCVIWVTGLSGSGKSTLACALNQMLY-QKGKLCYILD   60 (200)
T ss_dssp             SCCEEEEEECSTTSSHHHHHHHHHHHHH-HTTCCEEEEE
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHHH-hcCceEEEec
Confidence            5677899999999999999999999886 3334334554

>2orv_A Thymidine kinase; TP4A (P1-(5'-adenosyl)P4-(5'- (2'deoxythymidil))tetraphosphate, transferase; HET: 4TA; 2.30A {Homo sapiens} SCOP: c.37.1.24 g.39.1.14

Probab=96.66  E-value=0.0014  Score=59.97  Aligned_cols=103  Identities=17%  Similarity=0.153  Sum_probs=48.9

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccC-CCCHHHHHHHHHHHhcCCCCC---CcHHHHHHHHHHHH
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNS-VRNAASVYETIVNELKLKPGG---KSERHQLGAILKYF  293 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~-~~~~~~l~~~i~~~l~~~~~~---~s~~~~~~~l~~~l  293 (490)
                      .+...+++|+.|+||||.+-..+..... .+..++.+.-.. .+...    .+...++.....   ....++.+.    .
T Consensus        18 ~g~l~v~~G~MgsGKTT~lL~~~~r~~~-~g~kvli~kp~~D~Ryg~----~i~sr~G~~~~a~~i~~~~di~~~----~   88 (234)
T 2orv_A           18 RGQIQVILGPMFSGKSTELMRRVRRFQI-AQYKCLVIKYAKDTRYSS----SFCTHDRNTMEALPACLLRDVAQE----A   88 (234)
T ss_dssp             CCEEEEEECCTTSCHHHHHHHHHHHHHT-TTCCEEEEEETTCCCC---------------CEEEEESSGGGGHHH----H
T ss_pred             ceEEEEEECCCCCcHHHHHHHHHHHHHH-CCCeEEEEeecCCccchH----HHHhhcCCeeEEEecCCHHHHHHH----h
Confidence            4567889999999999766666555532 334444443222 12112    233333221100   111222222    2


Q ss_pred             hcCCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEEEe
Q psy200          294 DTKHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGV  337 (490)
Q Consensus       294 ~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI~~  337 (490)
                         +..-+|+|||++.+..  ...+..++.   ..+..|++-|.
T Consensus        89 ---~~~dvViIDEaQF~~~--v~el~~~l~---~~gi~VI~~GL  124 (234)
T 2orv_A           89 ---LGVAVIGIDEGQFFPD--IVEFCEAMA---NAGKTVIVAAL  124 (234)
T ss_dssp             ---TTCSEEEESSGGGCTT--HHHHHHHHH---HTTCEEEEECC
T ss_pred             ---ccCCEEEEEchhhhhh--HHHHHHHHH---hCCCEEEEEec
Confidence               2345999999999963  333334333   23444554443

>2p5t_B PEZT; postsegregational killing system, phosphoryltransferase, HEL helix motif, transcription regulator; 3.20A {Streptococcus pneumoniae}

Probab=96.65  E-value=0.0018  Score=60.71  Aligned_cols=27  Identities=15%  Similarity=0.302  Sum_probs=24.0

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      .+..++|.|+||+||||+++.++..+.
T Consensus        31 ~~~~i~l~G~~GsGKSTla~~L~~~l~   57 (253)
T 2p5t_B           31 QPIAILLGGQSGAGKTTIHRIKQKEFQ   57 (253)
T ss_dssp             SCEEEEEESCGGGTTHHHHHHHHHHTT
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHhcC
Confidence            456789999999999999999998874

>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=96.64  E-value=0.0013  Score=57.27  Aligned_cols=25  Identities=20%  Similarity=0.166  Sum_probs=22.6

Q ss_pred             CeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          220 GSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       220 ~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      ..|+|.|++|+||||+++.+++.++
T Consensus         2 ~~i~l~G~~GsGKsT~~~~L~~~l~   26 (173)
T 3kb2_A            2 TLIILEGPDCCFKSTVAAKLSKELK   26 (173)
T ss_dssp             CEEEEECSSSSSHHHHHHHHHHHHC
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhC
Confidence            3688999999999999999998875

>3bor_A Human initiation factor 4A-II; translation initiation, DEAD BOX, structural genomics, helic binding, HOST-virus interaction, hydrolase; 1.85A {Homo sapiens} PDB: 2g9n_A*

Probab=96.64  E-value=0.002  Score=59.62  Aligned_cols=40  Identities=28%  Similarity=0.440  Sum_probs=23.7

Q ss_pred             CeEEEEEecCccccccC-HHHHHHhHhCCCCCCCcEEEEEec
Q psy200          298 KSILLILDEIDALESRK-QTILYTIFEWPSIPGSKLVLVGVA  338 (490)
Q Consensus       298 ~~~vI~IDEid~l~~~~-~~~L~~l~~~~~~~~~~vilI~~t  338 (490)
                      ...+|||||+|.+.... ...+..++.... ...+++++.+|
T Consensus       173 ~~~~lViDEah~~~~~~~~~~l~~i~~~~~-~~~~~i~~SAT  213 (237)
T 3bor_A          173 WIKMFVLDEADEMLSRGFKDQIYEIFQKLN-TSIQVVLLSAT  213 (237)
T ss_dssp             TCCEEEEESHHHHHHTTCHHHHHHHHHHSC-TTCEEEEECSS
T ss_pred             cCcEEEECCchHhhccCcHHHHHHHHHhCC-CCCeEEEEEEe
Confidence            35699999999886442 344445544321 34455665555

>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=96.64  E-value=0.00057  Score=67.55  Aligned_cols=86  Identities=14%  Similarity=0.198  Sum_probs=46.5

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcC
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFDTK  296 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~  296 (490)
                      ...+.++|+||.|+||||+++.++..+.....-.++.+.-......... ..+   +.....+.....+.+.+..++.  
T Consensus       121 ~~~g~i~I~GptGSGKTTlL~~l~g~~~~~~~~~i~t~ed~~e~~~~~~-~~~---v~q~~~~~~~~~~~~~La~aL~--  194 (356)
T 3jvv_A          121 VPRGLVLVTGPTGSGKSTTLAAMLDYLNNTKYHHILTIEDPIEFVHESK-KCL---VNQREVHRDTLGFSEALRSALR--  194 (356)
T ss_dssp             CSSEEEEEECSTTSCHHHHHHHHHHHHHHHCCCEEEEEESSCCSCCCCS-SSE---EEEEEBTTTBSCHHHHHHHHTT--
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHhcccCCCCcEEEEccCcHHhhhhcc-ccc---eeeeeeccccCCHHHHHHHHhh--
Confidence            3456899999999999999999998876432233333321110000000 000   0000001111234446666665  


Q ss_pred             CCeEEEEEecCc
Q psy200          297 HKSILLILDEID  308 (490)
Q Consensus       297 ~~~~vI~IDEid  308 (490)
                      ..|-+|++||+-
T Consensus       195 ~~PdvillDEp~  206 (356)
T 3jvv_A          195 EDPDIILVGEMR  206 (356)
T ss_dssp             SCCSEEEESCCC
T ss_pred             hCcCEEecCCCC
Confidence            457799999996

>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=96.63  E-value=0.037  Score=53.78  Aligned_cols=91  Identities=16%  Similarity=0.212  Sum_probs=52.3

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCC-CHHHHHHHHHHHhcCC----CCCCc-HHHHHHHHHH
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVR-NAASVYETIVNELKLK----PGGKS-ERHQLGAILK  291 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~-~~~~l~~~i~~~l~~~----~~~~s-~~~~~~~l~~  291 (490)
                      .+..+.|.||.|+||||+++.++..+... ...+....+.... ...+.+..+...++..    ..+.. ...+.+.+..
T Consensus       128 ~g~vi~lvG~nGaGKTTll~~Lag~l~~~-~g~V~l~g~D~~r~~a~eql~~~~~~~gv~~v~q~~~~~p~~~v~e~l~~  206 (328)
T 3e70_C          128 KPYVIMFVGFNGSGKTTTIAKLANWLKNH-GFSVVIAASDTFRAGAIEQLEEHAKRIGVKVIKHSYGADPAAVAYDAIQH  206 (328)
T ss_dssp             SSEEEEEECCTTSSHHHHHHHHHHHHHHT-TCCEEEEEECCSSTTHHHHHHHHHHHTTCEEECCCTTCCHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHhc-CCEEEEEeecccccchHHHHHHHHHHcCceEEeccccCCHHHHHHHHHHH
Confidence            46688899999999999999999887533 2344444443332 3344455555555531    11122 2233444443


Q ss_pred             HHhcCCCeEEEEEecCcccc
Q psy200          292 YFDTKHKSILLILDEIDALE  311 (490)
Q Consensus       292 ~l~~~~~~~vI~IDEid~l~  311 (490)
                      .....  .-+++||......
T Consensus       207 ~~~~~--~d~vliDtaG~~~  224 (328)
T 3e70_C          207 AKARG--IDVVLIDTAGRSE  224 (328)
T ss_dssp             HHHHT--CSEEEEEECCSCC
T ss_pred             HHhcc--chhhHHhhccchh
Confidence            33322  2367789877654

>2ius_A DNA translocase FTSK; nucleotide-binding, chromosome partition, ATP-binding, DNA- binding, cell division, transmembrane, inner membrane; HET: DNA; 2.7A {Escherichia coli} PDB: 2j5p_A*

Probab=96.62  E-value=0.028  Score=57.93  Aligned_cols=73  Identities=19%  Similarity=0.261  Sum_probs=43.6

Q ss_pred             EEEEEecCccccccC----HHHHHHhHhCCCCCCCcEEEEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHH
Q psy200          300 ILLILDEIDALESRK----QTILYTIFEWPSIPGSKLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEI  375 (490)
Q Consensus       300 ~vI~IDEid~l~~~~----~~~L~~l~~~~~~~~~~vilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~i  375 (490)
                      ++|+|||++.+....    .+.+..+....  ....+.+|.+|.+... +-+...++..|.   .+|.|.--+..+...+
T Consensus       299 ivlvIDE~~~ll~~~~~~~~~~l~~Lar~g--Ra~GI~LIlaTQrp~~-dvl~~~i~~n~~---~RI~lrv~s~~dsr~i  372 (512)
T 2ius_A          299 IVVLVDEFADLMMTVGKKVEELIARLAQKA--RAAGIHLVLATQRPSV-DVITGLIKANIP---TRIAFTVSSKIDSRTI  372 (512)
T ss_dssp             EEEEEETHHHHHHHHHHHHHHHHHHHHHHC--GGGTEEEEEEESCCCT-TTSCHHHHHHCC---EEEEECCSSHHHHHHH
T ss_pred             EEEEEeCHHHHHhhhhHHHHHHHHHHHHHh--hhCCcEEEEEecCCcc-ccccHHHHhhcC---CeEEEEcCCHHHHHHh
Confidence            699999998876422    23333443333  2235666666765431 223344555555   4788888899888877


Q ss_pred             HHH
Q psy200          376 ISQ  378 (490)
Q Consensus       376 l~~  378 (490)
                      +..
T Consensus       373 lg~  375 (512)
T 2ius_A          373 LDQ  375 (512)
T ss_dssp             HSS
T ss_pred             cCC
Confidence            653

>4gp7_A Metallophosphoesterase; polynucleotide kinase phosphatase, RNA repair, transferase; HET: ATP CIT; 2.00A {Clostridium thermocellum} PDB: 4gp6_A*

Probab=96.60  E-value=0.0014  Score=57.39  Aligned_cols=22  Identities=23%  Similarity=0.282  Sum_probs=19.3

Q ss_pred             CCCeEEEECCCCCcHHHHHHHH
Q psy200          218 TSGSMYISGPPGTGKSASLNLL  239 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l  239 (490)
                      .+..+.|.|++|+||||+++.+
T Consensus         8 ~gei~~l~G~nGsGKSTl~~~~   29 (171)
T 4gp7_A            8 ELSLVVLIGSSGSGKSTFAKKH   29 (171)
T ss_dssp             SSEEEEEECCTTSCHHHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHHHH
Confidence            4668899999999999999964

>3b6e_A Interferon-induced helicase C domain-containing P; DECH, DEXD/H RNA-binding helicase, innate immunity, IFIH1, S genomics; 1.60A {Homo sapiens}

Probab=96.59  E-value=0.0015  Score=59.00  Aligned_cols=40  Identities=23%  Similarity=0.247  Sum_probs=27.6

Q ss_pred             CChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHh
Q psy200          197 PGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRA  243 (490)
Q Consensus       197 vgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l  243 (490)
                      .-+.-+.+.+..++.       ++.++|.+|+|+|||.++-.++..+
T Consensus        33 ~l~~~Q~~~i~~~~~-------~~~~li~~~tGsGKT~~~~~~~~~~   72 (216)
T 3b6e_A           33 QLRPYQMEVAQPALE-------GKNIIICLPTGSGKTRVAVYIAKDH   72 (216)
T ss_dssp             CCCHHHHHHHHHHHT-------TCCEEEECSCHHHHHHHHHHHHHHH
T ss_pred             CchHHHHHHHHHHhc-------CCCEEEEcCCCCCHHHHHHHHHHHH
Confidence            334445444444442       3579999999999999988777654

>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=96.59  E-value=0.0017  Score=57.23  Aligned_cols=27  Identities=26%  Similarity=0.449  Sum_probs=24.0

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      ....|+|+|++|+||||+++.+++.++
T Consensus        10 ~~~~i~i~G~~GsGKst~~~~l~~~~~   36 (180)
T 3iij_A           10 LLPNILLTGTPGVGKTTLGKELASKSG   36 (180)
T ss_dssp             CCCCEEEECSTTSSHHHHHHHHHHHHC
T ss_pred             cCCeEEEEeCCCCCHHHHHHHHHHHhC
Confidence            356799999999999999999998874

>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=96.58  E-value=0.0058  Score=61.74  Aligned_cols=27  Identities=26%  Similarity=0.325  Sum_probs=23.5

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      .+..|+|+|+||+||||+++.+++.++
T Consensus       257 ~~~lIil~G~pGSGKSTla~~L~~~~~  283 (416)
T 3zvl_A          257 NPEVVVAVGFPGAGKSTFIQEHLVSAG  283 (416)
T ss_dssp             SCCEEEEESCTTSSHHHHHHHHTGGGT
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHhcC
Confidence            457899999999999999999987753

>1rz3_A Hypothetical protein rbstp0775; MCSG, structural genomics, PSI, protein structure initiative; 1.90A {Geobacillus stearothermophilus} SCOP: c.37.1.6

Probab=96.57  E-value=0.0026  Score=57.25  Aligned_cols=46  Identities=15%  Similarity=0.128  Sum_probs=34.8

Q ss_pred             ChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          198 GREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       198 gre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      .+.+.++.|.+.+... ....+..+.|.|++|+||||+++.++..+.
T Consensus         2 ~~~~~~~~l~~~~~~~-~~~~~~~i~i~G~~GsGKstl~~~l~~~~~   47 (201)
T 1rz3_A            2 ELRDRIDFLCKTILAI-KTAGRLVLGIDGLSRSGKTTLANQLSQTLR   47 (201)
T ss_dssp             CHHHHHHHHHHHHHTS-CCSSSEEEEEEECTTSSHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHHh-ccCCCeEEEEECCCCCCHHHHHHHHHHHHh
Confidence            3556777777777542 223456788999999999999999998774

>1kag_A SKI, shikimate kinase I; transferase, structural genomics, PSI, protein structure initiative; 2.05A {Escherichia coli} SCOP: c.37.1.2

Probab=96.54  E-value=0.0015  Score=57.13  Aligned_cols=26  Identities=27%  Similarity=0.501  Sum_probs=23.2

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      +..++|+|++|+||||+++.++..++
T Consensus         4 ~~~i~l~G~~GsGKSTl~~~La~~l~   29 (173)
T 1kag_A            4 KRNIFLVGPMGAGKSTIGRQLAQQLN   29 (173)
T ss_dssp             CCCEEEECCTTSCHHHHHHHHHHHTT
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHhC
Confidence            45789999999999999999998864

>3l0o_A Transcription termination factor RHO; helicase, RHO factor, RNA capture mechanism, ATP-binding, hydrolase, nucleotide-binding, RN binding; 2.35A {Thermotoga maritima}

Probab=96.53  E-value=0.0016  Score=64.14  Aligned_cols=97  Identities=13%  Similarity=0.139  Sum_probs=55.9

Q ss_pred             cCCCCeEEEECCCCCcHHHHHHHHHHHhhh-cCCceEEEEeccCCCC-HHHHHHHHHHHhcCCCCCCcH-HH-----HHH
Q psy200          216 NETSGSMYISGPPGTGKSASLNLLVSRAEI-KDAFKTIYINCNSVRN-AASVYETIVNELKLKPGGKSE-RH-----QLG  287 (490)
Q Consensus       216 ~~~~~~ill~GppGtGKTtla~~l~~~l~~-~~~~~~~~v~~~~~~~-~~~l~~~i~~~l~~~~~~~s~-~~-----~~~  287 (490)
                      -+.++.++|.|++|+|||+|+..+++.... .+++.++++-+..-.. ..++++.+...+-........ ..     ..-
T Consensus       172 igrGQR~lIfg~~g~GKT~Ll~~Ia~~i~~~~~dv~~V~~lIGER~~EV~d~~~~~~G~VV~atadep~~~r~~~a~~al  251 (427)
T 3l0o_A          172 IGKGQRGMIVAPPKAGKTTILKEIANGIAENHPDTIRIILLIDERPEEVTDIRESTNAIVIAAPFDMPPDKQVKVAELTL  251 (427)
T ss_dssp             CBTTCEEEEEECTTCCHHHHHHHHHHHHHHHCTTSEEEEEECSCCHHHHSSSSSSCCSEEEECCTTSCHHHHHHHHHHHH
T ss_pred             ccCCceEEEecCCCCChhHHHHHHHHHHhhcCCCeEEEEEEeccCcchHHHHHHHhCCeEEEECCCCCHHHHHHHHHHHH
Confidence            357889999999999999999999987653 3566666665543211 011111111000001111111 11     111


Q ss_pred             HHHHHHhcCCCeEEEEEecCccccc
Q psy200          288 AILKYFDTKHKSILLILDEIDALES  312 (490)
Q Consensus       288 ~l~~~l~~~~~~~vI~IDEid~l~~  312 (490)
                      .+.+++...++.++|++|++-++..
T Consensus       252 tiAEyfrd~G~dVLil~DslTR~A~  276 (427)
T 3l0o_A          252 EMAKRLVEFNYDVVILLDSLTRLAR  276 (427)
T ss_dssp             HHHHHHHHTTCEEEEEEECHHHHHH
T ss_pred             HHHHHHHHcCCCEEEecccchHHHH
Confidence            2344555568899999999988753

>3fmo_B ATP-dependent RNA helicase DDX19B; nuclear porin, nuclear pore complex, nucleocytoplasmic trans mRNA export, protein interaction, beta-propeller; HET: ADP; 2.51A {Homo sapiens}

Probab=96.53  E-value=0.016  Score=55.73  Aligned_cols=28  Identities=29%  Similarity=0.484  Sum_probs=20.4

Q ss_pred             CCCCeEEEECCCCCcHHHHHH-HHHHHhh
Q psy200          217 ETSGSMYISGPPGTGKSASLN-LLVSRAE  244 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~-~l~~~l~  244 (490)
                      +.++.+++.+|.|+|||...- .+++.+.
T Consensus       129 ~~~~~~l~~a~TGsGKT~a~~lp~l~~l~  157 (300)
T 3fmo_B          129 EPPQNLIAQSQSGTGKTAAFVLAMLSQVE  157 (300)
T ss_dssp             SSCCCEEEECCTTSSHHHHHHHHHHHHCC
T ss_pred             CCCCeEEEECCCCCCccHHHHHHHHHhhh
Confidence            345789999999999997643 4445543

>2xb4_A Adenylate kinase; ATP-binding, nucleotide-binding, transferase; HET: SRT; 1.80A {Desulfovibrio gigas} PDB: 3l0s_A* 3l0p_A*

Probab=96.53  E-value=0.014  Score=53.33  Aligned_cols=24  Identities=33%  Similarity=0.580  Sum_probs=21.9

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHhh
Q psy200          221 SMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      .++|.|++|+||||+++.+++.++
T Consensus         2 ~I~l~G~~GsGKsT~a~~La~~lg   25 (223)
T 2xb4_A            2 NILIFGPNGSGKGTQGNLVKDKYS   25 (223)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhC
Confidence            578999999999999999999874

>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=96.50  E-value=0.0022  Score=56.85  Aligned_cols=25  Identities=28%  Similarity=0.616  Sum_probs=22.9

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHH
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~  242 (490)
                      .+..++|+|++|+||||+++.+++.
T Consensus         9 ~~~~I~l~G~~GsGKSTv~~~La~~   33 (184)
T 1y63_A            9 KGINILITGTPGTGKTSMAEMIAAE   33 (184)
T ss_dssp             SSCEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHh
Confidence            4568999999999999999999987

>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=96.49  E-value=0.0017  Score=57.58  Aligned_cols=26  Identities=23%  Similarity=0.474  Sum_probs=23.5

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      +..++|.|++|+||||+++.+++.++
T Consensus         3 ~~~I~i~G~~GsGKsT~~~~L~~~l~   28 (192)
T 1kht_A            3 NKVVVVTGVPGVGSTTSSQLAMDNLR   28 (192)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHH
Confidence            45789999999999999999999875

>1via_A Shikimate kinase; structural genomics, transferase; HET: MSE; 1.57A {Campylobacter jejuni} SCOP: c.37.1.2

Probab=96.47  E-value=0.0021  Score=56.33  Aligned_cols=25  Identities=24%  Similarity=0.304  Sum_probs=22.7

Q ss_pred             CeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          220 GSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       220 ~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      ..++|.|++|+||||+++.+++.++
T Consensus         5 ~~i~i~G~~GsGKsTla~~La~~l~   29 (175)
T 1via_A            5 KNIVFIGFMGSGKSTLARALAKDLD   29 (175)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHHHHT
T ss_pred             CEEEEEcCCCCCHHHHHHHHHHHcC
Confidence            3689999999999999999999875

>1zuh_A Shikimate kinase; alpha-beta protein, transferase; 1.80A {Helicobacter pylori} PDB: 1zui_A* 3hr7_A 3muf_A* 3mrs_A 3n2e_A*

Probab=96.47  E-value=0.0021  Score=55.89  Aligned_cols=27  Identities=22%  Similarity=0.175  Sum_probs=23.5

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      ...+++|.|++|+||||+++.+++.++
T Consensus         6 ~~~~i~l~G~~GsGKSTva~~La~~lg   32 (168)
T 1zuh_A            6 HMQHLVLIGFMGSGKSSLAQELGLALK   32 (168)
T ss_dssp             --CEEEEESCTTSSHHHHHHHHHHHHT
T ss_pred             ccceEEEECCCCCCHHHHHHHHHHHhC
Confidence            356899999999999999999999876

>3c8u_A Fructokinase; YP_612366.1, putative fructose transport system kinase, STRU genomics, joint center for structural genomics, JCSG; 1.95A {Silicibacter SP}

Probab=96.47  E-value=0.0023  Score=58.03  Aligned_cols=28  Identities=32%  Similarity=0.425  Sum_probs=24.8

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      ..+..+.|.|++|+|||||++.++..+.
T Consensus        20 ~~g~~v~I~G~sGsGKSTl~~~l~~~~~   47 (208)
T 3c8u_A           20 PGRQLVALSGAPGSGKSTLSNPLAAALS   47 (208)
T ss_dssp             CSCEEEEEECCTTSCTHHHHHHHHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHHh
Confidence            4567888999999999999999998875

>3vkw_A Replicase large subunit; alpha/beta domain, helicase, transferase; 1.90A {Tomato mosaic virus}

Probab=96.46  E-value=0.0046  Score=62.38  Aligned_cols=107  Identities=15%  Similarity=0.150  Sum_probs=56.0

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCC----CCCCcHHHHHHHHHHHH
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLK----PGGKSERHQLGAILKYF  293 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~----~~~~s~~~~~~~l~~~l  293 (490)
                      ..+..+|.|+||+|||+++..+++.    .  ..+.+.     -......+|.+.+...    ........+..++.+..
T Consensus       160 ~~~v~~I~G~aGsGKTt~I~~~~~~----~--~~lVlT-----pT~~aa~~l~~kl~~~~~~~~~~~~V~T~dsfL~~~~  228 (446)
T 3vkw_A          160 SAKVVLVDGVPGCGKTKEILSRVNF----E--EDLILV-----PGRQAAEMIRRRANASGIIVATKDNVRTVDSFLMNYG  228 (446)
T ss_dssp             CSEEEEEEECTTSCHHHHHHHHCCT----T--TCEEEE-----SCHHHHHHHHHHHTTTSCCCCCTTTEEEHHHHHHTTT
T ss_pred             cccEEEEEcCCCCCHHHHHHHHhcc----C--CeEEEe-----CCHHHHHHHHHHhhhcCccccccceEEEeHHhhcCCC
Confidence            5568889999999999999877642    1  112221     1133344454555321    11112223333332211


Q ss_pred             hcC-CCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEEEecCC
Q psy200          294 DTK-HKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVANA  340 (490)
Q Consensus       294 ~~~-~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI~~tn~  340 (490)
                      ... ...-+|||||+..+...   .+..++...  ...+++++|-.+-
T Consensus       229 ~~~~~~~d~liiDE~sm~~~~---~l~~l~~~~--~~~~vilvGD~~Q  271 (446)
T 3vkw_A          229 KGARCQFKRLFIDEGLMLHTG---CVNFLVEMS--LCDIAYVYGDTQQ  271 (446)
T ss_dssp             SSCCCCCSEEEEETGGGSCHH---HHHHHHHHT--TCSEEEEEECTTS
T ss_pred             CCCCCcCCEEEEeCcccCCHH---HHHHHHHhC--CCCEEEEecCccc
Confidence            100 01359999999977543   333333222  2378899887763

>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=96.46  E-value=0.0021  Score=57.13  Aligned_cols=27  Identities=26%  Similarity=0.431  Sum_probs=23.9

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      .+..|+|.|++|+||||+++.+++.++
T Consensus         4 ~~~~I~l~G~~GsGKST~~~~L~~~l~   30 (193)
T 2rhm_A            4 TPALIIVTGHPATGKTTLSQALATGLR   30 (193)
T ss_dssp             CCEEEEEEESTTSSHHHHHHHHHHHHT
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHcC
Confidence            356789999999999999999998874

>2j37_W Signal recognition particle 54 kDa protein (SRP54); ribosome, SRP, translation/RNA; 8.00A {Canis SP} PDB: 1wgw_A

Probab=96.45  E-value=0.035  Score=57.15  Aligned_cols=90  Identities=14%  Similarity=0.178  Sum_probs=52.9

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCH-HHHHHHHHHHhcCC----CCCCcHHHH-HHHHHHH
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNA-ASVYETIVNELKLK----PGGKSERHQ-LGAILKY  292 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~-~~l~~~i~~~l~~~----~~~~s~~~~-~~~l~~~  292 (490)
                      +..|+|+|.+|+||||++..++..+... +..+..+++-..... .+.+.......+.+    ..+....++ .+.+..+
T Consensus       101 ~~vI~ivG~~GvGKTTl~~kLA~~l~~~-G~kVllVd~D~~r~aa~~qL~~~~~~~~i~v~~~~~~~dp~~i~~~al~~~  179 (504)
T 2j37_W          101 QNVIMFVGLQGSGKTTTCSKLAYYYQRK-GWKTCLICADTFRAGAFDQLKQNATKARIPFYGSYTEMDPVIIASEGVEKF  179 (504)
T ss_dssp             -EEEEEECSTTSSHHHHHHHHHHHHHHT-TCCEEEEEECCSSSHHHHHHHHHHHHHTCCEEECCCCSCHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHhC-CCeEEEEeccccchhHHHHHHHHhhccCceEEccCCCCCHHHHHHHHHHHH
Confidence            4578899999999999999999888633 456677776554432 23333333333332    122223232 2333333


Q ss_pred             HhcCCCeEEEEEecCcccc
Q psy200          293 FDTKHKSILLILDEIDALE  311 (490)
Q Consensus       293 l~~~~~~~vI~IDEid~l~  311 (490)
                      ..  ...-++|||-...+.
T Consensus       180 ~~--~~~DvvIIDTpG~~~  196 (504)
T 2j37_W          180 KN--ENFEIIIVDTSGRHK  196 (504)
T ss_dssp             HH--TTCCEEEEEECCCCT
T ss_pred             HH--CCCcEEEEeCCCCcc
Confidence            21  224599999988764

>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=96.43  E-value=0.0025  Score=55.41  Aligned_cols=24  Identities=38%  Similarity=0.580  Sum_probs=20.8

Q ss_pred             CeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          220 GSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       220 ~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      ..++|.|++|+||||+++.+ +.++
T Consensus         2 ~~I~l~G~~GsGKsT~a~~L-~~~g   25 (179)
T 3lw7_A            2 KVILITGMPGSGKSEFAKLL-KERG   25 (179)
T ss_dssp             CEEEEECCTTSCHHHHHHHH-HHTT
T ss_pred             cEEEEECCCCCCHHHHHHHH-HHCC
Confidence            36889999999999999999 6654

>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=96.41  E-value=0.0023  Score=56.57  Aligned_cols=25  Identities=28%  Similarity=0.329  Sum_probs=22.8

Q ss_pred             CeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          220 GSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       220 ~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      ..|+|+|++|+||||+++.+++.++
T Consensus         3 ~~I~l~G~~GsGKsT~a~~La~~lg   27 (184)
T 2iyv_A            3 PKAVLVGLPGSGKSTIGRRLAKALG   27 (184)
T ss_dssp             CSEEEECSTTSSHHHHHHHHHHHHT
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHcC
Confidence            4689999999999999999999875

>2oxc_A Probable ATP-dependent RNA helicase DDX20; DEAD, structural genomics, structural genomics consortium, SGC, hydrolase; HET: ADP; 1.30A {Homo sapiens} PDB: 3b7g_A*

Probab=96.41  E-value=0.011  Score=54.17  Aligned_cols=36  Identities=11%  Similarity=0.275  Sum_probs=22.6

Q ss_pred             CCeEEEECCCCCcHHHHH-HHHHHHhhh-cCCceEEEE
Q psy200          219 SGSMYISGPPGTGKSASL-NLLVSRAEI-KDAFKTIYI  254 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla-~~l~~~l~~-~~~~~~~~v  254 (490)
                      ++.+++.+|.|+|||... -.+...+.. .....++++
T Consensus        61 ~~~~l~~a~TGsGKT~~~~l~~l~~l~~~~~~~~~lil   98 (230)
T 2oxc_A           61 GLDLIVQAKSGTGKTCVFSTIALDSLVLENLSTQILIL   98 (230)
T ss_dssp             TCCEEEECCTTSSHHHHHHHHHHHHCCTTSCSCCEEEE
T ss_pred             CCCEEEECCCCCcHHHHHHHHHHHHHHhcCCCceEEEE
Confidence            367999999999999873 334444422 222345555

>3eiq_A Eukaryotic initiation factor 4A-I; PDCD4, anti-oncogene, apoptosis, cell cycle, nucleus, phosph RNA-binding, ATP-binding, helicase, hydrolase; 3.50A {Homo sapiens}

Probab=96.40  E-value=0.0098  Score=59.44  Aligned_cols=40  Identities=28%  Similarity=0.452  Sum_probs=24.1

Q ss_pred             CeEEEEEecCccccccC-HHHHHHhHhCCCCCCCcEEEEEec
Q psy200          298 KSILLILDEIDALESRK-QTILYTIFEWPSIPGSKLVLVGVA  338 (490)
Q Consensus       298 ~~~vI~IDEid~l~~~~-~~~L~~l~~~~~~~~~~vilI~~t  338 (490)
                      ...+|||||+|.+.... ...+..++... ....+++++.+|
T Consensus       183 ~~~~vViDEah~~~~~~~~~~~~~~~~~~-~~~~~~i~~SAT  223 (414)
T 3eiq_A          183 YIKMFVLDEADEMLSRGFKDQIYDIFQKL-NSNTQVVLLSAT  223 (414)
T ss_dssp             TCCEEEECSHHHHHHTTTHHHHHHHHTTS-CTTCEEEEECSC
T ss_pred             cCcEEEEECHHHhhccCcHHHHHHHHHhC-CCCCeEEEEEEe
Confidence            34599999999986543 34444454432 244566666555

>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=96.39  E-value=0.0029  Score=56.89  Aligned_cols=27  Identities=26%  Similarity=0.487  Sum_probs=24.0

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      .+..|+|+|++|+||||+++.+++.++
T Consensus        19 ~~~~I~l~G~~GsGKST~a~~La~~l~   45 (201)
T 2cdn_A           19 SHMRVLLLGPPGAGKGTQAVKLAEKLG   45 (201)
T ss_dssp             SCCEEEEECCTTSSHHHHHHHHHHHHT
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHhC
Confidence            455789999999999999999999875

>3fe2_A Probable ATP-dependent RNA helicase DDX5; DEAD, ADP, ATP-binding, hydrolase, nucleotide- RNA-binding, methylation, mRNA processing, mRNA S nucleus; HET: ADP; 2.60A {Homo sapiens} PDB: 4a4d_A

Probab=96.36  E-value=0.03  Score=51.68  Aligned_cols=40  Identities=18%  Similarity=0.292  Sum_probs=24.9

Q ss_pred             CeEEEEEecCccccccC-HHHHHHhHhCCCCCCCcEEEEEec
Q psy200          298 KSILLILDEIDALESRK-QTILYTIFEWPSIPGSKLVLVGVA  338 (490)
Q Consensus       298 ~~~vI~IDEid~l~~~~-~~~L~~l~~~~~~~~~~vilI~~t  338 (490)
                      ...+|||||+|.+.... ...+..++... ....+++++.+|
T Consensus       176 ~~~~lViDEah~l~~~~~~~~~~~i~~~~-~~~~q~~~~SAT  216 (242)
T 3fe2_A          176 RTTYLVLDEADRMLDMGFEPQIRKIVDQI-RPDRQTLMWSAT  216 (242)
T ss_dssp             TCCEEEETTHHHHHHTTCHHHHHHHHTTS-CSSCEEEEEESC
T ss_pred             cccEEEEeCHHHHhhhCcHHHHHHHHHhC-CccceEEEEEee
Confidence            45599999999987643 34444555433 234566666665

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19

Probab=96.34  E-value=0.0098  Score=54.06  Aligned_cols=40  Identities=15%  Similarity=0.167  Sum_probs=24.4

Q ss_pred             CeEEEEEecCccccccC-HHHHHHhHhCCCCCCCcEEEEEec
Q psy200          298 KSILLILDEIDALESRK-QTILYTIFEWPSIPGSKLVLVGVA  338 (490)
Q Consensus       298 ~~~vI~IDEid~l~~~~-~~~L~~l~~~~~~~~~~vilI~~t  338 (490)
                      ...+|||||+|.+.... ...+..++.... ...+++++.+|
T Consensus       150 ~~~~lViDEah~~~~~~~~~~l~~i~~~~~-~~~~~l~~SAT  190 (219)
T 1q0u_A          150 TAHILVVDEADLMLDMGFITDVDQIAARMP-KDLQMLVFSAT  190 (219)
T ss_dssp             GCCEEEECSHHHHHHTTCHHHHHHHHHTSC-TTCEEEEEESC
T ss_pred             cceEEEEcCchHHhhhChHHHHHHHHHhCC-cccEEEEEecC
Confidence            34589999999987543 344445544322 34556666666

>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=96.34  E-value=0.003  Score=57.65  Aligned_cols=27  Identities=37%  Similarity=0.519  Sum_probs=24.1

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      .+..|+|.|++|+||||+++.+++.++
T Consensus         3 ~~~~I~l~G~~GsGKsT~a~~La~~l~   29 (220)
T 1aky_A            3 ESIRMVLIGPPGAGKGTQAPNLQERFH   29 (220)
T ss_dssp             CCCEEEEECCTTSSHHHHHHHHHHHHC
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHcC
Confidence            456789999999999999999999875

>2c95_A Adenylate kinase 1; transferase, AP4A, nucleotide kinase, transferase ATP-bindi; HET: B4P; 1.71A {Homo sapiens} PDB: 1z83_A* 3adk_A

Probab=96.34  E-value=0.0029  Score=56.37  Aligned_cols=27  Identities=22%  Similarity=0.556  Sum_probs=24.2

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      .+..|+|.|++|+||||+++.+++.++
T Consensus         8 ~~~~I~l~G~~GsGKsT~~~~La~~l~   34 (196)
T 2c95_A            8 KTNIIFVVGGPGSGKGTQCEKIVQKYG   34 (196)
T ss_dssp             TSCEEEEEECTTSSHHHHHHHHHHHHC
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHhC
Confidence            456899999999999999999998874

>3cm0_A Adenylate kinase; ATP-binding, cytoplasm, nucleotide biosynthesis, nucleotide-binding, transferase, structural genomics; 1.80A {Thermus thermophilus}

Probab=96.33  E-value=0.0025  Score=56.35  Aligned_cols=26  Identities=27%  Similarity=0.520  Sum_probs=23.1

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      +..++|.|++|+||||+++.+++.++
T Consensus         4 g~~I~l~G~~GsGKST~~~~La~~l~   29 (186)
T 3cm0_A            4 GQAVIFLGPPGAGKGTQASRLAQELG   29 (186)
T ss_dssp             EEEEEEECCTTSCHHHHHHHHHHHHT
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhC
Confidence            45788999999999999999998874

>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=96.32  E-value=0.0031  Score=54.90  Aligned_cols=25  Identities=16%  Similarity=0.288  Sum_probs=22.8

Q ss_pred             CeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          220 GSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       220 ~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      ..|+|+|++|+||||+++.+++.++
T Consensus         3 ~~I~l~G~~GsGKsT~a~~La~~lg   27 (173)
T 1e6c_A            3 EPIFMVGARGCGMTTVGRELARALG   27 (173)
T ss_dssp             CCEEEESCTTSSHHHHHHHHHHHHT
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHhC
Confidence            4689999999999999999999875

>3pey_A ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, ATPase, helicase, mRNA-export, nuclear pore, hydrolase-RNA complex; HET: ADP; 1.40A {Saccharomyces cerevisiae} PDB: 3pew_A* 3pex_A* 3pez_A* 3rrm_A* 3rrn_A* 2kbe_A 3gfp_A 2kbf_A 3pev_A* 3peu_A*

Probab=96.31  E-value=0.015  Score=57.42  Aligned_cols=24  Identities=29%  Similarity=0.501  Sum_probs=18.7

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHH
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLV  240 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~  240 (490)
                      +.++.+++.+|+|+|||..+-..+
T Consensus        42 ~~~~~~lv~a~TGsGKT~~~~~~~   65 (395)
T 3pey_A           42 NPPRNMIAQSQSGTGKTAAFSLTM   65 (395)
T ss_dssp             SSCCCEEEECCTTSCHHHHHHHHH
T ss_pred             CCCCeEEEECCCCCcHHHHHHHHH
Confidence            345789999999999998765433

>3lfu_A DNA helicase II; SF1 helicase, ATP-binding, DNA damage, DNA REP replication, DNA-binding, hydrolase, nucleotide-B SOS response; HET: DNA; 1.80A {Escherichia coli} PDB: 2is6_A* 2is2_A* 2is1_A* 2is4_A*

Probab=96.31  E-value=0.0083  Score=64.13  Aligned_cols=36  Identities=14%  Similarity=0.204  Sum_probs=24.5

Q ss_pred             eEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEEEec
Q psy200          299 SILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVA  338 (490)
Q Consensus       299 ~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI~~t  338 (490)
                      .-.|+|||+|.+.......+..+..    .+.+++++|-.
T Consensus       214 ~~~ilVDE~QD~~~~q~~ll~~l~~----~~~~l~~vGD~  249 (647)
T 3lfu_A          214 FTNILVDEFQDTNNIQYAWIRLLAG----DTGKVMIVGDD  249 (647)
T ss_dssp             CCEEEESSGGGCCHHHHHHHHHHHT----TTCEEEEEECG
T ss_pred             CCEEEEECcccCCHHHHHHHHHHhc----CCCEEEEEcCc
Confidence            4589999999997665566655543    34467777654

>3t61_A Gluconokinase; PSI-biology, structural genomics, protein structure initiati YORK structural genomics research consortium, nysgrc; 2.20A {Sinorhizobium meliloti}

Probab=96.30  E-value=0.0027  Score=57.13  Aligned_cols=27  Identities=26%  Similarity=0.409  Sum_probs=23.9

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      .+..++|.|++|+||||+++.++..++
T Consensus        17 ~~~~I~l~G~~GsGKSTla~~L~~~lg   43 (202)
T 3t61_A           17 FPGSIVVMGVSGSGKSSVGEAIAEACG   43 (202)
T ss_dssp             CSSCEEEECSTTSCHHHHHHHHHHHHT
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHhC
Confidence            356899999999999999999998874

>3dkp_A Probable ATP-dependent RNA helicase DDX52; DEAD, ADP, structural genomics, structural GEN consortium, SGC, rRNA, ATP-binding, hydrolase; HET: ADP; 2.10A {Homo sapiens}

Probab=96.30  E-value=0.03  Score=51.71  Aligned_cols=41  Identities=20%  Similarity=0.145  Sum_probs=24.5

Q ss_pred             CeEEEEEecCcccccc----CHHHHHHhHhCCCCCCCcEEEEEec
Q psy200          298 KSILLILDEIDALESR----KQTILYTIFEWPSIPGSKLVLVGVA  338 (490)
Q Consensus       298 ~~~vI~IDEid~l~~~----~~~~L~~l~~~~~~~~~~vilI~~t  338 (490)
                      ...+|||||+|.+...    -...+..++........+++++.+|
T Consensus       175 ~~~~lViDEah~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~SAT  219 (245)
T 3dkp_A          175 SVEWLVVDESDKLFEDGKTGFRDQLASIFLACTSHKVRRAMFSAT  219 (245)
T ss_dssp             TCCEEEESSHHHHHHHC--CHHHHHHHHHHHCCCTTCEEEEEESS
T ss_pred             cCcEEEEeChHHhcccccccHHHHHHHHHHhcCCCCcEEEEEecc
Confidence            3558999999999752    2334444443333345566666655

>1ly1_A Polynucleotide kinase; PNK, phosphatase, transferase; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.1

Probab=96.29  E-value=0.0022  Score=56.29  Aligned_cols=22  Identities=27%  Similarity=0.428  Sum_probs=20.4

Q ss_pred             CeEEEECCCCCcHHHHHHHHHH
Q psy200          220 GSMYISGPPGTGKSASLNLLVS  241 (490)
Q Consensus       220 ~~ill~GppGtGKTtla~~l~~  241 (490)
                      ..++|.|+||+||||+++.+++
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            4688999999999999999987

>1kgd_A CASK, peripheral plasma membrane CASK; maguk, guanylate kinase like domain, protein binding; 1.31A {Homo sapiens} SCOP: c.37.1.1

Probab=96.28  E-value=0.0026  Score=56.22  Aligned_cols=26  Identities=19%  Similarity=0.409  Sum_probs=23.0

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHh
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRA  243 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l  243 (490)
                      .+..++|+||+|+|||||++.++..+
T Consensus         4 ~g~~i~i~GpsGsGKSTL~~~L~~~~   29 (180)
T 1kgd_A            4 MRKTLVLLGAHGVGRRHIKNTLITKH   29 (180)
T ss_dssp             CCCEEEEECCTTSSHHHHHHHHHHHC
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHhhC
Confidence            35688999999999999999998875

>2pbr_A DTMP kinase, thymidylate kinase; transferase, nucleotide biosynthesis, TMP-binding, A binding, structural genomics, NPPSFA; 1.96A {Aquifex aeolicus}

Probab=96.27  E-value=0.007  Score=53.64  Aligned_cols=35  Identities=14%  Similarity=0.168  Sum_probs=27.0

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEec
Q psy200          221 SMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINC  256 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~  256 (490)
                      .++|.|++|+||||+++.+++.+.. .++.++....
T Consensus         2 ~I~l~G~~GsGKsT~~~~L~~~l~~-~g~~~i~~d~   36 (195)
T 2pbr_A            2 LIAFEGIDGSGKTTQAKKLYEYLKQ-KGYFVSLYRE   36 (195)
T ss_dssp             EEEEECSTTSCHHHHHHHHHHHHHH-TTCCEEEEES
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHH-CCCeEEEEeC
Confidence            5789999999999999999998731 2355665543

>2qor_A Guanylate kinase; phosphotransferase, purine metabolism, structural genomics, structural genomics of pathogenic protozoa consortium; HET: 5GP POP; 1.80A {Plasmodium vivax}

Probab=96.26  E-value=0.0025  Score=57.52  Aligned_cols=27  Identities=22%  Similarity=0.452  Sum_probs=24.1

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      .+..++|+|++|+||||+++.++..+.
T Consensus        11 ~~~~i~l~G~sGsGKsTl~~~L~~~~~   37 (204)
T 2qor_A           11 RIPPLVVCGPSGVGKGTLIKKVLSEFP   37 (204)
T ss_dssp             CCCCEEEECCTTSCHHHHHHHHHHHCT
T ss_pred             cCCEEEEECCCCCCHHHHHHHHHHhCc
Confidence            567899999999999999999998763

>1nks_A Adenylate kinase; thermophilic, transferase; HET: AMP ADP; 2.57A {Sulfolobus acidocaldarius} SCOP: c.37.1.1

Probab=96.25  E-value=0.0023  Score=56.72  Aligned_cols=34  Identities=24%  Similarity=0.300  Sum_probs=26.8

Q ss_pred             CeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEE
Q psy200          220 GSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYI  254 (490)
Q Consensus       220 ~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v  254 (490)
                      ..|+|.|++|+||||+++.+++.+.. .++.+.++
T Consensus         2 ~~I~i~G~~GsGKsT~~~~L~~~l~~-~g~~~~~~   35 (194)
T 1nks_A            2 KIGIVTGIPGVGKSTVLAKVKEILDN-QGINNKII   35 (194)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHHHHHT-TTCCEEEE
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHh-cCceEEEE
Confidence            36889999999999999999998852 23445555

>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=96.24  E-value=0.006  Score=54.66  Aligned_cols=36  Identities=17%  Similarity=0.222  Sum_probs=27.9

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEec
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINC  256 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~  256 (490)
                      .+..|+|.|++|+||||+++.+++.+   .++.++.+..
T Consensus         3 ~~~~I~l~G~~GsGKsT~~~~L~~~l---~g~~~~~~~~   38 (204)
T 2v54_A            3 RGALIVFEGLDKSGKTTQCMNIMESI---PANTIKYLNF   38 (204)
T ss_dssp             CCCEEEEECCTTSSHHHHHHHHHHTS---CGGGEEEEES
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHHH---CCCceEEEec
Confidence            35688999999999999999999886   2245555543

>1s2m_A Putative ATP-dependent RNA helicase DHH1; ATP-binding, RNA-binding, RNA binding protein; 2.10A {Saccharomyces cerevisiae} SCOP: c.37.1.19 c.37.1.19 PDB: 2wax_A* 2way_A

Probab=96.24  E-value=0.02  Score=56.93  Aligned_cols=21  Identities=24%  Similarity=0.385  Sum_probs=16.7

Q ss_pred             CeEEEECCCCCcHHHHHHHHH
Q psy200          220 GSMYISGPPGTGKSASLNLLV  240 (490)
Q Consensus       220 ~~ill~GppGtGKTtla~~l~  240 (490)
                      +.+++.+|+|+|||..+-..+
T Consensus        59 ~~~li~a~TGsGKT~~~~~~~   79 (400)
T 1s2m_A           59 RDILARAKNGTGKTAAFVIPT   79 (400)
T ss_dssp             CCEEEECCTTSCHHHHHHHHH
T ss_pred             CCEEEECCCCcHHHHHHHHHH
Confidence            469999999999998654443

>2ze6_A Isopentenyl transferase; crown GALL tumor, cytokinin biosynthesis; HET: DST AMP; 2.10A {Agrobacterium tumefaciens} PDB: 2ze5_A* 2ze7_A* 2ze8_A

Probab=96.23  E-value=0.0029  Score=59.37  Aligned_cols=24  Identities=21%  Similarity=0.277  Sum_probs=22.1

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHhh
Q psy200          221 SMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      .++|.|++|+||||+++.++..++
T Consensus         3 li~I~G~~GSGKSTla~~La~~~~   26 (253)
T 2ze6_A            3 LHLIYGPTCSGKTDMAIQIAQETG   26 (253)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHC
T ss_pred             EEEEECCCCcCHHHHHHHHHhcCC
Confidence            688999999999999999999875

>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=96.23  E-value=0.0046  Score=54.34  Aligned_cols=37  Identities=14%  Similarity=0.241  Sum_probs=29.2

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEe
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYIN  255 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~  255 (490)
                      .+..++|+|++|+||||+++.++..+.. .++.++.++
T Consensus         4 ~g~~i~l~G~~GsGKST~~~~L~~~l~~-~g~~~i~~d   40 (179)
T 2pez_A            4 RGCTVWLTGLSGAGKTTVSMALEEYLVC-HGIPCYTLD   40 (179)
T ss_dssp             CCEEEEEECCTTSSHHHHHHHHHHHHHH-TTCCEEEEE
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHhh-CCCcEEEEC
Confidence            4567889999999999999999988742 345666665

>2vli_A Antibiotic resistance protein; transferase, tunicamycin, phosphotransferase; 1.95A {Deinococcus radiodurans}

Probab=96.23  E-value=0.002  Score=56.71  Aligned_cols=26  Identities=35%  Similarity=0.554  Sum_probs=19.6

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      +..|+|.|++|+||||+++.+++.++
T Consensus         5 ~~~I~l~G~~GsGKST~a~~La~~l~   30 (183)
T 2vli_A            5 SPIIWINGPFGVGKTHTAHTLHERLP   30 (183)
T ss_dssp             CCEEEEECCC----CHHHHHHHHHST
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHhcC
Confidence            56789999999999999999998875

>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=96.22  E-value=0.0023  Score=56.89  Aligned_cols=35  Identities=23%  Similarity=0.379  Sum_probs=26.7

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEe
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYIN  255 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~  255 (490)
                      ..+..++|.|++|+||||+++.++..+    +...++++
T Consensus         7 ~~g~~i~l~G~~GsGKSTl~~~La~~~----~~g~i~i~   41 (191)
T 1zp6_A            7 LGGNILLLSGHPGSGKSTIAEALANLP----GVPKVHFH   41 (191)
T ss_dssp             CTTEEEEEEECTTSCHHHHHHHHHTCS----SSCEEEEC
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHhcc----CCCeEEEc
Confidence            346689999999999999999998753    23445554

>2plr_A DTMP kinase, probable thymidylate kinase; TMP-binding, ATP-binding, structural GEN NPPSFA; HET: 1PE PGE EPE PG4; 1.60A {Sulfolobus tokodaii}

Probab=96.20  E-value=0.0029  Score=57.06  Aligned_cols=26  Identities=31%  Similarity=0.367  Sum_probs=23.7

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      +..|+|.|++|+||||+++.+++.++
T Consensus         4 ~~~I~i~G~~GsGKsT~~~~L~~~l~   29 (213)
T 2plr_A            4 GVLIAFEGIDGSGKSSQATLLKDWIE   29 (213)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHT
T ss_pred             CeEEEEEcCCCCCHHHHHHHHHHHHh
Confidence            45788999999999999999999886

>2bwj_A Adenylate kinase 5; phosphoryl transfer reaction, transferase; HET: AMP; 2.3A {Homo sapiens}

Probab=96.20  E-value=0.0036  Score=55.89  Aligned_cols=26  Identities=31%  Similarity=0.556  Sum_probs=23.6

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      +..|+|.|++|+||||+++.+++.++
T Consensus        12 ~~~I~l~G~~GsGKsT~a~~L~~~l~   37 (199)
T 2bwj_A           12 CKIIFIIGGPGSGKGTQCEKLVEKYG   37 (199)
T ss_dssp             SCEEEEEECTTSSHHHHHHHHHHHHT
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHhC
Confidence            46899999999999999999999875

>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=96.20  E-value=0.0031  Score=55.14  Aligned_cols=27  Identities=22%  Similarity=0.282  Sum_probs=23.5

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      .+..++|+|++|+||||+++.++..++
T Consensus         7 ~g~~i~l~G~~GsGKSTl~~~l~~~~g   33 (175)
T 1knq_A            7 DHHIYVLMGVSGSGKSAVASEVAHQLH   33 (175)
T ss_dssp             TSEEEEEECSTTSCHHHHHHHHHHHHT
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHhhC
Confidence            356789999999999999999988763

>3ber_A Probable ATP-dependent RNA helicase DDX47; DEAD, AMP, structural genomics, structural GEN consortium, SGC, ATP-binding, hydrolase; HET: AMP PGE; 1.40A {Homo sapiens}

Probab=96.19  E-value=0.04  Score=51.18  Aligned_cols=40  Identities=20%  Similarity=0.217  Sum_probs=23.9

Q ss_pred             CeEEEEEecCccccccC-HHHHHHhHhCCCCCCCcEEEEEec
Q psy200          298 KSILLILDEIDALESRK-QTILYTIFEWPSIPGSKLVLVGVA  338 (490)
Q Consensus       298 ~~~vI~IDEid~l~~~~-~~~L~~l~~~~~~~~~~vilI~~t  338 (490)
                      ...+|||||+|.+.... ...+..++.... ...+++++.+|
T Consensus       186 ~~~~lViDEah~l~~~~~~~~l~~i~~~~~-~~~~~l~~SAT  226 (249)
T 3ber_A          186 ALKYLVMDEADRILNMDFETEVDKILKVIP-RDRKTFLFSAT  226 (249)
T ss_dssp             TCCEEEECSHHHHHHTTCHHHHHHHHHSSC-SSSEEEEEESS
T ss_pred             ccCEEEEcChhhhhccChHHHHHHHHHhCC-CCCeEEEEecc
Confidence            34589999999886542 344445554332 24556666555

>4b3f_X DNA-binding protein smubp-2; hydrolase, helicase; 2.50A {Homo sapiens} PDB: 4b3g_A

Probab=96.18  E-value=0.0052  Score=65.83  Aligned_cols=62  Identities=24%  Similarity=0.307  Sum_probs=37.3

Q ss_pred             HHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHH
Q psy200          200 EVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETI  269 (490)
Q Consensus       200 e~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i  269 (490)
                      +.+.+.+...|..      ....+|.||||||||+++-.+..++... +.. +.+.+.+......++..|
T Consensus       192 ~~Q~~AV~~al~~------~~~~lI~GPPGTGKT~ti~~~I~~l~~~-~~~-ILv~a~TN~AvD~i~erL  253 (646)
T 4b3f_X          192 TSQKEAVLFALSQ------KELAIIHGPPGTGKTTTVVEIILQAVKQ-GLK-VLCCAPSNIAVDNLVERL  253 (646)
T ss_dssp             HHHHHHHHHHHHC------SSEEEEECCTTSCHHHHHHHHHHHHHHT-TCC-EEEEESSHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcC------CCceEEECCCCCCHHHHHHHHHHHHHhC-CCe-EEEEcCchHHHHHHHHHH
Confidence            4566666666642      3478999999999998877777666432 223 333333322334444444

>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=96.17  E-value=0.062  Score=51.43  Aligned_cols=90  Identities=18%  Similarity=0.231  Sum_probs=54.5

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCH-HHHHHHHHHHhcCCC----CCCcHHHHH-HHHHHH
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNA-ASVYETIVNELKLKP----GGKSERHQL-GAILKY  292 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~-~~l~~~i~~~l~~~~----~~~s~~~~~-~~l~~~  292 (490)
                      +..++|+|++|+||||++..++..+.. .+..+..+++...... ...+..+....+...    .+....++. +.+..+
T Consensus        98 ~~vi~i~G~~G~GKTT~~~~la~~~~~-~g~~v~l~~~D~~r~~a~~ql~~~~~~~~v~v~~~~~~~~p~~~~~~~l~~~  176 (297)
T 1j8m_F           98 PYVIMLVGVQGTGKTTTAGKLAYFYKK-KGFKVGLVGADVYRPAALEQLQQLGQQIGVPVYGEPGEKDVVGIAKRGVEKF  176 (297)
T ss_dssp             SEEEEEECSSCSSTTHHHHHHHHHHHH-TTCCEEEEECCCSSSHHHHHHHHHHHHHTCCEECCTTCCCHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHH-CCCeEEEEecCCCCHHHHHHHHHHhccCCeEEEecCCCCCHHHHHHHHHHHH
Confidence            457889999999999999999988753 3456777776655432 223444444444321    123344443 333333


Q ss_pred             HhcCCCeEEEEEecCcccc
Q psy200          293 FDTKHKSILLILDEIDALE  311 (490)
Q Consensus       293 l~~~~~~~vI~IDEid~l~  311 (490)
                      ..  ...-+||||=...+.
T Consensus       177 ~~--~~~D~ViIDTpg~~~  193 (297)
T 1j8m_F          177 LS--EKMEIIIVDTAGRHG  193 (297)
T ss_dssp             HH--TTCSEEEEECCCSCC
T ss_pred             Hh--CCCCEEEEeCCCCcc
Confidence            21  223499999987765

>2xxa_A Signal recognition particle protein; protein transport, RNA/RNA binding protein, hydrolase, gtpas; HET: GCP; 3.94A {Escherichia coli} PDB: 2j28_9

Probab=96.16  E-value=0.034  Score=56.22  Aligned_cols=92  Identities=18%  Similarity=0.199  Sum_probs=56.2

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCH-HHHHHHHHHHhcCC----CCCCcHHHH-HHHHHH
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNA-ASVYETIVNELKLK----PGGKSERHQ-LGAILK  291 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~-~~l~~~i~~~l~~~----~~~~s~~~~-~~~l~~  291 (490)
                      .+..++|+|++|+||||++..++..+....+.++..++|...... .+.+..+....+..    ..+.+...+ .+.+..
T Consensus        99 ~~~vI~ivG~~GvGKTT~a~~LA~~l~~~~G~kVllvd~D~~r~~a~~ql~~~~~~~~l~v~~~~~~~dp~~i~~~~l~~  178 (433)
T 2xxa_A           99 PPAVVLMAGLQGAGKTTSVGKLGKFLREKHKKKVLVVSADVYRPAAIKQLETLAEQVGVDFFPSDVGQKPVDIVNAALKE  178 (433)
T ss_dssp             SSEEEEEECSTTSSHHHHHHHHHHHHHHTSCCCEEEEECCCSSTTHHHHHHHHHHHHTCEECCCCSSSCHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHhcCCeEEEEecCCCCccHHHHHHhhcccCCeeEEeCCCCCCHHHHHHHHHHH
Confidence            356888999999999999999999987543678888888766533 22233333333321    112233444 333433


Q ss_pred             HHhcCCCeEEEEEecCcccc
Q psy200          292 YFDTKHKSILLILDEIDALE  311 (490)
Q Consensus       292 ~l~~~~~~~vI~IDEid~l~  311 (490)
                      +...  ..-+||||=...+.
T Consensus       179 ~~~~--~~D~VIIDTpG~l~  196 (433)
T 2xxa_A          179 AKLK--FYDVLLVDTAGRLH  196 (433)
T ss_dssp             HHHT--TCSEEEEECCCCCT
T ss_pred             HHhC--CCCEEEEECCCccc
Confidence            3221  23489999876654

>3iuy_A Probable ATP-dependent RNA helicase DDX53; REC-A-like, DEAD-BOX, structural genomics, structural genomi consortium, SGC, ATP-binding, hydrolase; HET: AMP; 2.40A {Homo sapiens}

Probab=96.16  E-value=0.013  Score=53.54  Aligned_cols=40  Identities=18%  Similarity=0.245  Sum_probs=24.5

Q ss_pred             CeEEEEEecCccccccC-HHHHHHhHhCCCCCCCcEEEEEec
Q psy200          298 KSILLILDEIDALESRK-QTILYTIFEWPSIPGSKLVLVGVA  338 (490)
Q Consensus       298 ~~~vI~IDEid~l~~~~-~~~L~~l~~~~~~~~~~vilI~~t  338 (490)
                      ...+|||||+|.+.... ...+..++... ....+++++.+|
T Consensus       167 ~~~~lViDEah~~~~~~~~~~~~~i~~~~-~~~~~~l~~SAT  207 (228)
T 3iuy_A          167 SITYLVIDEADKMLDMEFEPQIRKILLDV-RPDRQTVMTSAT  207 (228)
T ss_dssp             TCCEEEECCHHHHHHTTCHHHHHHHHHHS-CSSCEEEEEESC
T ss_pred             cceEEEEECHHHHhccchHHHHHHHHHhC-CcCCeEEEEEee
Confidence            35689999999987553 34444444332 234566666666

>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=96.15  E-value=0.003  Score=57.20  Aligned_cols=28  Identities=29%  Similarity=0.451  Sum_probs=24.4

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      ..+..++|+||+|+||||+++.++..+.
T Consensus         6 ~~g~~i~l~GpsGsGKsTl~~~L~~~~~   33 (208)
T 3tau_A            6 ERGLLIVLSGPSGVGKGTVREAVFKDPE   33 (208)
T ss_dssp             CCCCEEEEECCTTSCHHHHHHHHHHSTT
T ss_pred             CCCcEEEEECcCCCCHHHHHHHHHhhCC
Confidence            4567899999999999999999998763

>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=96.12  E-value=0.0041  Score=55.08  Aligned_cols=26  Identities=23%  Similarity=0.475  Sum_probs=23.2

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      +..|+|.|++|+||||+++.+++.++
T Consensus         6 ~~~I~l~G~~GsGKsT~~~~L~~~l~   31 (194)
T 1qf9_A            6 PNVVFVLGGPGSGKGTQCANIVRDFG   31 (194)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHHHHHC
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHhC
Confidence            45789999999999999999998874

>1zd8_A GTP:AMP phosphotransferase mitochondrial; ATP:AMP phosphotransferase, myokinase, structural genomics, structural genomics consortium, SGC; 1.48A {Homo sapiens} PDB: 2ak3_A*

Probab=96.12  E-value=0.0037  Score=57.37  Aligned_cols=27  Identities=26%  Similarity=0.361  Sum_probs=23.5

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      .+..|+|.|++|+||||+++.+++.++
T Consensus         6 ~~~~I~l~G~~GsGKsT~a~~La~~l~   32 (227)
T 1zd8_A            6 RLLRAVIMGAPGSGKGTVSSRITTHFE   32 (227)
T ss_dssp             -CCEEEEEECTTSSHHHHHHHHHHHSS
T ss_pred             cCcEEEEECCCCCCHHHHHHHHHHHcC
Confidence            356799999999999999999998864

>1t6n_A Probable ATP-dependent RNA helicase; RECA-like fold, PRE-mRNA processing protein; HET: FLC; 1.94A {Homo sapiens} SCOP: c.37.1.19

Probab=96.11  E-value=0.033  Score=50.39  Aligned_cols=23  Identities=22%  Similarity=0.273  Sum_probs=18.1

Q ss_pred             CeEEEECCCCCcHHHHHHHHHHH
Q psy200          220 GSMYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       220 ~~ill~GppGtGKTtla~~l~~~  242 (490)
                      +.+++.+|.|+|||..+-..+-.
T Consensus        52 ~~~li~~~TGsGKT~~~~~~~~~   74 (220)
T 1t6n_A           52 MDVLCQAKSGMGKTAVFVLATLQ   74 (220)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHHH
T ss_pred             CCEEEECCCCCchhhhhhHHHHH
Confidence            56999999999999876555443

>1ukz_A Uridylate kinase; transferase; HET: ADP AMP; 1.90A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 1uky_A*

Probab=96.11  E-value=0.0042  Score=55.74  Aligned_cols=27  Identities=26%  Similarity=0.498  Sum_probs=23.7

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      .+..|+|.|++|+||||+++.+++.++
T Consensus        14 ~~~~I~l~G~~GsGKsT~~~~L~~~~g   40 (203)
T 1ukz_A           14 QVSVIFVLGGPGAGKGTQCEKLVKDYS   40 (203)
T ss_dssp             TCEEEEEECSTTSSHHHHHHHHHHHSS
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHcC
Confidence            456789999999999999999998864

>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=96.10  E-value=0.0055  Score=56.51  Aligned_cols=27  Identities=26%  Similarity=0.383  Sum_probs=24.2

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      .+..|+|.|++|+||||+++.+++.++
T Consensus        15 ~~~~I~l~G~~GsGKsT~a~~La~~l~   41 (233)
T 1ak2_A           15 KGVRAVLLGPPGAGKGTQAPKLAKNFC   41 (233)
T ss_dssp             CCCEEEEECCTTSSHHHHHHHHHHHHT
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHhC
Confidence            456799999999999999999999875

>2yvu_A Probable adenylyl-sulfate kinase; transferase, structural genomics, NPPSFA, national P protein structural and functional analyses; 2.10A {Aeropyrum pernix}

Probab=96.10  E-value=0.0037  Score=55.34  Aligned_cols=38  Identities=18%  Similarity=0.429  Sum_probs=29.1

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEe
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYIN  255 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~  255 (490)
                      ..+..++|.|++|+||||+++.++..+.. .++.+.+++
T Consensus        11 ~~~~~i~l~G~~GsGKsT~~~~L~~~l~~-~~~~~~~~~   48 (186)
T 2yvu_A           11 EKGIVVWLTGLPGSGKTTIATRLADLLQK-EGYRVEVLD   48 (186)
T ss_dssp             SCCEEEEEECCTTSSHHHHHHHHHHHHHH-TTCCEEEEE
T ss_pred             CCCcEEEEEcCCCCCHHHHHHHHHHHHHh-cCCeEEEee
Confidence            35678899999999999999999998853 233445553

>1zak_A Adenylate kinase; ATP:AMP-phosphotransferase, transferase; HET: AP5; 3.50A {Zea mays} SCOP: c.37.1.1 g.41.2.1

Probab=96.09  E-value=0.0033  Score=57.45  Aligned_cols=27  Identities=26%  Similarity=0.487  Sum_probs=24.1

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      .+..|+|.|++|+||||+++.+++.++
T Consensus         4 ~~~~I~l~G~~GsGKsT~~~~La~~l~   30 (222)
T 1zak_A            4 DPLKVMISGAPASGKGTQCELIKTKYQ   30 (222)
T ss_dssp             CSCCEEEEESTTSSHHHHHHHHHHHHC
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHhC
Confidence            456799999999999999999999875

>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=96.09  E-value=0.0041  Score=56.37  Aligned_cols=39  Identities=13%  Similarity=0.192  Sum_probs=30.1

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEe
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYIN  255 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~  255 (490)
                      ..+..++|.|++|+||||+++.++..+....++.+++++
T Consensus        23 ~~~~~i~~~G~~GsGKsT~~~~l~~~l~~~~g~~~~~~~   61 (211)
T 1m7g_A           23 QRGLTIWLTGLSASGKSTLAVELEHQLVRDRRVHAYRLD   61 (211)
T ss_dssp             SSCEEEEEECSTTSSHHHHHHHHHHHHHHHHCCCEEEEC
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHHHhccccCCcEEEEC
Confidence            456788999999999999999999987522344466664

>2wwf_A Thymidilate kinase, putative; transferase, malaria; HET: TMP ADP; 1.89A {Plasmodium falciparum} PDB: 2wwg_A* 2wwh_A* 2wwi_A*

Probab=96.08  E-value=0.0035  Score=56.65  Aligned_cols=27  Identities=26%  Similarity=0.305  Sum_probs=24.3

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      .+..|+|.|++|+||||+++.+++.++
T Consensus         9 ~~~~I~l~G~~GsGKST~~~~L~~~l~   35 (212)
T 2wwf_A            9 KGKFIVFEGLDRSGKSTQSKLLVEYLK   35 (212)
T ss_dssp             CSCEEEEEESTTSSHHHHHHHHHHHHH
T ss_pred             cCCEEEEEcCCCCCHHHHHHHHHHHHH
Confidence            356899999999999999999999876

>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=96.06  E-value=0.031  Score=56.59  Aligned_cols=96  Identities=14%  Similarity=0.304  Sum_probs=59.3

Q ss_pred             cCCCCeEEEECCCCCcHHHHHHHHHHHhhh-cCCceEEEEeccCCC-CHHHHHHHHHHHhcCC-------------CCCC
Q psy200          216 NETSGSMYISGPPGTGKSASLNLLVSRAEI-KDAFKTIYINCNSVR-NAASVYETIVNELKLK-------------PGGK  280 (490)
Q Consensus       216 ~~~~~~ill~GppGtGKTtla~~l~~~l~~-~~~~~~~~v~~~~~~-~~~~l~~~i~~~l~~~-------------~~~~  280 (490)
                      -..++.++|.|++|+|||+|+..+++.... ..++ ++++-|..-. ...+|++++...=...             ....
T Consensus       150 igkGQr~~Ifgg~G~GKT~L~~~i~~~~~~~~~~v-~V~~~iGER~rEv~e~~~~~~~~~~l~~~~~~~rtvvV~~t~d~  228 (482)
T 2ck3_D          150 YAKGGKIGLFGGAGVGKTVLIMELINNVAKAHGGY-SVFAGVGERTREGNDLYHEMIESGVINLKDATSKVALVYGQMNE  228 (482)
T ss_dssp             EETTCEEEEEECTTSSHHHHHHHHHHHTTTTCSSE-EEEEEESCCHHHHHHHHHHHHHHTSSCSSSSCCCEEEEEECTTS
T ss_pred             cccCCeeeeecCCCCChHHHHHHHHHhhHhhCCCE-EEEEECCCcchHHHHHHHHhhhccccccccCCceEEEEEECCCC
Confidence            357889999999999999999999987632 2344 4555554432 3456666665531111             0011


Q ss_pred             c-HH-----HHHHHHHHHHhc-CCCeEEEEEecCccccc
Q psy200          281 S-ER-----HQLGAILKYFDT-KHKSILLILDEIDALES  312 (490)
Q Consensus       281 s-~~-----~~~~~l~~~l~~-~~~~~vI~IDEid~l~~  312 (490)
                      . ..     ...-.+.+++.. .++.++|++|++-++..
T Consensus       229 p~~~r~~~~~~a~tiAEyfrd~~G~dVLll~DsitR~A~  267 (482)
T 2ck3_D          229 PPGARARVALTGLTVAEYFRDQEGQDVLLFIDNIFRFTQ  267 (482)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHTTCSCEEEEEECTHHHHH
T ss_pred             CHHHHHHHHHHHHHHHHHHHHhcCCcEEEEeccHHHHHH
Confidence            1 11     112234455665 68999999999887753

>2qe7_A ATP synthase subunit alpha; blockage of ATP hydrolysis, F1-ATPase, single analysis, thermoalkaliphilic, hydrolase; 3.06A {Bacillus SP} PDB: 1sky_B

Probab=96.05  E-value=0.016  Score=59.03  Aligned_cols=95  Identities=20%  Similarity=0.242  Sum_probs=59.7

Q ss_pred             ccCCCCeEEEECCCCCcHHHH-HHHHHHHhhhcCCceEEEEeccCCC-CHHHHHHHHHHHhcC--------CCCCCcHHH
Q psy200          215 NNETSGSMYISGPPGTGKSAS-LNLLVSRAEIKDAFKTIYINCNSVR-NAASVYETIVNELKL--------KPGGKSERH  284 (490)
Q Consensus       215 ~~~~~~~ill~GppGtGKTtl-a~~l~~~l~~~~~~~~~~v~~~~~~-~~~~l~~~i~~~l~~--------~~~~~s~~~  284 (490)
                      .-+.++.++|.|++|+|||+| +..+++...  .++.++++-+..-. ...++++++...=..        .........
T Consensus       158 PigrGQR~~Ifg~~g~GKT~Lal~~I~~~~~--~dv~~V~~~iGeR~~Ev~~~~~~~~~~g~m~~tvvV~atad~p~~~r  235 (502)
T 2qe7_A          158 PIGRGQRELIIGDRQTGKTTIAIDTIINQKG--QDVICIYVAIGQKQSTVAGVVETLRQHDALDYTIVVTASASEPAPLL  235 (502)
T ss_dssp             CCBTTCBCEEEECSSSCHHHHHHHHHHGGGS--CSEEEEEEEESCCHHHHHHHHHHHHHTTCSTTEEEEEECTTSCHHHH
T ss_pred             ccccCCEEEEECCCCCCchHHHHHHHHHhhc--CCcEEEEEECCCcchHHHHHHHHHhhCCCcceeEEEEECCCCCHHHH
Confidence            345788999999999999999 668877753  56666777666542 334556665542111        111111111


Q ss_pred             H-----HHHHHHHHhcCCCeEEEEEecCcccc
Q psy200          285 Q-----LGAILKYFDTKHKSILLILDEIDALE  311 (490)
Q Consensus       285 ~-----~~~l~~~l~~~~~~~vI~IDEid~l~  311 (490)
                      +     .-.+.+++...++.++|++|++-++.
T Consensus       236 ~~a~~~a~tiAEyfrd~G~dVLl~~Dsltr~A  267 (502)
T 2qe7_A          236 YLAPYAGCAMGEYFMYKGKHALVVYDDLSKQA  267 (502)
T ss_dssp             HHHHHHHHHHHHHHHTTTCEEEEEEECHHHHH
T ss_pred             HHHHHHHHHHHHHHHHcCCcEEEEEecHHHHH
Confidence            1     12345566667899999999987765

>2pt5_A Shikimate kinase, SK; aromatic amino acid biosynthesis, P-loop kinase, SHI kinase, shikimate pathway; 2.10A {Aquifex aeolicus}

Probab=96.03  E-value=0.0048  Score=53.44  Aligned_cols=24  Identities=29%  Similarity=0.354  Sum_probs=22.0

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHhh
Q psy200          221 SMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      .|+|+|++|+||||+++.+++.++
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~l~   25 (168)
T 2pt5_A            2 RIYLIGFMCSGKSTVGSLLSRSLN   25 (168)
T ss_dssp             EEEEESCTTSCHHHHHHHHHHHHT
T ss_pred             eEEEECCCCCCHHHHHHHHHHHhC
Confidence            588999999999999999999875

>2xau_A PRE-mRNA-splicing factor ATP-dependent RNA helica; hydrolase, ribosome biogenesis, ATPase, ATP-binding, OB-fold; HET: ADP; 1.90A {Saccharomyces cerevisiae} PDB: 3kx2_B*

Probab=96.02  E-value=0.038  Score=60.30  Aligned_cols=25  Identities=24%  Similarity=0.372  Sum_probs=20.3

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHh
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRA  243 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l  243 (490)
                      +..++|.||+|+|||+++..++...
T Consensus       109 ~~~vii~gpTGSGKTtllp~ll~~~  133 (773)
T 2xau_A          109 NQIMVFVGETGSGKTTQIPQFVLFD  133 (773)
T ss_dssp             CSEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHh
Confidence            4689999999999999777775443

>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=96.02  E-value=0.0042  Score=57.82  Aligned_cols=27  Identities=26%  Similarity=0.378  Sum_probs=24.2

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      .+..++|.|++|+||||+++.+++.++
T Consensus        26 ~~~~i~l~G~~GsGKSTl~k~La~~lg   52 (246)
T 2bbw_A           26 KLLRAVILGPPGSGKGTVCQRIAQNFG   52 (246)
T ss_dssp             CCCEEEEECCTTSSHHHHHHHHHHHHC
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHhC
Confidence            457899999999999999999998875

>2ck3_A ATP synthase subunit alpha\, mitochondrial; hydrolase; HET: ANP ADP; 1.9A {Bos taurus} SCOP: a.69.1.1 b.49.1.1 c.37.1.11 PDB: 1bmf_A* 1e1q_A* 1e1r_A* 1e79_A* 1h8h_A* 1nbm_A* 1ohh_A* 1qo1_A 1w0j_A* 1w0k_A* 1h8e_A* 2jdi_A* 2wss_A* 2w6j_A 2w6e_A 2w6g_A 2w6f_A 2w6h_A 2w6i_A 1cow_A* ...

Probab=96.01  E-value=0.019  Score=58.66  Aligned_cols=97  Identities=16%  Similarity=0.279  Sum_probs=60.3

Q ss_pred             cCCCCeEEEECCCCCcHHHH-HHHHHHHhhh------cCCceEEEEeccCCC-CHHHHHHHHHHHhcC--------CCCC
Q psy200          216 NETSGSMYISGPPGTGKSAS-LNLLVSRAEI------KDAFKTIYINCNSVR-NAASVYETIVNELKL--------KPGG  279 (490)
Q Consensus       216 ~~~~~~ill~GppGtGKTtl-a~~l~~~l~~------~~~~~~~~v~~~~~~-~~~~l~~~i~~~l~~--------~~~~  279 (490)
                      -+.++.++|.|++|+|||+| +..+++....      ..++.++++-+..-. ...++++.+...=..        ....
T Consensus       159 igrGQR~~I~g~~g~GKT~Lal~~I~~q~~~~~~~~~~~d~~~V~~~IGeR~~Ev~~~~~~~~~~g~m~~tvvV~atad~  238 (510)
T 2ck3_A          159 IGRGQRELIIGDRQTGKTSIAIDTIINQKRFNDGTDEKKKLYCIYVAIGQKRSTVAQLVKRLTDADAMKYTIVVSATASD  238 (510)
T ss_dssp             CBTTCBCEEEESTTSSHHHHHHHHHHHTHHHHTSCCTTTCCEEEEEEESCCHHHHHHHHHHHHHTTCGGGEEEEEECTTS
T ss_pred             cccCCEEEEecCCCCCchHHHHHHHHHHHhhccccccCCCeEEEEEECCCCcHHHHHHHHHHHhcCCcccceEEEECCCC
Confidence            45788999999999999999 6677777652      245666777666542 334556655542100        1111


Q ss_pred             CcHHHH-----HHHHHHHHhcCCCeEEEEEecCccccc
Q psy200          280 KSERHQ-----LGAILKYFDTKHKSILLILDEIDALES  312 (490)
Q Consensus       280 ~s~~~~-----~~~l~~~l~~~~~~~vI~IDEid~l~~  312 (490)
                      .....+     .-.+.+++...++.++|++|++-++..
T Consensus       239 p~~~r~~a~~~a~tiAEyfrd~G~dVLli~Dsltr~A~  276 (510)
T 2ck3_A          239 AAPLQYLAPYSGCSMGEYFRDNGKHALIIYDDLSKQAV  276 (510)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHTTTCEEEEEEETHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHHHHHHcCCcEEEEEcCHHHHHH
Confidence            111111     123455566678999999999877653

>1tf7_A KAIC; homohexamer, hexamer, circadian clock protein; HET: ATP; 2.80A {Synechococcus SP} SCOP: c.37.1.11 c.37.1.11 PDB: 3s1a_A* 1u9i_A* 2gbl_A* 3dvl_A* 3k0a_A* 3k09_A* 3jzm_A* 3k0e_A* 4dug_A* 3ua2_A* 3k0c_A* 3k0f_A*

Probab=96.01  E-value=0.011  Score=61.60  Aligned_cols=113  Identities=14%  Similarity=0.208  Sum_probs=61.5

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCC----------------CCCCc
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLK----------------PGGKS  281 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~----------------~~~~s  281 (490)
                      .+..++|.|++|+|||||++.++...... +..++++....  ....+...+ ..++..                ....+
T Consensus       280 ~G~i~~i~G~~GsGKSTLl~~l~g~~~~~-G~~vi~~~~ee--~~~~l~~~~-~~~g~~~~~~~~~g~~~~~~~~p~~LS  355 (525)
T 1tf7_A          280 KDSIILATGATGTGKTLLVSRFVENACAN-KERAILFAYEE--SRAQLLRNA-YSWGMDFEEMERQNLLKIVCAYPESAG  355 (525)
T ss_dssp             SSCEEEEEECTTSSHHHHHHHHHHHHHTT-TCCEEEEESSS--CHHHHHHHH-HTTSCCHHHHHHTTSEEECCCCGGGSC
T ss_pred             CCcEEEEEeCCCCCHHHHHHHHHHHHHhC-CCCEEEEEEeC--CHHHHHHHH-HHcCCCHHHHHhCCCEEEEEeccccCC
Confidence            56789999999999999999999876532 33455554322  233333222 111110                00123


Q ss_pred             HHHHHHHHHHHHhcCCCeEEEEEecCcccccc-----CHHHHHHhHhCCCCCCCcEEEE
Q psy200          282 ERHQLGAILKYFDTKHKSILLILDEIDALESR-----KQTILYTIFEWPSIPGSKLVLV  335 (490)
Q Consensus       282 ~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~-----~~~~L~~l~~~~~~~~~~vilI  335 (490)
                      ..+....+...... .++-+||||=+..|...     ....+..++......+..++++
T Consensus       356 ~g~~q~~~~a~~l~-~~p~llilDp~~~Ld~~~~~~~~~~~i~~ll~~l~~~g~tvilv  413 (525)
T 1tf7_A          356 LEDHLQIIKSEIND-FKPARIAIDSLSALARGVSNNAFRQFVIGVTGYAKQEEITGLFT  413 (525)
T ss_dssp             HHHHHHHHHHHHHT-TCCSEEEEECHHHHTSSSCHHHHHHHHHHHHHHHHHTTCEEEEE
T ss_pred             HHHHHHHHHHHHHh-hCCCEEEEcChHHHHhhCChHHHHHHHHHHHHHHHhCCCEEEEE
Confidence            34444333332222 45779999977777665     4555555544332233444444

>3tr0_A Guanylate kinase, GMP kinase; purines, pyrimidines, nucleosides, nucleotides, transferase; HET: 5GP; 1.85A {Coxiella burnetii}

Probab=96.01  E-value=0.0044  Score=55.61  Aligned_cols=26  Identities=31%  Similarity=0.503  Sum_probs=23.0

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHh
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRA  243 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l  243 (490)
                      .+..+.|.||+|+||||+++.++..+
T Consensus         6 ~g~ii~l~Gp~GsGKSTl~~~L~~~~   31 (205)
T 3tr0_A            6 KANLFIISAPSGAGKTSLVRALVKAL   31 (205)
T ss_dssp             CCCEEEEECCTTSCHHHHHHHHHHHS
T ss_pred             CCcEEEEECcCCCCHHHHHHHHHhhC
Confidence            45688899999999999999998864

>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=96.00  E-value=0.0089  Score=55.05  Aligned_cols=36  Identities=25%  Similarity=0.431  Sum_probs=28.9

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEe
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYIN  255 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~  255 (490)
                      .+..++|.|++|+||||+++.+++.+..  ++.++...
T Consensus        25 ~g~~i~i~G~~GsGKsT~~~~l~~~l~~--~~~~~~~~   60 (229)
T 4eaq_A           25 MSAFITFEGPEGSGKTTVINEVYHRLVK--DYDVIMTR   60 (229)
T ss_dssp             CCEEEEEECCTTSCHHHHHHHHHHHHTT--TSCEEEEC
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHHhc--CCCceeec
Confidence            4667889999999999999999999864  45555443

>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=96.00  E-value=0.0042  Score=56.17  Aligned_cols=27  Identities=22%  Similarity=0.229  Sum_probs=24.4

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      .+..|+|.|++|+||||+++.+++.+.
T Consensus         8 ~~~~I~l~G~~GsGKsT~~~~L~~~l~   34 (215)
T 1nn5_A            8 RGALIVLEGVDRAGKSTQSRKLVEALC   34 (215)
T ss_dssp             CCCEEEEEESTTSSHHHHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHH
Confidence            456899999999999999999999875

>3fb4_A Adenylate kinase; psychrophIle, phosphotransferase, ATP-binding, nucleotide-binding, transferase; HET: AP5; 2.00A {Marinibacillus marinus}

Probab=96.00  E-value=0.0038  Score=56.69  Aligned_cols=24  Identities=25%  Similarity=0.585  Sum_probs=21.7

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHhh
Q psy200          221 SMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      .|+|+|++|+||||+++.+++.++
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~~~   25 (216)
T 3fb4_A            2 NIVLMGLPGAGKGTQAEQIIEKYE   25 (216)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhC
Confidence            478999999999999999998874

>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=95.99  E-value=0.083  Score=53.15  Aligned_cols=90  Identities=17%  Similarity=0.185  Sum_probs=53.1

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHH-HHHHHHHHHhcCC----CCCCcHHHH-HHHHHHH
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAA-SVYETIVNELKLK----PGGKSERHQ-LGAILKY  292 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~-~l~~~i~~~l~~~----~~~~s~~~~-~~~l~~~  292 (490)
                      +..++|+|+.|+||||++..++..+... +..+..+++....... ..+..+....+.+    ..+....++ .+.+..+
T Consensus        98 ~~vi~i~G~~GsGKTT~~~~LA~~l~~~-g~~Vllvd~D~~r~aa~~qL~~~~~~~gv~v~~~~~~~~p~~i~~~~l~~~  176 (425)
T 2ffh_A           98 RNLWFLVGLQGSGKTTTAAKLALYYKGK-GRRPLLVAADTQRPAAREQLRLLGEKVGVPVLEVMDGESPESIRRRVEEKA  176 (425)
T ss_dssp             SEEEEEECCTTSSHHHHHHHHHHHHHTT-TCCEEEEECCSSCHHHHHHHHHHHHHHTCCEEECCTTCCHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHc-CCeEEEeeccccCchhHHHHHHhcccCCccEEecCCCCCHHHHHHHHHHHH
Confidence            5578899999999999999999988633 4566777764443222 2234444444432    112233444 3344433


Q ss_pred             HhcCCCeEEEEEecCcccc
Q psy200          293 FDTKHKSILLILDEIDALE  311 (490)
Q Consensus       293 l~~~~~~~vI~IDEid~l~  311 (490)
                      ..  ...-+||||=...+.
T Consensus       177 ~~--~~~DvVIIDTaG~l~  193 (425)
T 2ffh_A          177 RL--EARDLILVDTAGRLQ  193 (425)
T ss_dssp             HH--TTCSEEEEECCCCSS
T ss_pred             HH--CCCCEEEEcCCCccc
Confidence            22  223489999776654

>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=95.99  E-value=0.073  Score=46.71  Aligned_cols=23  Identities=22%  Similarity=0.315  Sum_probs=20.5

Q ss_pred             CeEEEECCCCCcHHHHHHHHHHH
Q psy200          220 GSMYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       220 ~~ill~GppGtGKTtla~~l~~~  242 (490)
                      -.|+|.|.+|+|||+|++.+...
T Consensus        23 ~ki~v~G~~~~GKSsli~~l~~~   45 (188)
T 1zd9_A           23 MELTLVGLQYSGKTTFVNVIASG   45 (188)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHS
T ss_pred             cEEEEECCCCCCHHHHHHHHHcC
Confidence            46889999999999999999864

>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=95.98  E-value=0.081  Score=46.26  Aligned_cols=25  Identities=20%  Similarity=0.248  Sum_probs=22.0

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHH
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVS  241 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~  241 (490)
                      .....++|.|.+|+|||+|++.+..
T Consensus        14 ~~~~~i~v~G~~~~GKssl~~~l~~   38 (187)
T 1zj6_A           14 HQEHKVIIVGLDNAGKTTILYQFSM   38 (187)
T ss_dssp             TSCEEEEEEESTTSSHHHHHHHHHT
T ss_pred             CCccEEEEECCCCCCHHHHHHHHhc
Confidence            4567899999999999999999974

>2jaq_A Deoxyguanosine kinase; transferase, deoxyribonucleoside kinase; HET: DCP; 2.3A {Mycoplasma mycoides subsp} PDB: 2jat_A* 2jas_A*

Probab=95.94  E-value=0.0045  Score=55.42  Aligned_cols=24  Identities=25%  Similarity=0.306  Sum_probs=22.2

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHhh
Q psy200          221 SMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      .|+|.|++|+||||+++.+++.++
T Consensus         2 ~I~i~G~~GsGKsT~~~~L~~~l~   25 (205)
T 2jaq_A            2 KIAIFGTVGAGKSTISAEISKKLG   25 (205)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHC
T ss_pred             EEEEECCCccCHHHHHHHHHHhcC
Confidence            578999999999999999999885

>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=95.93  E-value=0.045  Score=52.36  Aligned_cols=92  Identities=15%  Similarity=0.165  Sum_probs=53.9

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHH-HHHHHHHHHhcCCC----CCCcHHHH-HHHHHH
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAA-SVYETIVNELKLKP----GGKSERHQ-LGAILK  291 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~-~l~~~i~~~l~~~~----~~~s~~~~-~~~l~~  291 (490)
                      .+..+.|+|++|+||||++..++..+.. .+..+..+++....... ..+..+....+...    .+....++ ...+..
T Consensus        97 ~~~~i~i~g~~G~GKTT~~~~la~~~~~-~~~~v~l~~~d~~~~~~~~ql~~~~~~~~l~~~~~~~~~~p~~l~~~~l~~  175 (295)
T 1ls1_A           97 DRNLWFLVGLQGSGKTTTAAKLALYYKG-KGRRPLLVAADTQRPAAREQLRLLGEKVGVPVLEVMDGESPESIRRRVEEK  175 (295)
T ss_dssp             SSEEEEEECCTTTTHHHHHHHHHHHHHH-TTCCEEEEECCSSCHHHHHHHHHHHHHHTCCEEECCTTCCHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHH-cCCeEEEecCCcccHhHHHHHHHhcccCCeEEEEcCCCCCHHHHHHHHHHH
Confidence            3557889999999999999999988763 23456666654433221 12334444444321    12234344 334444


Q ss_pred             HHhcCCCeEEEEEecCccccc
Q psy200          292 YFDTKHKSILLILDEIDALES  312 (490)
Q Consensus       292 ~l~~~~~~~vI~IDEid~l~~  312 (490)
                      +...  .+-+||||+...+..
T Consensus       176 ~~~~--~~D~viiDtpp~~~~  194 (295)
T 1ls1_A          176 ARLE--ARDLILVDTAGRLQI  194 (295)
T ss_dssp             HHHH--TCCEEEEECCCCSSC
T ss_pred             HHhC--CCCEEEEeCCCCccc
Confidence            3322  245999999977643

>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=95.92  E-value=0.0052  Score=55.11  Aligned_cols=27  Identities=26%  Similarity=0.446  Sum_probs=24.0

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHh
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRA  243 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l  243 (490)
                      ..+..++|+||+|+|||||++.++...
T Consensus        17 ~~g~~ivl~GPSGaGKsTL~~~L~~~~   43 (197)
T 3ney_A           17 QGRKTLVLIGASGVGRSHIKNALLSQN   43 (197)
T ss_dssp             CSCCEEEEECCTTSSHHHHHHHHHHHC
T ss_pred             CCCCEEEEECcCCCCHHHHHHHHHhhC
Confidence            356789999999999999999998875

>2j41_A Guanylate kinase; GMP, GMK, transferase, ATP-binding, nucleotide- binding; HET: 5GP; 1.9A {Staphylococcus aureus}

Probab=95.90  E-value=0.0045  Score=55.59  Aligned_cols=26  Identities=23%  Similarity=0.397  Sum_probs=23.2

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHh
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRA  243 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l  243 (490)
                      .+..+.|.|++|+||||+++.++..+
T Consensus         5 ~g~~i~l~G~~GsGKSTl~~~L~~~~   30 (207)
T 2j41_A            5 KGLLIVLSGPSGVGKGTVRKRIFEDP   30 (207)
T ss_dssp             CCCEEEEECSTTSCHHHHHHHHHHCT
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHhh
Confidence            45688999999999999999998876

>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=95.89  E-value=0.028  Score=57.15  Aligned_cols=97  Identities=13%  Similarity=0.244  Sum_probs=61.0

Q ss_pred             cCCCCeEEEECCCCCcHHHHHHHHHHHhhh-cCCceEEEEeccCCC-CHHHHHHHHHHHhcCC--------------CCC
Q psy200          216 NETSGSMYISGPPGTGKSASLNLLVSRAEI-KDAFKTIYINCNSVR-NAASVYETIVNELKLK--------------PGG  279 (490)
Q Consensus       216 ~~~~~~ill~GppGtGKTtla~~l~~~l~~-~~~~~~~~v~~~~~~-~~~~l~~~i~~~l~~~--------------~~~  279 (490)
                      -..++.+.|.|++|+|||+|+..+++.... ..++ ++++-|..-. ...+|++++...=...              ...
T Consensus       162 igkGqr~gIfgg~GvGKT~L~~~l~~~~a~~~~~v-~V~~~iGER~rEv~e~~~~~~~~~~l~~~~l~~~rtvvV~~t~d  240 (498)
T 1fx0_B          162 YRRGGKIGLFGGAGVGKTVLIMELINNIAKAHGGV-SVFGGVGERTREGNDLYMEMKESGVINEQNIAESKVALVYGQMN  240 (498)
T ss_dssp             CCTTCCEEEEECSSSSHHHHHHHHHHHTTTTCSSC-EEEEEESCCSHHHHHHHHHHHHTTSSCSSTTCCCCEEEEEECTT
T ss_pred             cccCCeEEeecCCCCCchHHHHHHHHHHHhhCCCE-EEEEEcccCcHHHHHHHHhhhcccccccccccccceEEEEeCCC
Confidence            357889999999999999999999987642 2233 4555554432 4456777766531111              000


Q ss_pred             Cc------HHHHHHHHHHHHhc-CCCeEEEEEecCcccccc
Q psy200          280 KS------ERHQLGAILKYFDT-KHKSILLILDEIDALESR  313 (490)
Q Consensus       280 ~s------~~~~~~~l~~~l~~-~~~~~vI~IDEid~l~~~  313 (490)
                      ..      .....-.+.+++.. .++.++||+|++-++...
T Consensus       241 ~p~~~R~~~~~~altiAEyfrd~~G~dVLl~~DsitR~A~A  281 (498)
T 1fx0_B          241 EPPGARMRVGLTALTMAEYFRDVNEQDVLLFIDNIFRFVQA  281 (498)
T ss_dssp             SCHHHHTTHHHHHHHTHHHHTTTSCCEEEEEEECSHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHhcCCcEEEEeccHHHHHHH
Confidence            11      11122245566766 689999999999887643

>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=95.89  E-value=0.017  Score=58.97  Aligned_cols=95  Identities=15%  Similarity=0.234  Sum_probs=59.7

Q ss_pred             cCCCCeEEEECCCCCcHHHH-HHHHHHHhhhcCCceEEEEeccCCC-CHHHHHHHHHHHhcC--------CCCCCcHHHH
Q psy200          216 NETSGSMYISGPPGTGKSAS-LNLLVSRAEIKDAFKTIYINCNSVR-NAASVYETIVNELKL--------KPGGKSERHQ  285 (490)
Q Consensus       216 ~~~~~~ill~GppGtGKTtl-a~~l~~~l~~~~~~~~~~v~~~~~~-~~~~l~~~i~~~l~~--------~~~~~s~~~~  285 (490)
                      -+.++.++|.|++|+|||+| +..+++...  .++.++++-+..-. ...++++.+...=..        .........+
T Consensus       172 igrGQR~~I~g~~g~GKT~Lal~~I~~~~~--~dv~~V~~~IGeR~~Ev~e~~~~~~~~g~m~rtvvV~atad~p~~~r~  249 (515)
T 2r9v_A          172 IGRGQRELIIGDRQTGKTAIAIDTIINQKG--QGVYCIYVAIGQKKSAIARIIDKLRQYGAMEYTTVVVASASDPASLQY  249 (515)
T ss_dssp             EETTCBEEEEEETTSSHHHHHHHHHHTTTT--TTEEEEEEEESCCHHHHHHHHHHHHHTTGGGGEEEEEECTTSCHHHHH
T ss_pred             cccCCEEEEEcCCCCCccHHHHHHHHHhhc--CCcEEEEEEcCCCcHHHHHHHHHHHhCCCcceeEEEEECCCCCHHHHH
Confidence            35788999999999999999 568877753  55666777666543 334556665542100        1111111111


Q ss_pred             -----HHHHHHHHhcCCCeEEEEEecCccccc
Q psy200          286 -----LGAILKYFDTKHKSILLILDEIDALES  312 (490)
Q Consensus       286 -----~~~l~~~l~~~~~~~vI~IDEid~l~~  312 (490)
                           .-.+.+++...++.++|++|++-++..
T Consensus       250 ~a~~~a~tiAEyfrd~G~dVLli~DslTr~A~  281 (515)
T 2r9v_A          250 IAPYAGCAMGEYFAYSGRDALVVYDDLSKHAV  281 (515)
T ss_dssp             HHHHHHHHHHHHHHTTTCEEEEEEETHHHHHH
T ss_pred             HHHHHHHHHHHHHHHcCCcEEEEeccHHHHHH
Confidence                 123455666678999999999877653

>1rif_A DAR protein, DNA helicase UVSW; bacteriophage, RECG, SF2, DNA binding protein; HET: DNA; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.23

Probab=95.87  E-value=0.02  Score=54.27  Aligned_cols=52  Identities=17%  Similarity=0.087  Sum_probs=34.3

Q ss_pred             CCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEE
Q psy200          196 LPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYI  254 (490)
Q Consensus       196 lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v  254 (490)
                      +.-+.-+.+.+..++..       +..+|.+++|+|||.++-.++..........++++
T Consensus       112 ~~l~~~Q~~ai~~~l~~-------~~~ll~~~tGsGKT~~~~~~~~~~~~~~~~~~lil  163 (282)
T 1rif_A          112 IEPHWYQKDAVFEGLVN-------RRRILNLPTSAGRSLIQALLARYYLENYEGKILII  163 (282)
T ss_dssp             CCCCHHHHHHHHHHHHH-------SEEEECCCTTSCHHHHHHHHHHHHHHHCSSEEEEE
T ss_pred             cCccHHHHHHHHHHHhc-------CCeEEEcCCCCCcHHHHHHHHHHHHHcCCCeEEEE
Confidence            34555566666666642       34578999999999999777766433333356655

>2pl3_A Probable ATP-dependent RNA helicase DDX10; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; HET: ADP; 2.15A {Homo sapiens}

Probab=95.86  E-value=0.058  Score=49.38  Aligned_cols=40  Identities=18%  Similarity=0.238  Sum_probs=24.2

Q ss_pred             CeEEEEEecCccccccC-HHHHHHhHhCCCCCCCcEEEEEec
Q psy200          298 KSILLILDEIDALESRK-QTILYTIFEWPSIPGSKLVLVGVA  338 (490)
Q Consensus       298 ~~~vI~IDEid~l~~~~-~~~L~~l~~~~~~~~~~vilI~~t  338 (490)
                      ...+|||||+|.+.... ...+..++.... ...+++++.+|
T Consensus       171 ~~~~lViDEah~~~~~~~~~~~~~i~~~~~-~~~~~l~~SAT  211 (236)
T 2pl3_A          171 DLQMLVLDEADRILDMGFADTMNAVIENLP-KKRQTLLFSAT  211 (236)
T ss_dssp             TCCEEEETTHHHHHHTTTHHHHHHHHHTSC-TTSEEEEEESS
T ss_pred             cccEEEEeChHHHhcCCcHHHHHHHHHhCC-CCCeEEEEEee
Confidence            34599999999986543 344555554332 34456666555

>1zu4_A FTSY; GTPase, signal recognition particle, SRP, receptor, protein transport; 1.95A {Mycoplasma mycoides} PDB: 1zu5_A

Probab=95.86  E-value=0.08  Score=51.21  Aligned_cols=41  Identities=20%  Similarity=0.289  Sum_probs=31.8

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCC
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSV  259 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~  259 (490)
                      .+..++|+|++|+||||++..++..+.. .+..++.+++...
T Consensus       104 ~~~vI~ivG~~G~GKTT~~~~LA~~l~~-~g~kVllid~D~~  144 (320)
T 1zu4_A          104 RLNIFMLVGVNGTGKTTSLAKMANYYAE-LGYKVLIAAADTF  144 (320)
T ss_dssp             SCEEEEEESSTTSSHHHHHHHHHHHHHH-TTCCEEEEECCCS
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHH-CCCeEEEEeCCCc
Confidence            4567889999999999999999998863 3456666766543

>2j0s_A ATP-dependent RNA helicase DDX48; mRNA processing, phosphorylation, rRNA processing, mRNA splicing, mRNA transport; HET: ANP; 2.21A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB: 2j0q_A* 2hyi_C* 3ex7_C* 2xb2_A* 2hxy_A 2j0u_A 2j0u_B 2zu6_A

Probab=95.85  E-value=0.024  Score=56.55  Aligned_cols=41  Identities=22%  Similarity=0.519  Sum_probs=25.3

Q ss_pred             CeEEEEEecCccccccC-HHHHHHhHhCCCCCCCcEEEEEecC
Q psy200          298 KSILLILDEIDALESRK-QTILYTIFEWPSIPGSKLVLVGVAN  339 (490)
Q Consensus       298 ~~~vI~IDEid~l~~~~-~~~L~~l~~~~~~~~~~vilI~~tn  339 (490)
                      ...+|||||+|.+.... ...+..++... ....+++++.+|-
T Consensus       179 ~~~~vViDEah~~~~~~~~~~~~~i~~~~-~~~~~~i~~SAT~  220 (410)
T 2j0s_A          179 AIKMLVLDEADEMLNKGFKEQIYDVYRYL-PPATQVVLISATL  220 (410)
T ss_dssp             TCCEEEEETHHHHTSTTTHHHHHHHHTTS-CTTCEEEEEESCC
T ss_pred             heeEEEEccHHHHHhhhhHHHHHHHHHhC-ccCceEEEEEcCC
Confidence            35699999999986554 34455555432 2345666666653

>1fuu_A Yeast initiation factor 4A; IF4A, helicase, DEAD-box protein, translation; 2.50A {Saccharomyces cerevisiae} SCOP: c.37.1.19 PDB: 2vso_A* 2vsx_A*

Probab=95.84  E-value=0.016  Score=57.44  Aligned_cols=35  Identities=17%  Similarity=0.332  Sum_probs=21.9

Q ss_pred             CeEEEECCCCCcHHHHH-HHHHHHhhhc-CCceEEEE
Q psy200          220 GSMYISGPPGTGKSASL-NLLVSRAEIK-DAFKTIYI  254 (490)
Q Consensus       220 ~~ill~GppGtGKTtla-~~l~~~l~~~-~~~~~~~v  254 (490)
                      +.+++.+|+|+|||..+ -.+++.+... ....++++
T Consensus        59 ~~~lv~~~TGsGKT~~~~~~~~~~l~~~~~~~~~lil   95 (394)
T 1fuu_A           59 HDVLAQAQSGTGKTGTFSIAALQRIDTSVKAPQALML   95 (394)
T ss_dssp             CCEEECCCSSHHHHHHHHHHHHHHCCTTCCSCCEEEE
T ss_pred             CCEEEECCCCChHHHHHHHHHHHHhhccCCCCCEEEE
Confidence            56899999999999874 3344444321 22344555

>1lvg_A Guanylate kinase, GMP kinase; transferase; HET: ADP 5GP; 2.10A {Mus musculus} SCOP: c.37.1.1

Probab=95.83  E-value=0.0051  Score=55.23  Aligned_cols=25  Identities=36%  Similarity=0.590  Sum_probs=22.0

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHh
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRA  243 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l  243 (490)
                      +..+.|+||+|+|||||++.+...+
T Consensus         4 g~~i~lvGpsGaGKSTLl~~L~~~~   28 (198)
T 1lvg_A            4 PRPVVLSGPSGAGKSTLLKKLFQEH   28 (198)
T ss_dssp             -CCEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhhC
Confidence            5678999999999999999998865

>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=95.81  E-value=0.0073  Score=55.15  Aligned_cols=25  Identities=24%  Similarity=0.456  Sum_probs=22.6

Q ss_pred             CeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          220 GSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       220 ~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      ..+.|+|++|+||||+++.++..++
T Consensus         6 ~~i~i~G~~GsGKSTl~~~L~~~~g   30 (227)
T 1cke_A            6 PVITIDGPSGAGKGTLCKAMAEALQ   30 (227)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHHT
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhC
Confidence            4788999999999999999998764

>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=95.81  E-value=0.043  Score=56.07  Aligned_cols=27  Identities=22%  Similarity=0.378  Sum_probs=24.1

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      .+..++|+|+.|+|||||++.++..+.
T Consensus       292 ~GeVI~LVGpNGSGKTTLl~~LAgll~  318 (503)
T 2yhs_A          292 APFVILMVGVNGVGKTTTIGKLARQFE  318 (503)
T ss_dssp             TTEEEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCcccHHHHHHHHHHHhh
Confidence            456888999999999999999998875

>3crm_A TRNA delta(2)-isopentenylpyrophosphate transferase; ATP-binding, nucleotide-binding, nucleotidyltransferase, tRNA processing; 1.90A {Pseudomonas aeruginosa} PDB: 3crq_A 3crr_A

Probab=95.80  E-value=0.0076  Score=58.33  Aligned_cols=33  Identities=18%  Similarity=0.379  Sum_probs=26.6

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEe
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYIN  255 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~  255 (490)
                      ...++|+||+|+||||++..+++.++    ..++.++
T Consensus         5 ~~~i~i~GptGsGKTtla~~La~~l~----~~iis~D   37 (323)
T 3crm_A            5 PPAIFLMGPTAAGKTDLAMALADALP----CELISVD   37 (323)
T ss_dssp             CEEEEEECCTTSCHHHHHHHHHHHSC----EEEEEEC
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHcC----CcEEecc
Confidence            34789999999999999999999874    4455554

>3nwj_A ATSK2; P loop, shikimate, nucleoside monophosphate kinase, shikimat ATP binding, chloroplast, transferase; 2.35A {Arabidopsis thaliana}

Probab=95.79  E-value=0.0074  Score=56.38  Aligned_cols=26  Identities=27%  Similarity=0.462  Sum_probs=24.0

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      +..++|+|++|+||||+++.++..++
T Consensus        48 g~~i~l~G~~GsGKSTl~~~La~~lg   73 (250)
T 3nwj_A           48 GRSMYLVGMMGSGKTTVGKIMARSLG   73 (250)
T ss_dssp             TCCEEEECSTTSCHHHHHHHHHHHHT
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHhcC
Confidence            56899999999999999999999875

>2v6i_A RNA helicase; membrane, hydrolase, transmembrane, RNA replication, viral replication, nucleotide-binding; 2.10A {Kokobera virus} PDB: 2v6j_A

Probab=95.76  E-value=0.022  Score=57.69  Aligned_cols=49  Identities=22%  Similarity=0.303  Sum_probs=29.9

Q ss_pred             CCeEEEECCCCCcHHHHH-HHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHh
Q psy200          219 SGSMYISGPPGTGKSASL-NLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNEL  273 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla-~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l  273 (490)
                      ++.+++.||.|+|||..+ -.+++.+. ..+..++++.-     ...+..++...+
T Consensus         2 g~~~lv~a~TGsGKT~~~l~~~l~~~~-~~g~~~lvl~P-----t~~La~Q~~~~~   51 (431)
T 2v6i_A            2 RELTVLDLHPGAGKTRRVLPQLVREAV-KKRLRTVILAP-----TRVVASEMYEAL   51 (431)
T ss_dssp             CCEEEEECCTTSCTTTTHHHHHHHHHH-HTTCCEEEEES-----SHHHHHHHHHHT
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHHHHH-hCCCCEEEECc-----HHHHHHHHHHHh
Confidence            568999999999999985 54554432 23345555531     233455555555

>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=95.75  E-value=0.013  Score=56.07  Aligned_cols=28  Identities=25%  Similarity=0.376  Sum_probs=24.5

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      ..+..+.|.|++|+||||+++.++..+.
T Consensus        29 ~~~~ii~I~G~sGsGKSTla~~L~~~l~   56 (290)
T 1odf_A           29 KCPLFIFFSGPQGSGKSFTSIQIYNHLM   56 (290)
T ss_dssp             CSCEEEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHhh
Confidence            3556788999999999999999998886

>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin nucleotide-binding; 2.30A {Sulfolobus solfataricus}

Probab=95.74  E-value=0.024  Score=61.38  Aligned_cols=35  Identities=26%  Similarity=0.456  Sum_probs=24.8

Q ss_pred             CCeEEEECCCCCcHHHHHHHHH-HHhhhcCCceEEEE
Q psy200          219 SGSMYISGPPGTGKSASLNLLV-SRAEIKDAFKTIYI  254 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~-~~l~~~~~~~~~~v  254 (490)
                      +..++|.||+|+|||+.+-..+ +.+. ..+..++++
T Consensus        46 ~~~~lv~apTGsGKT~~~~l~il~~~~-~~~~~il~i   81 (715)
T 2va8_A           46 GNRLLLTSPTGSGKTLIAEMGIISFLL-KNGGKAIYV   81 (715)
T ss_dssp             TCCEEEECCTTSCHHHHHHHHHHHHHH-HSCSEEEEE
T ss_pred             CCcEEEEcCCCCcHHHHHHHHHHHHHH-HCCCeEEEE
Confidence            6789999999999999985444 3332 134566666

>3oaa_A ATP synthase subunit alpha; rossmann fold, hydrolase, hydrolase-transport PROT complex; HET: ANP ADP; 3.26A {Escherichia coli DH1} PDB: 2a7u_A

Probab=95.73  E-value=0.03  Score=56.97  Aligned_cols=95  Identities=18%  Similarity=0.272  Sum_probs=59.1

Q ss_pred             cCCCCeEEEECCCCCcHHHH-HHHHHHHhhhcCCceEEEEeccCCC-CHHHHHHHHHHHhcC--------CCCCCcHHHH
Q psy200          216 NETSGSMYISGPPGTGKSAS-LNLLVSRAEIKDAFKTIYINCNSVR-NAASVYETIVNELKL--------KPGGKSERHQ  285 (490)
Q Consensus       216 ~~~~~~ill~GppGtGKTtl-a~~l~~~l~~~~~~~~~~v~~~~~~-~~~~l~~~i~~~l~~--------~~~~~s~~~~  285 (490)
                      -+.++.++|.|++|+|||++ +..+++.-  ..++.++++-+..-. ...+|+.++...=..        .........+
T Consensus       159 igrGQR~~Ifg~~g~GKT~l~l~~I~n~~--~~dv~~V~~~IGeR~~ev~e~~~~l~~~g~m~~tvvV~atad~p~~~r~  236 (513)
T 3oaa_A          159 IGRGQRELIIGDRQTGKTALAIDAIINQR--DSGIKCIYVAIGQKASTISNVVRKLEEHGALANTIVVVATASESAALQY  236 (513)
T ss_dssp             CBTTCBCEEEESSSSSHHHHHHHHHHTTS--SSSCEEEEEEESCCHHHHHHHHHHHHHHSCSTTEEEEEECTTSCHHHHH
T ss_pred             cccCCEEEeecCCCCCcchHHHHHHHhhc--cCCceEEEEEecCChHHHHHHHHHHhhcCcccceEEEEECCCCChHHHH
Confidence            35788999999999999999 46777653  355666777666542 345566665443111        1111111111


Q ss_pred             -----HHHHHHHHhcCCCeEEEEEecCccccc
Q psy200          286 -----LGAILKYFDTKHKSILLILDEIDALES  312 (490)
Q Consensus       286 -----~~~l~~~l~~~~~~~vI~IDEid~l~~  312 (490)
                           .-.+.+++...++.++|++|++-+...
T Consensus       237 ~a~~~a~tiAEyfrd~G~dVLli~Dsltr~A~  268 (513)
T 3oaa_A          237 LAPYAGCAMGEYFRDRGEDALIIYDDLSKQAV  268 (513)
T ss_dssp             HHHHHHHHHHHHHHHTTCEEEEEEETHHHHHH
T ss_pred             HHHHHHHHHHHHHHhcCCCEEEEecChHHHHH
Confidence                 123455566678999999999877653

>1tf7_A KAIC; homohexamer, hexamer, circadian clock protein; HET: ATP; 2.80A {Synechococcus SP} SCOP: c.37.1.11 c.37.1.11 PDB: 3s1a_A* 1u9i_A* 2gbl_A* 3dvl_A* 3k0a_A* 3k09_A* 3jzm_A* 3k0e_A* 4dug_A* 3ua2_A* 3k0c_A* 3k0f_A*

Probab=95.68  E-value=0.0099  Score=61.95  Aligned_cols=40  Identities=18%  Similarity=0.184  Sum_probs=27.9

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHH-HHhhhcCCceEEEEeccC
Q psy200          218 TSGSMYISGPPGTGKSASLNLLV-SRAEIKDAFKTIYINCNS  258 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~-~~l~~~~~~~~~~v~~~~  258 (490)
                      .+..++|.|++|+|||||++.++ .-+.. .+-..++++...
T Consensus        38 ~Ge~~~l~G~nGsGKSTL~~~~ll~Gl~~-~~~g~i~v~g~~   78 (525)
T 1tf7_A           38 IGRSTLVSGTSGTGKTLFSIQFLYNGIIE-FDEPGVFVTFEE   78 (525)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHHHHH-HCCCEEEEESSS
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHHHHh-CCCCEEEEEEeC
Confidence            57789999999999999999952 32321 123457776544

>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=95.67  E-value=0.13  Score=43.58  Aligned_cols=22  Identities=23%  Similarity=0.279  Sum_probs=19.6

Q ss_pred             eEEEECCCCCcHHHHHHHHHHH
Q psy200          221 SMYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~  242 (490)
                      .++|.|++|+|||+|++.+...
T Consensus         2 ki~~~G~~~~GKssl~~~l~~~   23 (164)
T 1r8s_A            2 RILMVGLDAAGKTTILYKLKLG   23 (164)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            4789999999999999999764

>2fwr_A DNA repair protein RAD25; DNA unwinding, XPB, DNA binding protein; HET: DNA; 2.60A {Archaeoglobus fulgidus} SCOP: c.37.1.19 c.37.1.19 PDB: 2fzl_A*

Probab=95.66  E-value=0.019  Score=58.73  Aligned_cols=105  Identities=18%  Similarity=0.217  Sum_probs=55.3

Q ss_pred             ChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCC-
Q psy200          198 GREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLK-  276 (490)
Q Consensus       198 gre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~-  276 (490)
                      -+..+.+.+..++.       .+.++|.|+.|+|||.++-.++..+.    ..++.+ |+...-..++...+.. ++.. 
T Consensus        94 l~~~Q~~ai~~i~~-------~~~~ll~~~TGsGKT~~~l~~i~~~~----~~~Lvl-~P~~~L~~Q~~~~~~~-~~~~~  160 (472)
T 2fwr_A           94 LRDYQEKALERWLV-------DKRGCIVLPTGSGKTHVAMAAINELS----TPTLIV-VPTLALAEQWKERLGI-FGEEY  160 (472)
T ss_dssp             BCHHHHHHHHHHTT-------TTEEEEECCTTSCHHHHHHHHHHHHC----SCEEEE-ESSHHHHHHHHHHGGG-GCGGG
T ss_pred             cCHHHHHHHHHHHh-------cCCEEEEeCCCCCHHHHHHHHHHHcC----CCEEEE-ECCHHHHHHHHHHHHh-CCCcc
Confidence            34455555554443       24599999999999999988877653    344444 2221112233333322 3221 


Q ss_pred             ---CCC----------CcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCHHHH
Q psy200          277 ---PGG----------KSERHQLGAILKYFDTKHKSILLILDEIDALESRKQTIL  318 (490)
Q Consensus       277 ---~~~----------~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L  318 (490)
                         ..+          .+.+.+...+.. +.  .+..+|||||+|.+.......+
T Consensus       161 v~~~~g~~~~~~~Ivv~T~~~l~~~~~~-~~--~~~~liIvDEaH~~~~~~~~~~  212 (472)
T 2fwr_A          161 VGEFSGRIKELKPLTVSTYDSAYVNAEK-LG--NRFMLLIFDEVHHLPAESYVQI  212 (472)
T ss_dssp             EEEBSSSCBCCCSEEEEEHHHHHHTHHH-HT--TTCSEEEEETGGGTTSTTTHHH
T ss_pred             eEEECCCcCCcCCEEEEEcHHHHHHHHH-hc--CCCCEEEEECCcCCCChHHHHH
Confidence               000          022333332222 21  2355999999999976544333

>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=95.64  E-value=0.0051  Score=54.53  Aligned_cols=24  Identities=33%  Similarity=0.545  Sum_probs=20.8

Q ss_pred             CeEEEECCCCCcHHHHHHHHHHHh
Q psy200          220 GSMYISGPPGTGKSASLNLLVSRA  243 (490)
Q Consensus       220 ~~ill~GppGtGKTtla~~l~~~l  243 (490)
                      ..++|.|++|+||||+++.++...
T Consensus         3 ~ii~l~G~~GaGKSTl~~~L~~~~   26 (189)
T 2bdt_A            3 KLYIITGPAGVGKSTTCKRLAAQL   26 (189)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHS
T ss_pred             eEEEEECCCCCcHHHHHHHHhccc
Confidence            467899999999999999998743

>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=95.64  E-value=0.0077  Score=54.64  Aligned_cols=24  Identities=17%  Similarity=0.430  Sum_probs=21.8

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHhh
Q psy200          221 SMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      .|+|.|++|+||||+++.+++.++
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~~g   25 (214)
T 1e4v_A            2 RIILLGAPVAGKGTQAQFIMEKYG   25 (214)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhC
Confidence            478999999999999999999874

>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=95.63  E-value=0.052  Score=46.43  Aligned_cols=24  Identities=29%  Similarity=0.317  Sum_probs=20.9

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHH
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~  242 (490)
                      ...++|.|++|+|||+|++.+...
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            457899999999999999999764

>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=95.59  E-value=0.01  Score=54.69  Aligned_cols=26  Identities=35%  Similarity=0.394  Sum_probs=23.5

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      +..+.|.||+|+||||+++.+++.++
T Consensus         9 ~~~i~i~G~~GsGKsTla~~la~~lg   34 (233)
T 3r20_A            9 SLVVAVDGPAGTGKSSVSRGLARALG   34 (233)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHHT
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhC
Confidence            45789999999999999999999875

>3fht_A ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box helicase, RNA dependent ATPase, mRNA export, nucleocytoplasmic transport, NUP214, CAN; HET: ANP; 2.20A {Homo sapiens} PDB: 3ews_A* 3g0h_A* 3fhc_B

Probab=95.59  E-value=0.034  Score=55.38  Aligned_cols=27  Identities=26%  Similarity=0.448  Sum_probs=20.1

Q ss_pred             CCCeEEEECCCCCcHHHHH-HHHHHHhh
Q psy200          218 TSGSMYISGPPGTGKSASL-NLLVSRAE  244 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla-~~l~~~l~  244 (490)
                      .++.+++.+|+|+|||..+ -.+++.+.
T Consensus        63 ~~~~~lv~apTGsGKT~~~~~~~~~~~~   90 (412)
T 3fht_A           63 PPQNLIAQSQSGTGKTAAFVLAMLSQVE   90 (412)
T ss_dssp             SCCCEEEECCTTSCHHHHHHHHHHHHCC
T ss_pred             CCCeEEEECCCCchHHHHHHHHHHHHhh
Confidence            4578999999999999875 33444443

>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=95.58  E-value=0.0091  Score=53.56  Aligned_cols=23  Identities=22%  Similarity=0.348  Sum_probs=20.9

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHhh
Q psy200          221 SMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      .+.|+|++|+||||+++.++. ++
T Consensus         3 ~i~i~G~~GsGKSTl~~~L~~-~g   25 (204)
T 2if2_A            3 RIGLTGNIGCGKSTVAQMFRE-LG   25 (204)
T ss_dssp             EEEEEECTTSSHHHHHHHHHH-TT
T ss_pred             EEEEECCCCcCHHHHHHHHHH-CC
Confidence            688999999999999999988 63

>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=95.58  E-value=0.042  Score=48.32  Aligned_cols=25  Identities=20%  Similarity=0.234  Sum_probs=21.4

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHh
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRA  243 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l  243 (490)
                      .-.|+|.|.+|+|||+|++.+....
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            3478899999999999999987654

>1wrb_A DJVLGB; RNA helicase, DEAD BOX, VASA, structural genomics, NPPSFA, N project on protein structural and functional analyses; 2.40A {Dugesia japonica} SCOP: c.37.1.19

Probab=95.57  E-value=0.072  Score=49.34  Aligned_cols=40  Identities=18%  Similarity=0.336  Sum_probs=23.7

Q ss_pred             eEEEEEecCccccccC-HHHHHHhHhCCCCC---CCcEEEEEec
Q psy200          299 SILLILDEIDALESRK-QTILYTIFEWPSIP---GSKLVLVGVA  338 (490)
Q Consensus       299 ~~vI~IDEid~l~~~~-~~~L~~l~~~~~~~---~~~vilI~~t  338 (490)
                      ..+|||||+|.+.... ...+..++......   ..+++++.+|
T Consensus       175 ~~~lViDEah~~~~~~~~~~~~~i~~~~~~~~~~~~q~l~~SAT  218 (253)
T 1wrb_A          175 CKYIVLDEADRMLDMGFEPQIRKIIEESNMPSGINRQTLMFSAT  218 (253)
T ss_dssp             CCEEEEETHHHHHHTTCHHHHHHHHHSSCCCCGGGCEEEEEESS
T ss_pred             CCEEEEeCHHHHHhCchHHHHHHHHhhccCCCCCCcEEEEEEEe
Confidence            4589999999986543 34455555432222   3455665555

>3ly5_A ATP-dependent RNA helicase DDX18; alpha-beta, structural genomics, structural genomics consort ATP-binding, hydrolase, nucleotide-binding, RNA-B; 2.80A {Homo sapiens}

Probab=95.57  E-value=0.065  Score=50.13  Aligned_cols=40  Identities=18%  Similarity=0.206  Sum_probs=23.6

Q ss_pred             CeEEEEEecCccccccC-HHHHHHhHhCCCCCCCcEEEEEec
Q psy200          298 KSILLILDEIDALESRK-QTILYTIFEWPSIPGSKLVLVGVA  338 (490)
Q Consensus       298 ~~~vI~IDEid~l~~~~-~~~L~~l~~~~~~~~~~vilI~~t  338 (490)
                      +..+|||||+|.+.... ...+..++.... ...+++++.+|
T Consensus       201 ~l~~lViDEah~l~~~~~~~~l~~i~~~~~-~~~q~l~~SAT  241 (262)
T 3ly5_A          201 NLQCLVIDEADRILDVGFEEELKQIIKLLP-TRRQTMLFSAT  241 (262)
T ss_dssp             TCCEEEECSHHHHHHTTCHHHHHHHHHHSC-SSSEEEEECSS
T ss_pred             cCCEEEEcChHHHhhhhHHHHHHHHHHhCC-CCCeEEEEEec
Confidence            45689999999987653 344444444322 33455555555

>3gmt_A Adenylate kinase; ssgcid, ATP-BIN cytoplasm, nucleotide biosynthesis, nucleotide-BIND transferase, structural genomics; 2.10A {Burkholderia pseudomallei 1710B}

Probab=95.57  E-value=0.045  Score=50.19  Aligned_cols=25  Identities=24%  Similarity=0.498  Sum_probs=22.1

Q ss_pred             CeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          220 GSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       220 ~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      ..+.|.|+||+||||+++.+++.++
T Consensus         9 ~~~~~~G~pGsGKsT~a~~L~~~~g   33 (230)
T 3gmt_A            9 MRLILLGAPGAGKGTQANFIKEKFG   33 (230)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHHT
T ss_pred             cceeeECCCCCCHHHHHHHHHHHhC
Confidence            3567999999999999999999874

>1wp9_A ATP-dependent RNA helicase, putative; ATPase, DNA replication, DNA repair, DNA recombina hydrolase; 2.90A {Pyrococcus furiosus} SCOP: c.37.1.19 c.37.1.19

Probab=95.52  E-value=0.034  Score=56.31  Aligned_cols=52  Identities=15%  Similarity=0.093  Sum_probs=31.6

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHh
Q psy200          221 SMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNEL  273 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l  273 (490)
                      .++|.+|.|+|||..+-.++..........++++. +...-..++..++...+
T Consensus        25 ~~ll~~~tG~GKT~~~~~~~~~~~~~~~~~~liv~-P~~~L~~q~~~~~~~~~   76 (494)
T 1wp9_A           25 NCLIVLPTGLGKTLIAMMIAEYRLTKYGGKVLMLA-PTKPLVLQHAESFRRLF   76 (494)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHHHHHSCSCEEEEC-SSHHHHHHHHHHHHHHB
T ss_pred             CEEEEcCCCCCHHHHHHHHHHHHHhcCCCeEEEEE-CCHHHHHHHHHHHHHHh
Confidence            78899999999999988887665322334555552 22112234445554444

>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=95.52  E-value=0.0085  Score=54.78  Aligned_cols=27  Identities=26%  Similarity=0.441  Sum_probs=23.9

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      .+..+.|.||.|+|||||++.++..+.
T Consensus        15 ~G~ii~l~GpsGsGKSTLlk~L~g~~~   41 (219)
T 1s96_A           15 QGTLYIVSAPSGAGKSSLIQALLKTQP   41 (219)
T ss_dssp             CCCEEEEECCTTSCHHHHHHHHHHHSC
T ss_pred             CCcEEEEECCCCCCHHHHHHHHhccCC
Confidence            567899999999999999999988763

>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=95.51  E-value=0.02  Score=56.79  Aligned_cols=28  Identities=18%  Similarity=0.248  Sum_probs=24.6

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      ..+..++|+||+|+||||+++.++..+.
T Consensus       167 ~~~~~i~l~G~~GsGKSTl~~~l~~~~~  194 (377)
T 1svm_A          167 PKKRYWLFKGPIDSGKTTLAAALLELCG  194 (377)
T ss_dssp             TTCCEEEEECSTTSSHHHHHHHHHHHHC
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHhhcC
Confidence            4567899999999999999999998753

>3asz_A Uridine kinase; cytidine phosphorylation, transferase; HET: C5P; 2.25A {Thermus thermophilus} PDB: 3asy_A*

Probab=95.50  E-value=0.0079  Score=54.31  Aligned_cols=27  Identities=19%  Similarity=0.185  Sum_probs=23.6

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      .+..+.|.|+.|+||||+++.++..+.
T Consensus         5 ~~~~i~i~G~~GsGKSTl~~~l~~~~~   31 (211)
T 3asz_A            5 KPFVIGIAGGTASGKTTLAQALARTLG   31 (211)
T ss_dssp             CCEEEEEEESTTSSHHHHHHHHHHHHG
T ss_pred             CcEEEEEECCCCCCHHHHHHHHHHHhC
Confidence            456788999999999999999988764

>2z0m_A 337AA long hypothetical ATP-dependent RNA helicase DEAD; ATP-binding, hydrolase, nucleotide-binding, RNA binding protein, structural genomics; 1.90A {Sulfolobus tokodaii}

Probab=95.49  E-value=0.032  Score=53.77  Aligned_cols=24  Identities=17%  Similarity=0.391  Sum_probs=19.1

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHH
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~  242 (490)
                      ++.+++.+|+|+|||.++-..+-+
T Consensus        31 ~~~~lv~~~TGsGKT~~~~~~~~~   54 (337)
T 2z0m_A           31 GKNVVVRAKTGSGKTAAYAIPILE   54 (337)
T ss_dssp             TCCEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCCEEEEcCCCCcHHHHHHHHHHh
Confidence            357999999999999877655544

>2hf9_A Probable hydrogenase nickel incorporation protein HYPB; alpha and beta protein; HET: GSP; 1.90A {Methanocaldococcus jannaschii} PDB: 2hf8_A*

Probab=95.48  E-value=0.025  Score=51.39  Aligned_cols=40  Identities=18%  Similarity=0.238  Sum_probs=29.3

Q ss_pred             HHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          201 VQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       201 ~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      +..+.+...+.    ......++|.|.+|+|||||+..++....
T Consensus        24 ~~a~~~r~~~~----~~~~~~i~ivG~~gvGKTtl~~~l~~~~~   63 (226)
T 2hf9_A           24 RLADKNRKLLN----KHGVVAFDFMGAIGSGKTLLIEKLIDNLK   63 (226)
T ss_dssp             HHHHHHHHHHH----HTTCEEEEEEESTTSSHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHH----hCCCeEEEEEcCCCCCHHHHHHHHHHHhc
Confidence            33444444443    34567788999999999999999998864

>4e22_A Cytidylate kinase; P-loop, CMP/ATP binding, transferase; 2.32A {Yersinia pseudotuberculosis}

Probab=95.47  E-value=0.0094  Score=55.71  Aligned_cols=27  Identities=22%  Similarity=0.427  Sum_probs=24.2

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      .+..+.|.|++|+||||+++.+++.++
T Consensus        26 ~g~~I~I~G~~GsGKSTl~k~La~~Lg   52 (252)
T 4e22_A           26 IAPVITVDGPSGAGKGTLCKALAESLN   52 (252)
T ss_dssp             TSCEEEEECCTTSSHHHHHHHHHHHTT
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHhcC
Confidence            456889999999999999999998875

>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=95.47  E-value=0.009  Score=53.94  Aligned_cols=27  Identities=30%  Similarity=0.462  Sum_probs=23.4

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHh
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRA  243 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l  243 (490)
                      ..+..+.|.||.|+|||||++.++..+
T Consensus        18 ~~Gei~~l~GpnGsGKSTLl~~l~gl~   44 (207)
T 1znw_A           18 AVGRVVVLSGPSAVGKSTVVRCLRERI   44 (207)
T ss_dssp             -CCCEEEEECSTTSSHHHHHHHHHHHS
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHhhC
Confidence            346788999999999999999998876

>3foz_A TRNA delta(2)-isopentenylpyrophosphate transferas; nucleoside modification, isopentenyl-tRNA transferase, transferase-RNA complex; 2.50A {Escherichia coli k-12} PDB: 2zxu_A* 2zm5_A

Probab=95.46  E-value=0.012  Score=56.47  Aligned_cols=27  Identities=22%  Similarity=0.337  Sum_probs=23.7

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      .+..++|+||+|+|||+|+..+++.+.
T Consensus         9 ~~~~i~i~GptgsGKt~la~~La~~~~   35 (316)
T 3foz_A            9 LPKAIFLMGPTASGKTALAIELRKILP   35 (316)
T ss_dssp             CCEEEEEECCTTSCHHHHHHHHHHHSC
T ss_pred             CCcEEEEECCCccCHHHHHHHHHHhCC
Confidence            346788999999999999999999864

>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=95.44  E-value=0.031  Score=56.30  Aligned_cols=97  Identities=10%  Similarity=0.154  Sum_probs=60.8

Q ss_pred             cCCCCeEEEECCCCCcHHHHHHHHHHHhhh---cCCceEEEEeccCCC-CHHHHHHHHHHH--hc-----CCCCCCc-HH
Q psy200          216 NETSGSMYISGPPGTGKSASLNLLVSRAEI---KDAFKTIYINCNSVR-NAASVYETIVNE--LK-----LKPGGKS-ER  283 (490)
Q Consensus       216 ~~~~~~ill~GppGtGKTtla~~l~~~l~~---~~~~~~~~v~~~~~~-~~~~l~~~i~~~--l~-----~~~~~~s-~~  283 (490)
                      -..++.++|.|++|+|||+|+..+++....   .+++.++++-|..-. ...+|+.++...  +.     ....... ..
T Consensus       148 igrGQr~~Ifgg~G~GKt~L~~~Ia~~~~~~~d~~~~~~V~~~iGeR~~Ev~e~~~~~~~~g~~~rtvvV~atsd~p~~~  227 (465)
T 3vr4_D          148 LVRGQKLPVFSGSGLPHKELAAQIARQATVLDSSDDFAVVFAAIGITFEEAEFFMEDFRQTGAIDRSVMFMNLANDPAIE  227 (465)
T ss_dssp             CBTTCBCCEEECTTSCHHHHHHHHHHHCBCSSCSSCEEEEEEEEEECHHHHHHHHHHHHHHTGGGGEEEEEEETTSCHHH
T ss_pred             cccCCEEEEeCCCCcChHHHHHHHHHHHHhccCCCceEEEEEEecCCcHHHHHHHHHHhhcCCccceEEEEECCCCCHHH
Confidence            356778889999999999999999988653   345566777666532 345566665443  11     0001111 11


Q ss_pred             HH-----HHHHHHHHhc-CCCeEEEEEecCccccc
Q psy200          284 HQ-----LGAILKYFDT-KHKSILLILDEIDALES  312 (490)
Q Consensus       284 ~~-----~~~l~~~l~~-~~~~~vI~IDEid~l~~  312 (490)
                      .+     .-.+.+++.. .++.++|++|++-++..
T Consensus       228 r~~a~~~a~tiAEyfrd~~G~~VLl~~DslTr~A~  262 (465)
T 3vr4_D          228 RIATPRMALTAAEYLAYEKGMHVLVIMTDMTNYAE  262 (465)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCCEEEEEEECHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHhcCCeEEEEEcChHHHHH
Confidence            11     1235566665 48899999999987653

>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=95.44  E-value=0.0095  Score=51.44  Aligned_cols=27  Identities=22%  Similarity=0.374  Sum_probs=24.2

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHh
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRA  243 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l  243 (490)
                      ..+..+.|.||.|+|||||++.++..+
T Consensus        31 ~~Ge~v~L~G~nGaGKTTLlr~l~g~l   57 (158)
T 1htw_A           31 EKAIMVYLNGDLGAGKTTLTRGMLQGI   57 (158)
T ss_dssp             SSCEEEEEECSTTSSHHHHHHHHHHHT
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHHhC
Confidence            456688899999999999999999987

>3tqc_A Pantothenate kinase; biosynthesis of cofactors, prosthetic groups, carriers, TRAN; HET: ADP; 2.30A {Coxiella burnetii}

Probab=95.43  E-value=0.013  Score=56.85  Aligned_cols=27  Identities=22%  Similarity=0.226  Sum_probs=23.2

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      .+..+.|.|++|+||||+++.+...+.
T Consensus        91 ~p~iigI~GpsGSGKSTl~~~L~~ll~  117 (321)
T 3tqc_A           91 VPYIIGIAGSVAVGKSTTSRVLKALLS  117 (321)
T ss_dssp             CCEEEEEECCTTSSHHHHHHHHHHHHT
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHhc
Confidence            344788999999999999999988775

>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=95.43  E-value=0.13  Score=45.17  Aligned_cols=24  Identities=21%  Similarity=0.218  Sum_probs=21.1

Q ss_pred             CeEEEECCCCCcHHHHHHHHHHHh
Q psy200          220 GSMYISGPPGTGKSASLNLLVSRA  243 (490)
Q Consensus       220 ~~ill~GppGtGKTtla~~l~~~l  243 (490)
                      -.|+|.|.+|+|||+|++.+...-
T Consensus        24 ~ki~v~G~~~~GKSsli~~l~~~~   47 (191)
T 3dz8_A           24 FKLLIIGNSSVGKTSFLFRYADDT   47 (191)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHHT
T ss_pred             eEEEEECCCCcCHHHHHHHHhcCC
Confidence            368899999999999999998754

>3a8t_A Adenylate isopentenyltransferase; rossmann fold protein; HET: ATP; 2.37A {Humulus lupulus}

Probab=95.41  E-value=0.0089  Score=58.10  Aligned_cols=27  Identities=26%  Similarity=0.245  Sum_probs=23.7

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      .+..++|.||+|+|||+|+..|++.++
T Consensus        39 ~~~lIvI~GPTgsGKTtLa~~LA~~l~   65 (339)
T 3a8t_A           39 KEKLLVLMGATGTGKSRLSIDLAAHFP   65 (339)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHTTSC
T ss_pred             CCceEEEECCCCCCHHHHHHHHHHHCC
Confidence            345899999999999999999998864

>1z6g_A Guanylate kinase; structural genomics, SGC, structural genom consortium, transferase; HET: EPE; 2.18A {Plasmodium falciparum}

Probab=95.41  E-value=0.0091  Score=54.48  Aligned_cols=27  Identities=26%  Similarity=0.470  Sum_probs=23.4

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHh
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRA  243 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l  243 (490)
                      ..+..+.|+||.|+|||||++.++..+
T Consensus        21 ~~G~~~~lvGpsGsGKSTLl~~L~g~~   47 (218)
T 1z6g_A           21 NNIYPLVICGPSGVGKGTLIKKLLNEF   47 (218)
T ss_dssp             -CCCCEEEECSTTSSHHHHHHHHHHHS
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHhhC
Confidence            356789999999999999999998865

>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=95.41  E-value=0.073  Score=46.33  Aligned_cols=24  Identities=21%  Similarity=0.257  Sum_probs=20.8

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHH
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~  242 (490)
                      .-.++|.|.+|+|||+|++.+...
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            347899999999999999999754

>4a4z_A Antiviral helicase SKI2; hydrolase, ATPase, mRNA degradation, exosome; HET: ANP; 2.40A {Saccharomyces cerevisiae} PDB: 4a4k_A

Probab=95.39  E-value=0.026  Score=63.26  Aligned_cols=117  Identities=13%  Similarity=0.211  Sum_probs=58.6

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCC-----CCC-----------CcH
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLK-----PGG-----------KSE  282 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~-----~~~-----------~s~  282 (490)
                      ++.+++.||.|+|||.++...+..+. ..+..++++. +...-..+.+..+...+...     ..+           .+.
T Consensus        54 g~~vlv~apTGsGKTlv~~~~i~~~~-~~g~~vlvl~-PtraLa~Q~~~~l~~~~~~~~v~~l~G~~~~~~~~~IlV~Tp  131 (997)
T 4a4z_A           54 GDSVFVAAHTSAGKTVVAEYAIAMAH-RNMTKTIYTS-PIKALSNQKFRDFKETFDDVNIGLITGDVQINPDANCLIMTT  131 (997)
T ss_dssp             TCEEEEECCTTSCSHHHHHHHHHHHH-HTTCEEEEEE-SCGGGHHHHHHHHHTTC--CCEEEECSSCEECTTSSEEEEEH
T ss_pred             CCCEEEEECCCCcHHHHHHHHHHHHH-hcCCeEEEEe-CCHHHHHHHHHHHHHHcCCCeEEEEeCCCccCCCCCEEEECH
Confidence            46899999999999987655544432 1233444442 22223344555544433210     000           123


Q ss_pred             HHHHHHHHHHHhcCCCeEEEEEecCccccccCHH-HHHHhHhCCCCCCCcEEEEEec
Q psy200          283 RHQLGAILKYFDTKHKSILLILDEIDALESRKQT-ILYTIFEWPSIPGSKLVLVGVA  338 (490)
Q Consensus       283 ~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~~-~L~~l~~~~~~~~~~vilI~~t  338 (490)
                      ..+...+...........+|||||+|.+...... .+..++... ....+++++.+|
T Consensus       132 e~L~~~l~~~~~~l~~l~lvViDEaH~l~d~~~g~~~e~ii~~l-~~~v~iIlLSAT  187 (997)
T 4a4z_A          132 EILRSMLYRGADLIRDVEFVIFDEVHYVNDQDRGVVWEEVIIML-PQHVKFILLSAT  187 (997)
T ss_dssp             HHHHHHHHHTCSGGGGEEEEEECCTTCCCTTCTTCCHHHHHHHS-CTTCEEEEEECC
T ss_pred             HHHHHHHHhCchhhcCCCEEEEECcccccccchHHHHHHHHHhc-ccCCCEEEEcCC
Confidence            3343333321111134679999999998654211 122222211 134567776666

>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=95.37  E-value=0.064  Score=55.17  Aligned_cols=95  Identities=21%  Similarity=0.349  Sum_probs=58.5

Q ss_pred             cCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCC-HHHHHHHHHH----Hhc----------CCCCCC
Q psy200          216 NETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRN-AASVYETIVN----ELK----------LKPGGK  280 (490)
Q Consensus       216 ~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~-~~~l~~~i~~----~l~----------~~~~~~  280 (490)
                      -..++.++|.|++|+|||+|+..+++...  .+ .++++-|..-.. ..+++.++-+    .++          ......
T Consensus       224 igkGqr~~I~g~~g~GKT~L~~~ia~~~~--~~-~~V~~~iGER~~Ev~e~~~~~~el~d~~~g~~~m~rtvvV~~tsd~  300 (588)
T 3mfy_A          224 QAKGGTAAIPGPAGSGKTVTQHQLAKWSD--AQ-VVIYIGCGERGNEMTDVLEEFPKLKDPKTGKPLMERTVLIANTSNM  300 (588)
T ss_dssp             EETTCEEEECSCCSHHHHHHHHHHHHHSS--CS-EEEEEECCSSSSHHHHHHHHTTTCEETTTTEEGGGGEEEEECCTTS
T ss_pred             cccCCeEEeecCCCCCHHHHHHHHHhccC--CC-EEEEEEecccHHHHHHHHHHHHHhcccccccccccceEEEEECCCC
Confidence            35688999999999999999999987642  23 456666665543 3455555422    011          001111


Q ss_pred             cH-HHH-----HHHHHHHHhcCCCeEEEEEecCcccccc
Q psy200          281 SE-RHQ-----LGAILKYFDTKHKSILLILDEIDALESR  313 (490)
Q Consensus       281 s~-~~~-----~~~l~~~l~~~~~~~vI~IDEid~l~~~  313 (490)
                      .. ...     .-.+.+++...++.++|++|++-++...
T Consensus       301 p~~~r~~~~~~a~tiAEyfrd~G~dVLl~~DsltR~A~A  339 (588)
T 3mfy_A          301 PVAAREASIYTGITIAEYFRDMGYDVALMADSTSRWAEA  339 (588)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHTTCEEEEEEECTTTCCCC
T ss_pred             CHHHHHHHHHHHHHHHHHHHHcCCCEEEeecchHHHHHH
Confidence            11 111     1234455666688999999999877654

>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=95.34  E-value=0.099  Score=46.98  Aligned_cols=27  Identities=33%  Similarity=0.581  Sum_probs=23.1

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHh
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRA  243 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l  243 (490)
                      .....++|.|++|+|||+|++.+....
T Consensus        10 ~~~~~i~~~G~~g~GKTsl~~~l~~~~   36 (218)
T 1nrj_B           10 SYQPSIIIAGPQNSGKTSLLTLLTTDS   36 (218)
T ss_dssp             CCCCEEEEECSTTSSHHHHHHHHHHSS
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            345689999999999999999998754

>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=95.32  E-value=0.03  Score=50.83  Aligned_cols=39  Identities=23%  Similarity=0.297  Sum_probs=29.3

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEecc
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCN  257 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~  257 (490)
                      .+..|.|.|++|+||||+++.+++.+.. .++.++...-+
T Consensus         5 ~g~~i~~eG~~gsGKsT~~~~l~~~l~~-~~~~v~~~~~p   43 (213)
T 4edh_A            5 TGLFVTLEGPEGAGKSTNRDYLAERLRE-RGIEVQLTREP   43 (213)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHHHHHT-TTCCEEEEESS
T ss_pred             CceEEEEEcCCCCCHHHHHHHHHHHHHH-cCCCcccccCC
Confidence            3567889999999999999999998862 33555554433

>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=95.31  E-value=0.083  Score=46.10  Aligned_cols=25  Identities=24%  Similarity=0.324  Sum_probs=21.3

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHH
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~  242 (490)
                      ....++|.|++|+|||+|++.+...
T Consensus        15 ~~~ki~ivG~~~vGKSsL~~~l~~~   39 (181)
T 1fzq_A           15 QEVRILLLGLDNAGKTTLLKQLASE   39 (181)
T ss_dssp             SCEEEEEEESTTSSHHHHHHHHCCS
T ss_pred             CceEEEEECCCCCCHHHHHHHHhcC
Confidence            4557899999999999999998654

>3fmp_B ATP-dependent RNA helicase DDX19B; nuclear porin, nuclear pore complex, nucleocytoplasmic trans mRNA export, protein interaction, beta-propeller; HET: ADP; 3.19A {Homo sapiens}

Probab=95.30  E-value=0.041  Score=56.33  Aligned_cols=27  Identities=26%  Similarity=0.448  Sum_probs=20.1

Q ss_pred             CCCCeEEEECCCCCcHHHHH-HHHHHHh
Q psy200          217 ETSGSMYISGPPGTGKSASL-NLLVSRA  243 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla-~~l~~~l  243 (490)
                      +.++.+++.||.|+|||... -.++..+
T Consensus       129 ~~~~~~l~~a~TGsGKT~~~~l~il~~l  156 (479)
T 3fmp_B          129 EPPQNLIAQSQSGTGKTAAFVLAMLSQV  156 (479)
T ss_dssp             BSCCEEEEECCSSSSHHHHHHHHHHTTC
T ss_pred             CCCCcEEEEcCCCCchhHHHHHHHHHHH
Confidence            34689999999999999874 3444444

>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=95.27  E-value=0.014  Score=52.18  Aligned_cols=26  Identities=27%  Similarity=0.355  Sum_probs=22.4

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      ...+.|+|++|+||||+++.+++.++
T Consensus        12 ~~iIgltG~~GSGKSTva~~L~~~lg   37 (192)
T 2grj_A           12 HMVIGVTGKIGTGKSTVCEILKNKYG   37 (192)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHHHC
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHhcC
Confidence            34678999999999999999988754

>3v9p_A DTMP kinase, thymidylate kinase; ssgcid, STRU genomics, seattle structural genomics center for infectious transferase; 1.90A {Burkholderia thailandensis}

Probab=95.26  E-value=0.023  Score=52.20  Aligned_cols=54  Identities=13%  Similarity=0.170  Sum_probs=32.1

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhc---CCceEEEEeccCCCCHHHHHHHHHH
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIK---DAFKTIYINCNSVRNAASVYETIVN  271 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~---~~~~~~~v~~~~~~~~~~l~~~i~~  271 (490)
                      .+..|.|.|++|+||||+++.+++.+...   .++.++...-+........+.+++.
T Consensus        24 ~g~~I~~eG~~GsGKsT~~~~l~~~l~~~~~~~g~~v~~~rep~~t~~g~~ir~~l~   80 (227)
T 3v9p_A           24 RGKFITFEGIDGAGKTTHLQWFCDRLQERLGPAGRHVVVTREPGGTRLGETLREILL   80 (227)
T ss_dssp             CCCEEEEECCC---CHHHHHHHHHHHHHHHGGGTCCEEEEESSSSSHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHhhccccceeeeeecCCCCChHHHHHHHHHH
Confidence            45678899999999999999999998632   1455555544432222333444443

>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=95.25  E-value=0.011  Score=55.22  Aligned_cols=27  Identities=22%  Similarity=0.178  Sum_probs=24.0

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      ....|.|.|++|+||||+++.+++.++
T Consensus        21 ~~~iI~I~G~~GSGKST~a~~L~~~lg   47 (252)
T 1uj2_A           21 EPFLIGVSGGTASGKSSVCAKIVQLLG   47 (252)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHHHTT
T ss_pred             CcEEEEEECCCCCCHHHHHHHHHHHhh
Confidence            455788999999999999999999876

>2wsm_A Hydrogenase expression/formation protein (HYPB); metal binding protein; 2.30A {Archaeoglobus fulgidus}

Probab=95.24  E-value=0.022  Score=51.64  Aligned_cols=46  Identities=22%  Similarity=0.222  Sum_probs=33.7

Q ss_pred             CCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          195 ELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       195 ~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      .+-...+..+.+...+..    .....++|.|.+|+||||++..++..+.
T Consensus        10 ~l~~~~~~~~~~~~~~~~----~~~~~i~i~G~~g~GKTTl~~~l~~~~~   55 (221)
T 2wsm_A           10 LLAENKRLAEKNREALRE----SGTVAVNIMGAIGSGKTLLIERTIERIG   55 (221)
T ss_dssp             -CHHHHHHHHHHHHHHHH----HTCEEEEEEECTTSCHHHHHHHHHHHHT
T ss_pred             HHhhcHHHHHHHHHhhcc----cCceEEEEEcCCCCCHHHHHHHHHHHhc
Confidence            344455566666665532    3567889999999999999999998864

>2z83_A Helicase/nucleoside triphosphatase; hydrolase, membrane, nucleotide-binding, RNA replication, transmembrane, viral protein; 1.80A {Japanese encephalitis virus} PDB: 2v8o_A 2qeq_A

Probab=95.23  E-value=0.025  Score=57.80  Aligned_cols=51  Identities=18%  Similarity=0.280  Sum_probs=32.2

Q ss_pred             CCCeEEEECCCCCcHHHH-HHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhc
Q psy200          218 TSGSMYISGPPGTGKSAS-LNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELK  274 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtl-a~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~  274 (490)
                      .++.+++.||+|+|||+. +-.+++.+.. .+..++++.     -...+..++...+.
T Consensus        20 ~~~~vlv~a~TGsGKT~~~~l~il~~~~~-~~~~~lvl~-----Ptr~La~Q~~~~l~   71 (459)
T 2z83_A           20 KRQMTVLDLHPGSGKTRKILPQIIKDAIQ-QRLRTAVLA-----PTRVVAAEMAEALR   71 (459)
T ss_dssp             TTCEEEECCCTTSCTTTTHHHHHHHHHHH-TTCCEEEEE-----CSHHHHHHHHHHTT
T ss_pred             cCCcEEEECCCCCCHHHHHHHHHHHHHHh-CCCcEEEEC-----chHHHHHHHHHHhc
Confidence            467899999999999997 4555554431 234455553     12446666666664

>3exa_A TRNA delta(2)-isopentenylpyrophosphate transferase; alpha-beta protein, structural genomics, PSI-2, protein structure initiative; 2.30A {Bacillus halodurans} PDB: 2qgn_A

Probab=95.22  E-value=0.012  Score=56.47  Aligned_cols=26  Identities=27%  Similarity=0.433  Sum_probs=23.0

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      ...++|.||+|+|||+|+..+++.+.
T Consensus         3 ~~~i~i~GptgsGKt~la~~La~~~~   28 (322)
T 3exa_A            3 EKLVAIVGPTAVGKTKTSVMLAKRLN   28 (322)
T ss_dssp             CEEEEEECCTTSCHHHHHHHHHHTTT
T ss_pred             CcEEEEECCCcCCHHHHHHHHHHhCc
Confidence            35788999999999999999998864

>2eyu_A Twitching motility protein PILT; pilus retraction motor, C-terminal domain PILT, protein transport; 1.87A {Aquifex aeolicus}

Probab=95.20  E-value=0.012  Score=55.39  Aligned_cols=28  Identities=25%  Similarity=0.623  Sum_probs=25.0

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      ..+..++|+||.|+||||+++.++..+.
T Consensus        23 ~~g~~v~i~Gp~GsGKSTll~~l~g~~~   50 (261)
T 2eyu_A           23 RKMGLILVTGPTGSGKSTTIASMIDYIN   50 (261)
T ss_dssp             CSSEEEEEECSTTCSHHHHHHHHHHHHH
T ss_pred             CCCCEEEEECCCCccHHHHHHHHHHhCC
Confidence            4567899999999999999999998775

>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=95.20  E-value=0.044  Score=47.63  Aligned_cols=25  Identities=28%  Similarity=0.308  Sum_probs=21.4

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHH
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVS  241 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~  241 (490)
                      .....++|.|++|+|||+|++.+..
T Consensus        16 ~~~~~i~v~G~~~~GKssli~~l~~   40 (183)
T 1moz_A           16 NKELRILILGLDGAGKTTILYRLQI   40 (183)
T ss_dssp             SSCEEEEEEEETTSSHHHHHHHTCC
T ss_pred             CCccEEEEECCCCCCHHHHHHHHhc
Confidence            4566899999999999999988863

>2xgj_A ATP-dependent RNA helicase DOB1; hydrolase-RNA complex, hydrolase, tramp, exosome, DEAD, nucleotide-binding; HET: ADP; 2.90A {Saccharomyces cerevisiae}

Probab=95.16  E-value=0.11  Score=58.41  Aligned_cols=117  Identities=12%  Similarity=0.188  Sum_probs=58.6

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcC---CCCC-----------CcHHH
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKL---KPGG-----------KSERH  284 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~---~~~~-----------~s~~~  284 (490)
                      +..+++.+|.|+|||.++...+.... ..+..++++.- .-.-..+.+..+...++.   -..+           .+.+.
T Consensus       101 g~~vLV~apTGSGKTlva~lai~~~l-~~g~rvL~l~P-tkaLa~Q~~~~l~~~~~~vglltGd~~~~~~~~IvV~Tpe~  178 (1010)
T 2xgj_A          101 GESVLVSAHTSAGKTVVAEYAIAQSL-KNKQRVIYTSP-IKALSNQKYRELLAEFGDVGLMTGDITINPDAGCLVMTTEI  178 (1010)
T ss_dssp             TCEEEEECCTTSCHHHHHHHHHHHHH-HTTCEEEEEES-SHHHHHHHHHHHHHHHSCEEEECSSCEECTTCSEEEEEHHH
T ss_pred             CCCEEEECCCCCChHHHHHHHHHHHh-ccCCeEEEECC-hHHHHHHHHHHHHHHhCCEEEEeCCCccCCCCCEEEEcHHH
Confidence            45799999999999998755444322 23445666532 111123334444333321   0000           12333


Q ss_pred             HHHHHHHHHhcCCCeEEEEEecCccccccCHHH-HHHhHhCCCCCCCcEEEEEec
Q psy200          285 QLGAILKYFDTKHKSILLILDEIDALESRKQTI-LYTIFEWPSIPGSKLVLVGVA  338 (490)
Q Consensus       285 ~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~-L~~l~~~~~~~~~~vilI~~t  338 (490)
                      +...+.........-.+|||||+|.+....... +..++... ....+++++.+|
T Consensus       179 L~~~L~~~~~~l~~l~lVViDEaH~l~d~~rg~~~e~il~~l-~~~~~il~LSAT  232 (1010)
T 2xgj_A          179 LRSMLYRGSEVMREVAWVIFDEVHYMRDKERGVVWEETIILL-PDKVRYVFLSAT  232 (1010)
T ss_dssp             HHHHHHHTCTTGGGEEEEEEETGGGGGCTTTHHHHHHHHHHS-CTTCEEEEEECC
T ss_pred             HHHHHHcCcchhhcCCEEEEechhhhcccchhHHHHHHHHhc-CCCCeEEEEcCC
Confidence            333332211111345699999999997653222 22222221 234566666666

>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=95.16  E-value=0.015  Score=52.18  Aligned_cols=24  Identities=25%  Similarity=0.396  Sum_probs=22.3

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHhh
Q psy200          221 SMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      .+.|.|++|+||||+++.++..++
T Consensus         4 ~i~i~G~~GsGKst~~~~la~~lg   27 (208)
T 3ake_A            4 IVTIDGPSASGKSSVARRVAAALG   27 (208)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHHhcC
Confidence            788999999999999999999875

>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=95.12  E-value=0.025  Score=57.68  Aligned_cols=95  Identities=16%  Similarity=0.234  Sum_probs=58.2

Q ss_pred             CCCCeEEEECCCCCcHHHH-HHHHHHHhhhcCCceEEEEeccCCC-CHHHHHHHHHHHhcC--------CCCC-----Cc
Q psy200          217 ETSGSMYISGPPGTGKSAS-LNLLVSRAEIKDAFKTIYINCNSVR-NAASVYETIVNELKL--------KPGG-----KS  281 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtl-a~~l~~~l~~~~~~~~~~v~~~~~~-~~~~l~~~i~~~l~~--------~~~~-----~s  281 (490)
                      +.++.++|.|++|+|||+| +..+++...  .++.++++-+..-. ...++++++...=..        ....     .-
T Consensus       161 grGQR~~Ifg~~g~GKT~Lal~~I~~~~~--~dv~~V~~~iGeR~~Ev~~~~~~~~~~g~m~rtvvV~atad~p~~~r~~  238 (507)
T 1fx0_A          161 GRGQRELIIGDRQTGKTAVATDTILNQQG--QNVICVYVAIGQKASSVAQVVTNFQERGAMEYTIVVAETADSPATLQYL  238 (507)
T ss_dssp             BTTCBCBEEESSSSSHHHHHHHHHHTCCT--TTCEEEEEEESCCHHHHHHHHHHTGGGTGGGSEEEEEECTTSCGGGTTH
T ss_pred             ccCCEEEEecCCCCCccHHHHHHHHHhhc--CCcEEEEEEcCCCchHHHHHHHHHHhcCccccceEEEECCCCCHHHHHH
Confidence            5678899999999999999 568877653  56666777666542 233445444331000        0100     01


Q ss_pred             HHHHHHHHHHHHhcCCCeEEEEEecCcccccc
Q psy200          282 ERHQLGAILKYFDTKHKSILLILDEIDALESR  313 (490)
Q Consensus       282 ~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~  313 (490)
                      .....-.+.+++...++.++|++|++-++...
T Consensus       239 a~~~a~tiAEyfrd~G~dVLli~Dsltr~A~A  270 (507)
T 1fx0_A          239 APYTGAALAEYFMYRERHTLIIYDDLSKQAQA  270 (507)
T ss_dssp             HHHHHHHHHHHHHHTTCEEEEEEECHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCcEEEEEecHHHHHHH
Confidence            11222344555666689999999998776543

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A*

Probab=95.11  E-value=0.063  Score=53.73  Aligned_cols=23  Identities=22%  Similarity=0.284  Sum_probs=17.6

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHH
Q psy200          219 SGSMYISGPPGTGKSASLNLLVS  241 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~  241 (490)
                      ++.+++.+|.|+|||...-..+.
T Consensus        36 ~~~~lv~apTGsGKT~~~l~~~~   58 (414)
T 3oiy_A           36 GKSFTMVAPTGVGKTTFGMMTAL   58 (414)
T ss_dssp             TCCEECCSCSSSSHHHHHHHHHH
T ss_pred             CCCEEEEeCCCCCHHHHHHHHHH
Confidence            45799999999999995544433

>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=95.10  E-value=0.0089  Score=53.84  Aligned_cols=26  Identities=23%  Similarity=0.188  Sum_probs=22.5

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHh
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRA  243 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l  243 (490)
                      .+..+.|+|++|+||||+++.++..+
T Consensus        20 ~~~~i~i~G~~GsGKSTl~~~L~~~~   45 (207)
T 2qt1_A           20 KTFIIGISGVTNSGKTTLAKNLQKHL   45 (207)
T ss_dssp             CCEEEEEEESTTSSHHHHHHHHHTTS
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHhc
Confidence            45578899999999999999998764

>2zj8_A DNA helicase, putative SKI2-type helicase; RECA fold, ATP-binding, hydrolase, nucleotide- binding; 2.00A {Pyrococcus furiosus} PDB: 2zj5_A* 2zj2_A 2zja_A*

Probab=95.10  E-value=0.043  Score=59.47  Aligned_cols=36  Identities=28%  Similarity=0.343  Sum_probs=24.6

Q ss_pred             CCeEEEECCCCCcHHHHHH-HHHHHhhhcCCceEEEEe
Q psy200          219 SGSMYISGPPGTGKSASLN-LLVSRAEIKDAFKTIYIN  255 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~-~l~~~l~~~~~~~~~~v~  255 (490)
                      +..++|.||.|+|||+.+. .+++.+.. .+..++++.
T Consensus        39 ~~~~lv~apTGsGKT~~~~l~il~~~~~-~~~~~l~i~   75 (720)
T 2zj8_A           39 GKNALISIPTASGKTLIAEIAMVHRILT-QGGKAVYIV   75 (720)
T ss_dssp             TCEEEEECCGGGCHHHHHHHHHHHHHHH-HCSEEEEEC
T ss_pred             CCcEEEEcCCccHHHHHHHHHHHHHHHh-CCCEEEEEc
Confidence            5789999999999999884 44444321 234566663

>3b9q_A Chloroplast SRP receptor homolog, alpha subunit CPFTSY; protein translocation, GTP-binding, nucleotide-binding, protein transport; 1.75A {Arabidopsis thaliana}

Probab=95.08  E-value=0.033  Score=53.51  Aligned_cols=27  Identities=33%  Similarity=0.491  Sum_probs=24.0

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      .+..+.|.|+.|+||||+++.++..+.
T Consensus        99 ~g~vi~lvG~nGsGKTTll~~Lag~l~  125 (302)
T 3b9q_A           99 KPAVIMIVGVNGGGKTTSLGKLAHRLK  125 (302)
T ss_dssp             SCEEEEEECCTTSCHHHHHHHHHHHHH
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHHHH
Confidence            345788999999999999999999876

>3l9o_A ATP-dependent RNA helicase DOB1; REC-A fold, winged-helix-turn-helix, antiparallel-coiled-COI domain, ATP-binding, helicase, hydrolase; 3.39A {Saccharomyces cerevisiae}

Probab=95.07  E-value=0.032  Score=63.29  Aligned_cols=117  Identities=12%  Similarity=0.195  Sum_probs=59.5

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcC---CCC------C-----CcHHH
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKL---KPG------G-----KSERH  284 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~---~~~------~-----~s~~~  284 (490)
                      +..+++.|+.|+|||.++...+.... ..+..++++. +.-.-..+.+..+...++.   -..      +     .+...
T Consensus       199 g~dvLV~ApTGSGKTlva~l~i~~~l-~~g~rvlvl~-PtraLa~Q~~~~l~~~~~~VglltGd~~~~~~~~IlV~Tpe~  276 (1108)
T 3l9o_A          199 GESVLVSAHTSAGKTVVAEYAIAQSL-KNKQRVIYTS-PIKALSNQKYRELLAEFGDVGLMTGDITINPDAGCLVMTTEI  276 (1108)
T ss_dssp             TCCEEEECCSSSHHHHHHHHHHHHHH-HTTCEEEEEE-SSHHHHHHHHHHHHHHTSSEEEECSSCBCCCSCSEEEEEHHH
T ss_pred             CCCEEEECCCCCChHHHHHHHHHHHH-hcCCeEEEEc-CcHHHHHHHHHHHHHHhCCccEEeCccccCCCCCEEEeChHH
Confidence            56899999999999998765554432 2334555552 2111123334444443321   000      0     13334


Q ss_pred             HHHHHHHHHhcCCCeEEEEEecCccccccCHH-HHHHhHhCCCCCCCcEEEEEec
Q psy200          285 QLGAILKYFDTKHKSILLILDEIDALESRKQT-ILYTIFEWPSIPGSKLVLVGVA  338 (490)
Q Consensus       285 ~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~~-~L~~l~~~~~~~~~~vilI~~t  338 (490)
                      +...+......-....+|||||+|.+...... .+..++... ....+++++.+|
T Consensus       277 L~~~L~~~~~~l~~l~lVVIDEaH~l~d~~rg~~~e~ii~~l-~~~~qvl~lSAT  330 (1108)
T 3l9o_A          277 LRSMLYRGSEVMREVAWVIFDEVHYMRDKERGVVWEETIILL-PDKVRYVFLSAT  330 (1108)
T ss_dssp             HHHHHHHCSSHHHHEEEEEEETGGGTTSHHHHHHHHHHHHHS-CTTSEEEEEECS
T ss_pred             HHHHHHcCccccccCCEEEEhhhhhccccchHHHHHHHHHhc-CCCceEEEEcCC
Confidence            44433321000023559999999999754322 222233222 245667777666

>3hjn_A DTMP kinase, thymidylate kinase; ATP-binding, nucleotide biosynth nucleotide-binding, transferase, structural genomics; HET: ADP TYD; 2.10A {Thermotoga maritima}

Probab=95.05  E-value=0.06  Score=48.17  Aligned_cols=48  Identities=23%  Similarity=0.263  Sum_probs=33.3

Q ss_pred             EEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHH
Q psy200          222 MYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIV  270 (490)
Q Consensus       222 ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~  270 (490)
                      |.|-|.-|+||||.++.+++.+.. .+..++...-+...........++
T Consensus         3 I~~EG~DGsGKsTq~~~L~~~L~~-~g~~v~~treP~~t~~~~~ir~~l   50 (197)
T 3hjn_A            3 ITFEGIDGSGKSTQIQLLAQYLEK-RGKKVILKREPGGTETGEKIRKIL   50 (197)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHHH-TTCCEEEEESSCSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHH-CCCcEEEEECCCCCcHHHHHHHHh
Confidence            668899999999999999998863 345666665554434444444444

>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=95.01  E-value=0.06  Score=54.21  Aligned_cols=97  Identities=10%  Similarity=0.167  Sum_probs=60.1

Q ss_pred             cCCCCeEEEECCCCCcHHHHHHHHHHHhhh----------cCCceEEEEeccCCC-CHHHHHHHHHHH--hc------CC
Q psy200          216 NETSGSMYISGPPGTGKSASLNLLVSRAEI----------KDAFKTIYINCNSVR-NAASVYETIVNE--LK------LK  276 (490)
Q Consensus       216 ~~~~~~ill~GppGtGKTtla~~l~~~l~~----------~~~~~~~~v~~~~~~-~~~~l~~~i~~~--l~------~~  276 (490)
                      -..++.+.|.|++|+|||+|+..+++....          ..++.++++-|..-. ...+|+.++...  +.      ..
T Consensus       144 igrGQr~~Ifgg~G~GKt~L~~~Ia~~~~a~~~~~~~~~d~~~~~~V~~~iGeR~~Ev~e~~~~l~~~g~~~rtvvv~~t  223 (464)
T 3gqb_B          144 LVRGQKLPIFSGSGLPANEIAAQIARQATVRPDLSGEGEKEEPFAVVFAAMGITQRELSYFIQEFERTGALSRSVLFLNK  223 (464)
T ss_dssp             CBTTCBCCEEEETTSCHHHHHHHHHHHCBCCHHHHCCCSTTCCEEEEEEEEEECHHHHHHHHHHHHHTSGGGGEEEEEEE
T ss_pred             cccCCEEEEecCCCCCchHHHHHHHHHHHhcccccccccCCCceEEEEEEecCchHHHHHHHHHhhhcccccceEEEEEC
Confidence            356778889999999999999999988653          345566777665432 345566655432  10      00


Q ss_pred             CCCCcHHHH-----HHHHHHHHhc-CCCeEEEEEecCccccc
Q psy200          277 PGGKSERHQ-----LGAILKYFDT-KHKSILLILDEIDALES  312 (490)
Q Consensus       277 ~~~~s~~~~-----~~~l~~~l~~-~~~~~vI~IDEid~l~~  312 (490)
                      ........+     .-.+.+++.. .++.++|++|++-++..
T Consensus       224 ~d~p~~~r~~~~~~a~tiAEyfrd~~G~~VLl~~DdlTr~A~  265 (464)
T 3gqb_B          224 ADDPTIERILTPRMALTVAEYLAFEHDYHVLVILTDMTNYSE  265 (464)
T ss_dssp             TTSCTHHHHHHHHHHHHHHHHHHHTTCCEEEEEEETHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHhcCCeEEEEEcChHHHHH
Confidence            111111111     1234566665 58899999999977653

>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=95.01  E-value=0.024  Score=54.55  Aligned_cols=27  Identities=19%  Similarity=0.306  Sum_probs=24.3

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      .+..+.|+||.|+||||+++.++..+.
T Consensus       101 ~g~vi~lvG~nGsGKTTll~~Lagll~  127 (304)
T 1rj9_A          101 KGRVVLVVGVNGVGKTTTIAKLGRYYQ  127 (304)
T ss_dssp             SSSEEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHHHH
Confidence            456888999999999999999998876

>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=95.01  E-value=0.013  Score=52.27  Aligned_cols=26  Identities=35%  Similarity=0.346  Sum_probs=22.6

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHH
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~  242 (490)
                      .....|.|+|++|+||||+++.+++.
T Consensus         6 ~~~~~I~i~G~~GsGKST~~~~La~~   31 (203)
T 1uf9_A            6 KHPIIIGITGNIGSGKSTVAALLRSW   31 (203)
T ss_dssp             CCCEEEEEEECTTSCHHHHHHHHHHT
T ss_pred             cCceEEEEECCCCCCHHHHHHHHHHC
Confidence            34567899999999999999999875

>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=95.00  E-value=0.089  Score=54.33  Aligned_cols=93  Identities=16%  Similarity=0.283  Sum_probs=55.4

Q ss_pred             cCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCC-CHHHHHHHHHHHhcCCCCC---------------
Q psy200          216 NETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVR-NAASVYETIVNELKLKPGG---------------  279 (490)
Q Consensus       216 ~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~-~~~~l~~~i~~~l~~~~~~---------------  279 (490)
                      -..++.+.|.|++|+|||+|+..+++...  .+ .++++-|..-. ...+++.++-+ +..+..|               
T Consensus       229 igrGqr~~Ifgg~g~GKT~L~~~ia~~~~--~~-v~V~~~iGER~~Ev~e~~~~~~e-l~d~~~G~~~m~rtvvV~~tsd  304 (600)
T 3vr4_A          229 VTKGGAAAVPGPFGAGKTVVQHQIAKWSD--VD-LVVYVGCGERGNEMTDVVNEFPE-LIDPNTGESLMERTVLIANTSN  304 (600)
T ss_dssp             CBTTCEEEEECCTTSCHHHHHHHHHHHSS--CS-EEEEEEEEECHHHHHHHHHHTTT-CBCTTTCSBGGGGEEEEEEETT
T ss_pred             ccCCCEEeeecCCCccHHHHHHHHHhccC--CC-EEEEEEecccHHHHHHHHHHHHh-hcccccccccccceEEEEECCC
Confidence            35688999999999999999999988743  23 35666555431 23344443211 1111111               


Q ss_pred             Cc-HHHH-----HHHHHHHHhcCCCeEEEEEecCccccc
Q psy200          280 KS-ERHQ-----LGAILKYFDTKHKSILLILDEIDALES  312 (490)
Q Consensus       280 ~s-~~~~-----~~~l~~~l~~~~~~~vI~IDEid~l~~  312 (490)
                      .. ....     .-.+.+++...++.++|++|.+-++..
T Consensus       305 ~p~~~R~~~~~~altiAEyfrd~G~dVLl~~Ds~tR~A~  343 (600)
T 3vr4_A          305 MPVAAREASIYTGITIAEYFRDMGYDVAIMADSTSRWAE  343 (600)
T ss_dssp             SCHHHHHHHHHHHHHHHHHHHTTTCEEEEEEECHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHcCCCEEEEecchHHHHH
Confidence            11 1111     123445666668899999999986653

>2gk6_A Regulator of nonsense transcripts 1; UPF1, helicase, NMD, hydrolase; HET: ADP; 2.40A {Homo sapiens} PDB: 2gjk_A* 2gk7_A 2xzo_A* 2xzp_A

Probab=95.00  E-value=0.036  Score=58.95  Aligned_cols=38  Identities=29%  Similarity=0.463  Sum_probs=28.4

Q ss_pred             HHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          200 EVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       200 e~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      +.+.+.+...+.       .+.++|.||||||||+++..++..+.
T Consensus       183 ~~Q~~av~~~l~-------~~~~li~GppGTGKT~~~~~~i~~l~  220 (624)
T 2gk6_A          183 HSQVYAVKTVLQ-------RPLSLIQGPPGTGKTVTSATIVYHLA  220 (624)
T ss_dssp             HHHHHHHHHHHT-------CSEEEEECCTTSCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhc-------CCCeEEECCCCCCHHHHHHHHHHHHH
Confidence            445555555442       35789999999999999998888765

>3def_A T7I23.11 protein; chloroplast, TOC33, GTPase, hydrolase; HET: GDP; 1.96A {Arabidopsis thaliana} PDB: 3bb3_A* 3bb4_A* 2j3e_A*

Probab=95.00  E-value=0.058  Score=50.49  Aligned_cols=25  Identities=32%  Similarity=0.538  Sum_probs=21.6

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHH
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~  242 (490)
                      ..-.|+|.|.+|+|||||++++...
T Consensus        35 ~~~~I~lvG~~g~GKSSLin~l~~~   59 (262)
T 3def_A           35 NSMTVLVLGKGGVGKSSTVNSLIGE   59 (262)
T ss_dssp             CEEEEEEEECTTSSHHHHHHHHHTS
T ss_pred             CCcEEEEECCCCCCHHHHHHHHhCC
Confidence            3457899999999999999999864

>3ld9_A DTMP kinase, thymidylate kinase; ssgcid, NIH, niaid, SBRI, UW, emerald biostructures, ehrlich chaffeensis; 2.15A {Ehrlichia chaffeensis}

Probab=94.99  E-value=0.024  Score=51.89  Aligned_cols=30  Identities=23%  Similarity=0.245  Sum_probs=25.7

Q ss_pred             cCCCCeEEEECCCCCcHHHHHHHHHHHhhh
Q psy200          216 NETSGSMYISGPPGTGKSASLNLLVSRAEI  245 (490)
Q Consensus       216 ~~~~~~ill~GppGtGKTtla~~l~~~l~~  245 (490)
                      ...+..|.|.|+.|+||||+++.+++.+..
T Consensus        18 ~~~~~~i~~~G~~g~GKst~~~~l~~~l~~   47 (223)
T 3ld9_A           18 GPGSMFITFEGIDGSGKTTQSHLLAEYLSE   47 (223)
T ss_dssp             -CCCEEEEEECSTTSSHHHHHHHHHHHHHH
T ss_pred             CCCCeEEEEECCCCCCHHHHHHHHHHHHhh
Confidence            446778889999999999999999999864

>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=94.99  E-value=0.0069  Score=54.70  Aligned_cols=24  Identities=25%  Similarity=0.325  Sum_probs=22.1

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHhh
Q psy200          221 SMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      .|.|.|++|+||||+++.++..+.
T Consensus         2 ~I~i~G~~GsGKsTl~~~L~~~l~   25 (214)
T 1gtv_A            2 LIAIEGVDGAGKRTLVEKLSGAFR   25 (214)
T ss_dssp             EEEEEEEEEEEHHHHHHHHHHHHH
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHHH
Confidence            578999999999999999999885

>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=94.98  E-value=0.017  Score=50.35  Aligned_cols=36  Identities=14%  Similarity=0.188  Sum_probs=27.6

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEe
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYIN  255 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~  255 (490)
                      ...+.|.|++|+||||++..++..+.. .++.+..+.
T Consensus         4 ~~~i~i~G~sGsGKTTl~~~L~~~l~~-~g~~v~~ik   39 (169)
T 1xjc_A            4 MNVWQVVGYKHSGKTTLMEKWVAAAVR-EGWRVGTVK   39 (169)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHHHH-TTCCEEEEE
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHhhHh-cCCeeeEEE
Confidence            457889999999999999999998752 234444443

>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=94.96  E-value=0.013  Score=52.69  Aligned_cols=21  Identities=29%  Similarity=0.474  Sum_probs=19.4

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q psy200          221 SMYISGPPGTGKSASLNLLVS  241 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~  241 (490)
                      .+.|+|++|+||||+++.++.
T Consensus         4 ~i~l~G~~GsGKST~~~~La~   24 (206)
T 1jjv_A            4 IVGLTGGIGSGKTTIANLFTD   24 (206)
T ss_dssp             EEEEECSTTSCHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            578999999999999999976

>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=94.95  E-value=0.031  Score=53.93  Aligned_cols=28  Identities=18%  Similarity=0.198  Sum_probs=24.6

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      ..+..+.|.|++|+|||||++.++..+.
T Consensus        88 ~~g~ivgI~G~sGsGKSTL~~~L~gll~  115 (312)
T 3aez_A           88 PVPFIIGVAGSVAVGKSTTARVLQALLA  115 (312)
T ss_dssp             CCCEEEEEECCTTSCHHHHHHHHHHHHH
T ss_pred             CCCEEEEEECCCCchHHHHHHHHHhhcc
Confidence            4566888999999999999999998875

>2c61_A A-type ATP synthase non-catalytic subunit B; hydrolase, H+ ATPase, A1AO, ATP synthesis, hydrogen ION transport, ION transport; 1.5A {Methanosarcina mazei GO1} PDB: 3dsr_A* 3b2q_A* 2rkw_A* 3eiu_A*

Probab=94.95  E-value=0.047  Score=55.30  Aligned_cols=96  Identities=13%  Similarity=0.140  Sum_probs=58.2

Q ss_pred             cCCCCeEEEECCCCCcHHHHHHHHHHHhhhc---CCceEEEEeccCCC-CHHHHHHHHHHHhcC--------CCCCCcHH
Q psy200          216 NETSGSMYISGPPGTGKSASLNLLVSRAEIK---DAFKTIYINCNSVR-NAASVYETIVNELKL--------KPGGKSER  283 (490)
Q Consensus       216 ~~~~~~ill~GppGtGKTtla~~l~~~l~~~---~~~~~~~v~~~~~~-~~~~l~~~i~~~l~~--------~~~~~s~~  283 (490)
                      -..++.++|.|++|+|||+|+..+++.....   .++.++++-|..-. ...+|++++...=..        ........
T Consensus       149 igrGQr~~Ifgg~G~GKt~Ll~~Ia~~~~~n~~~~~~~~V~~~iGER~~Ev~e~~~~~~~~g~m~rtvvV~~tsd~p~~~  228 (469)
T 2c61_A          149 LVRGQKLPIFSASGLPHNEIALQIARQASVPGSESAFAVVFAAMGITNEEAQYFMSDFEKTGALERAVVFLNLADDPAVE  228 (469)
T ss_dssp             CBTTCBCCEEECTTSCHHHHHHHHHHHCBCTTCSSCEEEEEEEEEECHHHHHHHHHHHHHHSGGGGEEEEEEETTSCHHH
T ss_pred             cccCCEEEEECCCCCCHHHHHHHHHHHHhhccCCCCcEEEEEEccCCcHHHHHHHHHHHhccCccceEEEEECCCCCHHH
Confidence            3567788889999999999999999886521   13456666665532 345666666543110        11111111


Q ss_pred             H-----HHHHHHHHHh-cCCCeEEEEEecCcccc
Q psy200          284 H-----QLGAILKYFD-TKHKSILLILDEIDALE  311 (490)
Q Consensus       284 ~-----~~~~l~~~l~-~~~~~~vI~IDEid~l~  311 (490)
                      .     ..-.+.+++. ..++.++|++|++-++.
T Consensus       229 r~~~~~~a~tiAEyfrdd~G~dVLl~~DsltR~A  262 (469)
T 2c61_A          229 RIVTPRMALTAAEYLAYEHGMHVLVILTDITNYA  262 (469)
T ss_dssp             HHHHHHHHHHHHHHHHHHHCCEEEEEEECHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHhcCCeEEEEEeCHHHHH
Confidence            1     1123445565 35889999999876654

>3lnc_A Guanylate kinase, GMP kinase; ALS collaborative crystallography, emerald biostructures, ATP-binding, cytoplasm, nucleotide-binding; HET: 5GP; 1.95A {Anaplasma phagocytophilum}

Probab=94.94  E-value=0.01  Score=54.60  Aligned_cols=26  Identities=27%  Similarity=0.449  Sum_probs=17.1

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHH-HHh
Q psy200          218 TSGSMYISGPPGTGKSASLNLLV-SRA  243 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~-~~l  243 (490)
                      .+..+.|+||+|+||||+++.++ ..+
T Consensus        26 ~G~ii~l~Gp~GsGKSTl~~~L~~~~~   52 (231)
T 3lnc_A           26 VGVILVLSSPSGCGKTTVANKLLEKQK   52 (231)
T ss_dssp             CCCEEEEECSCC----CHHHHHHC---
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHhcCC
Confidence            46788999999999999999998 664

>1xti_A Probable ATP-dependent RNA helicase P47; alpha-beta fold, gene regulation; 1.95A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB: 1xtj_A* 1xtk_A

Probab=94.88  E-value=0.053  Score=53.55  Aligned_cols=23  Identities=22%  Similarity=0.257  Sum_probs=17.8

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHH
Q psy200          219 SGSMYISGPPGTGKSASLNLLVS  241 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~  241 (490)
                      ++.+++.+|+|+|||..+-..+-
T Consensus        45 ~~~~lv~a~TGsGKT~~~~~~~~   67 (391)
T 1xti_A           45 GMDVLCQAKSGMGKTAVFVLATL   67 (391)
T ss_dssp             TCCEEEECSSCSSHHHHHHHHHH
T ss_pred             CCcEEEECCCCCcHHHHHHHHHH
Confidence            36799999999999987644433

>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=94.87  E-value=0.018  Score=55.34  Aligned_cols=27  Identities=33%  Similarity=0.453  Sum_probs=24.5

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHh
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRA  243 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l  243 (490)
                      ..+..+.|+||+|+|||||++.++..+
T Consensus       124 ~~Ge~vaIvGpsGsGKSTLl~lL~gl~  150 (305)
T 2v9p_A          124 PKKNCLAFIGPPNTGKSMLCNSLIHFL  150 (305)
T ss_dssp             TTCSEEEEECSSSSSHHHHHHHHHHHH
T ss_pred             cCCCEEEEECCCCCcHHHHHHHHhhhc
Confidence            567889999999999999999999876

>3iqw_A Tail-anchored protein targeting factor GET3; ATPase, Zn binding, protein transport; HET: ANP; 3.00A {Chaetomium thermophilum} PDB: 3iqx_A* 3ibg_A*

Probab=94.86  E-value=0.08  Score=51.55  Aligned_cols=47  Identities=13%  Similarity=0.233  Sum_probs=35.4

Q ss_pred             cCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHH
Q psy200          216 NETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAA  263 (490)
Q Consensus       216 ~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~  263 (490)
                      ......+++.|.+|+||||++-.++..+.. .+.+++.+++-...+..
T Consensus        13 ~~~~~i~~~sgkGGvGKTt~a~~lA~~la~-~g~~vllid~D~~~~l~   59 (334)
T 3iqw_A           13 QRSLRWIFVGGKGGVGKTTTSCSLAIQLAK-VRRSVLLLSTDPAHNLS   59 (334)
T ss_dssp             CTTCCEEEEECSTTSSHHHHHHHHHHHHTT-SSSCEEEEECCSSCHHH
T ss_pred             CCCeEEEEEeCCCCccHHHHHHHHHHHHHh-CCCcEEEEECCCCCChh
Confidence            345678899999999999999999998863 34577777776443333

>2p6r_A Afuhel308 helicase; protein-DNA complex, SF2 helicase, archaeal helicase, DNA repair,, DNA binding protein/DNA complex; 3.00A {Archaeoglobus fulgidus} SCOP: a.4.5.43 a.289.1.2 c.37.1.19 c.37.1.19 PDB: 2p6u_A

Probab=94.85  E-value=0.033  Score=60.12  Aligned_cols=35  Identities=20%  Similarity=0.352  Sum_probs=24.5

Q ss_pred             CCeEEEECCCCCcHHHHHHHH-HHHhhhcCCceEEEEe
Q psy200          219 SGSMYISGPPGTGKSASLNLL-VSRAEIKDAFKTIYIN  255 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l-~~~l~~~~~~~~~~v~  255 (490)
                      ++.++|.||+|+|||+.+-.. .+.+.  .+..++++.
T Consensus        40 ~~~~lv~apTGsGKT~~~~l~il~~~~--~~~~~l~i~   75 (702)
T 2p6r_A           40 GKNLLLAMPTAAGKTLLAEMAMVREAI--KGGKSLYVV   75 (702)
T ss_dssp             CSCEEEECSSHHHHHHHHHHHHHHHHH--TTCCEEEEE
T ss_pred             CCcEEEEcCCccHHHHHHHHHHHHHHH--hCCcEEEEe
Confidence            578999999999999998443 34433  234566663

>3kw6_A 26S protease regulatory subunit 8; structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium, NESG; 2.10A {Homo sapiens}

Probab=94.85  E-value=0.074  Score=39.66  Aligned_cols=74  Identities=11%  Similarity=0.098  Sum_probs=54.6

Q ss_pred             CCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhC-CHHHHHHHHHHHHHHHHhccccCCcccccCHHHHHHH
Q psy200          365 APYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSG-DIRKAIDITNHLIDLTYDNVKENGEVTGIGLKEVLGV  443 (490)
Q Consensus       365 ~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~G-d~r~ai~ll~~a~~~a~~~~~~~~~~~~It~~~v~~a  443 (490)
                      +.++.++..+||+.++......   ++..++.|++   .+.| .-..+-++|..|...|..++     ...|+.+||..|
T Consensus         1 plPd~~~R~~Il~~~l~~~~~~---~~~dl~~la~---~t~G~SGADi~~l~~eA~~~a~~~~-----~~~i~~~d~~~A   69 (78)
T 3kw6_A            1 PPPNEEARLDILKIHSRKMNLT---RGINLRKIAE---LMPGASGAEVKGVCTEAGMYALRER-----RVHVTQEDFEMA   69 (78)
T ss_dssp             CCCCHHHHHHHHHHHHTTSEEC---TTCCHHHHHH---TCTTCCHHHHHHHHHHHHHHHHHTT-----CSEECHHHHHHH
T ss_pred             CcCCHHHHHHHHHHHhcCCCCC---CccCHHHHHH---HcCCCCHHHHHHHHHHHHHHHHHhC-----CCCCCHHHHHHH
Confidence            3578899999999888765211   2334777877   3344 23444568999999999888     678999999999


Q ss_pred             HHHhcc
Q psy200          444 ISSVYC  449 (490)
Q Consensus       444 ~~~~~~  449 (490)
                      +..+..
T Consensus        70 l~~v~~   75 (78)
T 3kw6_A           70 VAKVMQ   75 (78)
T ss_dssp             HHHHHC
T ss_pred             HHHHHh
Confidence            998764

>4tmk_A Protein (thymidylate kinase); ATP:DTMP phosphotransferase, transferase; HET: T5A; 1.98A {Escherichia coli} SCOP: c.37.1.1 PDB: 5tmp_A*

Probab=94.85  E-value=0.052  Score=49.26  Aligned_cols=52  Identities=19%  Similarity=0.271  Sum_probs=34.0

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHhhhcCCc-eEEEEeccCCCCHHHHHHHHHH
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRAEIKDAF-KTIYINCNSVRNAASVYETIVN  271 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l~~~~~~-~~~~v~~~~~~~~~~l~~~i~~  271 (490)
                      +..|.|.|+.|+||||+++.+++.+... ++ .++...-+........++.++.
T Consensus         3 g~~i~~eG~~gsGKsT~~~~l~~~l~~~-~~~~v~~~rep~~t~~g~~ir~~l~   55 (213)
T 4tmk_A            3 SKYIVIEGLEGAGKTTARNVVVETLEQL-GIRDMVFTREPGGTQLAEKLRSLLL   55 (213)
T ss_dssp             CCEEEEEECTTSCHHHHHHHHHHHHHHT-TCCCEEEEESSCSSHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHc-CCCcceeeeCCCCCHHHHHHHHHHh
Confidence            4678899999999999999999998633 33 3444433332223444555544

>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=94.84  E-value=0.026  Score=56.79  Aligned_cols=28  Identities=29%  Similarity=0.570  Sum_probs=24.9

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      ..++.++|+||.|+||||++++++..+.
T Consensus       165 ~~ggii~I~GpnGSGKTTlL~allg~l~  192 (418)
T 1p9r_A          165 RPHGIILVTGPTGSGKSTTLYAGLQELN  192 (418)
T ss_dssp             SSSEEEEEECSTTSCHHHHHHHHHHHHC
T ss_pred             hcCCeEEEECCCCCCHHHHHHHHHhhcC
Confidence            4567899999999999999999999875

>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=94.84  E-value=0.055  Score=53.23  Aligned_cols=39  Identities=21%  Similarity=0.294  Sum_probs=29.0

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEec
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINC  256 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~  256 (490)
                      +....+.|+|.+|+||||++..++..+.. .+.++..+.+
T Consensus        77 ~~~~~I~i~G~~G~GKSTl~~~L~~~l~~-~g~kV~vi~~  115 (355)
T 3p32_A           77 GNAHRVGITGVPGVGKSTAIEALGMHLIE-RGHRVAVLAV  115 (355)
T ss_dssp             CCSEEEEEECCTTSSHHHHHHHHHHHHHT-TTCCEEEEEE
T ss_pred             CCceEEEEECCCCCCHHHHHHHHHHHHHh-CCCceEEEec
Confidence            45668899999999999999999988742 2334444444

>2og2_A Putative signal recognition particle receptor; nucleotide-binding, protein transport; 2.00A {Arabidopsis thaliana}

Probab=94.83  E-value=0.042  Score=54.03  Aligned_cols=27  Identities=33%  Similarity=0.491  Sum_probs=24.0

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      .+..+.|+|+.|+||||+++.++..+.
T Consensus       156 ~g~vi~lvG~nGsGKTTll~~Lag~l~  182 (359)
T 2og2_A          156 KPAVIMIVGVNGGGKTTSLGKLAHRLK  182 (359)
T ss_dssp             SSEEEEEECCTTSCHHHHHHHHHHHHH
T ss_pred             CCeEEEEEcCCCChHHHHHHHHHhhcc
Confidence            355788999999999999999999876

>1q3t_A Cytidylate kinase; nucleotide monophosphate kinase, CMP kinase, transferase; NMR {Streptococcus pneumoniae} SCOP: c.37.1.1

Probab=94.83  E-value=0.025  Score=52.10  Aligned_cols=28  Identities=21%  Similarity=0.360  Sum_probs=24.5

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      ..+..+.|.|++|+||||+++.++..++
T Consensus        14 ~~~~~i~i~G~~gsGKst~~~~l~~~lg   41 (236)
T 1q3t_A           14 MKTIQIAIDGPASSGKSTVAKIIAKDFG   41 (236)
T ss_dssp             CCCCEEEEECSSCSSHHHHHHHHHHHHC
T ss_pred             cCCcEEEEECCCCCCHHHHHHHHHHHcC
Confidence            3566899999999999999999998875

>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=94.83  E-value=0.021  Score=51.73  Aligned_cols=25  Identities=24%  Similarity=0.292  Sum_probs=21.6

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      +..|.|.|++|+||||+++.++. ++
T Consensus         4 ~~~I~i~G~~GSGKST~~~~L~~-lg   28 (218)
T 1vht_A            4 RYIVALTGGIGSGKSTVANAFAD-LG   28 (218)
T ss_dssp             CEEEEEECCTTSCHHHHHHHHHH-TT
T ss_pred             ceEEEEECCCCCCHHHHHHHHHH-cC
Confidence            45788999999999999999976 53

>2jlq_A Serine protease subunit NS3; ribonucleoprotein, nucleotide-binding, viral nucleoprotein, endoplasmic reticulum, helicase, hydrolase; 1.67A {Dengue virus 4} PDB: 2jly_A* 2jls_A* 2jlu_A 2jlv_A* 2jlw_A 2jlx_A* 2jlz_A* 2jlr_A* 2bmf_A 2bhr_A

Probab=94.78  E-value=0.037  Score=56.36  Aligned_cols=50  Identities=20%  Similarity=0.313  Sum_probs=29.7

Q ss_pred             CCeEEEECCCCCcHHHH-HHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhc
Q psy200          219 SGSMYISGPPGTGKSAS-LNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELK  274 (490)
Q Consensus       219 ~~~ill~GppGtGKTtl-a~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~  274 (490)
                      ...+++.||+|+|||+. +-.++..+.. .+..++++.     -...+..++...+.
T Consensus        19 ~~~~lv~a~TGsGKT~~~~~~~l~~~~~-~~~~~lvl~-----Ptr~La~Q~~~~l~   69 (451)
T 2jlq_A           19 KRLTIMDLHPGAGKTKRILPSIVREALL-RRLRTLILA-----PTRVVAAEMEEALR   69 (451)
T ss_dssp             TCEEEECCCTTSSCCTTHHHHHHHHHHH-TTCCEEEEE-----SSHHHHHHHHHHTT
T ss_pred             CCeEEEECCCCCCHhhHHHHHHHHHHHh-cCCcEEEEC-----CCHHHHHHHHHHhc
Confidence            45679999999999993 4444444322 233455553     12446666666663

>2oap_1 GSPE-2, type II secretion system protein; hexameric ATPase, hydrolase; HET: ANP; 2.95A {Archaeoglobus fulgidus} PDB: 2oaq_1

Probab=94.77  E-value=0.032  Score=57.68  Aligned_cols=36  Identities=22%  Similarity=0.254  Sum_probs=27.8

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEec
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINC  256 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~  256 (490)
                      +.+++|+||+|+||||++++++..+.  +...++.+..
T Consensus       260 g~~i~I~GptGSGKTTlL~aL~~~i~--~~~giitied  295 (511)
T 2oap_1          260 KFSAIVVGETASGKTTTLNAIMMFIP--PDAKVVSIED  295 (511)
T ss_dssp             TCCEEEEESTTSSHHHHHHHHGGGSC--TTCCEEEEES
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhhCC--CCCCEEEEcC
Confidence            55799999999999999999988774  3344555543

>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=94.77  E-value=0.13  Score=45.25  Aligned_cols=25  Identities=20%  Similarity=0.232  Sum_probs=21.1

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHH
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVS  241 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~  241 (490)
                      ...-.++|.|++|+|||+|++.+..
T Consensus        27 ~~~~ki~v~G~~~vGKSsLi~~l~~   51 (192)
T 2b6h_A           27 KKQMRILMVGLDAAGKTTILYKLKL   51 (192)
T ss_dssp             TSCEEEEEEESTTSSHHHHHHHHCS
T ss_pred             CCccEEEEECCCCCCHHHHHHHHHh
Confidence            3456799999999999999998854

>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=94.75  E-value=0.079  Score=46.96  Aligned_cols=23  Identities=26%  Similarity=0.304  Sum_probs=20.5

Q ss_pred             CeEEEECCCCCcHHHHHHHHHHH
Q psy200          220 GSMYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       220 ~~ill~GppGtGKTtla~~l~~~  242 (490)
                      ..|+|.|++|+|||+|++.+...
T Consensus        15 ~ki~v~G~~~~GKSsli~~l~~~   37 (206)
T 2bov_A           15 HKVIMVGSGGVGKSALTLQFMYD   37 (206)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHHhC
Confidence            46889999999999999999764

>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=94.73  E-value=0.036  Score=53.40  Aligned_cols=28  Identities=21%  Similarity=0.254  Sum_probs=24.1

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      ..+..+.|.|+.|+||||+++.++..+.
T Consensus        78 ~~g~iigI~G~~GsGKSTl~~~L~~~l~  105 (308)
T 1sq5_A           78 RIPYIISIAGSVAVGKSTTARVLQALLS  105 (308)
T ss_dssp             CCCEEEEEEECTTSSHHHHHHHHHHHHT
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHHh
Confidence            4556888999999999999999988764

>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=94.71  E-value=0.017  Score=55.35  Aligned_cols=24  Identities=25%  Similarity=0.426  Sum_probs=21.4

Q ss_pred             CeEEEECCCCCcHHHHHHHHHHHh
Q psy200          220 GSMYISGPPGTGKSASLNLLVSRA  243 (490)
Q Consensus       220 ~~ill~GppGtGKTtla~~l~~~l  243 (490)
                      ..++|.|+||+||||+++.+++.+
T Consensus         3 ~~I~l~G~~GsGKST~a~~L~~~~   26 (301)
T 1ltq_A            3 KIILTIGCPGSGKSTWAREFIAKN   26 (301)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHS
T ss_pred             eEEEEECCCCCCHHHHHHHHHHhC
Confidence            468899999999999999998853

>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=94.70  E-value=0.28  Score=43.87  Aligned_cols=23  Identities=22%  Similarity=0.273  Sum_probs=20.1

Q ss_pred             CeEEEECCCCCcHHHHHHHHHHH
Q psy200          220 GSMYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       220 ~~ill~GppGtGKTtla~~l~~~  242 (490)
                      -.|+|.|.+|+|||+|++.+...
T Consensus        26 ~ki~vvG~~~~GKSsLi~~l~~~   48 (217)
T 2f7s_A           26 IKLLALGDSGVGKTTFLYRYTDN   48 (217)
T ss_dssp             EEEEEESCTTSSHHHHHHHHHCS
T ss_pred             EEEEEECcCCCCHHHHHHHHhcC
Confidence            46889999999999999998753

>4hlc_A DTMP kinase, thymidylate kinase; TMK, MRSA, pipiridine, transfera transferase inhibitor complex; HET: T05; 1.55A {Staphylococcus aureus subsp} PDB: 2cck_A 4gfd_A* 4gsy_A* 4hdc_A* 4hej_A* 2ccj_A* 4hld_A* 2ccg_A*

Probab=94.70  E-value=0.053  Score=48.84  Aligned_cols=49  Identities=20%  Similarity=0.303  Sum_probs=34.1

Q ss_pred             CeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHH
Q psy200          220 GSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIV  270 (490)
Q Consensus       220 ~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~  270 (490)
                      .-|.|-|.-|+||||+++.+++.+.  .++.++...-+........+..++
T Consensus         3 kFI~~EG~dGsGKsTq~~~L~~~L~--~~~~v~~~~eP~~t~~g~~ir~~l   51 (205)
T 4hlc_A            3 AFITFEGPEGSGKTTVINEVYHRLV--KDYDVIMTREPGGVPTGEEIRKIV   51 (205)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHHHT--TTSCEEEEESSTTCHHHHHHHHHH
T ss_pred             CEEEEECCCCCcHHHHHHHHHHHHH--CCCCEEEeeCCCCChHHHHHHHHH
Confidence            4577899999999999999999985  456666665444333334444443

>2jeo_A Uridine-cytidine kinase 1; UCK, transferase, ATP-binding, nucleoside kinase, nucleotide-binding; 2.50A {Homo sapiens} PDB: 2uvq_A*

Probab=94.69  E-value=0.02  Score=53.15  Aligned_cols=28  Identities=18%  Similarity=0.134  Sum_probs=24.0

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      ..+..+.|.||.|+||||+++.++..++
T Consensus        23 ~~g~iigI~G~~GsGKSTl~k~L~~~lG   50 (245)
T 2jeo_A           23 MRPFLIGVSGGTASGKSTVCEKIMELLG   50 (245)
T ss_dssp             CCSEEEEEECSTTSSHHHHHHHHHHHHT
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHhc
Confidence            3456788999999999999999988764

>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=94.69  E-value=0.04  Score=57.86  Aligned_cols=39  Identities=13%  Similarity=0.142  Sum_probs=29.7

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEe
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYIN  255 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~  255 (490)
                      ..+..|+|+|.+|+||||+++.+++.+.......++.++
T Consensus       394 q~~~~I~l~GlsGSGKSTiA~~La~~L~~~G~~~~~~lD  432 (573)
T 1m8p_A          394 TQGFTIFLTGYMNSGKDAIARALQVTLNQQGGRSVSLLL  432 (573)
T ss_dssp             TCCEEEEEECSTTSSHHHHHHHHHHHHHHHCSSCEEEEE
T ss_pred             ccceEEEeecCCCCCHHHHHHHHHHHhcccCCceEEEEC
Confidence            345678899999999999999999998633224455564

>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=94.68  E-value=0.061  Score=47.84  Aligned_cols=24  Identities=25%  Similarity=0.475  Sum_probs=20.6

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHH
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVS  241 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~  241 (490)
                      ....++|.|++|+|||+|++.+..
T Consensus        24 ~~~ki~lvG~~~vGKSsLi~~l~~   47 (198)
T 1f6b_A           24 KTGKLVFLGLDNAGKTTLLHMLKD   47 (198)
T ss_dssp             CCEEEEEEEETTSSHHHHHHHHSC
T ss_pred             CCcEEEEECCCCCCHHHHHHHHhc
Confidence            445788999999999999999864

>2qmh_A HPR kinase/phosphorylase; V267F mutation, ATP-binding, carbohydrate metabolism, magnesium, metal-binding, multifunctional enzyme; 2.60A {Lactobacillus casei} PDB: 1jb1_A 1kkl_A 1kkm_A*

Probab=94.66  E-value=0.015  Score=52.04  Aligned_cols=26  Identities=35%  Similarity=0.434  Sum_probs=23.0

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHh
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRA  243 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l  243 (490)
                      .+..++|.||+|+|||+|+..+++..
T Consensus        33 ~g~~ilI~GpsGsGKStLA~~La~~g   58 (205)
T 2qmh_A           33 YGLGVLITGDSGVGKSETALELVQRG   58 (205)
T ss_dssp             TTEEEEEECCCTTTTHHHHHHHHTTT
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHhC
Confidence            45679999999999999999998765

>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=94.64  E-value=0.069  Score=46.58  Aligned_cols=26  Identities=19%  Similarity=0.261  Sum_probs=21.6

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHH
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~  242 (490)
                      .....++|.|++|+|||+|++.+...
T Consensus        16 ~~~~~i~v~G~~~~GKssl~~~l~~~   41 (186)
T 1ksh_A           16 ERELRLLMLGLDNAGKTTILKKFNGE   41 (186)
T ss_dssp             -CCEEEEEECSTTSSHHHHHHHHTTC
T ss_pred             CCeeEEEEECCCCCCHHHHHHHHhcC
Confidence            34567899999999999999998754

>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=94.64  E-value=0.03  Score=55.52  Aligned_cols=29  Identities=24%  Similarity=0.580  Sum_probs=25.3

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHhhh
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRAEI  245 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l~~  245 (490)
                      ..+..++|+||+|+||||+++.++..+..
T Consensus       134 ~~g~~i~ivG~~GsGKTTll~~l~~~~~~  162 (372)
T 2ewv_A          134 RKMGLILVTGPTGSGKSTTIASMIDYINQ  162 (372)
T ss_dssp             SSSEEEEEECSSSSSHHHHHHHHHHHHHH
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHHhhcCc
Confidence            45678999999999999999999998753

>3d3q_A TRNA delta(2)-isopentenylpyrophosphate transferase; alpha-beta protein, structural genomics, PSI-2; 2.70A {Staphylococcus epidermidis atcc 12228}

Probab=94.64  E-value=0.023  Score=55.25  Aligned_cols=25  Identities=20%  Similarity=0.244  Sum_probs=22.8

Q ss_pred             CeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          220 GSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       220 ~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      ..++|.||+|+||||++..++..++
T Consensus         8 ~lI~I~GptgSGKTtla~~La~~l~   32 (340)
T 3d3q_A            8 FLIVIVGPTASGKTELSIEVAKKFN   32 (340)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHTT
T ss_pred             ceEEEECCCcCcHHHHHHHHHHHcC
Confidence            4788999999999999999999874

>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=94.64  E-value=0.057  Score=49.83  Aligned_cols=39  Identities=18%  Similarity=0.281  Sum_probs=29.2

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCce-EEEEecc
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFK-TIYINCN  257 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~-~~~v~~~  257 (490)
                      .+..|.|.|++|+||||+++.+++.+... ++. ++...-+
T Consensus        26 ~~~~i~~eG~~GsGKsT~~~~l~~~l~~~-~~~~~~~~rep   65 (236)
T 3lv8_A           26 NAKFIVIEGLEGAGKSTAIQVVVETLQQN-GIDHITRTREP   65 (236)
T ss_dssp             CCCEEEEEESTTSCHHHHHHHHHHHHHHT-TCCCEEEEESS
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHhc-CCCeeeeecCC
Confidence            45688899999999999999999988632 344 4444433

>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=94.63  E-value=0.017  Score=53.35  Aligned_cols=27  Identities=33%  Similarity=0.517  Sum_probs=23.5

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHh
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRA  243 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l  243 (490)
                      ..+..+.|.||.|+|||||++.++..+
T Consensus        29 ~~Ge~~~iiG~nGsGKSTLl~~l~Gl~   55 (235)
T 3tif_A           29 KEGEFVSIMGPSGSGKSTMLNIIGCLD   55 (235)
T ss_dssp             CTTCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             cCCCEEEEECCCCCcHHHHHHHHhcCC
Confidence            456789999999999999999998655

>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=94.63  E-value=0.025  Score=49.62  Aligned_cols=26  Identities=23%  Similarity=0.225  Sum_probs=23.3

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      ...+.|.|++|+||||+++.++..+.
T Consensus         6 ~~~i~i~G~sGsGKTTl~~~l~~~l~   31 (174)
T 1np6_A            6 IPLLAFAAWSGTGKTTLLKKLIPALC   31 (174)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHHHH
T ss_pred             ceEEEEEeCCCCCHHHHHHHHHHhcc
Confidence            46788999999999999999998875

>2ged_A SR-beta, signal recognition particle receptor beta subunit; protein transport, G protein, proline isomerization, circular permutation; 2.20A {Saccharomyces cerevisiae}

Probab=94.62  E-value=0.031  Score=49.20  Aligned_cols=25  Identities=36%  Similarity=0.610  Sum_probs=21.8

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHH
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~  242 (490)
                      ....++|.|++|+|||+|++.+...
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            4457899999999999999999865

>2h92_A Cytidylate kinase; rossmann fold, transferase; HET: C5P PG4; 2.30A {Staphylococcus aureus}

Probab=94.60  E-value=0.028  Score=50.93  Aligned_cols=26  Identities=23%  Similarity=0.365  Sum_probs=23.0

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      +..+.|+|++|+||||+++.+++.++
T Consensus         3 ~~~i~i~G~~gsGkst~~~~l~~~~g   28 (219)
T 2h92_A            3 AINIALDGPAAAGKSTIAKRVASELS   28 (219)
T ss_dssp             CCCEEEECCTTSSHHHHHHHHHHHTT
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHhcC
Confidence            34789999999999999999998864

>2oca_A DAR protein, ATP-dependent DNA helicase UVSW; ATP-dependant helicase, T4-bacteriophage, recombination, hydrolase; 2.70A {Enterobacteria phage T4}

Probab=94.60  E-value=0.063  Score=55.39  Aligned_cols=51  Identities=18%  Similarity=0.070  Sum_probs=34.0

Q ss_pred             CChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEE
Q psy200          197 PGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYI  254 (490)
Q Consensus       197 vgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v  254 (490)
                      .-+..+.+.+..++..       ..++|.|+.|+|||.++-.++..........++++
T Consensus       113 ~l~~~Q~~ai~~~~~~-------~~~ll~~~tGsGKT~~~~~~~~~~~~~~~~~vlvl  163 (510)
T 2oca_A          113 EPHWYQKDAVFEGLVN-------RRRILNLPTSAGRSLIQALLARYYLENYEGKILII  163 (510)
T ss_dssp             CCCHHHHHHHHHHHHH-------SEEEEECCSTTTHHHHHHHHHHHHHHHCSSEEEEE
T ss_pred             CCCHHHHHHHHHHHhc-------CCcEEEeCCCCCHHHHHHHHHHHHHhCCCCeEEEE
Confidence            3455666666666642       57899999999999998777665432233355555

>3clv_A RAB5 protein, putative; malaria, GTPase, structural genomics, GTP-binding, nucleotide-binding, signaling protein; HET: GDP; 1.89A {Plasmodium falciparum}

Probab=94.59  E-value=0.042  Score=48.45  Aligned_cols=24  Identities=25%  Similarity=0.223  Sum_probs=21.3

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHH
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~  242 (490)
                      .-.|+|.|++|+|||+|++++...
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            456889999999999999999875

>3eph_A TRNA isopentenyltransferase; transferase, alternative initiation, ATP-binding, cytoplasm, mitochondrion, nucleotide-binding, nucleus; 2.95A {Saccharomyces cerevisiae} PDB: 3epj_A 3epk_A* 3epl_A*

Probab=94.58  E-value=0.025  Score=56.25  Aligned_cols=25  Identities=28%  Similarity=0.356  Sum_probs=22.8

Q ss_pred             CeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          220 GSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       220 ~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      ..++|.||+|+|||+|+..+++.+.
T Consensus         3 ~~i~i~GptgsGKttla~~La~~~~   27 (409)
T 3eph_A            3 KVIVIAGTTGVGKSQLSIQLAQKFN   27 (409)
T ss_dssp             EEEEEEECSSSSHHHHHHHHHHHHT
T ss_pred             cEEEEECcchhhHHHHHHHHHHHCC
Confidence            4688999999999999999999875

>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=94.58  E-value=0.37  Score=46.19  Aligned_cols=26  Identities=38%  Similarity=0.507  Sum_probs=22.2

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHH
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~  242 (490)
                      .+.+.+.|+|.+|+|||||++++...
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            34567889999999999999999764

>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=94.57  E-value=0.034  Score=57.25  Aligned_cols=48  Identities=8%  Similarity=-0.109  Sum_probs=33.7

Q ss_pred             CCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhh
Q psy200          196 LPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEI  245 (490)
Q Consensus       196 lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~  245 (490)
                      ...+.+..+.+.+....  ....+..|+|.|.+|+||||+++++++.+..
T Consensus       374 ~f~rpeV~~vLr~~~~~--~~~~~~~I~l~GlsGsGKSTIa~~La~~L~~  421 (511)
T 1g8f_A          374 WFSYPEVVKILRESNPP--RPKQGFSIVLGNSLTVSREQLSIALLSTFLQ  421 (511)
T ss_dssp             TTSCHHHHHHHHHHSCC--GGGCCEEEEECTTCCSCHHHHHHHHHHHHTT
T ss_pred             cccChhhHHHHHHhccc--ccccceEEEecccCCCCHHHHHHHHHHHHHH
Confidence            34445555455554321  1235578999999999999999999999974

>2eyq_A TRCF, transcription-repair coupling factor; MFD, SF2 ATPase, hydrolase; HET: EPE; 3.20A {Escherichia coli} SCOP: b.34.18.1 c.37.1.19 c.37.1.19 c.37.1.19 c.37.1.19 d.315.1.1

Probab=94.55  E-value=0.37  Score=54.90  Aligned_cols=132  Identities=14%  Similarity=0.108  Sum_probs=65.1

Q ss_pred             hHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCC--
Q psy200          199 REVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLK--  276 (490)
Q Consensus       199 re~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~--  276 (490)
                      +..+.+.+..++... ..+.+..++|+|+.|+|||.++-..+-... ..+..++++ ++...-..+++..+...+...  
T Consensus       605 t~~Q~~ai~~il~~~-~~g~p~d~ll~~~TGsGKT~val~aa~~~~-~~g~~vlvl-vPt~~La~Q~~~~~~~~~~~~~i  681 (1151)
T 2eyq_A          605 TPDQAQAINAVLSDM-CQPLAMDRLVCGDVGFGKTEVAMRAAFLAV-DNHKQVAVL-VPTTLLAQQHYDNFRDRFANWPV  681 (1151)
T ss_dssp             CHHHHHHHHHHHHHH-HSSSCCEEEEECCCCTTTHHHHHHHHHHHH-TTTCEEEEE-CSSHHHHHHHHHHHHHHSTTTTC
T ss_pred             CHHHHHHHHHHHHHH-hcCCcCcEEEECCCCCCHHHHHHHHHHHHH-HhCCeEEEE-echHHHHHHHHHHHHHHhhcCCC
Confidence            455555555555432 234556899999999999988764443322 123344444 222212334455554443221  


Q ss_pred             -----CCCCcHHHHHHHHHHH--------------Hhc---CCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEE
Q psy200          277 -----PGGKSERHQLGAILKY--------------FDT---KHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVL  334 (490)
Q Consensus       277 -----~~~~s~~~~~~~l~~~--------------l~~---~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vil  334 (490)
                           ....+..+....+...              +..   .....+|||||+|.+.......+..+.     ....+++
T Consensus       682 ~v~~l~~~~~~~~~~~~~~~l~~g~~dIvV~T~~ll~~~~~~~~l~lvIiDEaH~~g~~~~~~l~~l~-----~~~~vl~  756 (1151)
T 2eyq_A          682 RIEMISRFRSAKEQTQILAEVAEGKIDILIGTHKLLQSDVKFKDLGLLIVDEEHRFGVRHKERIKAMR-----ANVDILT  756 (1151)
T ss_dssp             CEEEESTTSCHHHHHHHHHHHHTTCCSEEEECTHHHHSCCCCSSEEEEEEESGGGSCHHHHHHHHHHH-----TTSEEEE
T ss_pred             eEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHhCCccccccceEEEechHhcChHHHHHHHHhc-----CCCCEEE
Confidence                 0111222322222221              111   134569999999997544333333332     2345555


Q ss_pred             EEec
Q psy200          335 VGVA  338 (490)
Q Consensus       335 I~~t  338 (490)
                      +.+|
T Consensus       757 lSAT  760 (1151)
T 2eyq_A          757 LTAT  760 (1151)
T ss_dssp             EESS
T ss_pred             EcCC
Confidence            5555

>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=94.53  E-value=0.026  Score=53.60  Aligned_cols=26  Identities=23%  Similarity=0.225  Sum_probs=22.0

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      .+..|.|+|++|+||||+++.++ .++
T Consensus        74 ~~~iI~I~G~~GSGKSTva~~La-~lg   99 (281)
T 2f6r_A           74 GLYVLGLTGISGSGKSSVAQRLK-NLG   99 (281)
T ss_dssp             TCEEEEEEECTTSCHHHHHHHHH-HHT
T ss_pred             CCEEEEEECCCCCCHHHHHHHHH-HCC
Confidence            34578999999999999999998 443

>2pcj_A ABC transporter, lipoprotein-releasing system ATP-binding protein; structural genomics; 1.70A {Aquifex aeolicus} PDB: 2pcl_A

Probab=94.49  E-value=0.017  Score=52.94  Aligned_cols=26  Identities=31%  Similarity=0.337  Sum_probs=22.8

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHh
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRA  243 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l  243 (490)
                      .+..+.|.||.|+|||||++.++..+
T Consensus        29 ~Ge~~~iiG~nGsGKSTLl~~l~Gl~   54 (224)
T 2pcj_A           29 KGEFVSIIGASGSGKSTLLYILGLLD   54 (224)
T ss_dssp             TTCEEEEEECTTSCHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            56788899999999999999998655

>3h1t_A Type I site-specific restriction-modification system, R (restriction) subunit; hydrolase, restriction enzyme HSDR, ATP-binding; 2.30A {Vibrio vulnificus}

Probab=94.43  E-value=0.033  Score=58.75  Aligned_cols=47  Identities=17%  Similarity=0.089  Sum_probs=31.8

Q ss_pred             CCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          196 LPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       196 lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      +.-|..+.+.+...+....  ...+.++|+++.|+|||.++-.++..+.
T Consensus       177 ~~lr~~Q~~ai~~~~~~~~--~~~~~~ll~~~TGsGKT~~~~~~~~~l~  223 (590)
T 3h1t_A          177 YSPRYYQQIAINRAVQSVL--QGKKRSLITMATGTGKTVVAFQISWKLW  223 (590)
T ss_dssp             --CCHHHHHHHHHHHHHHH--TTCSEEEEEECTTSCHHHHHHHHHHHHH
T ss_pred             CCchHHHHHHHHHHHHHHh--cCCCceEEEecCCCChHHHHHHHHHHHH
Confidence            3556666666666555432  2346688999999999999888777664

>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=94.43  E-value=0.02  Score=52.92  Aligned_cols=28  Identities=25%  Similarity=0.411  Sum_probs=24.0

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      ..+..+.|.||.|+|||||++.++..+.
T Consensus        29 ~~Ge~~~i~G~nGsGKSTLl~~l~Gl~~   56 (237)
T 2cbz_A           29 PEGALVAVVGQVGCGKSSLLSALLAEMD   56 (237)
T ss_dssp             CTTCEEEEECSTTSSHHHHHHHHTTCSE
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHhcCCC
Confidence            3567899999999999999999987653

>4bas_A ADP-ribosylation factor, putative (small GTPase, putative); hydrolase; HET: GNP; 2.00A {Trypanosoma brucei TREU927}

Probab=94.42  E-value=0.049  Score=48.07  Aligned_cols=25  Identities=20%  Similarity=0.295  Sum_probs=21.1

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHH
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~  242 (490)
                      ....|+|.|.+|+|||+|++.+...
T Consensus        16 ~~~ki~v~G~~~~GKSsl~~~l~~~   40 (199)
T 4bas_A           16 TKLQVVMCGLDNSGKTTIINQVKPA   40 (199)
T ss_dssp             CEEEEEEECCTTSCHHHHHHHHSCC
T ss_pred             CCcEEEEECCCCCCHHHHHHHHhcC
Confidence            3457899999999999999998653

>2wjy_A Regulator of nonsense transcripts 1; nonsense mediated decay, zinc-finger, ATP-binding, metal-BIN UPF2, UPF1, helicase, hydrolase; 2.50A {Homo sapiens} PDB: 2wjv_A 2iyk_A

Probab=94.39  E-value=0.056  Score=59.09  Aligned_cols=38  Identities=29%  Similarity=0.463  Sum_probs=28.4

Q ss_pred             HHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          200 EVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       200 e~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      +.+.+.+...+.       .+.++|.||||||||+++..++..+.
T Consensus       359 ~~Q~~Av~~~l~-------~~~~lI~GppGTGKT~ti~~~i~~l~  396 (800)
T 2wjy_A          359 HSQVYAVKTVLQ-------RPLSLIQGPPGTGKTVTSATIVYHLA  396 (800)
T ss_dssp             HHHHHHHHHHHT-------SSEEEEECCTTSCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcc-------CCeEEEEcCCCCCHHHHHHHHHHHHH
Confidence            445555554442       35789999999999999998888775

>3b85_A Phosphate starvation-inducible protein; PHOH2, ATPase, PFAM: PF02562, ST genomics, PSI-2, protein structure initiative; 2.35A {Corynebacterium glutamicum atcc 13032}

Probab=94.38  E-value=0.02  Score=51.79  Aligned_cols=24  Identities=21%  Similarity=0.302  Sum_probs=22.0

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHH
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~  242 (490)
                      +..+.|.||.|+|||||++.++..
T Consensus        22 Ge~~~liG~nGsGKSTLl~~l~Gl   45 (208)
T 3b85_A           22 NTIVFGLGPAGSGKTYLAMAKAVQ   45 (208)
T ss_dssp             CSEEEEECCTTSSTTHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcC
Confidence            568889999999999999999876

>1gm5_A RECG; helicase, replication restart; HET: DNA ADP; 3.24A {Thermotoga maritima} SCOP: a.24.21.1 b.40.4.9 c.37.1.19 c.37.1.19

Probab=94.37  E-value=0.19  Score=54.71  Aligned_cols=38  Identities=21%  Similarity=0.366  Sum_probs=25.0

Q ss_pred             cCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEE
Q psy200          216 NETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYI  254 (490)
Q Consensus       216 ~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v  254 (490)
                      .+.+..++|.|+.|+|||.++-..+-..-. .+..++++
T Consensus       386 ~~~~~~~Ll~a~TGSGKTlvall~il~~l~-~g~qvlvl  423 (780)
T 1gm5_A          386 SEKPMNRLLQGDVGSGKTVVAQLAILDNYE-AGFQTAFM  423 (780)
T ss_dssp             SSSCCCCEEECCSSSSHHHHHHHHHHHHHH-HTSCEEEE
T ss_pred             ccCCCcEEEEcCCCCCHHHHHHHHHHHHHH-cCCeEEEE
Confidence            344568999999999999987655443311 23445555

>3dmq_A RNA polymerase-associated protein RAPA; SWF2/SNF2, transcription factor, RNA polymerase recycling, activator, ATP-binding, DNA-binding; 3.20A {Escherichia coli K12}

Probab=94.36  E-value=0.22  Score=55.72  Aligned_cols=73  Identities=11%  Similarity=0.117  Sum_probs=47.6

Q ss_pred             CCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCc-eEEEEeccCCCCHHHHHHHHHHHhc
Q psy200          196 LPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAF-KTIYINCNSVRNAASVYETIVNELK  274 (490)
Q Consensus       196 lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~-~~~~v~~~~~~~~~~l~~~i~~~l~  274 (490)
                      +--+..+.+.+...+.     .....++|.++.|+|||..+-.++..+...... .++.+ |+. .-..++..++...++
T Consensus       152 ~~LrpyQ~eav~~~l~-----~~~~~~LLad~tGlGKTi~Ai~~i~~l~~~g~~~rvLIV-vP~-sLl~Qw~~E~~~~f~  224 (968)
T 3dmq_A          152 TSLIPHQLNIAHDVGR-----RHAPRVLLADEVGLGKTIEAGMILHQQLLSGAAERVLII-VPE-TLQHQWLVEMLRRFN  224 (968)
T ss_dssp             SCCCHHHHHHHHHHHH-----SSSCEEEECCCTTSCHHHHHHHHHHHHHHTSSCCCEEEE-CCT-TTHHHHHHHHHHHSC
T ss_pred             CCCcHHHHHHHHHHHH-----hcCCCEEEECCCCCcHHHHHHHHHHHHHHhCCCCeEEEE-eCH-HHHHHHHHHHHHHhC
Confidence            4445666666665554     235678999999999999998888776433322 44444 444 456777777766664


Q ss_pred             C
Q psy200          275 L  275 (490)
Q Consensus       275 ~  275 (490)
                      .
T Consensus       225 l  225 (968)
T 3dmq_A          225 L  225 (968)
T ss_dssp             C
T ss_pred             C
Confidence            3

>2whx_A Serine protease/ntpase/helicase NS3; transcription, hydrolase, ATP-binding, reticulum, nucleotidyltransferase, multifunctional enzyme; HET: ADP; 2.20A {Dengue virus 4} PDB: 2vbc_A 2wzq_A

Probab=94.35  E-value=0.037  Score=58.71  Aligned_cols=50  Identities=20%  Similarity=0.264  Sum_probs=31.4

Q ss_pred             CCCeEEEECCCCCcHHHH-HHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHh
Q psy200          218 TSGSMYISGPPGTGKSAS-LNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNEL  273 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtl-a~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l  273 (490)
                      .++.+++.+++|+|||+. +-.+++.+.. .+..++++.     -...+..++...+
T Consensus       185 ~g~dvlv~a~TGSGKT~~~~lpil~~l~~-~~~~vLvl~-----PtreLa~Qi~~~l  235 (618)
T 2whx_A          185 KKRLTIMDLHPGAGKTKRILPSIVREALK-RRLRTLILA-----PTRVVAAEMEEAL  235 (618)
T ss_dssp             TTCEEEECCCTTSSTTTTHHHHHHHHHHH-TTCCEEEEE-----SSHHHHHHHHHHT
T ss_pred             cCCeEEEEcCCCCCHHHHHHHHHHHHHHh-CCCeEEEEc-----ChHHHHHHHHHHh
Confidence            467899999999999996 3445444432 333455553     1244666666666

>1b0u_A Histidine permease; ABC transporter, transport protein; HET: ATP; 1.50A {Salmonella typhimurium} SCOP: c.37.1.12

Probab=94.33  E-value=0.022  Score=53.56  Aligned_cols=27  Identities=26%  Similarity=0.335  Sum_probs=23.5

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHh
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRA  243 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l  243 (490)
                      ..+..+.|.||.|+|||||++.++..+
T Consensus        30 ~~Ge~~~liG~nGsGKSTLlk~l~Gl~   56 (262)
T 1b0u_A           30 RAGDVISIIGSSGSGKSTFLRCINFLE   56 (262)
T ss_dssp             CTTCEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            456788999999999999999998765

>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=94.30  E-value=0.021  Score=51.92  Aligned_cols=26  Identities=23%  Similarity=0.434  Sum_probs=23.0

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHh
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRA  243 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l  243 (490)
                      .+..+.|.||.|+|||||++.++..+
T Consensus        34 ~Ge~~~iiG~NGsGKSTLlk~l~Gl~   59 (214)
T 1sgw_A           34 KGNVVNFHGPNGIGKTTLLKTISTYL   59 (214)
T ss_dssp             TTCCEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            56788899999999999999998765

>2krk_A 26S protease regulatory subunit 8; structural genomics, northeast structural genomics consortium (NESG), target HR3102A, PSI-2; NMR {Homo sapiens}

Probab=94.26  E-value=0.059  Score=41.16  Aligned_cols=78  Identities=9%  Similarity=0.056  Sum_probs=57.1

Q ss_pred             EEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCC-HHHHHHHHHHHHHHHHhccccCCcccccCHHHH
Q psy200          362 MNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGD-IRKAIDITNHLIDLTYDNVKENGEVTGIGLKEV  440 (490)
Q Consensus       362 i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd-~r~ai~ll~~a~~~a~~~~~~~~~~~~It~~~v  440 (490)
                      ..-.|++.++..+||+..+......   ++..++.|++   .+.|- -..+-++|+.|...|.++.     ...|+.+||
T Consensus         6 ~~~~~Pd~~~R~~IL~~~l~~~~l~---~dvdl~~LA~---~T~G~SGADL~~l~~eAa~~alr~~-----~~~I~~~df   74 (86)
T 2krk_A            6 HHHSHPNEEARLDILKIHSRKMNLT---RGINLRKIAE---LMPGASGAEVKGVCTEAGMYALRER-----RVHVTQEDF   74 (86)
T ss_dssp             CCCCCCCHHHHHHHHHHHTTTSEEC---TTCCCHHHHH---TCSSCCHHHHHHHHHHHHHHHHHTT-----CSEECHHHH
T ss_pred             CCCCCcCHHHHHHHHHHHHcCCCCC---cccCHHHHHH---HcCCCCHHHHHHHHHHHHHHHHHHc-----CCCCCHHHH
Confidence            4457999999999999988765211   2233677776   33342 3344568999999999887     678999999


Q ss_pred             HHHHHHhccC
Q psy200          441 LGVISSVYCT  450 (490)
Q Consensus       441 ~~a~~~~~~~  450 (490)
                      ..|+..+.+.
T Consensus        75 ~~Al~~v~p~   84 (86)
T 2krk_A           75 EMAVAKVMQK   84 (86)
T ss_dssp             HHHHHHHHCC
T ss_pred             HHHHHHHccC
Confidence            9999988653

>2gza_A Type IV secretion system protein VIRB11; ATPase, hydrolase; 2.60A {Brucella suis}

Probab=94.25  E-value=0.027  Score=55.59  Aligned_cols=36  Identities=19%  Similarity=0.325  Sum_probs=28.3

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEe
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYIN  255 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~  255 (490)
                      .+..++|+|+.|+||||+++.++..+.  .....+.++
T Consensus       174 ~G~~i~ivG~sGsGKSTll~~l~~~~~--~~~g~I~ie  209 (361)
T 2gza_A          174 LERVIVVAGETGSGKTTLMKALMQEIP--FDQRLITIE  209 (361)
T ss_dssp             TTCCEEEEESSSSCHHHHHHHHHTTSC--TTSCEEEEE
T ss_pred             cCCEEEEECCCCCCHHHHHHHHHhcCC--CCceEEEEC
Confidence            467899999999999999999988764  333455555

>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=94.23  E-value=0.05  Score=52.97  Aligned_cols=81  Identities=15%  Similarity=0.171  Sum_probs=46.2

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCC
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFDTKHK  298 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~  298 (490)
                      +..++|+|+.|+||||+++.++..+.  +.-..+.++.......... .   +.+..-. + ........+..++.  .+
T Consensus       171 g~~v~i~G~~GsGKTTll~~l~g~~~--~~~g~i~i~~~~e~~~~~~-~---~~i~~~~-g-gg~~~r~~la~aL~--~~  240 (330)
T 2pt7_A          171 GKNVIVCGGTGSGKTTYIKSIMEFIP--KEERIISIEDTEEIVFKHH-K---NYTQLFF-G-GNITSADCLKSCLR--MR  240 (330)
T ss_dssp             TCCEEEEESTTSCHHHHHHHGGGGSC--TTSCEEEEESSCCCCCSSC-S---SEEEEEC-B-TTBCHHHHHHHHTT--SC
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCCc--CCCcEEEECCeeccccccc-h---hEEEEEe-C-CChhHHHHHHHHhh--hC
Confidence            56899999999999999999988764  3334556654321110000 0   0000000 0 11233444555554  45


Q ss_pred             eEEEEEecCcc
Q psy200          299 SILLILDEIDA  309 (490)
Q Consensus       299 ~~vI~IDEid~  309 (490)
                      |-+|++||.-.
T Consensus       241 p~ilildE~~~  251 (330)
T 2pt7_A          241 PDRIILGELRS  251 (330)
T ss_dssp             CSEEEECCCCS
T ss_pred             CCEEEEcCCCh
Confidence            77999999876

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens}

Probab=94.22  E-value=0.13  Score=51.13  Aligned_cols=18  Identities=22%  Similarity=0.497  Sum_probs=15.2

Q ss_pred             CCeEEEECCCCCcHHHHH
Q psy200          219 SGSMYISGPPGTGKSASL  236 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla  236 (490)
                      ++.+++.+|.|+|||...
T Consensus        52 ~~~~lv~a~TGsGKT~~~   69 (417)
T 2i4i_A           52 KRDLMACAQTGSGKTAAF   69 (417)
T ss_dssp             TCCEEEECCTTSCHHHHH
T ss_pred             CCCEEEEcCCCCHHHHHH
Confidence            467999999999999743

>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=94.21  E-value=0.028  Score=52.93  Aligned_cols=26  Identities=35%  Similarity=0.457  Sum_probs=23.2

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHH
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~  242 (490)
                      ..+..+.|.||.|+|||||++.++..
T Consensus        44 ~~Ge~~~l~G~NGsGKSTLlk~l~Gl   69 (267)
T 2zu0_C           44 HPGEVHAIMGPNGSGKSTLSATLAGR   69 (267)
T ss_dssp             CTTCEEEEECCTTSSHHHHHHHHHTC
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHhCC
Confidence            45678999999999999999999875

>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=94.21  E-value=0.03  Score=49.07  Aligned_cols=26  Identities=27%  Similarity=0.290  Sum_probs=22.5

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      .+..+|+|+.|+||||++++|+-.+.
T Consensus        26 ~g~~~i~G~NGsGKStll~ai~~~l~   51 (182)
T 3kta_A           26 KGFTAIVGANGSGKSNIGDAILFVLG   51 (182)
T ss_dssp             SSEEEEEECTTSSHHHHHHHHHHHTT
T ss_pred             CCcEEEECCCCCCHHHHHHHHHHHHc
Confidence            34788999999999999999987664

>3cr8_A Sulfate adenylyltranferase, adenylylsulfate kinase; APS kinase, transferase, sulfate metabolism, nucleotide 2 kinase; 2.95A {Thiobacillus denitrificans}

Probab=94.19  E-value=0.041  Score=57.41  Aligned_cols=28  Identities=25%  Similarity=0.398  Sum_probs=25.0

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      ..+..++|+|++|+||||+++.++..+.
T Consensus       367 ~~G~iI~LiG~sGSGKSTLar~La~~L~  394 (552)
T 3cr8_A          367 RQGFTVFFTGLSGAGKSTLARALAARLM  394 (552)
T ss_dssp             GSCEEEEEEESSCHHHHHHHHHHHHHHH
T ss_pred             ccceEEEEECCCCChHHHHHHHHHHhhc
Confidence            3567899999999999999999999886

>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=94.19  E-value=1.7  Score=41.41  Aligned_cols=24  Identities=46%  Similarity=0.583  Sum_probs=21.0

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHH
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~  242 (490)
                      .+.+.|.|.+|+|||||++++...
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            356889999999999999999764

>2db3_A ATP-dependent RNA helicase VASA; DEAD-BOX, protein-RNA complex, ATPase, riken structural genomics/proteomics initiative, RSGI; HET: ANP; 2.20A {Drosophila melanogaster}

Probab=94.16  E-value=0.23  Score=50.02  Aligned_cols=42  Identities=14%  Similarity=0.255  Sum_probs=25.5

Q ss_pred             CCeEEEEEecCccccccC-HHHHHHhHhCCC-CCCCcEEEEEec
Q psy200          297 HKSILLILDEIDALESRK-QTILYTIFEWPS-IPGSKLVLVGVA  338 (490)
Q Consensus       297 ~~~~vI~IDEid~l~~~~-~~~L~~l~~~~~-~~~~~vilI~~t  338 (490)
                      .+..+|||||+|.+.... ...+..++.... ....+++++.+|
T Consensus       202 ~~~~~lVlDEah~~~~~gf~~~~~~i~~~~~~~~~~q~l~~SAT  245 (434)
T 2db3_A          202 EDTRFVVLDEADRMLDMGFSEDMRRIMTHVTMRPEHQTLMFSAT  245 (434)
T ss_dssp             TTCCEEEEETHHHHTSTTTHHHHHHHHHCTTSCSSCEEEEEESC
T ss_pred             ccCCeEEEccHhhhhccCcHHHHHHHHHhcCCCCCceEEEEecc
Confidence            345699999999987653 344555554332 234456666555

>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=94.15  E-value=0.025  Score=53.15  Aligned_cols=27  Identities=30%  Similarity=0.415  Sum_probs=23.6

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHh
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRA  243 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l  243 (490)
                      ..+..+.|.||.|+|||||++.++..+
T Consensus        48 ~~Gei~~liG~NGsGKSTLlk~l~Gl~   74 (263)
T 2olj_A           48 REGEVVVVIGPSGSGKSTFLRCLNLLE   74 (263)
T ss_dssp             CTTCEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             cCCCEEEEEcCCCCcHHHHHHHHHcCC
Confidence            466789999999999999999998765

>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=94.13  E-value=0.029  Score=52.35  Aligned_cols=25  Identities=28%  Similarity=0.414  Sum_probs=22.6

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHH
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~  242 (490)
                      .+..+.|.||.|+|||||++.++..
T Consensus        28 ~Ge~~~l~G~nGsGKSTLlk~l~Gl   52 (250)
T 2d2e_A           28 KGEVHALMGPNGAGKSTLGKILAGD   52 (250)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHHTC
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCC
Confidence            5678899999999999999999875

>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=94.11  E-value=0.024  Score=53.08  Aligned_cols=26  Identities=31%  Similarity=0.517  Sum_probs=23.0

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHh
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRA  243 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l  243 (490)
                      .+..+.|.||.|+|||||++.++..+
T Consensus        32 ~Ge~~~liG~nGsGKSTLlk~l~Gl~   57 (257)
T 1g6h_A           32 KGDVTLIIGPNGSGKSTLINVITGFL   57 (257)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCCC
Confidence            56788899999999999999998765

>2onk_A Molybdate/tungstate ABC transporter, ATP-binding protein; membrane protein; 3.10A {Archaeoglobus fulgidus} SCOP: c.37.1.12

Probab=94.10  E-value=0.03  Score=51.84  Aligned_cols=26  Identities=31%  Similarity=0.470  Sum_probs=22.8

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHh
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRA  243 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l  243 (490)
                      .. ..+.|.||.|+|||||++.++..+
T Consensus        23 ~~-e~~~liG~nGsGKSTLl~~l~Gl~   48 (240)
T 2onk_A           23 GR-DYCVLLGPTGAGKSVFLELIAGIV   48 (240)
T ss_dssp             CS-SEEEEECCTTSSHHHHHHHHHTSS
T ss_pred             CC-EEEEEECCCCCCHHHHHHHHhCCC
Confidence            35 788899999999999999998765

>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=94.10  E-value=0.025  Score=51.94  Aligned_cols=27  Identities=22%  Similarity=0.479  Sum_probs=23.6

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      .+..+.|.||.|+|||||++.++..+.
T Consensus        33 ~Ge~~~i~G~nGsGKSTLl~~l~Gl~~   59 (229)
T 2pze_A           33 RGQLLAVAGSTGAGKTSLLMMIMGELE   59 (229)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHTTSSC
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCCCc
Confidence            567889999999999999999987653

>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=94.09  E-value=0.055  Score=50.35  Aligned_cols=38  Identities=26%  Similarity=0.401  Sum_probs=29.7

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEecc
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCN  257 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~  257 (490)
                      ....+++.|.+|+||||++..++..+.  .+.++..+++-
T Consensus        13 ~~~i~~~~GkgGvGKTTl~~~La~~l~--~g~~v~vvd~D   50 (262)
T 1yrb_A           13 ASMIVVFVGTAGSGKTTLTGEFGRYLE--DNYKVAYVNLD   50 (262)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHHHHT--TTSCEEEEECC
T ss_pred             ceEEEEEeCCCCCCHHHHHHHHHHHHH--CCCeEEEEeCC
Confidence            445788999999999999999998886  44566666543

>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=94.09  E-value=0.035  Score=55.64  Aligned_cols=39  Identities=23%  Similarity=0.239  Sum_probs=28.4

Q ss_pred             HHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHh
Q psy200          203 LEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRA  243 (490)
Q Consensus       203 ~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l  243 (490)
                      ...+.++|....  .....+.|.|++|+|||||++.++...
T Consensus        55 ~~~i~~~L~~~~--~~~~~valvG~nGaGKSTLln~L~Gl~   93 (413)
T 1tq4_A           55 NSAISDALKEID--SSVLNVAVTGETGSGKSSFINTLRGIG   93 (413)
T ss_dssp             HHHHHHHHHHHH--HCCEEEEEEECTTSSHHHHHHHHHTCC
T ss_pred             chhhhhhhhhcc--cCCeEEEEECCCCCcHHHHHHHHhCCC
Confidence            344555555432  345688899999999999999998743

>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=94.08  E-value=0.025  Score=52.39  Aligned_cols=26  Identities=19%  Similarity=0.381  Sum_probs=23.0

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHh
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRA  243 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l  243 (490)
                      .+..+.|.||.|+|||||++.++..+
T Consensus        31 ~Ge~~~l~G~nGsGKSTLl~~l~Gl~   56 (240)
T 1ji0_A           31 RGQIVTLIGANGAGKTTTLSAIAGLV   56 (240)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCCC
Confidence            56788899999999999999998765

>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=94.06  E-value=0.026  Score=53.47  Aligned_cols=27  Identities=22%  Similarity=0.202  Sum_probs=23.4

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHh
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRA  243 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l  243 (490)
                      ..+..+.|.||.|+|||||++.++..+
T Consensus        32 ~~Ge~~~iiGpnGsGKSTLl~~l~Gl~   58 (275)
T 3gfo_A           32 KRGEVTAILGGNGVGKSTLFQNFNGIL   58 (275)
T ss_dssp             ETTSEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHHcCC
Confidence            356788999999999999999998755

>1a7j_A Phosphoribulokinase; transferase, calvin cycle; 2.50A {Rhodobacter sphaeroides} SCOP: c.37.1.6

Probab=94.05  E-value=0.021  Score=54.50  Aligned_cols=41  Identities=15%  Similarity=0.232  Sum_probs=26.4

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCC
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSV  259 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~  259 (490)
                      ....|.|.|++|+||||+++.+++.++.. ++.+..++...+
T Consensus         4 ~~~iIgItG~sGSGKSTva~~L~~~lg~~-~~~~~vI~~D~~   44 (290)
T 1a7j_A            4 KHPIISVTGSSGAGTSTVKHTFDQIFRRE-GVKAVSIEGDAF   44 (290)
T ss_dssp             TSCEEEEESCC---CCTHHHHHHHHHHHH-TCCEEEEEGGGG
T ss_pred             CceEEEEECCCCCCHHHHHHHHHHHHhhc-CCCeeEeecchh
Confidence            34578899999999999999999877521 223455555444

>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=94.03  E-value=0.026  Score=52.54  Aligned_cols=26  Identities=27%  Similarity=0.309  Sum_probs=23.1

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHh
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRA  243 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l  243 (490)
                      .+..+.|.||.|+|||||++.++..+
T Consensus        34 ~Ge~~~i~G~nGsGKSTLl~~l~Gl~   59 (247)
T 2ff7_A           34 QGEVIGIVGRSGSGKSTLTKLIQRFY   59 (247)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            56788999999999999999997765

>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=94.02  E-value=0.025  Score=52.45  Aligned_cols=27  Identities=30%  Similarity=0.470  Sum_probs=23.5

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHh
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRA  243 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l  243 (490)
                      ..+..+.|.||.|+|||||++.++..+
T Consensus        26 ~~Ge~~~i~G~nGsGKSTLl~~l~Gl~   52 (243)
T 1mv5_A           26 QPNSIIAFAGPSGGGKSTIFSLLERFY   52 (243)
T ss_dssp             CTTEEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            356788999999999999999998765

>2ihy_A ABC transporter, ATP-binding protein; ATPase, ABC cassette, hydrolase; HET: MSE; 1.90A {Staphylococcus aureus}

Probab=94.01  E-value=0.034  Score=52.73  Aligned_cols=28  Identities=25%  Similarity=0.376  Sum_probs=23.8

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      ..+..+.|.||.|+|||||++.++..+.
T Consensus        45 ~~Ge~~~liG~NGsGKSTLlk~l~Gl~~   72 (279)
T 2ihy_A           45 AKGDKWILYGLNGAGKTTLLNILNAYEP   72 (279)
T ss_dssp             ETTCEEEEECCTTSSHHHHHHHHTTSSC
T ss_pred             cCCCEEEEECCCCCcHHHHHHHHhCCCC
Confidence            3567889999999999999999987653

>2ghi_A Transport protein; multidrug resistance protein, MDR, structural genomics, structural genomics consortium, SGC; 2.20A {Plasmodium yoelii yoelii str}

Probab=94.01  E-value=0.028  Score=52.80  Aligned_cols=27  Identities=26%  Similarity=0.321  Sum_probs=23.7

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHh
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRA  243 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l  243 (490)
                      ..+..+.|.||.|+|||||++.++..+
T Consensus        44 ~~Ge~~~i~G~nGsGKSTLl~~l~Gl~   70 (260)
T 2ghi_A           44 PSGTTCALVGHTGSGKSTIAKLLYRFY   70 (260)
T ss_dssp             CTTCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHhccC
Confidence            466789999999999999999998754

>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=93.99  E-value=0.028  Score=52.58  Aligned_cols=27  Identities=26%  Similarity=0.509  Sum_probs=23.5

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHh
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRA  243 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l  243 (490)
                      ..+..+.|.||.|+|||||++.++..+
T Consensus        39 ~~Gei~~l~G~NGsGKSTLlk~l~Gl~   65 (256)
T 1vpl_A           39 EEGEIFGLIGPNGAGKTTTLRIISTLI   65 (256)
T ss_dssp             CTTCEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             cCCcEEEEECCCCCCHHHHHHHHhcCC
Confidence            456788999999999999999998765

>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=93.98  E-value=0.027  Score=52.45  Aligned_cols=26  Identities=27%  Similarity=0.456  Sum_probs=23.0

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHh
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRA  243 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l  243 (490)
                      .+..+.|.||.|+|||||++.++..+
T Consensus        25 ~Ge~~~liG~NGsGKSTLlk~l~Gl~   50 (249)
T 2qi9_C           25 AGEILHLVGPNGAGKSTLLARMAGMT   50 (249)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhCCC
Confidence            56788999999999999999998765

>2ixe_A Antigen peptide transporter 1; ABC ATPase, hydrolase; HET: ATP; 2.0A {Rattus norvegicus} PDB: 2ixg_A* 2ixf_A* 1jj7_A*

Probab=93.96  E-value=0.028  Score=53.08  Aligned_cols=27  Identities=30%  Similarity=0.362  Sum_probs=23.7

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHh
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRA  243 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l  243 (490)
                      ..+..+.|.||.|+|||||++.++..+
T Consensus        43 ~~Ge~~~i~G~nGsGKSTLlk~l~Gl~   69 (271)
T 2ixe_A           43 YPGKVTALVGPNGSGKSTVAALLQNLY   69 (271)
T ss_dssp             CTTCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            467789999999999999999998765

>3fdi_A Uncharacterized protein; cytidylate kinase like protein, PSI, MCSG, PRK04182 class ME structural genomics, protein structure initiative; 2.20A {Eubacterium ventriosum}

Probab=93.96  E-value=0.042  Score=49.38  Aligned_cols=26  Identities=15%  Similarity=0.074  Sum_probs=23.6

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      ...|.|.|+.|+|||++++.+++.++
T Consensus         6 ~~iI~i~g~~GsGk~ti~~~la~~lg   31 (201)
T 3fdi_A            6 QIIIAIGREFGSGGHLVAKKLAEHYN   31 (201)
T ss_dssp             CCEEEEEECTTSSHHHHHHHHHHHTT
T ss_pred             CeEEEEeCCCCCCHHHHHHHHHHHhC
Confidence            35788999999999999999999986

>2ocp_A DGK, deoxyguanosine kinase; protein-nucleotide complex, transferase; HET: DTP; 2.80A {Homo sapiens} SCOP: c.37.1.1

Probab=93.94  E-value=0.03  Score=51.71  Aligned_cols=26  Identities=27%  Similarity=0.328  Sum_probs=23.2

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      +..|+|.|..|+||||+++.+++.+.
T Consensus         2 ~~~i~~~G~~g~GKtt~~~~l~~~l~   27 (241)
T 2ocp_A            2 PRRLSIEGNIAVGKSTFVKLLTKTYP   27 (241)
T ss_dssp             CEEEEEEECTTSSHHHHHHHHHHHCT
T ss_pred             CeEEEEEcCCCCCHHHHHHHHHHHcC
Confidence            45788999999999999999999873

>3bfv_A CAPA1, CAPB2, membrane protein CAPA1, protein tyrosine kinase; chimerical protein, P-loop protein, capsule biogenesis/degradation; HET: ADP; 1.80A {Staphylococcus aureus} PDB: 2ved_A*

Probab=93.94  E-value=0.13  Score=48.50  Aligned_cols=59  Identities=22%  Similarity=0.317  Sum_probs=43.0

Q ss_pred             HHHHHHHHHHHHhhhccCCCCeEEEECC-CCCcHHHHHHHHHHHhhhcCCceEEEEeccCC
Q psy200          200 EVQLEGIRQFLLGHVNNETSGSMYISGP-PGTGKSASLNLLVSRAEIKDAFKTIYINCNSV  259 (490)
Q Consensus       200 e~~~~~l~~~L~~~~~~~~~~~ill~Gp-pGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~  259 (490)
                      .+.+..|+..|.........+.++|+|+ +|+||||++-.++..+.. .+.+++.+++..-
T Consensus        63 ~Ea~r~lrt~l~~~~~~~~~kvI~vts~kgG~GKTt~a~nLA~~lA~-~G~rVLLID~D~~  122 (271)
T 3bfv_A           63 SEKFRGIRSNIMFANPDSAVQSIVITSEAPGAGKSTIAANLAVAYAQ-AGYKTLIVDGDMR  122 (271)
T ss_dssp             HHHHHHHHHHHHHSSTTCCCCEEEEECSSTTSSHHHHHHHHHHHHHH-TTCCEEEEECCSS
T ss_pred             HHHHHHHHHHHHhhccCCCCeEEEEECCCCCCcHHHHHHHHHHHHHh-CCCeEEEEeCCCC
Confidence            3566677777765434456678888876 899999999999998863 4557788877543

>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=93.94  E-value=0.028  Score=52.95  Aligned_cols=27  Identities=37%  Similarity=0.519  Sum_probs=23.5

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHh
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRA  243 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l  243 (490)
                      ..+..+.|.||.|+|||||++.++..+
T Consensus        35 ~~Ge~~~liG~nGsGKSTLl~~l~Gl~   61 (266)
T 4g1u_C           35 ASGEMVAIIGPNGAGKSTLLRLLTGYL   61 (266)
T ss_dssp             ETTCEEEEECCTTSCHHHHHHHHTSSS
T ss_pred             cCCCEEEEECCCCCcHHHHHHHHhcCC
Confidence            356788999999999999999998765

>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=93.93  E-value=0.03  Score=54.98  Aligned_cols=27  Identities=26%  Similarity=0.470  Sum_probs=23.5

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHh
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRA  243 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l  243 (490)
                      ..+..+.|.||.|+|||||++.++..+
T Consensus        28 ~~Ge~~~llGpsGsGKSTLLr~iaGl~   54 (359)
T 3fvq_A           28 DPGEILFIIGASGCGKTTLLRCLAGFE   54 (359)
T ss_dssp             CTTCEEEEEESTTSSHHHHHHHHHTSS
T ss_pred             cCCCEEEEECCCCchHHHHHHHHhcCC
Confidence            356788899999999999999998765

>3i5x_A ATP-dependent RNA helicase MSS116; protein-RNA complex, RNA helicase, DEAD-BOX, ATP-binding, HE hydrolase, mitochondrion; HET: ANP; 1.90A {Saccharomyces cerevisiae} PDB: 3i5y_A* 3i61_A* 3i62_A* 3sqx_A* 4db2_A 4db4_A

Probab=93.92  E-value=0.24  Score=51.69  Aligned_cols=19  Identities=21%  Similarity=0.363  Sum_probs=16.4

Q ss_pred             CCCeEEEECCCCCcHHHHH
Q psy200          218 TSGSMYISGPPGTGKSASL  236 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla  236 (490)
                      .++.+++.+|.|+|||...
T Consensus       110 ~~~~~lv~apTGsGKTl~~  128 (563)
T 3i5x_A          110 EDHDVIARAKTGTGKTFAF  128 (563)
T ss_dssp             SSEEEEEECCTTSCHHHHH
T ss_pred             CCCeEEEECCCCCCccHHH
Confidence            4678999999999999853

>1yks_A Genome polyprotein [contains: flavivirin protease NS3 catalytic subunit]; helicase, flavivirus, DEAD-BOX, ATPase, rtpase, hydrolase; 1.80A {Yellow fever virus} SCOP: c.37.1.14 c.37.1.14 PDB: 1ymf_A*

Probab=93.87  E-value=0.048  Score=55.36  Aligned_cols=50  Identities=12%  Similarity=0.259  Sum_probs=30.9

Q ss_pred             CCCeEEEECCCCCcHHHHH-HHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHh
Q psy200          218 TSGSMYISGPPGTGKSASL-NLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNEL  273 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla-~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l  273 (490)
                      .++.+++.||.|+|||..+ -.+++.+.. .+...+++.     -...+..++...+
T Consensus         7 ~g~~vlv~a~TGSGKT~~~l~~~l~~~~~-~~~~~lil~-----Ptr~La~Q~~~~l   57 (440)
T 1yks_A            7 KGMTTVLDFHPGAGKTRRFLPQILAECAR-RRLRTLVLA-----PTRVVLSEMKEAF   57 (440)
T ss_dssp             TTCEEEECCCTTSSTTTTHHHHHHHHHHH-TTCCEEEEE-----SSHHHHHHHHHHT
T ss_pred             CCCCEEEEcCCCCCHHHHHHHHHHHHHHh-cCCeEEEEc-----chHHHHHHHHHHH
Confidence            4678999999999999984 445554432 334455553     1234555555555

>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=93.87  E-value=0.032  Score=49.62  Aligned_cols=22  Identities=27%  Similarity=0.439  Sum_probs=20.0

Q ss_pred             eEEEECCCCCcHHHHHHHHHHH
Q psy200          221 SMYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~  242 (490)
                      .++|.|++|+|||||++.++..
T Consensus         7 kv~lvG~~g~GKSTLl~~l~~~   28 (199)
T 2f9l_A            7 KVVLIGDSGVGKSNLLSRFTRN   28 (199)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHS
T ss_pred             EEEEECcCCCCHHHHHHHHhcC
Confidence            5789999999999999999875

>3gqb_A V-type ATP synthase alpha chain; A3B3, V-ATPase, ATP synthesis, ATP-binding, hydrogen ION TRA hydrolase, ION transport; 2.80A {Thermus thermophilus HB8} PDB: 3a5c_A* 3a5d_A 3j0j_A* 1um2_C

Probab=93.84  E-value=0.089  Score=54.10  Aligned_cols=93  Identities=20%  Similarity=0.281  Sum_probs=54.6

Q ss_pred             cCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCC-CHHHHHHHHHHHhcCCCCC---------------
Q psy200          216 NETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVR-NAASVYETIVNELKLKPGG---------------  279 (490)
Q Consensus       216 ~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~-~~~~l~~~i~~~l~~~~~~---------------  279 (490)
                      -..++.+.|.|++|+|||+|+..+++...  .+ .++++-|..-. ...+++.++-+ +..+..|               
T Consensus       218 igrGqr~~Ifg~~g~GKT~l~~~ia~~~~--~~-v~V~~~iGER~~Ev~e~~~~~~e-l~d~~~G~~~~~rtvvv~~tsd  293 (578)
T 3gqb_A          218 VAMGGTAAIPGPFGSGKSVTQQSLAKWSN--AD-VVVYVGSGERGNEMTDVLVEFPE-LTDPKTGGPLMHRTVLIANTSN  293 (578)
T ss_dssp             EETTCEEEECCCTTSCHHHHHHHHHHHSS--CS-EEEEEEEEECHHHHHHHHTTGGG-CBCTTTSSBSGGGEEEEEEETT
T ss_pred             ccCCCEEeeeCCCCccHHHHHHHHHhccC--CC-EEEEEEecccHHHHHHHHHHHHh-hcccccccccccceEEEEECCC
Confidence            35688999999999999999999988743  23 35566555431 22333333211 1111111               


Q ss_pred             CcH-HHH-----HHHHHHHHhcCCCeEEEEEecCccccc
Q psy200          280 KSE-RHQ-----LGAILKYFDTKHKSILLILDEIDALES  312 (490)
Q Consensus       280 ~s~-~~~-----~~~l~~~l~~~~~~~vI~IDEid~l~~  312 (490)
                      ... ...     .-.+.+++...++.++|++|.+-++..
T Consensus       294 ~p~~~R~~~~~~altiAEyfrd~G~dVLl~~Ds~tR~A~  332 (578)
T 3gqb_A          294 MPVAAREASIYVGVTIAEYFRDQGFSVALMADSTSRWAE  332 (578)
T ss_dssp             SCHHHHHHHHHHHHHHHHHHHHTTCEEEECCSCHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHcCCCEEEEecChHHHHH
Confidence            111 111     123445565668899999999886653

>2yz2_A Putative ABC transporter ATP-binding protein TM_0; cobalt transport, TM02 hydrolase, inner membrane, membrane, nucleotide-binding; 2.30A {Thermotoga maritima}

Probab=93.84  E-value=0.031  Score=52.66  Aligned_cols=27  Identities=22%  Similarity=0.479  Sum_probs=23.4

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHh
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRA  243 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l  243 (490)
                      ..+..+.|.||.|+|||||++.++..+
T Consensus        31 ~~Ge~~~liG~nGsGKSTLl~~i~Gl~   57 (266)
T 2yz2_A           31 NEGECLLVAGNTGSGKSTLLQIVAGLI   57 (266)
T ss_dssp             CTTCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             cCCCEEEEECCCCCcHHHHHHHHhCCC
Confidence            356788899999999999999998755

>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=93.79  E-value=0.031  Score=49.46  Aligned_cols=23  Identities=26%  Similarity=0.420  Sum_probs=20.5

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHh
Q psy200          221 SMYISGPPGTGKSASLNLLVSRA  243 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~l  243 (490)
                      .+.|.|++|+|||||++.++...
T Consensus        31 kv~lvG~~g~GKSTLl~~l~~~~   53 (191)
T 1oix_A           31 KVVLIGDSGVGKSNLLSRFTRNE   53 (191)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHSC
T ss_pred             EEEEECcCCCCHHHHHHHHhcCC
Confidence            57899999999999999998754

>2it1_A 362AA long hypothetical maltose/maltodextrin transport ATP-binding protein; structural genomics, NPPSFA; 1.94A {Pyrococcus horikoshii}

Probab=93.77  E-value=0.038  Score=54.46  Aligned_cols=27  Identities=30%  Similarity=0.421  Sum_probs=23.5

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHh
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRA  243 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l  243 (490)
                      ..+..+.|.||.|+|||||++.++..+
T Consensus        27 ~~Ge~~~llGpnGsGKSTLLr~iaGl~   53 (362)
T 2it1_A           27 KDGEFMALLGPSGSGKSTLLYTIAGIY   53 (362)
T ss_dssp             CTTCEEEEECCTTSSHHHHHHHHHTSS
T ss_pred             CCCCEEEEECCCCchHHHHHHHHhcCC
Confidence            356788899999999999999998765

>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=93.75  E-value=0.037  Score=54.41  Aligned_cols=27  Identities=26%  Similarity=0.444  Sum_probs=23.5

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHh
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRA  243 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l  243 (490)
                      ..+..+.|.||.|+|||||++.++..+
T Consensus        27 ~~Ge~~~llGpnGsGKSTLLr~iaGl~   53 (359)
T 2yyz_A           27 KDGEFVALLGPSGCGKTTTLLMLAGIY   53 (359)
T ss_dssp             CTTCEEEEECSTTSSHHHHHHHHHTSS
T ss_pred             cCCCEEEEEcCCCchHHHHHHHHHCCC
Confidence            356788899999999999999998765

>2nq2_C Hypothetical ABC transporter ATP-binding protein HI1470; putative iron chelatin ABC transporter, nucleotide binding domain; 2.40A {Haemophilus influenzae}

Probab=93.75  E-value=0.031  Score=52.18  Aligned_cols=27  Identities=30%  Similarity=0.447  Sum_probs=23.4

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      .+..+.|.||.|+|||||++.++..+.
T Consensus        30 ~Ge~~~l~G~nGsGKSTLl~~l~Gl~~   56 (253)
T 2nq2_C           30 KGDILAVLGQNGCGKSTLLDLLLGIHR   56 (253)
T ss_dssp             TTCEEEEECCSSSSHHHHHHHHTTSSC
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCCCC
Confidence            566888999999999999999987653

>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=93.74  E-value=0.038  Score=54.72  Aligned_cols=27  Identities=26%  Similarity=0.458  Sum_probs=23.6

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHh
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRA  243 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l  243 (490)
                      ..+..+.|.||.|+|||||++.++..+
T Consensus        27 ~~Ge~~~llGpsGsGKSTLLr~iaGl~   53 (381)
T 3rlf_A           27 HEGEFVVFVGPSGCGKSTLLRMIAGLE   53 (381)
T ss_dssp             CTTCEEEEECCTTSSHHHHHHHHHTSS
T ss_pred             CCCCEEEEEcCCCchHHHHHHHHHcCC
Confidence            356788899999999999999998765

>2dyk_A GTP-binding protein; GTPase, ribosome-binding protein, structural genomics; HET: GDP; 1.96A {Thermus thermophilus}

Probab=93.73  E-value=0.037  Score=46.85  Aligned_cols=22  Identities=36%  Similarity=0.614  Sum_probs=20.0

Q ss_pred             eEEEECCCCCcHHHHHHHHHHH
Q psy200          221 SMYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~  242 (490)
                      .++|.|++|+|||++++.+...
T Consensus         3 ki~v~G~~~~GKSsli~~l~~~   24 (161)
T 2dyk_A            3 KVVIVGRPNVGKSSLFNRLLKK   24 (161)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            5889999999999999999865

>1z47_A CYSA, putative ABC-transporter ATP-binding protein; alpha/beta motif, beta sandwich, ligand binding protein; 1.90A {Alicyclobacillus acidocaldarius}

Probab=93.71  E-value=0.037  Score=54.37  Aligned_cols=26  Identities=27%  Similarity=0.496  Sum_probs=23.0

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHh
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRA  243 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l  243 (490)
                      .+..+.|.||.|+|||||++.++..+
T Consensus        40 ~Ge~~~llGpnGsGKSTLLr~iaGl~   65 (355)
T 1z47_A           40 EGEMVGLLGPSGSGKTTILRLIAGLE   65 (355)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHHTSS
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhCCC
Confidence            56788899999999999999998765

>2xzl_A ATP-dependent helicase NAM7; hydrolase-RNA complex, NMD, RNA degradation, allosteric REGU; HET: ADP 1PE; 2.40A {Saccharomyces cerevisiae}

Probab=93.71  E-value=0.069  Score=58.40  Aligned_cols=26  Identities=35%  Similarity=0.551  Sum_probs=21.9

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      .+.++|.||||||||+++..++..+.
T Consensus       375 ~~~~lI~GppGTGKT~~i~~~i~~l~  400 (802)
T 2xzl_A          375 RPLSLIQGPPGTGKTVTSATIVYHLS  400 (802)
T ss_dssp             CSEEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             CCCEEEECCCCCCHHHHHHHHHHHHH
Confidence            45789999999999999888877664

>2obl_A ESCN; ATPase, hydrolase; 1.80A {Escherichia coli O127} PDB: 2obm_A*

Probab=93.70  E-value=0.066  Score=52.43  Aligned_cols=36  Identities=19%  Similarity=0.262  Sum_probs=28.6

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEE
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYI  254 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v  254 (490)
                      ..+..+.|.|+.|+|||||++.++....  ++..++.+
T Consensus        69 ~~Gq~~gIiG~nGaGKTTLl~~I~g~~~--~~~g~i~~  104 (347)
T 2obl_A           69 GIGQRIGIFAGSGVGKSTLLGMICNGAS--ADIIVLAL  104 (347)
T ss_dssp             ETTCEEEEEECTTSSHHHHHHHHHHHSC--CSEEEEEE
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHhcCCC--CCEEEEEE
Confidence            5678999999999999999999999864  34434444

>2f1r_A Molybdopterin-guanine dinucleotide biosynthesis protein B (MOBB); structural genomics, PSI, protein structure initiative; 2.10A {Archaeoglobus fulgidus}

Probab=93.69  E-value=0.023  Score=49.68  Aligned_cols=25  Identities=16%  Similarity=0.254  Sum_probs=22.7

Q ss_pred             CeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          220 GSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       220 ~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      ..+.|+|++|+|||||++.++..+.
T Consensus         3 ~~v~IvG~SGsGKSTL~~~L~~~~~   27 (171)
T 2f1r_A            3 LILSIVGTSDSGKTTLITRMMPILR   27 (171)
T ss_dssp             CEEEEEESCHHHHHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhh
Confidence            4688999999999999999998875

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus}

Probab=93.67  E-value=0.39  Score=49.55  Aligned_cols=25  Identities=24%  Similarity=0.361  Sum_probs=19.5

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHh
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRA  243 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l  243 (490)
                      ++.+++.+|.|+|||..+-..+-+.
T Consensus        19 ~~~~l~~~~tGsGKT~~~~~~~~~~   43 (555)
T 3tbk_A           19 GKNTIICAPTGCGKTFVSLLICEHH   43 (555)
T ss_dssp             TCCEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CCCEEEEeCCCChHHHHHHHHHHHH
Confidence            3579999999999998866655443

>3cio_A ETK, tyrosine-protein kinase ETK; WZC, escherichia coli tyrosine kinase domain, signaling protein, transferase, inner membrane, membrane; 2.50A {Escherichia coli}

Probab=93.67  E-value=0.13  Score=49.25  Aligned_cols=57  Identities=18%  Similarity=0.275  Sum_probs=41.7

Q ss_pred             HHHHHHHHHHHhhhccCCCCeEEEECC-CCCcHHHHHHHHHHHhhhcCCceEEEEeccC
Q psy200          201 VQLEGIRQFLLGHVNNETSGSMYISGP-PGTGKSASLNLLVSRAEIKDAFKTIYINCNS  258 (490)
Q Consensus       201 ~~~~~l~~~L~~~~~~~~~~~ill~Gp-pGtGKTtla~~l~~~l~~~~~~~~~~v~~~~  258 (490)
                      +.+..|+..|.........+.|+|+|. +|+||||++..++..+.. .+.+++.+++..
T Consensus        86 Ea~r~lrt~l~~~~~~~~~kvI~vts~kgG~GKTtva~nLA~~lA~-~G~rVLLID~D~  143 (299)
T 3cio_A           86 EAVRALRTSLHFAMMETENNILMITGATPDSGKTFVSSTLAAVIAQ-SDQKVLFIDADL  143 (299)
T ss_dssp             HHHHHHHHHHHHHTSSCSCCEEEEEESSSSSCHHHHHHHHHHHHHH-TTCCEEEEECCT
T ss_pred             HHHHHHHHHHHHhccCCCCeEEEEECCCCCCChHHHHHHHHHHHHh-CCCcEEEEECCC
Confidence            556666666654434456678888886 799999999999998863 356778887654

>3sop_A Neuronal-specific septin-3; hydrolase; HET: GDP; 2.88A {Homo sapiens}

Probab=93.66  E-value=0.035  Score=52.36  Aligned_cols=24  Identities=29%  Similarity=0.475  Sum_probs=21.4

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHhh
Q psy200          221 SMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      .+.|.||.|+|||||++.++....
T Consensus         4 ~v~lvG~nGaGKSTLln~L~g~~~   27 (270)
T 3sop_A            4 NIMVVGQSGLGKSTLVNTLFKSQV   27 (270)
T ss_dssp             EEEEEESSSSSHHHHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHhCCCC
Confidence            578999999999999999998763

>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=93.64  E-value=0.04  Score=54.44  Aligned_cols=27  Identities=22%  Similarity=0.528  Sum_probs=23.5

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHh
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRA  243 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l  243 (490)
                      ..+..+.|.||.|+|||||++.++..+
T Consensus        35 ~~Ge~~~llGpnGsGKSTLLr~iaGl~   61 (372)
T 1v43_A           35 KDGEFLVLLGPSGCGKTTTLRMIAGLE   61 (372)
T ss_dssp             CTTCEEEEECCTTSSHHHHHHHHHTSS
T ss_pred             CCCCEEEEECCCCChHHHHHHHHHcCC
Confidence            456788899999999999999998765

>2zpa_A Uncharacterized protein YPFI; RNA modification enzyme, RNA helicase, acetyltransferase, GCN5 acetyltransferase; HET: ACO ADP; 2.35A {Escherichia coli K12}

Probab=93.54  E-value=0.45  Score=50.38  Aligned_cols=97  Identities=16%  Similarity=0.228  Sum_probs=60.0

Q ss_pred             CeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCe
Q psy200          220 GSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFDTKHKS  299 (490)
Q Consensus       220 ~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~  299 (490)
                      +..+|+|++|.|||+++-.++..+.  ..   ++|.++...+...++......+  .+  ...+++.       ......
T Consensus       193 ~~~vlta~RGRGKSa~lG~~~a~~~--~~---~~vtAP~~~a~~~l~~~~~~~i--~~--~~Pd~~~-------~~~~~~  256 (671)
T 2zpa_A          193 GVAAVTAARGRGKSALAGQLISRIA--GR---AIVTAPAKASTDVLAQFAGEKF--RF--IAPDALL-------ASDEQA  256 (671)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHHSS--SC---EEEECSSCCSCHHHHHHHGGGC--CB--CCHHHHH-------HSCCCC
T ss_pred             CeEEEecCCCCCHHHHHHHHHHHHH--hC---cEEECCCHHHHHHHHHHhhCCe--EE--eCchhhh-------hCcccC
Confidence            5679999999999999999999875  22   4777777766665554432221  11  1222211       222234


Q ss_pred             EEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEEEecC
Q psy200          300 ILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVAN  339 (490)
Q Consensus       300 ~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI~~tn  339 (490)
                      -+|||||+=.+.-   ..|..++.    ...++++..+.+
T Consensus       257 dlliVDEAAaIp~---pll~~ll~----~~~~v~~~tTv~  289 (671)
T 2zpa_A          257 DWLVVDEAAAIPA---PLLHQLVS----RFPRTLLTTTVQ  289 (671)
T ss_dssp             SEEEEETGGGSCH---HHHHHHHT----TSSEEEEEEEBS
T ss_pred             CEEEEEchhcCCH---HHHHHHHh----hCCeEEEEecCC
Confidence            5999999999864   45555554    223566655555

>2dpy_A FLII, flagellum-specific ATP synthase; beta barrel, alpha-beta structure, hydrolase; HET: ADP; 2.40A {Salmonella typhimurium}

Probab=93.53  E-value=0.08  Score=53.58  Aligned_cols=39  Identities=15%  Similarity=0.137  Sum_probs=30.0

Q ss_pred             cCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEec
Q psy200          216 NETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINC  256 (490)
Q Consensus       216 ~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~  256 (490)
                      -..+..+.|.|+.|+|||||++.++....  .+...+.++.
T Consensus       154 i~~Gq~~~IvG~sGsGKSTLl~~Iag~~~--~~~G~i~~~G  192 (438)
T 2dpy_A          154 VGRGQRMGLFAGSGVGKSVLLGMMARYTR--ADVIVVGLIG  192 (438)
T ss_dssp             CBTTCEEEEEECTTSSHHHHHHHHHHHSC--CSEEEEEEES
T ss_pred             ecCCCEEEEECCCCCCHHHHHHHHhcccC--CCeEEEEEec
Confidence            35678899999999999999999999864  3344455543

>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=93.53  E-value=0.011  Score=65.39  Aligned_cols=23  Identities=26%  Similarity=0.202  Sum_probs=20.1

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHH
Q psy200          218 TSGSMYISGPPGTGKSASLNLLV  240 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~  240 (490)
                      .+..++|+||.|+||||+++.++
T Consensus       661 ~g~i~~ItGpNGsGKSTlLr~ia  683 (934)
T 3thx_A          661 KQMFHIITGPNMGGKSTYIRQTG  683 (934)
T ss_dssp             TBCEEEEECCTTSSHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHH
Confidence            34678999999999999999984

>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=93.52  E-value=0.041  Score=46.88  Aligned_cols=23  Identities=22%  Similarity=0.257  Sum_probs=20.4

Q ss_pred             CeEEEECCCCCcHHHHHHHHHHH
Q psy200          220 GSMYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       220 ~~ill~GppGtGKTtla~~l~~~  242 (490)
                      -.++|.|++|+|||+|++.+...
T Consensus         6 ~~i~v~G~~~~GKssl~~~l~~~   28 (168)
T 1z2a_A            6 IKMVVVGNGAVGKSSMIQRYCKG   28 (168)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHC
T ss_pred             EEEEEECcCCCCHHHHHHHHHcC
Confidence            36889999999999999999875

>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=93.51  E-value=0.034  Score=54.51  Aligned_cols=27  Identities=33%  Similarity=0.522  Sum_probs=23.5

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHh
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRA  243 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l  243 (490)
                      ..+..+.|.||.|+|||||++.++..+
T Consensus        24 ~~Ge~~~llGpnGsGKSTLLr~iaGl~   50 (348)
T 3d31_A           24 ESGEYFVILGPTGAGKTLFLELIAGFH   50 (348)
T ss_dssp             CTTCEEEEECCCTHHHHHHHHHHHTSS
T ss_pred             cCCCEEEEECCCCccHHHHHHHHHcCC
Confidence            456788899999999999999998765

>3io3_A DEHA2D07832P; chaperone, membrane traffic, ATPase; HET: ADP; 1.80A {Debaryomyces hansenii}

Probab=93.50  E-value=0.1  Score=51.05  Aligned_cols=44  Identities=11%  Similarity=0.311  Sum_probs=34.6

Q ss_pred             cCCCCeEEEECCCCCcHHHHHHHHHHHhhh-cCCceEEEEeccCC
Q psy200          216 NETSGSMYISGPPGTGKSASLNLLVSRAEI-KDAFKTIYINCNSV  259 (490)
Q Consensus       216 ~~~~~~ill~GppGtGKTtla~~l~~~l~~-~~~~~~~~v~~~~~  259 (490)
                      ....+.+++.|.+|+||||++..++..+.. ..+.+++.+++-..
T Consensus        15 ~~~~~i~~~~gkGGvGKTt~a~~lA~~la~~~~g~~vllid~D~~   59 (348)
T 3io3_A           15 HDSLKWIFVGGKGGVGKTTTSSSVAVQLALAQPNEQFLLISTDPA   59 (348)
T ss_dssp             CTTCSEEEEECSTTSSHHHHHHHHHHHHHHHCTTSCEEEEECCSS
T ss_pred             CCCcEEEEEeCCCCCcHHHHHHHHHHHHHHhcCCCeEEEEECCCC
Confidence            455689999999999999999999988862 44567777777543

>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=93.50  E-value=0.041  Score=54.41  Aligned_cols=26  Identities=27%  Similarity=0.557  Sum_probs=23.0

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHh
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRA  243 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l  243 (490)
                      .+..+.|.||.|+|||||++.++..+
T Consensus        28 ~Ge~~~llGpnGsGKSTLLr~iaGl~   53 (372)
T 1g29_1           28 DGEFMILLGPSGCGKTTTLRMIAGLE   53 (372)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHHTSS
T ss_pred             CCCEEEEECCCCcHHHHHHHHHHcCC
Confidence            56788899999999999999998765

>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=93.45  E-value=0.041  Score=47.29  Aligned_cols=23  Identities=30%  Similarity=0.456  Sum_probs=20.0

Q ss_pred             CeEEEECCCCCcHHHHHHHHHHH
Q psy200          220 GSMYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       220 ~~ill~GppGtGKTtla~~l~~~  242 (490)
                      ..++|.|++|+|||||++.+...
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            35789999999999999999753

>3tmk_A Thymidylate kinase; phosphotransferase; HET: T5A; 2.00A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 2tmk_A* 1tmk_A*

Probab=93.43  E-value=0.049  Score=49.49  Aligned_cols=27  Identities=26%  Similarity=0.399  Sum_probs=24.6

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      .+..|.|.|++|+||||+++.+++.+.
T Consensus         4 ~g~~i~~eG~~g~GKst~~~~l~~~l~   30 (216)
T 3tmk_A            4 RGKLILIEGLDRTGKTTQCNILYKKLQ   30 (216)
T ss_dssp             CCCEEEEEECSSSSHHHHHHHHHHHHC
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHhc
Confidence            467889999999999999999999986

>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=93.42  E-value=0.035  Score=48.71  Aligned_cols=21  Identities=33%  Similarity=0.607  Sum_probs=19.1

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q psy200          221 SMYISGPPGTGKSASLNLLVS  241 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~  241 (490)
                      .++|.|++|+|||||++.++.
T Consensus         4 kv~ivG~~gvGKStLl~~l~~   24 (184)
T 2zej_A            4 KLMIVGNTGSGKTTLLQQLMK   24 (184)
T ss_dssp             EEEEESCTTSSHHHHHHHHTC
T ss_pred             EEEEECCCCCCHHHHHHHHhc
Confidence            578999999999999999876

>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=93.40  E-value=0.045  Score=46.44  Aligned_cols=22  Identities=32%  Similarity=0.406  Sum_probs=19.8

Q ss_pred             eEEEECCCCCcHHHHHHHHHHH
Q psy200          221 SMYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~  242 (490)
                      .++|.|++|+|||+|++.+...
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            5889999999999999998764

>3tqf_A HPR(Ser) kinase; transferase, hydrolase; 2.80A {Coxiella burnetii}

Probab=93.38  E-value=0.044  Score=47.68  Aligned_cols=25  Identities=28%  Similarity=0.351  Sum_probs=22.4

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHH
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~  242 (490)
                      .+..++|.|++|+||||++..+.+.
T Consensus        15 ~G~gvli~G~SGaGKStlal~L~~r   39 (181)
T 3tqf_A           15 DKMGVLITGEANIGKSELSLALIDR   39 (181)
T ss_dssp             TTEEEEEEESSSSSHHHHHHHHHHT
T ss_pred             CCEEEEEEcCCCCCHHHHHHHHHHc
Confidence            4678999999999999999999874

>2wv9_A Flavivirin protease NS2B regulatory subunit, FLAV protease NS3 catalytic subunit; nucleotide-binding, capsid protein; 2.75A {Murray valley encephalitis virus}

Probab=93.38  E-value=0.13  Score=55.07  Aligned_cols=50  Identities=16%  Similarity=0.244  Sum_probs=31.1

Q ss_pred             CCCeEEEECCCCCcHHHHH-HHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHh
Q psy200          218 TSGSMYISGPPGTGKSASL-NLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNEL  273 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla-~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l  273 (490)
                      .++.+++.|+.|+|||..+ -.+++.+.. ....++++. +    ...+..++...+
T Consensus       240 ~g~dvlv~apTGSGKTl~~ll~il~~l~~-~~~~~lila-P----Tr~La~Q~~~~l  290 (673)
T 2wv9_A          240 KRQLTVLDLHPGAGKTRRILPQIIKDAIQ-KRLRTAVLA-P----TRVVAAEMAEAL  290 (673)
T ss_dssp             TTCEEEECCCTTTTTTTTHHHHHHHHHHH-TTCCEEEEE-S----SHHHHHHHHHHT
T ss_pred             cCCeEEEEeCCCCCHHHHHHHHHHHHHHh-CCCcEEEEc-c----HHHHHHHHHHHH
Confidence            4789999999999999973 555554332 334455553 1    234555555555

>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=93.33  E-value=0.056  Score=51.86  Aligned_cols=24  Identities=33%  Similarity=0.472  Sum_probs=21.2

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHh
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRA  243 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l  243 (490)
                      +..+.|.|++|+|||||++.++ .+
T Consensus       165 G~i~~l~G~sG~GKSTLln~l~-~~  188 (302)
T 2yv5_A          165 GFICILAGPSGVGKSSILSRLT-GE  188 (302)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHH-SC
T ss_pred             CcEEEEECCCCCCHHHHHHHHH-Hh
Confidence            4578899999999999999998 54

>1f2t_A RAD50 ABC-ATPase; DNA double-strand break repair, replication; 1.60A {Pyrococcus furiosus} SCOP: c.37.1.12 PDB: 1f2u_A* 1us8_A*

Probab=93.32  E-value=0.049  Score=46.31  Aligned_cols=25  Identities=32%  Similarity=0.481  Sum_probs=21.8

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHh
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRA  243 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l  243 (490)
                      .+..+|+||.|+|||+++.++.-.+
T Consensus        23 ~g~~~I~G~NGsGKStil~Ai~~~l   47 (149)
T 1f2t_A           23 EGINLIIGQNGSGKSSLLDAILVGL   47 (149)
T ss_dssp             SEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHH
Confidence            4578899999999999999997655

>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=93.30  E-value=0.064  Score=56.61  Aligned_cols=37  Identities=14%  Similarity=0.241  Sum_probs=28.7

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEe
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYIN  255 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~  255 (490)
                      .+..|+|+|.+|+||||+++.+++.+.. .++.++.++
T Consensus        51 ~g~lIvLtGlsGSGKSTlAr~La~~L~~-~G~~~v~lD   87 (630)
T 1x6v_B           51 RGCTVWLTGLSGAGKTTVSMALEEYLVC-HGIPCYTLD   87 (630)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHHHHHH-TTCCEEEES
T ss_pred             CCCEEEEEeCCCCCHHHHHHHHHHHHHh-cCCeEEEec
Confidence            4567899999999999999999998731 235556654

>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=93.28  E-value=0.043  Score=46.47  Aligned_cols=23  Identities=30%  Similarity=0.424  Sum_probs=20.3

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHh
Q psy200          221 SMYISGPPGTGKSASLNLLVSRA  243 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~l  243 (490)
                      .++|.|++|+|||+|++.+....
T Consensus         5 ~i~v~G~~~~GKssl~~~l~~~~   27 (166)
T 2ce2_X            5 KLVVVGAGGVGKSALTIQLIQNH   27 (166)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHSS
T ss_pred             EEEEECCCCCCHHHHHHHHHhCc
Confidence            58899999999999999998653

>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=93.26  E-value=0.046  Score=47.01  Aligned_cols=23  Identities=26%  Similarity=0.527  Sum_probs=20.0

Q ss_pred             CeEEEECCCCCcHHHHHHHHHHH
Q psy200          220 GSMYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       220 ~~ill~GppGtGKTtla~~l~~~  242 (490)
                      -.++|.|++|+|||+|++.+...
T Consensus         5 ~ki~i~G~~~vGKSsl~~~l~~~   27 (175)
T 2nzj_A            5 YRVVLLGDPGVGKTSLASLFAGK   27 (175)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHCC
T ss_pred             EEEEEECCCCccHHHHHHHHhcC
Confidence            36889999999999999998754

>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=93.21  E-value=0.05  Score=46.93  Aligned_cols=23  Identities=30%  Similarity=0.407  Sum_probs=20.4

Q ss_pred             CeEEEECCCCCcHHHHHHHHHHH
Q psy200          220 GSMYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       220 ~~ill~GppGtGKTtla~~l~~~  242 (490)
                      -.++|.|++|+|||+|++.+...
T Consensus         8 ~~i~v~G~~~~GKSsli~~l~~~   30 (177)
T 1wms_A            8 FKVILLGDGGVGKSSLMNRYVTN   30 (177)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHS
T ss_pred             eEEEEECCCCCCHHHHHHHHHcC
Confidence            46889999999999999999764

>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=93.21  E-value=0.039  Score=53.04  Aligned_cols=27  Identities=33%  Similarity=0.505  Sum_probs=23.8

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHh
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRA  243 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l  243 (490)
                      ..+..+.|+||.|+|||||++.++..+
T Consensus        78 ~~Ge~vaivG~sGsGKSTLl~ll~gl~  104 (306)
T 3nh6_A           78 MPGQTLALVGPSGAGKSTILRLLFRFY  104 (306)
T ss_dssp             CTTCEEEEESSSCHHHHHHHHHHTTSS
T ss_pred             cCCCEEEEECCCCchHHHHHHHHHcCC
Confidence            467789999999999999999998765

>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=93.21  E-value=0.05  Score=46.23  Aligned_cols=23  Identities=26%  Similarity=0.304  Sum_probs=20.4

Q ss_pred             CeEEEECCCCCcHHHHHHHHHHH
Q psy200          220 GSMYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       220 ~~ill~GppGtGKTtla~~l~~~  242 (490)
                      ..++|.|++|+|||+|++.+...
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            46889999999999999999865

>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=93.20  E-value=0.05  Score=46.40  Aligned_cols=23  Identities=26%  Similarity=0.362  Sum_probs=20.2

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHh
Q psy200          221 SMYISGPPGTGKSASLNLLVSRA  243 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~l  243 (490)
                      .++|.|++|+|||+|++.+...-
T Consensus         5 ~i~v~G~~~~GKssli~~l~~~~   27 (170)
T 1ek0_A            5 KLVLLGEAAVGKSSIVLRFVSND   27 (170)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHhcCC
Confidence            58899999999999999998653

>2qm8_A GTPase/ATPase; G protein, G3E, metallochaperone, chaperone; HET: MSE; 1.70A {Methylobacterium extorquens} SCOP: c.37.1.10 PDB: 2qm7_A*

Probab=93.19  E-value=0.062  Score=52.45  Aligned_cols=28  Identities=32%  Similarity=0.415  Sum_probs=24.5

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      ..+..+.|.|++|+|||||++.++..+.
T Consensus        53 ~~g~~v~i~G~~GaGKSTLl~~l~g~~~   80 (337)
T 2qm8_A           53 GRAIRVGITGVPGVGKSTTIDALGSLLT   80 (337)
T ss_dssp             CCSEEEEEECCTTSCHHHHHHHHHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHhhh
Confidence            4667888999999999999999988764

>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=93.17  E-value=0.054  Score=56.19  Aligned_cols=27  Identities=19%  Similarity=0.255  Sum_probs=23.9

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      ....|+|+|.||+||||+++.+++.++
T Consensus        34 ~~~lIvlvGlpGSGKSTia~~La~~L~   60 (520)
T 2axn_A           34 SPTVIVMVGLPARGKTYISKKLTRYLN   60 (520)
T ss_dssp             CCEEEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHh
Confidence            345789999999999999999999875

>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=93.16  E-value=0.042  Score=52.42  Aligned_cols=28  Identities=25%  Similarity=0.504  Sum_probs=24.0

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      ..+..+.|.||.|+|||||++.++..+.
T Consensus        62 ~~Ge~~~i~G~NGsGKSTLlk~l~Gl~~   89 (290)
T 2bbs_A           62 ERGQLLAVAGSTGAGKTSLLMMIMGELE   89 (290)
T ss_dssp             CTTCEEEEEESTTSSHHHHHHHHTTSSC
T ss_pred             cCCCEEEEECCCCCcHHHHHHHHhcCCC
Confidence            3667889999999999999999987653

>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=93.16  E-value=0.052  Score=46.41  Aligned_cols=23  Identities=13%  Similarity=0.089  Sum_probs=20.4

Q ss_pred             CeEEEECCCCCcHHHHHHHHHHH
Q psy200          220 GSMYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       220 ~~ill~GppGtGKTtla~~l~~~  242 (490)
                      -.++|.|++|+|||+|++.+...
T Consensus         7 ~~i~v~G~~~~GKssli~~l~~~   29 (170)
T 1z08_A            7 FKVVLLGEGCVGKTSLVLRYCEN   29 (170)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHC
T ss_pred             eEEEEECcCCCCHHHHHHHHHcC
Confidence            36889999999999999999865

>2pjz_A Hypothetical protein ST1066; ATP binding protein, structural genomics, NPPSFA; 1.90A {Sulfolobus tokodaii}

Probab=93.15  E-value=0.044  Score=51.51  Aligned_cols=25  Identities=28%  Similarity=0.476  Sum_probs=22.3

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHh
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRA  243 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l  243 (490)
                      +..+.|.||.|+|||||++.++..+
T Consensus        30 Ge~~~i~G~NGsGKSTLlk~l~Gl~   54 (263)
T 2pjz_A           30 GEKVIILGPNGSGKTTLLRAISGLL   54 (263)
T ss_dssp             SSEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CEEEEEECCCCCCHHHHHHHHhCCC
Confidence            6688899999999999999998654

>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=93.15  E-value=0.052  Score=46.34  Aligned_cols=24  Identities=25%  Similarity=0.346  Sum_probs=20.9

Q ss_pred             CeEEEECCCCCcHHHHHHHHHHHh
Q psy200          220 GSMYISGPPGTGKSASLNLLVSRA  243 (490)
Q Consensus       220 ~~ill~GppGtGKTtla~~l~~~l  243 (490)
                      -.++|.|++|+|||+|++.+...-
T Consensus         7 ~~i~v~G~~~~GKSsli~~l~~~~   30 (170)
T 1z0j_A            7 LKVCLLGDTGVGKSSIMWRFVEDS   30 (170)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHSC
T ss_pred             eEEEEECcCCCCHHHHHHHHHcCC
Confidence            368899999999999999998753

>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=93.15  E-value=0.023  Score=53.35  Aligned_cols=27  Identities=30%  Similarity=0.354  Sum_probs=23.7

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      .+..|+|.|+.|+||||+++.+++.+.
T Consensus        23 ~~~~I~ieG~~GsGKST~~~~L~~~l~   49 (263)
T 1p5z_B           23 RIKKISIEGNIAAGKSTFVNILKQLCE   49 (263)
T ss_dssp             CCEEEEEECSTTSSHHHHHTTTGGGCT
T ss_pred             CceEEEEECCCCCCHHHHHHHHHHhcC
Confidence            456788999999999999999998873

>3o47_A ADP-ribosylation factor GTPase-activating protein ribosylation factor 1; structural genomics consortium, GTPase activation; HET: GDP; 2.80A {Homo sapiens}

Probab=93.14  E-value=0.28  Score=47.57  Aligned_cols=21  Identities=24%  Similarity=0.308  Sum_probs=18.8

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q psy200          221 SMYISGPPGTGKSASLNLLVS  241 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~  241 (490)
                      .|+|.|.+|+|||+|++.+..
T Consensus       167 kI~ivG~~~vGKSsLl~~l~~  187 (329)
T 3o47_A          167 RILMVGLDAAGKTTILYKLKL  187 (329)
T ss_dssp             EEEEEESTTSSHHHHHHHTCS
T ss_pred             eEEEECCCCccHHHHHHHHhC
Confidence            589999999999999998854

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A*

Probab=93.14  E-value=0.5  Score=50.62  Aligned_cols=25  Identities=24%  Similarity=0.361  Sum_probs=20.4

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHh
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRA  243 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l  243 (490)
                      ++.++|.+|.|+|||..+-.++.+.
T Consensus        28 g~~~iv~~~TGsGKTl~~~~~i~~~   52 (696)
T 2ykg_A           28 GKNTIICAPTGCGKTFVSLLICEHH   52 (696)
T ss_dssp             TCCEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CCCEEEEcCCCchHHHHHHHHHHHH
Confidence            4679999999999999887766543

>4dhe_A Probable GTP-binding protein ENGB; melioidosis, RAS-like GTPase, cell division, cell cycle, SEP GTP-binding; 2.20A {Burkholderia thailandensis}

Probab=93.11  E-value=0.31  Score=43.71  Aligned_cols=25  Identities=24%  Similarity=0.492  Sum_probs=21.6

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHH
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~  242 (490)
                      ....|+|.|.+|+|||+|++.+...
T Consensus        28 ~~~~i~v~G~~~~GKSslin~l~~~   52 (223)
T 4dhe_A           28 VQPEIAFAGRSNAGKSTAINVLCNQ   52 (223)
T ss_dssp             CSCEEEEEESCHHHHHHHHHHHTTC
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHhCC
Confidence            3457889999999999999999765

>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=93.07  E-value=0.073  Score=47.38  Aligned_cols=84  Identities=10%  Similarity=0.095  Sum_probs=47.6

Q ss_pred             eEEEE-CCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCe
Q psy200          221 SMYIS-GPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFDTKHKS  299 (490)
Q Consensus       221 ~ill~-GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~  299 (490)
                      .+.|+ +.+|+||||++-.++..+.. .+.+++.+++....+...++..-  .-...........+.+.+.....   ..
T Consensus         3 vi~v~s~kgG~GKTt~a~~la~~la~-~g~~vlliD~D~~~~~~~~~~~~--~~~~~~~~~~~~~l~~~l~~l~~---~y   76 (206)
T 4dzz_A            3 VISFLNPKGGSGKTTAVINIATALSR-SGYNIAVVDTDPQMSLTNWSKAG--KAAFDVFTAASEKDVYGIRKDLA---DY   76 (206)
T ss_dssp             EEEECCSSTTSSHHHHHHHHHHHHHH-TTCCEEEEECCTTCHHHHHHTTS--CCSSEEEECCSHHHHHTHHHHTT---TS
T ss_pred             EEEEEeCCCCccHHHHHHHHHHHHHH-CCCeEEEEECCCCCCHHHHHhcC--CCCCcEEecCcHHHHHHHHHhcC---CC
Confidence            44455 77899999999999999874 45688888876544433332200  00000000112444444444322   24


Q ss_pred             EEEEEecCccc
Q psy200          300 ILLILDEIDAL  310 (490)
Q Consensus       300 ~vI~IDEid~l  310 (490)
                      -+||||=-..+
T Consensus        77 D~viiD~~~~~   87 (206)
T 4dzz_A           77 DFAIVDGAGSL   87 (206)
T ss_dssp             SEEEEECCSSS
T ss_pred             CEEEEECCCCC
Confidence            48999976665

>3la6_A Tyrosine-protein kinase WZC; P-loop protein, nucleotide binding domain, walker A motif, B protein kinase, oligomerization; HET: ADP; 3.20A {Escherichia coli}

Probab=93.06  E-value=0.2  Score=47.54  Aligned_cols=59  Identities=14%  Similarity=0.220  Sum_probs=42.7

Q ss_pred             HHHHHHHHHHHHhhhccCCCCeEEEEC-CCCCcHHHHHHHHHHHhhhcCCceEEEEeccCC
Q psy200          200 EVQLEGIRQFLLGHVNNETSGSMYISG-PPGTGKSASLNLLVSRAEIKDAFKTIYINCNSV  259 (490)
Q Consensus       200 e~~~~~l~~~L~~~~~~~~~~~ill~G-ppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~  259 (490)
                      .+.+..|+..|.........+.|+|+| -+|+||||++-.++..+.. .+.+++.+++..-
T Consensus        73 ~Ea~r~lrt~l~~~~~~~~~kvI~vts~kgG~GKTtva~nLA~~lA~-~G~rVLLID~D~~  132 (286)
T 3la6_A           73 IEAIRSLRTSLHFAMMQAQNNVLMMTGVSPSIGMTFVCANLAAVISQ-TNKRVLLIDCDMR  132 (286)
T ss_dssp             HHHHHHHHHHHHHHSTTTTCCEEEEEESSSSSSHHHHHHHHHHHHHT-TTCCEEEEECCTT
T ss_pred             HHHHHHHHHHHhhhccCCCCeEEEEECCCCCCcHHHHHHHHHHHHHh-CCCCEEEEeccCC
Confidence            466677777776544445567777666 5799999999999998863 3567888887654

>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA dependent ATPase, RNA helicase; HET: ANP; 1.91A {Saccharomyces cerevisiae S288C}

Probab=93.05  E-value=0.49  Score=49.59  Aligned_cols=19  Identities=21%  Similarity=0.363  Sum_probs=16.4

Q ss_pred             CCCeEEEECCCCCcHHHHH
Q psy200          218 TSGSMYISGPPGTGKSASL  236 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla  236 (490)
                      .++.+++.+|.|+|||...
T Consensus        59 ~~~dvlv~apTGsGKTl~~   77 (579)
T 3sqw_A           59 EDHDVIARAKTGTGKTFAF   77 (579)
T ss_dssp             SSEEEEEECCTTSCHHHHH
T ss_pred             CCCeEEEEcCCCcHHHHHH
Confidence            4678999999999999853

>2o8b_B DNA mismatch repair protein MSH6; DNA damage response, somatic hypermutat protein-DNA complex, DNA mispair, cancer; HET: DNA ADP; 2.75A {Homo sapiens} PDB: 2o8c_B* 2o8d_B* 2o8e_B* 2o8f_B*

Probab=93.04  E-value=0.02  Score=64.25  Aligned_cols=21  Identities=24%  Similarity=0.365  Sum_probs=19.7

Q ss_pred             CCeEEEECCCCCcHHHHHHHH
Q psy200          219 SGSMYISGPPGTGKSASLNLL  239 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l  239 (490)
                      +..++|+||.|+||||+++.+
T Consensus       789 g~i~~ItGpNgsGKSTlLr~i  809 (1022)
T 2o8b_B          789 AYCVLVTGPNMGGKSTLMRQA  809 (1022)
T ss_dssp             CCEEEEECCTTSSHHHHHHHH
T ss_pred             CcEEEEECCCCCChHHHHHHH
Confidence            578999999999999999998

>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=93.03  E-value=0.035  Score=54.56  Aligned_cols=27  Identities=26%  Similarity=0.502  Sum_probs=23.4

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHh
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRA  243 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l  243 (490)
                      ..+..+.|.||.|+|||||++.++..+
T Consensus        29 ~~Ge~~~llGpnGsGKSTLLr~iaGl~   55 (353)
T 1oxx_K           29 ENGERFGILGPSGAGKTTFMRIIAGLD   55 (353)
T ss_dssp             CTTCEEEEECSCHHHHHHHHHHHHTSS
T ss_pred             CCCCEEEEECCCCCcHHHHHHHHhCCC
Confidence            356788899999999999999998754

>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=93.02  E-value=0.055  Score=46.77  Aligned_cols=25  Identities=24%  Similarity=0.339  Sum_probs=21.4

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHh
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRA  243 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l  243 (490)
                      ...++|.|++|+|||+|++.+....
T Consensus         8 ~~~i~v~G~~~~GKSsli~~l~~~~   32 (182)
T 1ky3_A            8 ILKVIILGDSGVGKTSLMHRYVNDK   32 (182)
T ss_dssp             EEEEEEECCTTSSHHHHHHHHHHSC
T ss_pred             eEEEEEECCCCCCHHHHHHHHHhCc
Confidence            4578899999999999999997653

>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=93.02  E-value=0.055  Score=46.02  Aligned_cols=22  Identities=32%  Similarity=0.404  Sum_probs=19.9

Q ss_pred             eEEEECCCCCcHHHHHHHHHHH
Q psy200          221 SMYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~  242 (490)
                      .++|.|.+|+|||+|++.+...
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            5889999999999999999864

>2lkc_A Translation initiation factor IF-2; NMR {Geobacillus stearothermophilus} PDB: 2lkd_A*

Probab=93.01  E-value=0.068  Score=46.09  Aligned_cols=25  Identities=20%  Similarity=0.250  Sum_probs=21.7

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHH
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~  242 (490)
                      ....|+|.|++|+|||+|++.+...
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            4567899999999999999999763

>3hdt_A Putative kinase; structura genomics, PSI-2, protein structure initiative, midwest CENT structural genomics, MCSG; 2.79A {Clostridium symbiosum atcc 14940}

Probab=92.99  E-value=0.082  Score=48.30  Aligned_cols=26  Identities=15%  Similarity=0.047  Sum_probs=23.5

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      ...|.|.|++|+|||++++.|++.++
T Consensus        14 ~~iI~i~g~~gsGk~~i~~~la~~lg   39 (223)
T 3hdt_A           14 NLIITIEREYGSGGRIVGKKLAEELG   39 (223)
T ss_dssp             CEEEEEEECTTSCHHHHHHHHHHHHT
T ss_pred             CeEEEEeCCCCCCHHHHHHHHHHHcC
Confidence            45788999999999999999999986

>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=92.96  E-value=0.062  Score=51.52  Aligned_cols=25  Identities=28%  Similarity=0.341  Sum_probs=21.4

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHh
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRA  243 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l  243 (490)
                      +..+.|.|++|+|||||++.++...
T Consensus       169 geiv~l~G~sG~GKSTll~~l~g~~  193 (301)
T 1u0l_A          169 GKISTMAGLSGVGKSSLLNAINPGL  193 (301)
T ss_dssp             SSEEEEECSTTSSHHHHHHHHSTTC
T ss_pred             CCeEEEECCCCCcHHHHHHHhcccc
Confidence            4578899999999999999997643

>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=92.95  E-value=0.051  Score=46.37  Aligned_cols=22  Identities=32%  Similarity=0.483  Sum_probs=19.7

Q ss_pred             eEEEECCCCCcHHHHHHHHHHH
Q psy200          221 SMYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~  242 (490)
                      .++|.|++|+|||+|++.+...
T Consensus         5 ~i~v~G~~~~GKssli~~l~~~   26 (170)
T 1g16_A            5 KILLIGDSGVGKSCLLVRFVED   26 (170)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHC
T ss_pred             EEEEECcCCCCHHHHHHHHHhC
Confidence            5889999999999999999754

>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=92.94  E-value=0.054  Score=53.89  Aligned_cols=27  Identities=22%  Similarity=0.324  Sum_probs=23.5

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHh
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRA  243 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l  243 (490)
                      ..+..+.|.||.|+|||||++.++..+
T Consensus        45 ~~Ge~~~llGpsGsGKSTLLr~iaGl~   71 (390)
T 3gd7_A           45 SPGQRVGLLGRTGSGKSTLLSAFLRLL   71 (390)
T ss_dssp             CTTCEEEEEESTTSSHHHHHHHHHTCS
T ss_pred             cCCCEEEEECCCCChHHHHHHHHhCCC
Confidence            467789999999999999999998654

>3o8b_A HCV NS3 protease/helicase; ntpase, RNA, translocation, protein-RNA compl protease/ntpase/helicase, hydrolase; 1.95A {Hepatitis c virus} PDB: 3o8c_A* 3o8d_A* 3o8r_A* 4b71_A* 4b73_A* 4b74_A* 4b76_A* 4b75_A* 4a92_A* 1cu1_A 4b6e_A* 4b6f_A* 2zjo_A* 1a1v_A* 1hei_A 3kqn_A* 3kql_A* 3kqu_A* 3kqh_A 3kqk_A ...

Probab=92.93  E-value=0.14  Score=54.46  Aligned_cols=22  Identities=23%  Similarity=0.363  Sum_probs=17.4

Q ss_pred             CCCeEEEECCCCCcHHHHHHHH
Q psy200          218 TSGSMYISGPPGTGKSASLNLL  239 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l  239 (490)
                      ..+.+++.|+.|+|||+.+-..
T Consensus       231 ~~~~vlv~ApTGSGKT~a~~l~  252 (666)
T 3o8b_A          231 SFQVAHLHAPTGSGKSTKVPAA  252 (666)
T ss_dssp             SCEEEEEECCTTSCTTTHHHHH
T ss_pred             cCCeEEEEeCCchhHHHHHHHH
Confidence            4567999999999999765543

>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=92.92  E-value=0.056  Score=47.69  Aligned_cols=25  Identities=24%  Similarity=0.449  Sum_probs=20.7

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHH
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~  242 (490)
                      ....++|.|++|+|||+|++.+...
T Consensus        22 ~~~ki~~vG~~~vGKSsli~~l~~~   46 (190)
T 1m2o_B           22 KHGKLLFLGLDNAGKTTLLHMLKND   46 (190)
T ss_dssp             --CEEEEEESTTSSHHHHHHHHHHS
T ss_pred             CccEEEEECCCCCCHHHHHHHHhcC
Confidence            3457899999999999999999863

>2erx_A GTP-binding protein DI-RAS2; GTP hydrolysis, transport protein; HET: GDP; 1.65A {Homo sapiens} SCOP: c.37.1.8

Probab=92.90  E-value=0.056  Score=46.17  Aligned_cols=22  Identities=27%  Similarity=0.357  Sum_probs=19.7

Q ss_pred             eEEEECCCCCcHHHHHHHHHHH
Q psy200          221 SMYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~  242 (490)
                      .++|.|++|+|||+|++.+...
T Consensus         5 ~i~v~G~~~~GKssli~~l~~~   26 (172)
T 2erx_A            5 RVAVFGAGGVGKSSLVLRFVKG   26 (172)
T ss_dssp             EEEEECCTTSSHHHHHHHHHTC
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            5889999999999999999763

>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=92.89  E-value=0.059  Score=45.94  Aligned_cols=23  Identities=22%  Similarity=0.239  Sum_probs=20.2

Q ss_pred             CeEEEECCCCCcHHHHHHHHHHH
Q psy200          220 GSMYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       220 ~~ill~GppGtGKTtla~~l~~~  242 (490)
                      -.++|.|.+|+|||+|++.+...
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            36889999999999999999864

>2www_A Methylmalonic aciduria type A protein, mitochondrial; transport protein, nucleotide-binding; HET: GDP 2PE; 2.64A {Homo sapiens}

Probab=92.87  E-value=0.13  Score=50.32  Aligned_cols=26  Identities=31%  Similarity=0.470  Sum_probs=22.9

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      ...+.|+|+||+|||||++.+...+.
T Consensus        74 ~~~v~lvG~pgaGKSTLln~L~~~~~   99 (349)
T 2www_A           74 AFRVGLSGPPGAGKSTFIEYFGKMLT   99 (349)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             ceEEEEEcCCCCCHHHHHHHHHHHhh
Confidence            56788999999999999999998654

>2gks_A Bifunctional SAT/APS kinase; transferase, sulfurylase; HET: ADP; 2.31A {Aquifex aeolicus}

Probab=92.83  E-value=0.089  Score=54.86  Aligned_cols=38  Identities=18%  Similarity=0.365  Sum_probs=28.7

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEe
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYIN  255 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~  255 (490)
                      ..+..++|+|.+|+||||+++.+++.+... +..+.+++
T Consensus       370 ~~~~~I~l~G~~GsGKSTia~~La~~L~~~-G~~~~~ld  407 (546)
T 2gks_A          370 KQGFCVWLTGLPCAGKSTIAEILATMLQAR-GRKVTLLD  407 (546)
T ss_dssp             GCCEEEEEECSTTSSHHHHHHHHHHHHHHT-TCCEEEEC
T ss_pred             ccceEEEccCCCCCCHHHHHHHHHHHhhhc-CCeEEEEC
Confidence            345678899999999999999999987532 23455554

>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=92.83  E-value=0.053  Score=46.99  Aligned_cols=24  Identities=42%  Similarity=0.607  Sum_probs=20.9

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHH
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~  242 (490)
                      +..++|.|++|+|||||++.+...
T Consensus         4 ~~ki~ivG~~g~GKStLl~~l~~~   27 (172)
T 2gj8_A            4 GMKVVIAGRPNAGKSSLLNALAGR   27 (172)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHHTS
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC
Confidence            446889999999999999999764

>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=92.83  E-value=0.057  Score=46.14  Aligned_cols=21  Identities=24%  Similarity=0.381  Sum_probs=18.7

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q psy200          221 SMYISGPPGTGKSASLNLLVS  241 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~  241 (490)
                      .++|.|++|+|||+|++.+..
T Consensus         4 ki~ivG~~~~GKSsli~~l~~   24 (169)
T 3q85_A            4 KVMLVGESGVGKSTLAGTFGG   24 (169)
T ss_dssp             EEEEECSTTSSHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHHh
Confidence            478999999999999999863

>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=92.79  E-value=0.06  Score=47.05  Aligned_cols=23  Identities=22%  Similarity=0.278  Sum_probs=20.5

Q ss_pred             CeEEEECCCCCcHHHHHHHHHHH
Q psy200          220 GSMYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       220 ~~ill~GppGtGKTtla~~l~~~  242 (490)
                      -.|+|.|++|+|||+|++.+...
T Consensus        12 ~ki~v~G~~~~GKSsli~~l~~~   34 (195)
T 3bc1_A           12 IKFLALGDSGVGKTSVLYQYTDG   34 (195)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHhcC
Confidence            46889999999999999999864

---

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	490
d1fnna2	276	c.37.1.20 (A:1-276) CDC6, N-domain {Archaeon Pyrob	1e-20
d1w5sa2	287	c.37.1.20 (A:7-293) CDC6-like protein APE0152, N-t	7e-16
d1njfa_	239	c.37.1.20 (A:) delta prime subunit of DNA polymera	2e-07
d1sxjd2	237	c.37.1.20 (D:26-262) Replication factor C2 {Baker'	9e-07
d1sxje2	252	c.37.1.20 (E:4-255) Replication factor C5 {Baker's	1e-04
d2fnaa2	283	c.37.1.20 (A:1-283) Archaeal ATPase SSO1545 {Sulfo	1e-04
d1w44a_	321	c.37.1.11 (A:) NTPase P4 {Bacteriophage phi-12 [Ta	4e-04
d1sxja2	253	c.37.1.20 (A:295-547) Replication factor C1 {Baker	0.004

>d1fnna2 c.37.1.20 (A:1-276) CDC6, N-domain {Archaeon Pyrobaculum aerophilum [TaxId: 13773]} Length = 276

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]

 Score = 89.5 bits (220), Expect = 1e-20
 Identities = 53/245 (21%), Positives = 101/245 (41%), Gaps = 13/245 (5%)

Query: 195 ELPGREVQLEGIRQFLLGHVNN--ETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTI 252
            LP RE QL+ +   L   + N         + G PGTGK+ +L  L    + K   + +
Sbjct: 17  RLPHREQQLQQLDILLGNWLRNPGHHYPRATLLGRPGTGKTVTLRKLWELYKDKTTARFV 76

Query: 253 YINCNSVRNAASVYETIVNE--LKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDAL 310
           YIN    RN  ++   I     +     G S    L  ++++   +   + L+LD+   L
Sbjct: 77  YINGFIYRNFTAIIGEIARSLNIPFPRRGLSRDEFLALLVEHLRERDLYMFLVLDDAFNL 136

Query: 311 ESRKQTILYTIFEW-PSIPGSKLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSR 369
                +    + +    +   ++ LV V +   + + + P  +    +   ++ F+PY++
Sbjct: 137 APDILSTFIRLGQEADKLGAFRIALVIVGHNDAVLNNLDPSTRGI--MGKYVIRFSPYTK 194

Query: 370 EQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVS------GDIRKAIDITNHLIDLTY 423
           +QI +I+  + K       ++   LQ++A    A +      GD R AIDI         
Sbjct: 195 DQIFDILLDRAKAGLAEGSYSEDILQMIADITGAQTPLDTNRGDARLAIDILYRSAYAAQ 254

Query: 424 DNVKE 428
            N ++
Sbjct: 255 QNGRK 259

>d1w5sa2 c.37.1.20 (A:7-293) CDC6-like protein APE0152, N-terminal domain {Aeropyrum pernix [TaxId: 56636]} Length = 287

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]

 Score = 75.9 bits (185), Expect = 7e-16
 Identities = 40/250 (16%), Positives = 90/250 (36%), Gaps = 23/250 (9%)

Query: 195 ELPGREVQLEGIRQFLLGHVNNETSGSM-----YISGPPGTGKSASLNLLVSR-----AE 244
           EL  R  + E + +  L  + +    S         G  G GK+      V R     A+
Sbjct: 17  ELRVRRGEAEALARIYLNRLLSGAGLSDVNMIYGSIGRVGIGKTTLAKFTVKRVSEAAAK 76

Query: 245 IKDAFKTIYINCNSVRNAASVYETIVNE--LKLKPGGKSERHQLGAILKYFDTKHKSILL 302
                K  Y+N  +  N  ++   IV +    ++  G      L A++     ++  +L+
Sbjct: 77  EGLTVKQAYVNAFNAPNLYTILSLIVRQTGYPIQVRGAPALDILKALVDNLYVENHYLLV 136

Query: 303 ILDEIDALESRKQTILYTIFEW--------PSIPGSKLVLVGVANALDLTDRMLPRLQAN 354
           ILDE  ++ S  +     ++               +++  + VA+ +     M  ++   
Sbjct: 137 ILDEFQSMLSSPRIAAEDLYTLLRVHEEIPSRDGVNRIGFLLVASDVRALSYMREKIPQV 196

Query: 355 VTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVA---AVSGDIRKA 411
            +     ++   Y   ++  I+ Q+ +   +  ++    L+L++          G  R+A
Sbjct: 197 ESQIGFKLHLPAYKSRELYTILEQRAELGLRDTVWEPRHLELISDVYGEDKGGDGSARRA 256

Query: 412 IDITNHLIDL 421
           I       ++
Sbjct: 257 IVALKMACEM 266

>d1njfa_ c.37.1.20 (A:) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]} Length = 239

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]

 Score = 49.7 bits (118), Expect = 2e-07
 Identities = 45/252 (17%), Positives = 84/252 (33%), Gaps = 30/252 (11%)

Query: 195 ELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYI 254
           ++ G+E  L  +   L          +   SG  G GK++   L      +         
Sbjct: 13  DVVGQEHVLTALANGLS---LGRIHHAYLFSGTRGVGKTSIARL--LAKGLNCETGITAT 67

Query: 255 NCNSVRNAASVYE-TIVNELKLKPGGKSERHQLGAILKYFDTK---HKSILLILDEIDAL 310
            C    N   + +   V+ +++    +++      +L          +  + ++DE+  L
Sbjct: 68  PCGVCDNCREIEQGRFVDLIEIDAASRTKVEDTRDLLDNVQYAPARGRFKVYLIDEVHML 127

Query: 311 ESRKQTILYTIFEWPSIPGSKLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSRE 370
                  L    E P     K +L     A     ++   +  +  LQ  L         
Sbjct: 128 SRHSFNALLKTLEEPP-EHVKFLL-----ATTDPQKLPVTIL-SRCLQFHLKALDVEQIR 180

Query: 371 QILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITNHLIDLTYDNVKENG 430
             LE I  +     +       ALQLLA    A  G +R A+ +T+  I         +G
Sbjct: 181 HQLEHILNE-----EHIAHEPRALQLLA---RAAEGSLRDALSLTDQAI------ASGDG 226

Query: 431 EVTGIGLKEVLG 442
           +V+   +  +LG
Sbjct: 227 QVSTQAVSAMLG 238

>d1sxjd2 c.37.1.20 (D:26-262) Replication factor C2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 237

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]

 Score = 47.8 bits (112), Expect = 9e-07
 Identities = 39/249 (15%), Positives = 82/249 (32%), Gaps = 24/249 (9%)

Query: 195 ELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYI 254
           E+  ++  +  +++ L     +     M   GPPGTGK++++  L       D  K+  +
Sbjct: 13  EVTAQDHAVTVLKKTL----KSANLPHMLFYGPPGTGKTSTILALTKELYGPDLMKSRIL 68

Query: 255 NCNSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRK 314
             N+          +  ++K        +     +  Y    +K I  ILDE D++ +  
Sbjct: 69  ELNASDE--RGISIVREKVKNFARLTVSKPSKHDLENYPCPPYKII--ILDEADSMTADA 124

Query: 315 QTILYTIFEWPSIPGSKLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILE 374
           Q+ L    E  S                         +    L      F   + +    
Sbjct: 125 QSALRRTMETYSGVTRF------------CLICNYVTRIIDPLASQCSKFRFKALDASNA 172

Query: 375 IISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITNHLIDLTYDNVKENGEVTG 434
           I   +     +    +   L+ +       +GD+R+ I +           + +   +T 
Sbjct: 173 IDRLRFISEQENVKCDDGVLERIL---DISAGDLRRGITLLQSASKGA-QYLGDGKNITS 228

Query: 435 IGLKEVLGV 443
             ++E+ GV
Sbjct: 229 TQVEELAGV 237

>d1sxje2 c.37.1.20 (E:4-255) Replication factor C5 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 252

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]

 Score = 41.7 bits (96), Expect = 1e-04
 Identities = 29/230 (12%), Positives = 64/230 (27%), Gaps = 18/230 (7%)

Query: 195 ELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKT--- 251
            L   E     ++              + + GP GTGK      L+        ++    
Sbjct: 12  ALSHNEELTNFLKSLSD---QPRDLPHLLLYGPNGTGKKTRCMALLESIFGPGVYRLKID 68

Query: 252 ---IYINCNSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEID 308
                   N       V      E+     G ++R  +  +LK      +  +   D  D
Sbjct: 69  VRQFVTASNRKLELNVVSSPYHLEITPSDMGNNDRIVIQELLKEVAQMEQ--VDFQDSKD 126

Query: 309 ALESRKQTILYTIFEWPSIPGSKLVL----VGVANALDLTDRMLPRLQANVTLQPTLMNF 364
            L  R + ++       +      +         N   +                 L+  
Sbjct: 127 GLAHRYKCVIINEANSLTKDAQAALRRTMEKYSKNIRLIMVCDSMSPIIAPIKSQCLLIR 186

Query: 365 APYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDI 414
            P   +  +  I   +   ++  +     L+ +A    A +G++R ++ +
Sbjct: 187 CPAPSDSEISTILSDVVTNERIQLETKDILKRIA---QASNGNLRVSLLM 233

>d2fnaa2 c.37.1.20 (A:1-283) Archaeal ATPase SSO1545 {Sulfolobus solfataricus [TaxId: 2287]} Length = 283

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]

 Score = 41.6 bits (96), Expect = 1e-04
 Identities = 33/262 (12%), Positives = 75/262 (28%), Gaps = 27/262 (10%)

Query: 177 LLFSEDKPKVEEKAKDSCELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASL 236
           +LF    PK   K     +   RE ++E ++                + G   TGKS+  
Sbjct: 1   MLFDT-SPKDNRK-----DFFDREKEIEKLKGLRAPIT--------LVLGLRRTGKSS-- 44

Query: 237 NLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFDTK 296
            ++       +                  Y+  + EL+ +     +R    ++LK     
Sbjct: 45  -IIKIGINELNLPYIYLDLRKFEERNYISYKDFLLELQKEINKLVKRLP--SLLKALKNI 101

Query: 297 HKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVANALDLTD----RMLPRLQ 352
              +++  +       + +     + E         V++ +  A +L       +LP L 
Sbjct: 102 QGIVIMGNEIKFNWNRKDRLSFANLLESFEQASKDNVIIVLDEAQELVKLRGVNLLPALA 161

Query: 353 ANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAI 412
                   +      S   +L    +             S ++L          +  + +
Sbjct: 162 YAYDNLKRIKFIMSGSEMGLLYDYLRVEDPESPLFGRAFSTVELKPFSRE----EAIEFL 217

Query: 413 DITNHLIDLTYDNVKENGEVTG 434
                  D+ + + +   E  G
Sbjct: 218 RRGFQEADIDFKDYEVVYEKIG 239

>d1w44a_ c.37.1.11 (A:) NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]} Length = 321

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]

 Score = 40.4 bits (94), Expect = 4e-04
 Identities = 26/251 (10%), Positives = 72/251 (28%), Gaps = 41/251 (16%)

Query: 181 EDKPKVEEKAKDSCELP--GREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNL 238
            +   +++  +                + +F         SG + ++G   +GK+  ++ 
Sbjct: 86  VENGFMKQGHRGWLVDLTGELVGCSPVVAEFGGHRY---ASGMVIVTGKGNSGKTPLVHA 142

Query: 239 LVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFDTKHK 298
           L      KD + T+                                 +  I        +
Sbjct: 143 LGEALGGKDKYATV--------RFGEPLSGYN--------TDFNV-FVDDI---ARAMLQ 182

Query: 299 SILLILDEIDAL----------ESRKQTILYTIFEWPSIPGSKLVLVGVA-NALDLTDRM 347
             ++++D +  +              +     + +  ++  S+  +V  + N     D++
Sbjct: 183 HRVIVIDSLKNVIGAAGGNTTSGGISRGAFDLLSDIGAMAASRGCVVIASLNPTSNDDKI 242

Query: 348 LPRLQANVTLQPTLMNFAP--YSREQILEIISQKLKQT--DKFNMFN-ASALQLLAGKVA 402
           +  ++       T +  +       Q+L    + L++        +   S L +   K +
Sbjct: 243 VELVKEASRSNSTSLVISTDVDGEWQVLTRTGEGLQRLTHTLQTSYGEHSVLTIHTSKQS 302

Query: 403 AVSGDIRKAID 413
                  KAI 
Sbjct: 303 GGKQASGKAIQ 313

>d1sxja2 c.37.1.20 (A:295-547) Replication factor C1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 253

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]

 Score = 36.7 bits (83), Expect = 0.004
 Identities = 31/224 (13%), Positives = 72/224 (32%), Gaps = 28/224 (12%)

Query: 221 SMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKPGGK 280
           +  + GPPG GK+ + +L+          +      +     A V   + N         
Sbjct: 54  AAMLYGPPGIGKTTAAHLVAQELGYDILEQNASDVRSKTLLNAGVKNALDN--------M 105

Query: 281 SERHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVANA 340
           S         +  +   K  ++I+DE+D +    +  +  + ++     + L+L+     
Sbjct: 106 SVVGYFKHNEEAQNLNGKHFVIIMDEVDGMSGGDRGGVGQLAQFCRKTSTPLILICNERN 165

Query: 341 LDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGK 400
           L                +P   +         +    +K K            +  L   
Sbjct: 166 LPKMRPFDRVCLDIQFRRPDANSIKSRLMTIAIR---EKFKLDPN-------VIDRLI-- 213

Query: 401 VAAVSGDIRKAIDITNHLI----DLTYDNVKENGEVTGIGLKEV 440
                GDIR+ I++ + +      + ++N+    E++    K +
Sbjct: 214 -QTTRGDIRQVINLLSTISTTTKTINHENIN---EISKAWEKNI 253

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	490
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	99.94
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	99.92
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	99.91
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	99.9
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	99.9
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	99.89
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	99.89
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	99.88
d1lv7a_	256	AAA domain of cell division protein FtsH {Escheric	99.87
d1ixza_	247	AAA domain of cell division protein FtsH {Thermus	99.87
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	99.87
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	99.85
d1e32a2	258	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	99.84
d1sxje2	252	Replication factor C5 {Baker's yeast (Saccharomyce	99.83
d1r6bx2	268	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	99.78
d1r7ra3	265	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	99.73
d1a5ta2	207	delta prime subunit of DNA polymerase III, N-domai	99.7
d1d2na_	246	Hexamerization domain of N-ethylmalemide-sensitive	99.68
d1qvra2	387	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	99.65
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	99.61
d1jbka_	195	ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}	99.57
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	99.56
d1ny5a2	247	Transcriptional activator sigm54 (NtrC1), C-termin	99.56
d1r6bx3	315	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	99.52
d2a5yb3	277	CED-4, NB-ARC domain {Caenorhabditis elegans [TaxI	99.48
d1qvra3	315	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	99.47
d2fnaa2	283	Archaeal ATPase SSO1545 {Sulfolobus solfataricus [	99.45
d1w44a_	321	NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}	99.42
d1um8a_	364	ClpX {Helicobacter pylori [TaxId: 210]}	99.39
d1g8pa_	333	ATPase subunit of magnesium chelatase, BchI {Rhodo	99.37
d2gnoa2	198	gamma subunit of DNA polymerase III, N-domain {The	99.28
d1g41a_	443	HslU {Haemophilus influenzae [TaxId: 727]}	99.17
d1svma_	362	Papillomavirus large T antigen helicase domain {Si	98.81
d1ye8a1	178	Hypothetical kinase-like protein Aq_1292 {Aquifex	98.39
d1gvnb_	273	Plasmid maintenance system epsilon/zeta, toxin zet	98.14
d1a1va1	136	HCV helicase domain {Human hepatitis C virus (HCV)	97.81
d2qy9a2	211	GTPase domain of the signal recognition particle r	97.77
d1w36d1	359	Exodeoxyribonuclease V alpha chain (RecD) {Escheri	97.76
d1j8yf2	211	GTPase domain of the signal sequence recognition p	97.74
d1okkd2	207	GTPase domain of the signal recognition particle r	97.73
d1vmaa2	213	GTPase domain of the signal recognition particle r	97.73
d1ly1a_	152	Polynucleotide kinase, kinase domain {Bacteriophag	97.66
d1ls1a2	207	GTPase domain of the signal sequence recognition p	97.63
d1yj5a2	172	5' polynucleotide kinase-3' phosphatase, C-termina	97.63
d1kaga_	169	Shikimate kinase (AroK) {Escherichia coli [TaxId:	97.61
d2i3ba1	189	Cancer-related NTPase, C1orf57 {Human (Homo sapien	97.6
d1tf7a2	242	Circadian clock protein KaiC {Synechococcus sp. st	97.6
d1lw7a2	192	Transcriptional regulator NadR, ribosylnicotinamid	97.49
d1yksa1	140	YFV helicase domain {Yellow fever virus [TaxId: 11	97.49
d1rkba_	173	Adenylate kinase {Human (Homo sapiens), isoenzyme	97.45
d1m8pa3	183	ATP sulfurylase C-terminal domain {Fungus (Penicil	97.43
d1zp6a1	176	Hypothetical protein Atu3015 {Agrobacterium tumefa	97.4
d1knqa_	171	Gluconate kinase {Escherichia coli [TaxId: 562]}	97.34
d1xp8a1	268	RecA protein, ATPase-domain {Deinococcus radiodura	97.33
d1cr2a_	277	Gene 4 protein (g4p, DNA primase), helicase domain	97.32
d1qhxa_	178	Chloramphenicol phosphotransferase {Streptomyces v	97.3
d2bdta1	176	Hypothetical protein BH3686 {Bacillus halodurans [	97.28
d1y63a_	174	Probable kinase LmjF30.1890 {Leishmania major [Tax	97.28
d1u94a1	263	RecA protein, ATPase-domain {Escherichia coli [Tax	97.25
d1qf9a_	194	UMP/CMP kinase {Dictyostelium discoideum [TaxId: 4	97.24
d1wp9a1	200	putative ATP-dependent RNA helicase PF2015 {Pyroco	97.24
d1viaa_	161	Shikimate kinase (AroK) {Campylobacter jejuni [Tax	97.23
d1x6va3	195	Adenosine-5'phosphosulfate kinase (APS kinase) {Hu	97.21
d1e6ca_	170	Shikimate kinase (AroK) {Erwinia chrysanthemi [Tax	97.21
d1mo6a1	269	RecA protein, ATPase-domain {Mycobacterium tubercu	97.18
d1ak2a1	190	Adenylate kinase {Cow (Bos taurus), mitochondrial	97.13
d1tf7a1	242	Circadian clock protein KaiC {Synechococcus sp. st	97.07
d2iyva1	165	Shikimate kinase (AroK) {Mycobacterium tuberculosi	97.06
d1gkya_	186	Guanylate kinase {Baker's yeast (Saccharomyces cer	97.04
d2fz4a1	206	DNA repair protein RAD25 {Archaeoglobus fulgidus [	97.03
d1nlfa_	274	Hexameric replicative helicase repA {Escherichia c	97.0
d1rz3a_	198	Hypothetical protein rbstp0775 {Bacillus stearothe	96.97
d1np6a_	170	Molybdopterin-guanine dinucleotide biosynthesis pr	96.96
d1ckea_	225	CMP kinase {Escherichia coli [TaxId: 562]}	96.94
d1zaka1	189	Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}	96.94
d1khta_	190	Adenylate kinase {Archaeon Methanococcus voltae [T	96.94
d1ukza_	196	Uridylate kinase {Baker's yeast (Saccharomyces cer	96.92
d1htwa_	158	Hypothetical protein HI0065 {Haemophilus influenza	96.9
d1m7ga_	208	Adenosine-5'phosphosulfate kinase (APS kinase) {Fu	96.88
d3adka_	194	Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}	96.86
d1zina1	182	Adenylate kinase {Bacillus stearothermophilus [Tax	96.85
d1teva_	194	UMP/CMP kinase {Human (Homo sapiens) [TaxId: 9606]	96.82
d2jdid3	276	Central domain of beta subunit of F1 ATP synthase	96.82
d2cdna1	181	Adenylate kinase {Mycobacterium tuberculosis [TaxI	96.78
d2ak3a1	189	Adenylate kinase {Cow (Bos taurus), mitochondrial	96.71
d1szpa2	251	DNA repair protein Rad51, catalytic domain {Baker'	96.68
d1s3ga1	182	Adenylate kinase {Bacillus globisporus [TaxId: 145	96.67
d2p6ra3	202	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	96.59
d1bifa1	213	6-phosphofructo-2-kinase/fructose-2,6-bisphosphata	96.59
d1akya1	180	Adenylate kinase {Baker's yeast (Saccharomyces cer	96.59
d1nksa_	194	Adenylate kinase {Archaeon Sulfolobus acidocaldari	96.58
d1v5wa_	258	Meiotic recombination protein DMC1/LIM15 homolog {	96.54
d1q3ta_	223	CMP kinase {Streptococcus pneumoniae [TaxId: 1313]	96.5
d1e4va1	179	Adenylate kinase {Escherichia coli [TaxId: 562]}	96.49
d1l2ta_	230	MJ0796 {Archaeon Methanococcus jannaschii [TaxId:	96.41
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	96.41
d1xpua3	289	Transcription termination factor Rho, ATPase domai	96.39
d1nn5a_	209	Thymidylate kinase {Human (Homo sapiens) [TaxId: 9	96.38
d2i1qa2	258	DNA repair protein Rad51, catalytic domain {Archae	96.34
d1p9ra_	401	Extracellular secretion NTPase EpsE {Vibrio choler	96.32
d1gm5a3	264	RecG helicase domain {Thermotoga maritima [TaxId:	96.3
d4tmka_	210	Thymidylate kinase {Escherichia coli [TaxId: 562]}	96.28
d1lvga_	190	Guanylate kinase {Mouse (Mus musculus) [TaxId: 100	96.24
d1g6oa_	323	Hexameric traffic ATPase, HP0525 {Helicobacter pyl	96.22
d2p67a1	327	LAO/AO transport system kinase ArgK {Escherichia c	96.21
d1znwa1	182	Guanylate kinase {Mycobacterium tuberculosis [TaxI	96.19
d1xjca_	165	Molybdopterin-guanine dinucleotide biosynthesis pr	96.19
d2qm8a1	323	Metallochaperone MeaB {Methylobacterium extorquens	96.1
d2bmfa2	305	Dengue virus helicase {Dengue virus type 2 [TaxId:	96.09
d1pzna2	254	DNA repair protein Rad51, catalytic domain {Archae	96.03
d1wb9a2	234	DNA repair protein MutS, the C-terminal domain {Es	96.02
d2fh5b1	207	Signal recognition particle receptor beta-subunit	96.02
d1tuea_	205	Replication protein E1 helicase domain {Human papi	95.99
d1gkub1	237	Helicase-like "domain" of reverse gyrase {Archaeon	95.95
d1wf3a1	178	GTPase Era, N-terminal domain {Thermus thermophilu	95.93
d1h65a_	257	Chloroplast protein translocon GTPase Toc34 {Garde	95.88
d1n0wa_	242	DNA repair protein Rad51, catalytic domain {Human	95.77
d1yrba1	244	ATP(GTP)-binding protein PAB0955 {Pyrococcus abyss	95.74
d1odfa_	286	Hypothetical protein Ygr205W {Baker's yeast (Sacch	95.66
d1s96a_	205	Guanylate kinase {Escherichia coli [TaxId: 562]}	95.66
d1ksha_	165	ADP-ribosylation factor {Mouse (Mus musculus), ARL	95.66
d1fx0a3	276	Central domain of alpha subunit of F1 ATP synthase	95.66
d1ewqa2	224	DNA repair protein MutS, the C-terminal domain {Th	95.63
d1hv8a1	208	Putative DEAD box RNA helicase {Archaeon Methanoco	95.6
d1uj2a_	213	Uridine-cytidine kinase 2 {Human (Homo sapiens) [T	95.56
d2gj8a1	161	Probable tRNA modification GTPase TrmE (MnmE), G d	95.55
d1kgda_	178	Guanylate kinase-like domain of Cask {Human (Homo	95.46
d2jdia3	285	Central domain of alpha subunit of F1 ATP synthase	95.42
d1ihua1	296	Arsenite-translocating ATPase ArsA {Escherichia co	95.39
d1tmka_	214	Thymidylate kinase {Baker's yeast (Saccharomyces c	95.38
d1q0ua_	209	Probable DEAD box RNA helicase YqfR {Bacillus stea	95.35
d1s2ma1	206	Putative ATP-dependent RNA helicase DHH1 {Baker's	95.35
d1t6na_	207	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	95.31
d1fzqa_	176	ADP-ribosylation factor {Mouse (Mus musculus), ARL	95.28
d1e0sa_	173	ADP-ribosylation factor {Human (Homo sapiens), ARF	95.27
d1r8sa_	160	ADP-ribosylation factor {Human (Homo sapiens), ARF	95.26
d1qdea_	212	Initiation factor 4a {Baker's yeast (Saccharomyces	95.25
d2g9na1	218	Initiation factor 4a {Human (Homo sapiens) [TaxId:	95.22
d1veca_	206	DEAD box RNA helicase rck/p54 {Human (Homo sapiens	94.98
d1ihua2	279	Arsenite-translocating ATPase ArsA {Escherichia co	94.96
d1rifa_	282	DNA helicase UvsW {Bacteriophage T4 [TaxId: 10665]	94.96
d1zd9a1	164	ADP-ribosylation factor {Human (Homo sapiens), ARL	94.87
d1sgwa_	200	Putative ABC transporter PF0895 {Pyrococcus furios	94.78
d2qtvb1	166	SAR1 {Baker's yeast (Saccharomyces cerevisiae) [Ta	94.71
d2j0sa1	222	Probable ATP-dependent RNA helicase DDX48 {Human (	94.66
d2awna2	232	Maltose transport protein MalK, N-terminal domain	94.64
d1u0la2	225	Probable GTPase EngC (YjeQ), C-terminal domain {Th	94.64
d1upta_	169	ADP-ribosylation factor {Human (Homo sapiens), ARL	94.62
d1oywa2	206	RecQ helicase domain {Escherichia coli [TaxId: 562	94.61
d1v43a3	239	Hypothetical protein PH0022, N-terminal domain {Py	94.55
d1sq5a_	308	Pantothenate kinase PanK {Escherichia coli [TaxId:	94.55
d2a5ja1	173	Rab2b {Human (Homo sapiens) [TaxId: 9606]}	94.36
d2vp4a1	197	Deoxyribonucleoside kinase {Fruit fly (Drosophila	94.33
d1uaaa1	306	DEXX box DNA helicase {Escherichia coli, RepD [Tax	94.3
d1f6ba_	186	SAR1 {Chinese hamster (Cricetulus griseus) [TaxId:	94.29
d1g2912	240	Maltose transport protein MalK, N-terminal domain	94.25
d2onka1	240	Molybdate/tungstate import ATP-binding protein Wtp	94.15
d3b60a1	253	Multidrug resistance ABC transporter MsbA, C-termi	94.14
d1zj6a1	177	ADP-ribosylation factor {Human (Homo sapiens), ARL	94.13
d1z2aa1	164	Rab23 {Mouse (Mus musculus) [TaxId: 10090]}	94.11
d2pmka1	241	Haemolysin B ATP-binding protein {Escherichia coli	94.1
d1z0fa1	166	Rab14 {Human (Homo sapiens) [TaxId: 9606]}	94.05
d1xbta1	133	Thymidine kinase, TK1, N-terminal domain {Human (H	94.01
d1kaoa_	167	Rap2a {Human (Homo sapiens) [TaxId: 9606]}	93.98
d1jj7a_	251	Peptide transporter Tap1, C-terminal ABC domain {H	93.97
d1u0ja_	267	Rep 40 protein helicase domain {Adeno-associated v	93.95
d1nrjb_	209	Signal recognition particle receptor beta-subunit	93.94
d3d31a2	229	Sulfate/molybdate ABC transporter, ATP-binding pro	93.94
d1gsia_	208	Thymidylate kinase {Mycobacterium tuberculosis [Ta	93.88
d3dhwc1	240	Methionine import ATP-binding protein MetN {Escher	93.88
d3raba_	169	Rab3a {Rat (Rattus norvegicus) [TaxId: 10116]}	93.82
d2atva1	168	Ras-like estrogen-regulated growth inhibitor, RERG	93.78
d1z08a1	167	Rab21 {Human (Homo sapiens) [TaxId: 9606]}	93.76
d1moza_	182	ADP-ribosylation factor {Baker's yeast (Saccharomy	93.73
d1r0wa_	281	Cystic fibrosis transmembrane conductance regulato	93.71
d1kkma_	176	HPr kinase HprK C-terminal domain {Lactobacillus c	93.62
d2erya1	171	r-Ras2 {Human (Homo sapiens) [TaxId: 9606]}	93.61
d2ew1a1	171	Rab30 {Human (Homo sapiens) [TaxId: 9606]}	93.6
d1r2qa_	170	Rab5a {Human (Homo sapiens) [TaxId: 9606]}	93.58
d2f9la1	175	Rab11b {Human (Homo sapiens) [TaxId: 9606]}	93.58
d1pjra1	318	DEXX box DNA helicase {Bacillus stearothermophilus	93.56
d1uf9a_	191	Dephospho-CoA kinase {Thermus thermophilus [TaxId:	93.53
d1z06a1	165	Rab-33b {Mouse (Mus musculus) [TaxId: 10090]}	93.5
d2f7sa1	186	Rab27b {Human (Homo sapiens) [TaxId: 9606]}	93.49
d1mv5a_	242	Multidrug resistance ABC transporter LmrA, C-termi	93.48
d2fn4a1	173	r-Ras {Human (Homo sapiens) [TaxId: 9606]}	93.47
d1z0ja1	167	Rab-22a {Mouse (Mus musculus) [TaxId: 10090]}	93.46
d1ky3a_	175	Rab-related protein ypt7p {Baker's yeast (Saccharo	93.42
d2erxa1	171	di-Ras2 {Human (Homo sapiens) [TaxId: 9606]}	93.41
d2ocpa1	241	Deoxyguanosine kinase {Human (Homo sapiens) [TaxId	93.39
d1oxxk2	242	Glucose transport protein GlcV, N-terminal domain	93.39
d1ctqa_	166	cH-p21 Ras protein {Human (Homo sapiens) [TaxId: 9	93.39
d1g16a_	166	Rab-related protein Sec4 {Baker's yeast (Saccharom	93.37
d1mkya1	171	Probable GTPase Der, N-terminal and middle domains	93.36
d1cp2a_	269	Nitrogenase iron protein {Clostridium pasteurianum	93.35
d1b0ua_	258	ATP-binding subunit of the histidine permease {Sal	93.26
d1yzqa1	164	Rab6 {Human (Homo sapiens) [TaxId: 9606]}	93.24
d1vg8a_	184	Rab7 {Rat (Rattus norvegicus) [TaxId: 10116]}	93.23
d2b8ta1	139	Thymidine kinase, TK1, N-terminal domain {Ureaplas	93.22
d1xtqa1	167	GTP-binding protein RheB {Human (Homo sapiens) [Ta	93.21
d1c1ya_	167	Rap1A {Human (Homo sapiens) [TaxId: 9606]}	93.13
d2cxxa1	184	GTP-binding protein engB {Pyrococcus horikoshii [T	93.02
d1ko7a2	169	HPr kinase HprK C-terminal domain {Staphylococcus	92.99
d1knxa2	177	HPr kinase HprK C-terminal domain {Mycoplasma pneu	92.98
d2g6ba1	170	Rab26 {Human (Homo sapiens) [TaxId: 9606]}	92.98
d1ek0a_	170	Ypt51 {Baker's yeast (Saccharomyces cerevisiae) [T	92.95
d1wmsa_	174	Rab9a {Human (Homo sapiens) [TaxId: 9606]}	92.93
d1ji0a_	240	Branched chain aminoacid ABC transporter {Thermoto	92.9
d1x3sa1	177	Rab18 {Human (Homo sapiens) [TaxId: 9606]}	92.89
d1mh1a_	183	Rac {Human (Homo sapiens) [TaxId: 9606]}	92.87
d1kmqa_	177	RhoA {Human (Homo sapiens) [TaxId: 9606]}	92.85
d2bmea1	174	Rab4a {Human (Homo sapiens) [TaxId: 9606]}	92.83
d2gjsa1	168	Rad {Human (Homo sapiens) [TaxId: 9606]}	92.83
d1u8za_	168	Ras-related protein RalA {Cotton-top tamarin (Sagu	92.81
d1p5zb_	241	Deoxycytidine kinase {Human (Homo sapiens) [TaxId:	92.75
d1wrba1	238	putative ATP-dependent RNA helicase VlgB {Flatworm	92.67
d2afhe1	289	Nitrogenase iron protein {Azotobacter vinelandii [	92.62
d2bcgy1	194	GTPase Ytp1 {Baker's yeast (Saccharomyces cerevisi	92.57
d1xx6a1	141	Thymidine kinase, TK1, N-terminal domain {Clostrid	92.56
d1x1ra1	169	Ras-related protein M-Ras (XRas) {Mouse (Mus muscu	92.52
d1svia_	195	Probable GTPase EngB {Bacillus subtilis [TaxId: 14	92.51
d1a7ja_	288	Phosphoribulokinase {Rhodobacter sphaeroides [TaxI	92.49
d2atxa1	185	RhoQ {Human (Homo sapiens) [TaxId: 9606]}	92.49
d2g3ya1	172	GTP-binding protein GEM {Human (Homo sapiens) [Tax	92.47
d1vpla_	238	Putative ABC transporter TM0544 {Thermotoga mariti	92.45
d2hyda1	255	Putative multidrug export ATP-binding/permease pro	92.43
d1egaa1	179	GTPase Era, N-terminal domain {Escherichia coli [T	92.39
d1m7ba_	179	RhoE (RND3) {Mouse (Mus musculus) [TaxId: 10090]}	92.18
d2fu5c1	173	Rab8a {Mouse (Mus musculus) [TaxId: 10090]}	92.17
d1deka_	241	Deoxynucleoside monophosphate kinase {Bacteriophag	92.14
g1f2t.1	292	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	92.02
d2ngra_	191	CDC42 {Human (Homo sapiens) [TaxId: 9606]}	91.95
d1l7vc_	231	ABC transporter involved in vitamin B12 uptake, Bt	91.85
d1vhta_	208	Dephospho-CoA kinase {Escherichia coli [TaxId: 562	91.83
d1g6ha_	254	MJ1267 {Archaeon Methanococcus jannaschii [TaxId:	91.77
d1i2ma_	170	Ran {Human (Homo sapiens) [TaxId: 9606]}	91.59
d1lnza2	185	Obg GTP-binding protein middle domain {Bacillus su	91.44
d1jjva_	205	Dephospho-CoA kinase {Haemophilus influenzae [TaxI	91.31
d1byia_	224	Dethiobiotin synthetase {Escherichia coli [TaxId:	91.28
d1nija1	222	Hypothetical protein YjiA, N-terminal domain {Esch	91.26
d1zcba2	200	Transducin (alpha subunit) {Mouse (Mus musculus) [	91.18
d1mkya2	186	Probable GTPase Der, N-terminal and middle domains	91.07
d1p6xa_	333	Thymidine kinase {Equine herpesvirus type 4 [TaxId	90.97
d1udxa2	180	Obg GTP-binding protein middle domain {Thermus the	90.83
d2dy1a2	267	Elongation factor G (EF-G), N-terminal (G) domain	90.82
d1xzpa2	160	TrmE GTPase domain {Thermotoga maritima [TaxId: 23	90.79
g1ii8.1	369	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	90.62
d2bmja1	175	Centaurin gamma 1, G domain {Human (Homo sapiens)	90.58
d1puia_	188	Probable GTPase EngB {Escherichia coli [TaxId: 562	90.46
d1t9ha2	231	Probable GTPase EngC (YjeQ), C-terminal domain {Ba	90.18
d2bv3a2	276	Elongation factor G (EF-G), N-terminal (G) domain	90.12
d1svsa1	195	Transducin (alpha subunit) {Rat (Rattus norvegicus	89.97
d2bcjq2	200	Transducin (alpha subunit) {Mouse (Mus musculus) [	89.89
g1xew.1	329	Smc head domain {Pyrococcus furiosus [TaxId: 2261]	89.74
d1e9ra_	433	Bacterial conjugative coupling protein TrwB {Esche	89.28
d1azta2	221	Transducin (alpha subunit) {Cow (Bos taurus) [TaxI	89.23
d1tq4a_	400	Interferon-inducible GTPase {Mouse (Mus musculus)	89.2
d1qhla_	222	Cell division protein MukB {Escherichia coli [TaxI	88.92
d1g3qa_	237	Cell division regulator MinD {Archaeon Pyrococcus	88.06
d1z63a1	230	Helicase of the SNF2/Rad54 hamily {Sulfolobus solf	87.95
d1hyqa_	232	Cell division regulator MinD {Archaeon Archaeoglob	87.86
d1z3ix2	298	Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxI	87.62
d1e69a_	308	Smc head domain {Thermotoga maritima [TaxId: 2336]	87.29
d1bg2a_	323	Kinesin {Human (Homo sapiens) [TaxId: 9606]}	87.25
d1lkxa_	684	Myosin S1, motor domain {Dictyostelium discoideum,	87.19
d1d0xa2	712	Myosin S1, motor domain {Dictyostelium discoideum	87.15
d1br2a2	710	Myosin S1, motor domain {Chicken (Gallus gallus),	86.6
d2mysa2	794	Myosin S1, motor domain {Chicken (Gallus gallus),	85.87
d1w1wa_	427	Smc head domain {Baker's yeast (Saccharomyces cere	85.54
d1goja_	354	Kinesin {Neurospora crassa [TaxId: 5141]}	85.53
d1kk8a2	789	Myosin S1, motor domain {Bay scallop (Aequipecten	85.2
d1osna_	331	Thymidine kinase {Varicella-zoster virus [TaxId: 1	84.96
d1f6va_	91	C-terminal domain of B transposition protein {Bact	84.83
d1wb1a4	179	Elongation factor SelB, N-terminal domain {Methano	84.7
d1w7ja2	730	Myosin S1, motor domain {Chicken (Gallus gallus),	84.69
d1f9va_	342	Kinesin motor Ncd (non-claret disjunctional) {Bake	83.93
d1x88a1	345	Kinesin {Human (Homo sapiens), mitotic kinesin eg5	83.37
d1ry6a_	330	Kinesin {Malaria parasite (Plasmodium falciparum)	83.14
d2zfia1	349	Kinesin {Mouse (Mus musculus), kif1a [TaxId: 10090	83.07
d1e2ka_	329	Thymidine kinase {Herpes simplex virus type 1, dif	82.53
d1v8ka_	362	Kinesin {Mouse (Mus musculus), kif2c [TaxId: 10090	82.01
d1sdma_	364	Kinesin heavy chain-like protein {Potato (Solanum	81.54
d1g8fa3	122	ATP sulfurylase C-terminal domain {Baker's yeast (	81.43
d1g7sa4	227	Initiation factor IF2/eIF5b, N-terminal (G) domain	81.41
g1qhh.1	623	DEXX box DNA helicase {Bacillus stearothermophilus	80.47

>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=99.94  E-value=2.4e-25  Score=212.02  Aligned_cols=248  Identities=23%  Similarity=0.289  Sum_probs=204.8

Q ss_pred             CCCCChHHHHHHHHHHHHhhhcc--CCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVNN--ETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVN  271 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~--~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~  271 (490)
                      +.++||+++++.|.++|..++..  ..+++++|+||||||||++++.+++.+.....+.+++++|........++..+..
T Consensus        16 ~~l~~Re~ei~~l~~~l~~~l~~~~~~~~~lll~GppGtGKT~l~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~   95 (276)
T d1fnna2          16 KRLPHREQQLQQLDILLGNWLRNPGHHYPRATLLGRPGTGKTVTLRKLWELYKDKTTARFVYINGFIYRNFTAIIGEIAR   95 (276)
T ss_dssp             SCCTTCHHHHHHHHHHHHHHHHSTTSSCCEEEEECCTTSSHHHHHHHHHHHHTTSCCCEEEEEETTTCCSHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHHHHhCCCCCCCceEEECCCCCCHHHHHHHHHHHHhcccCCcEEEecchhhhhhhhhhhhhHH
Confidence            67999999999999999887653  3568999999999999999999999998777889999999999999999999988


Q ss_pred             HhcCC--CCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCHHHHHHhHhCC-CCCCCcEEEEEecCCCChhHhhh
Q psy200          272 ELKLK--PGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWP-SIPGSKLVLVGVANALDLTDRML  348 (490)
Q Consensus       272 ~l~~~--~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~-~~~~~~vilI~~tn~~~~~~~l~  348 (490)
                      .++..  ..+.....+...+.+.+.......++++|+++.+.......+..++... ......+++|++++..++.+.+.
T Consensus        96 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~  175 (276)
T d1fnna2          96 SLNIPFPRRGLSRDEFLALLVEHLRERDLYMFLVLDDAFNLAPDILSTFIRLGQEADKLGAFRIALVIVGHNDAVLNNLD  175 (276)
T ss_dssp             HTTCCCCSSCCCHHHHHHHHHHHHHHTTCCEEEEEETGGGSCHHHHHHHHHHTTCHHHHSSCCEEEEEEESSTHHHHTSC
T ss_pred             hhhhhhhhhccchhHHHHHHHHHHhhcccccccchhHHHHhhhhhhhhHHHHHhccccccccceEEeecCCchhhhhhcc
Confidence            87653  3445667777777777766667889999999998776555555544322 33566788999999877788888


Q ss_pred             HHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHH------HhhCCHHHHHHHHHHHHHHH
Q psy200          349 PRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVA------AVSGDIRKAIDITNHLIDLT  422 (490)
Q Consensus       349 ~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~------~~~Gd~r~ai~ll~~a~~~a  422 (490)
                      +++.+|+..  ..+.|.+++.+++.+|+.+++........+++++++.|++...      ...||+|.++++|+.|+..|
T Consensus       176 ~~~~~r~~~--~~i~~~~~~~~e~~~il~~r~~~~~~~~~~~~~~l~~ia~~~~~~~~~~~~~G~~R~a~~ll~~a~~~A  253 (276)
T d1fnna2         176 PSTRGIMGK--YVIRFSPYTKDQIFDILLDRAKAGLAEGSYSEDILQMIADITGAQTPLDTNRGDARLAIDILYRSAYAA  253 (276)
T ss_dssp             HHHHHHHTT--CEEECCCCBHHHHHHHHHHHHHHHBCTTSSCHHHHHHHHHHHSBSSTTCTTSCCHHHHHHHHHHHHHHH
T ss_pred             hhhhhhhcc--hhccccchhHHHHHHHHHHHHHHhcccccccHHHHHHHHHHhhhhhhhhhcCCCHHHHHHHHHHHHHHH
Confidence            888888753  3699999999999999999988754456689999999998542      34699999999999999999


Q ss_pred             HhccccCCcccccCHHHHHHHHHHhc
Q psy200          423 YDNVKENGEVTGIGLKEVLGVISSVY  448 (490)
Q Consensus       423 ~~~~~~~~~~~~It~~~v~~a~~~~~  448 (490)
                      ..++     ...|+.+||.+|+.++.
T Consensus       254 ~~~~-----~~~I~~edv~~A~~~~~  274 (276)
T d1fnna2         254 QQNG-----RKHIAPEDVRKSSKEVL  274 (276)
T ss_dssp             HHTT-----CSSCCHHHHHHHHHHHS
T ss_pred             HHcC-----CCCcCHHHHHHHHHHHh
Confidence            9998     77999999999999874

>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=99.92  E-value=2.3e-23  Score=199.33  Aligned_cols=245  Identities=18%  Similarity=0.229  Sum_probs=189.1

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCC-----eEEEECCCCCcHHHHHHHHHHHhhh-----cCCceEEEEeccCCCCHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSG-----SMYISGPPGTGKSASLNLLVSRAEI-----KDAFKTIYINCNSVRNAA  263 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~-----~ill~GppGtGKTtla~~l~~~l~~-----~~~~~~~~v~~~~~~~~~  263 (490)
                      +.|+||++++++|..++...+..+...     +++|+||||||||++++++++++..     ...+.+++++|....+..
T Consensus        16 ~~~~~Re~e~~~l~~~l~~~~~~~~~~~~~~~~l~l~GppGtGKT~l~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~   95 (287)
T d1w5sa2          16 PELRVRRGEAEALARIYLNRLLSGAGLSDVNMIYGSIGRVGIGKTTLAKFTVKRVSEAAAKEGLTVKQAYVNAFNAPNLY   95 (287)
T ss_dssp             SSCSSSCHHHHHHHHHHHHHHHTSSCBCCEEEEEECTTCCSSSHHHHHHHHHHHHHHHHHHTTCCEEEEEEEGGGCCSHH
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHcCCCCCCcceEEEeECCCCCCHHHHHHHHHHHHHhhcccccCCceeeeeccccccchh
Confidence            789999999999999886655443221     4678899999999999999999852     234688899999999999


Q ss_pred             HHHHHHHHHhcCC--CCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccC---HHHHHH---hHhC--CCCCCCcEE
Q psy200          264 SVYETIVNELKLK--PGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRK---QTILYT---IFEW--PSIPGSKLV  333 (490)
Q Consensus       264 ~l~~~i~~~l~~~--~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~---~~~L~~---l~~~--~~~~~~~vi  333 (490)
                      ..+..+...++..  ..+.....+.+.+.+.....+...++++||+|.+....   .+.++.   ++++  .......+.
T Consensus        96 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~iide~d~l~~~~~~~~~~~~~l~~l~~~l~~~~~~~~~~  175 (287)
T d1w5sa2          96 TILSLIVRQTGYPIQVRGAPALDILKALVDNLYVENHYLLVILDEFQSMLSSPRIAAEDLYTLLRVHEEIPSRDGVNRIG  175 (287)
T ss_dssp             HHHHHHHHHHTCCCCCTTCCHHHHHHHHHHHHHHHTCEEEEEEESTHHHHSCTTSCHHHHHHHHTHHHHSCCTTSCCBEE
T ss_pred             hHHHHHhhhcccccccccchHHHHHHHHHHHHHhccCccccceeEEEEeccccccchhHHHHHHHHHHhcchhhccccee
Confidence            9888888887653  34556667777777666655778899999999997553   333333   2322  234456777


Q ss_pred             EEEecCCCChhHhh---hHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHH---hhCC
Q psy200          334 LVGVANALDLTDRM---LPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAA---VSGD  407 (490)
Q Consensus       334 lI~~tn~~~~~~~l---~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~---~~Gd  407 (490)
                      +|++++..++.+.+   .+++.+|+.   ..+.|.+|+.+++.+|+..++........+++++++.|+++...   ..||
T Consensus       176 ~i~i~~~~~~~~~~~~~~~~~~~r~~---~~i~f~~y~~~el~~Il~~r~~~~~~~~~~~~~al~~ia~~~~~~~~~~gd  252 (287)
T d1w5sa2         176 FLLVASDVRALSYMREKIPQVESQIG---FKLHLPAYKSRELYTILEQRAELGLRDTVWEPRHLELISDVYGEDKGGDGS  252 (287)
T ss_dssp             EEEEEEETHHHHHHHHHCHHHHTTCS---EEEECCCCCHHHHHHHHHHHHHHHBCTTSCCHHHHHHHHHHHCGGGTSCCC
T ss_pred             EEeecccHHHHHHHHhhccchhcccc---eeeeccCCcHHHHHHHHhhhHHHhhccCCCCHHHHHHHHHHHhccccCCCC
Confidence            77777755554433   467777776   58999999999999999999876544567899999999986643   3689


Q ss_pred             HHHHHHHHHHHHHHHHhccccCCcccccCHHHHHHHHHH
Q psy200          408 IRKAIDITNHLIDLTYDNVKENGEVTGIGLKEVLGVISS  446 (490)
Q Consensus       408 ~r~ai~ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~~~  446 (490)
                      +|.++++|+.|+..|..++     ...|+.+||.+|+.+
T Consensus       253 ~R~ai~~l~~a~~~A~~~~-----~~~It~~~V~~A~~e  286 (287)
T d1w5sa2         253 ARRAIVALKMACEMAEAMG-----RDSLSEDLVRKAVSE  286 (287)
T ss_dssp             HHHHHHHHHHHHHHHHHTT-----CSSCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHcC-----CCCCCHHHHHHHHhc
Confidence            9999999999999999888     779999999999975

>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=99.91  E-value=4.3e-24  Score=198.43  Aligned_cols=220  Identities=21%  Similarity=0.248  Sum_probs=167.6

Q ss_pred             cCCCCcchHHHhhcCCCCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCC-ceEEEEec
Q psy200          178 LFSEDKPKVEEKAKDSCELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDA-FKTIYINC  256 (490)
Q Consensus       178 ~~~~~~~~~~~~~l~~~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~-~~~~~v~~  256 (490)
                      .+|.++|+|...    ++++|+++.++.|..|+..    +...+++|+||+|+|||++++.+++++..... ..++..++
T Consensus         2 ~pw~ekyrP~~~----~divg~~~~~~~L~~~i~~----~~~~~lLl~Gp~G~GKttl~~~la~~l~~~~~~~~~~e~~~   73 (227)
T d1sxjc2           2 LPWVEKYRPETL----DEVYGQNEVITTVRKFVDE----GKLPHLLFYGPPGTGKTSTIVALAREIYGKNYSNMVLELNA   73 (227)
T ss_dssp             CCHHHHTCCSSG----GGCCSCHHHHHHHHHHHHT----TCCCCEEEECSSSSSHHHHHHHHHHHHHTTSHHHHEEEECT
T ss_pred             CchhhhhCCCCH----HHccCcHHHHHHHHHHHHc----CCCCeEEEECCCCCChhHHHHHHHHHhhcCCCcceeEEecc
Confidence            479999999988    9999999999999999864    55567999999999999999999999752221 24566666


Q ss_pred             cCCCCHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHh----cCCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcE
Q psy200          257 NSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFD----TKHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKL  332 (490)
Q Consensus       257 ~~~~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~----~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~v  332 (490)
                      +........                    ...+.....    ..++..+|||||++.+....+..|...++..   ...+
T Consensus        74 ~~~~~~~~~--------------------~~~~~~~~~~~~~~~~~~kiiiiDe~d~~~~~~~~~Ll~~le~~---~~~~  130 (227)
T d1sxjc2          74 SDDRGIDVV--------------------RNQIKDFASTRQIFSKGFKLIILDEADAMTNAAQNALRRVIERY---TKNT  130 (227)
T ss_dssp             TSCCSHHHH--------------------HTHHHHHHHBCCSSSCSCEEEEETTGGGSCHHHHHHHHHHHHHT---TTTE
T ss_pred             cccCCeeee--------------------ecchhhccccccccCCCeEEEEEeccccchhhHHHHHHHHhhhc---ccce
Confidence            655332221                    111111111    1234569999999999988888888887743   2356


Q ss_pred             EEEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHH
Q psy200          333 VLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAI  412 (490)
Q Consensus       333 ilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai  412 (490)
                      +++.++|.   ...+.+.+++||.    .+.|.+++.+++.+++.+.+..+  ...+++++++.|++   ...||+|.++
T Consensus       131 ~~~~~~~~---~~~i~~~i~sr~~----~i~~~~~~~~~i~~~l~~I~~~e--~i~i~~~~l~~i~~---~s~Gd~R~ai  198 (227)
T d1sxjc2         131 RFCVLANY---AHKLTPALLSQCT----RFRFQPLPQEAIERRIANVLVHE--KLKLSPNAEKALIE---LSNGDMRRVL  198 (227)
T ss_dssp             EEEEEESC---GGGSCHHHHTTSE----EEECCCCCHHHHHHHHHHHHHTT--TCCBCHHHHHHHHH---HHTTCHHHHH
T ss_pred             eeccccCc---HHHhHHHHHHHHh----hhccccccccccccccccccccc--cccCCHHHHHHHHH---HcCCcHHHHH
Confidence            66666663   4567788999985    89999999999999999999887  45689999999998   6789999999


Q ss_pred             HHHHHHHHHHHhccccCCcccccCHHHHHHHHH
Q psy200          413 DITNHLIDLTYDNVKENGEVTGIGLKEVLGVIS  445 (490)
Q Consensus       413 ~ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~~  445 (490)
                      ++|+.+...+...+     ...|+.++|.+++.
T Consensus       199 n~Lq~~~~~~~~~~-----~~~It~~~v~e~~g  226 (227)
T d1sxjc2         199 NVLQSCKATLDNPD-----EDEISDDVIYECCG  226 (227)
T ss_dssp             HHTTTTTTTTCSSS-----CCCBCHHHHHHHTT
T ss_pred             HHHHHHHHhcCCCC-----CCeeCHHHHHHHhC
Confidence            99988765555555     56899999998763

>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=99.90  E-value=2.9e-23  Score=193.84  Aligned_cols=233  Identities=17%  Similarity=0.170  Sum_probs=169.6

Q ss_pred             CCCCcchHHHhhcCCCCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhc--CCceEEEEec
Q psy200          179 FSEDKPKVEEKAKDSCELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIK--DAFKTIYINC  256 (490)
Q Consensus       179 ~~~~~~~~~~~~l~~~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~--~~~~~~~v~~  256 (490)
                      +|.++|+|...    ++++|+++.++.|..|+.    .+...+++|+||+|+|||++++.+++++...  ......++++
T Consensus         1 ~w~~ky~P~~~----~diig~~~~~~~l~~~i~----~~~~~~lll~Gp~G~GKTtl~~~i~~~l~~~~~~~~~~~~~~~   72 (237)
T d1sxjd2           1 PWVEKYRPKNL----DEVTAQDHAVTVLKKTLK----SANLPHMLFYGPPGTGKTSTILALTKELYGPDLMKSRILELNA   72 (237)
T ss_dssp             CHHHHTCCSST----TTCCSCCTTHHHHHHHTT----CTTCCCEEEECSTTSSHHHHHHHHHHHHHHHHHHTTSEEEECS
T ss_pred             CcchhhCCCCH----HHccCcHHHHHHHHHHHH----cCCCCeEEEECCCCCChHHHHHHHHHHHcCCcccccchhheec
Confidence            57889999888    999999999988888875    3556779999999999999999999997422  2346677887


Q ss_pred             cCCCCHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEEE
Q psy200          257 NSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVG  336 (490)
Q Consensus       257 ~~~~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI~  336 (490)
                      ........+...+-.............    .+.  .....+..+|||||+|.+....+..+..+++..   ....++|.
T Consensus        73 ~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~--~~~~~~~~viiiDe~d~l~~~~~~~l~~~~~~~---~~~~~~i~  143 (237)
T d1sxjd2          73 SDERGISIVREKVKNFARLTVSKPSKH----DLE--NYPCPPYKIIILDEADSMTADAQSALRRTMETY---SGVTRFCL  143 (237)
T ss_dssp             SSCCCHHHHTTHHHHHHHSCCCCCCTT----HHH--HSCCCSCEEEEETTGGGSCHHHHHHHHHHHHHT---TTTEEEEE
T ss_pred             cccccchHHHHHHHHHhhhhhhhhhHH----HHh--hccccCceEEEEecccccCHHHHHHHhhccccc---cccccccc
Confidence            776655444333322221111111110    011  111234558999999999988777777776643   23445555


Q ss_pred             ecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHHHHH
Q psy200          337 VANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITN  416 (490)
Q Consensus       337 ~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll~  416 (490)
                      +++.   ...+.+.+++||.    .+.|++++.+++.++|...+..+  ...+++++++.|++   ...||+|.++++|+
T Consensus       144 ~~~~---~~~~~~~l~sr~~----~i~f~~~~~~~~~~~L~~i~~~e--~i~i~~~~l~~ia~---~s~gd~R~ai~~L~  211 (237)
T d1sxjd2         144 ICNY---VTRIIDPLASQCS----KFRFKALDASNAIDRLRFISEQE--NVKCDDGVLERILD---ISAGDLRRGITLLQ  211 (237)
T ss_dssp             EESC---GGGSCHHHHHHSE----EEECCCCCHHHHHHHHHHHHHTT--TCCCCHHHHHHHHH---HTSSCHHHHHHHHH
T ss_pred             cccc---cccccccccchhh----hhccccccccccchhhhhhhhhh--cCcCCHHHHHHHHH---HcCCCHHHHHHHHH
Confidence            5552   4566788999985    89999999999999999998876  45689999999998   66799999999999


Q ss_pred             HHHHHHHhccccCCcccccCHHHHHHHH
Q psy200          417 HLIDLTYDNVKENGEVTGIGLKEVLGVI  444 (490)
Q Consensus       417 ~a~~~a~~~~~~~~~~~~It~~~v~~a~  444 (490)
                      .+...+...+.    ...|+.++|.+++
T Consensus       212 ~~~~~~~~~~~----~~~It~~~i~e~~  235 (237)
T d1sxjd2         212 SASKGAQYLGD----GKNITSTQVEELA  235 (237)
T ss_dssp             HTHHHHHHHCS----CCCCCHHHHHHHH
T ss_pred             HHHHhchhcCC----CCccCHHHHHHhh
Confidence            98877765542    3579999998775

>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=99.90  E-value=2.4e-23  Score=192.95  Aligned_cols=220  Identities=20%  Similarity=0.266  Sum_probs=165.8

Q ss_pred             cCCCCcchHHHhhcCCCCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcC-CceEEEEec
Q psy200          178 LFSEDKPKVEEKAKDSCELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKD-AFKTIYINC  256 (490)
Q Consensus       178 ~~~~~~~~~~~~~l~~~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~-~~~~~~v~~  256 (490)
                      .+|.++|+|...    ++++|+++.++.|..|+..    +...+++|+||+|+|||++|+.+++++.... .+.++++++
T Consensus         3 ~pw~eKyrP~~~----~d~ig~~~~~~~L~~~~~~----~~~~~~ll~Gp~G~GKTt~a~~la~~l~~~~~~~~~~~~n~   74 (224)
T d1sxjb2           3 LPWVEKYRPQVL----SDIVGNKETIDRLQQIAKD----GNMPHMIISGMPGIGKTTSVHCLAHELLGRSYADGVLELNA   74 (224)
T ss_dssp             CCHHHHTCCSSG----GGCCSCTHHHHHHHHHHHS----CCCCCEEEECSTTSSHHHHHHHHHHHHHGGGHHHHEEEECT
T ss_pred             CchHhHhCCCCH----HHhcCCHHHHHHHHHHHHc----CCCCeEEEECCCCCCchhhHHHHHHHHhccccccccccccc
Confidence            479999999998    9999999999999998864    5566799999999999999999999986321 235788888


Q ss_pred             cCCCCHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEEE
Q psy200          257 NSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVG  336 (490)
Q Consensus       257 ~~~~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI~  336 (490)
                      ........+...+........               .....+..+|||||+|.+....+..|...++..   ....++++
T Consensus        75 ~~~~~~~~i~~~~~~~~~~~~---------------~~~~~~~kviiiDe~d~~~~~~~~~ll~~~e~~---~~~~~~i~  136 (224)
T d1sxjb2          75 SDDRGIDVVRNQIKHFAQKKL---------------HLPPGKHKIVILDEADSMTAGAQQALRRTMELY---SNSTRFAF  136 (224)
T ss_dssp             TSCCSHHHHHTHHHHHHHBCC---------------CCCTTCCEEEEEESGGGSCHHHHHTTHHHHHHT---TTTEEEEE
T ss_pred             cccCCceehhhHHHHHHHhhc---------------cCCCcceEEEEEecccccchhHHHHHhhhcccc---ccceeeee
Confidence            776544333222111110000               001234669999999999998888887777643   33555555


Q ss_pred             ecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHHHHH
Q psy200          337 VANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITN  416 (490)
Q Consensus       337 ~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll~  416 (490)
                      +++.   ...+.+.+++||.    .+.|++++.+++..++...+..+  ...+++++++.|++   ...||+|.+|+.|+
T Consensus       137 ~~~~---~~~i~~~l~sr~~----~i~~~~~~~~~i~~~l~~i~~~e--~~~i~~~~l~~I~~---~s~Gd~R~ai~~Lq  204 (224)
T d1sxjb2         137 ACNQ---SNKIIEPLQSQCA----ILRYSKLSDEDVLKRLLQIIKLE--DVKYTNDGLEAIIF---TAEGDMRQAINNLQ  204 (224)
T ss_dssp             EESC---GGGSCHHHHTTSE----EEECCCCCHHHHHHHHHHHHHHH--TCCBCHHHHHHHHH---HHTTCHHHHHHHHH
T ss_pred             ccCc---hhhhhhHHHHHHH----HhhhcccchhhhHHHHHHHHHhc--ccCCCHHHHHHHHH---HcCCcHHHHHHHHH
Confidence            5652   4567789999995    89999999999999999999887  45689999999987   67899999999998


Q ss_pred             HHHHHHHhccccCCcccccCHHHHHHHHH
Q psy200          417 HLIDLTYDNVKENGEVTGIGLKEVLGVIS  445 (490)
Q Consensus       417 ~a~~~a~~~~~~~~~~~~It~~~v~~a~~  445 (490)
                      .++.   ..       ..|+.+.|.++++
T Consensus       205 ~~~~---~~-------~~i~~~~i~~~~d  223 (224)
T d1sxjb2         205 STVA---GH-------GLVNADNVFKIVD  223 (224)
T ss_dssp             HHHH---HH-------SSBCHHHHHHHHT
T ss_pred             HHHH---cC-------CCcCHHHHHHHhC
Confidence            7642   22       3688888877653

>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=99.89  E-value=6e-23  Score=191.12  Aligned_cols=212  Identities=19%  Similarity=0.237  Sum_probs=163.1

Q ss_pred             CCCCcchHHHhhcCCCCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhc-CCceEEEEecc
Q psy200          179 FSEDKPKVEEKAKDSCELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIK-DAFKTIYINCN  257 (490)
Q Consensus       179 ~~~~~~~~~~~~l~~~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~-~~~~~~~v~~~  257 (490)
                      +|.++|+|...    ++|+|+++.++.|..|+..    +..++++|+||||+|||++|+.+++++... ..+.+++++++
T Consensus        13 ~w~~ky~P~~~----~diig~~~~~~~l~~~i~~----~~~~~lll~Gp~G~GKTtla~~iak~l~~~~~~~~~~e~n~s   84 (231)
T d1iqpa2          13 PWVEKYRPQRL----DDIVGQEHIVKRLKHYVKT----GSMPHLLFAGPPGVGKTTAALALARELFGENWRHNFLELNAS   84 (231)
T ss_dssp             CHHHHTCCCST----TTCCSCHHHHHHHHHHHHH----TCCCEEEEESCTTSSHHHHHHHHHHHHHGGGHHHHEEEEETT
T ss_pred             hHHHHhCCCCH----HHccCcHHHHHHHHHHHHc----CCCCeEEEECCCCCcHHHHHHHHHHHHHhcccCCCeeEEecC
Confidence            68899999988    9999999999999999865    566789999999999999999999987522 23467888876


Q ss_pred             CCCCHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHH----hcCCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEE
Q psy200          258 SVRNAASVYETIVNELKLKPGGKSERHQLGAILKYF----DTKHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLV  333 (490)
Q Consensus       258 ~~~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l----~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vi  333 (490)
                      .......                    +...+....    ....+..+|+|||++.+....+..|..+++..   ..+++
T Consensus        85 ~~~~~~~--------------------~~~~~~~~~~~~~~~~~~~~iilide~d~~~~~~~~~ll~~l~~~---~~~~~  141 (231)
T d1iqpa2          85 DERGINV--------------------IREKVKEFARTKPIGGASFKIIFLDEADALTQDAQQALRRTMEMF---SSNVR  141 (231)
T ss_dssp             CHHHHHT--------------------THHHHHHHHHSCCGGGCSCEEEEEETGGGSCHHHHHHHHHHHHHT---TTTEE
T ss_pred             cccchhH--------------------HHHHHHHHHhhhhccCCCceEEeehhhhhcchhHHHHHhhhcccC---CcceE
Confidence            5321111                    111111111    12245779999999999998888888877643   44678


Q ss_pred             EEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHH
Q psy200          334 LVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAID  413 (490)
Q Consensus       334 lI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~  413 (490)
                      +|+++|.   ...+++.+.+||.    .+.|.+++.+++..++...+..+  ...+++++++.|++   ...||+|.+++
T Consensus       142 ~i~~~n~---~~~i~~~l~sR~~----~i~~~~~~~~~~~~~l~~~~~~e--~i~i~~~~l~~I~~---~~~gdiR~ai~  209 (231)
T d1iqpa2         142 FILSCNY---SSKIIEPIQSRCA----IFRFRPLRDEDIAKRLRYIAENE--GLELTEEGLQAILY---IAEGDMRRAIN  209 (231)
T ss_dssp             EEEEESC---GGGSCHHHHHTEE----EEECCCCCHHHHHHHHHHHHHTT--TCEECHHHHHHHHH---HHTTCHHHHHH
T ss_pred             EEeccCC---hhhchHhHhCccc----cccccccchhhHHHHHHHHHHHh--CCCCCHHHHHHHHH---HcCCCHHHHHH
Confidence            8888874   4566788999995    89999999999999999999877  45689999999998   67899999999


Q ss_pred             HHHHHHHHHHhccccCCcccccCHHHHHHH
Q psy200          414 ITNHLIDLTYDNVKENGEVTGIGLKEVLGV  443 (490)
Q Consensus       414 ll~~a~~~a~~~~~~~~~~~~It~~~v~~a  443 (490)
                      +|+.+...          ...|+.++|..+
T Consensus       210 ~Lq~~~~~----------~~~it~e~v~~v  229 (231)
T d1iqpa2         210 ILQAAAAL----------DKKITDENVFMV  229 (231)
T ss_dssp             HHHHHHTT----------CSEECHHHHHHH
T ss_pred             HHHHHHHc----------CCCcCHHHHHhh
Confidence            99877431          236888887654

>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=99.89  E-value=8.4e-22  Score=184.09  Aligned_cols=210  Identities=19%  Similarity=0.246  Sum_probs=163.4

Q ss_pred             CCCCChHHHHHHHHHHHHhhhc-cCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVN-NETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNE  272 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~-~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~  272 (490)
                      ++++|+++.++.|..|+..... ....+++|||||||||||++|+++++++.    +.+..++.......          
T Consensus         9 ~divGqe~~~~~l~~~i~~~~~~~~~~~~~L~~GPpGtGKT~lA~~la~~~~----~~~~~~~~~~~~~~----------   74 (238)
T d1in4a2           9 DEFIGQENVKKKLSLALEAAKMRGEVLDHVLLAGPPGLGKTTLAHIIASELQ----TNIHVTSGPVLVKQ----------   74 (238)
T ss_dssp             GGCCSCHHHHHHHHHHHHHHHHHTCCCCCEEEESSTTSSHHHHHHHHHHHHT----CCEEEEETTTCCSH----------
T ss_pred             HHcCChHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCcHHHHHHHHHhccC----CCcccccCcccccH----------
Confidence            7899999999999999986543 33567899999999999999999999986    55667776554332          


Q ss_pred             hcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCHHHHHHhHhCCCC---------------CCCcEEEEEe
Q psy200          273 LKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPSI---------------PGSKLVLVGV  337 (490)
Q Consensus       273 l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~---------------~~~~vilI~~  337 (490)
                                .++...    +....+..+++|||++.+....++.+...++....               ...++++|++
T Consensus        75 ----------~~~~~~----~~~~~~~~~~~ide~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~I~a  140 (238)
T d1in4a2          75 ----------GDMAAI----LTSLERGDVLFIDEIHRLNKAVEELLYSAIEDFQIDIMIGKGPSAKSIRIDIQPFTLVGA  140 (238)
T ss_dssp             ----------HHHHHH----HHHCCTTCEEEEETGGGCCHHHHHHHHHHHHTSCCCC---------------CCCEEEEE
T ss_pred             ----------HHHHHH----HHhhccCCchHHHHHHHhhhHHHhhcccceeeeeeeeeecCcccccccccCCCCeEEEEe
Confidence                      222222    22234457999999999988777777776653221               2347788988


Q ss_pred             cCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHHHHHH
Q psy200          338 ANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITNH  417 (490)
Q Consensus       338 tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll~~  417 (490)
                      ||.   ...+.+.+++||.   ..+.|.+++.+++..++...+...  ...+++++++.+++   ...||+|.++++|+.
T Consensus       141 t~~---~~~~~~~~~~r~~---~~~~~~~~~~~~~~~~l~~~~~~~--~~~~~~~~l~~i~~---~s~gd~R~ai~~l~~  209 (238)
T d1in4a2         141 TTR---SGLLSSPLRSRFG---IILELDFYTVKELKEIIKRAASLM--DVEIEDAAAEMIAK---RSRGTPRIAIRLTKR  209 (238)
T ss_dssp             ESC---GGGSCHHHHTTCS---EEEECCCCCHHHHHHHHHHHHHHT--TCCBCHHHHHHHHH---TSTTCHHHHHHHHHH
T ss_pred             cCC---Cccccccceeeee---EEEEecCCCHHHHHHHHHHhhhhc--cchhhHHHHHHHHH---hCCCCHHHHHHHHHH
Confidence            884   3445678888887   468999999999999999988876  45689999999987   678999999999999


Q ss_pred             HHHHHHhccccCCcccccCHHHHHHHHHHh
Q psy200          418 LIDLTYDNVKENGEVTGIGLKEVLGVISSV  447 (490)
Q Consensus       418 a~~~a~~~~~~~~~~~~It~~~v~~a~~~~  447 (490)
                      +...+...+     ...|+.+.+.+++..+
T Consensus       210 ~~~~~~~~~-----~~~it~~~~~~al~~l  234 (238)
T d1in4a2         210 VRDMLTVVK-----ADRINTDIVLKTMEVL  234 (238)
T ss_dssp             HHHHHHHHT-----CSSBCHHHHHHHHHHH
T ss_pred             HHHHHHHhc-----CCccCHHHHHHHHHhh
Confidence            988887777     5689999999998765

>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=99.88  E-value=5.7e-22  Score=185.41  Aligned_cols=226  Identities=16%  Similarity=0.199  Sum_probs=158.6

Q ss_pred             CcchHHHhhcCCCCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCC
Q psy200          182 DKPKVEEKAKDSCELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRN  261 (490)
Q Consensus       182 ~~~~~~~~~l~~~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~  261 (490)
                      ++|+|...    ++++|+++.++.|..++..   ...++.++|+||+|+|||++|+.+++.+.......     .... .
T Consensus         4 ~KyrP~~~----~dlig~~~~~~~L~~~i~~---~~~~~~~Ll~Gp~G~GKtt~a~~~~~~l~~~~~~~-----~~~~-~   70 (239)
T d1njfa_           4 RKWRPQTF----ADVVGQEHVLTALANGLSL---GRIHHAYLFSGTRGVGKTSIARLLAKGLNCETGIT-----ATPC-G   70 (239)
T ss_dssp             HHTCCSSG----GGSCSCHHHHHHHHHHHHT---TCCCSEEEEECSTTSSHHHHHHHHHHHHHCTTCSC-----SSCC-S
T ss_pred             hhhCCCCH----HHccChHHHHHHHHHHHHc---CCCCeeEEEECCCCCcHHHHHHHHHHHhcCccccc-----cCcc-c
Confidence            36777777    8999999999999988864   33456799999999999999999999885322110     0000 0


Q ss_pred             HHHHHHHHHHHhcC------CCCCCcHHHHHHHHHHHHh--cCCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEE
Q psy200          262 AASVYETIVNELKL------KPGGKSERHQLGAILKYFD--TKHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLV  333 (490)
Q Consensus       262 ~~~l~~~i~~~l~~------~~~~~s~~~~~~~l~~~l~--~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vi  333 (490)
                      .......+...-..      .......+.+.+.+..+..  ..++..||||||+|.|....+..|+..++.   ....++
T Consensus        71 ~~~~~~~i~~~~~~~~~~~~~~~~~~i~~ir~~~~~~~~~~~~~~~kviiIde~d~l~~~~q~~Llk~lE~---~~~~~~  147 (239)
T d1njfa_          71 VCDNCREIEQGRFVDLIEIDAASRTKVEDTRDLLDNVQYAPARGRFKVYLIDEVHMLSRHSFNALLKTLEE---PPEHVK  147 (239)
T ss_dssp             CSHHHHHHHHTCCTTEEEEETTCSSSHHHHHHHHHSCCCSCSSSSSEEEEEETGGGSCHHHHHHHHHHHHS---CCTTEE
T ss_pred             cchHHHHHHcCCCCeEEEecchhcCCHHHHHHHHHHHHhccccCCCEEEEEECcccCCHHHHHHHHHHHhc---CCCCeE
Confidence            00011111111000      0011223344433332211  124567999999999998888889888874   334667


Q ss_pred             EEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHH
Q psy200          334 LVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAID  413 (490)
Q Consensus       334 lI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~  413 (490)
                      +|++||.   ...+.+.+++||.    .+.|.+++.+++.+++...+..+  ...+++++++.|++   ...||+|.+++
T Consensus       148 ~il~tn~---~~~i~~~i~SRc~----~i~~~~~~~~~i~~~l~~i~~~e--~~~~~~~~l~~i~~---~s~Gd~R~ain  215 (239)
T d1njfa_         148 FLLATTD---PQKLPVTILSRCL----QFHLKALDVEQIRHQLEHILNEE--HIAHEPRALQLLAR---AAEGSLRDALS  215 (239)
T ss_dssp             EEEEESC---GGGSCHHHHTTSE----EEECCCCCHHHHHHHHHHHHHHH--TCCBCHHHHHHHHH---HTTTCHHHHHH
T ss_pred             EEEEcCC---ccccChhHhhhhc----ccccccCcHHHhhhHHHHHHhhh--ccCCCHHHHHHHHH---HcCCCHHHHHH
Confidence            7777873   5678899999995    89999999999999999999887  35689999999987   67899999999


Q ss_pred             HHHHHHHHHHhccccCCcccccCHHHHHHHH
Q psy200          414 ITNHLIDLTYDNVKENGEVTGIGLKEVLGVI  444 (490)
Q Consensus       414 ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~  444 (490)
                      +|+.+..    .+     ...|+.++|.+++
T Consensus       216 ~l~~~~~----~~-----~~~I~~~~v~~~l  237 (239)
T d1njfa_         216 LTDQAIA----SG-----DGQVSTQAVSAML  237 (239)
T ss_dssp             HHHHHHH----HT-----TTSBCHHHHHHHH
T ss_pred             HHHHHHH----hC-----CCCcCHHHHHHHh
Confidence            9987642    23     2379999998876

>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=99.87  E-value=5.4e-21  Score=179.49  Aligned_cols=217  Identities=12%  Similarity=0.150  Sum_probs=161.0

Q ss_pred             CCCCChHHHHHHHHHHHHhhh--------ccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHV--------NNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASV  265 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~--------~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l  265 (490)
                      ++++|.++.+++|.+.+....        ....++++|||||||||||++|++++++++    .+++++++..+.+    
T Consensus        12 ~Di~Gl~~~k~~l~e~v~~~~~~~~~~~~g~~~~~~iLL~GppGtGKT~la~~iA~~~~----~~~~~i~~~~l~~----   83 (256)
T d1lv7a_          12 ADVAGCDEAKEEVAELVEYLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGEAK----VPFFTISGSDFVE----   83 (256)
T ss_dssp             GGSCSCHHHHHHTHHHHHHHHCGGGC-----CCCCEEEEECCTTSCHHHHHHHHHHHHT----CCEEEECSCSSTT----
T ss_pred             HHHhchHHHHHHHHHHHHHHHCHHHHHHcCCCCCCeEEeeCCCCCCccHHHHHHHHHcC----CCEEEEEhHHhhh----
Confidence            689999999999987664321        123567899999999999999999999986    7889999887744    


Q ss_pred             HHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccC-----------HHH---HHHhHhCCCCCCCc
Q psy200          266 YETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRK-----------QTI---LYTIFEWPSIPGSK  331 (490)
Q Consensus       266 ~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~-----------~~~---L~~l~~~~~~~~~~  331 (490)
                                .+.|.+...+...|..+..  ..|+||||||+|.+....           ...   |...++-. ....+
T Consensus        84 ----------~~~g~~~~~l~~~f~~A~~--~~P~il~iDeiD~l~~~r~~~~~~~~~~~~~~~~~ll~~~d~~-~~~~~  150 (256)
T d1lv7a_          84 ----------MFVGVGASRVRDMFEQAKK--AAPCIIFIDEIDAVGRQRGAGLGGGHDEREQTLNQMLVEMDGF-EGNEG  150 (256)
T ss_dssp             ----------SCCCCCHHHHHHHHHHHHT--TCSEEEEETTHHHHTCCCSTTSCCTTCHHHHHHHHHHHHHHTC-CSSSC
T ss_pred             ----------cchhHHHHHHHHHHHHHHH--cCCEEEEEEChhhhCccCCCCCCCCcHHHHHHHHHHHHHhhCC-CCCCC
Confidence                      5677788888887776544  679999999999986431           112   33333322 24567


Q ss_pred             EEEEEecCCCChhHhhhHHhhh--ccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhC-CH
Q psy200          332 LVLVGVANALDLTDRMLPRLQA--NVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSG-DI  408 (490)
Q Consensus       332 vilI~~tn~~~~~~~l~~~l~~--R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~G-d~  408 (490)
                      +++|++||.   ++.+++.+.+  ||.   ..+.|++++.++..+|++..+.+....   .+..+..+++   .+.| ..
T Consensus       151 v~vIatTn~---~~~ld~al~R~gRfd---~~i~i~~P~~~~R~~il~~~l~~~~~~---~~~~~~~la~---~t~G~s~  218 (256)
T d1lv7a_         151 IIVIAATNR---PDVLDPALLRPGRFD---RQVVVGLPDVRGREQILKVHMRRVPLA---PDIDAAIIAR---GTPGFSG  218 (256)
T ss_dssp             EEEEEEESC---TTTSCGGGGSTTSSC---EEEECCCCCHHHHHHHHHHHHTTSCBC---TTCCHHHHHH---TCTTCCH
T ss_pred             EEEEEeCCC---cccCCHhHcCCCCCC---EEEECCCcCHHHHHHHHHHhccCCCcC---cccCHHHHHH---hCCCCCH
Confidence            999999995   4556666664  676   589999999999999999988765222   2334566666   3444 44


Q ss_pred             HHHHHHHHHHHHHHHhccccCCcccccCHHHHHHHHHHhc
Q psy200          409 RKAIDITNHLIDLTYDNVKENGEVTGIGLKEVLGVISSVY  448 (490)
Q Consensus       409 r~ai~ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~~~~~  448 (490)
                      +.+-++|+.|...|..++     ...|+.+||.+|+..+.
T Consensus       219 adi~~l~~~A~~~a~~~~-----~~~i~~~d~~~Al~rv~  253 (256)
T d1lv7a_         219 ADLANLVNEAALFAARGN-----KRVVSMVEFEKAKDKIM  253 (256)
T ss_dssp             HHHHHHHHHHHHHHHHTT-----CSSBCHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHcC-----CCccCHHHHHHHHHHHh
Confidence            555678898988888777     56899999999998875

>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=99.87  E-value=9.4e-22  Score=183.99  Aligned_cols=213  Identities=16%  Similarity=0.165  Sum_probs=151.5

Q ss_pred             CCCCChHHHHHHHHHHHHhhh--------ccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHV--------NNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASV  265 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~--------~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l  265 (490)
                      ++++|.++.++.|.+++....        ....++++||+||||||||++|++++++++    +.++++++..+      
T Consensus         9 ~di~G~~~~k~~l~~~i~~l~~~~~~~~~g~~~~~giLl~GppGtGKT~la~aia~~~~----~~~~~i~~~~l------   78 (247)
T d1ixza_           9 KDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEAR----VPFITASGSDF------   78 (247)
T ss_dssp             GGCCSCHHHHHHHHHHHHHHHCHHHHHHTTCCCCSEEEEECCTTSSHHHHHHHHHHHTT----CCEEEEEHHHH------
T ss_pred             HHHccHHHHHHHHHHHHHHHHCHHHHHHcCCCCCceEEEecCCCCChhHHHHHHHHHcC----CCEEEEEhHHh------
Confidence            679999999888877654321        123467899999999999999999999875    78888876532      


Q ss_pred             HHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccC-----------HHH---HHHhHhCCCCCCCc
Q psy200          266 YETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRK-----------QTI---LYTIFEWPSIPGSK  331 (490)
Q Consensus       266 ~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~-----------~~~---L~~l~~~~~~~~~~  331 (490)
                              ...+.|.+...+.+.|..+.  ...|+||||||+|.+....           ...   |...++-. ....+
T Consensus        79 --------~~~~~g~~~~~l~~~f~~a~--~~~p~Ii~iDeid~l~~~r~~~~~~~~~~~~~~~~~ll~~~d~~-~~~~~  147 (247)
T d1ixza_          79 --------VEMFVGVGAARVRDLFETAK--RHAPCIVFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMDGF-EKDTA  147 (247)
T ss_dssp             --------HHSCTTHHHHHHHHHHHHHT--TSSSEEEEEETHHHHHC---------CHHHHHHHHHHHHHHHTC-CTTCC
T ss_pred             --------hhccccHHHHHHHHHHHHHH--HcCCEEEEEEChhhhCccCCCCCCCCcHHHHHHHHHHHHHhhCC-CCCCC
Confidence                    12455556666666665543  3568999999999986542           112   22333322 34568


Q ss_pred             EEEEEecCCCChhHhhhHHhh--hccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhC-CH
Q psy200          332 LVLVGVANALDLTDRMLPRLQ--ANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSG-DI  408 (490)
Q Consensus       332 vilI~~tn~~~~~~~l~~~l~--~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~G-d~  408 (490)
                      ++||++||.   ++.+++.+.  +||.   ..|.|++|+.++..+|++..+......   .+..++.+++   .+.| ..
T Consensus       148 vivi~tTn~---~~~ld~al~R~~Rf~---~~i~~~~P~~~eR~~il~~~l~~~~~~---~~~~~~~la~---~t~g~s~  215 (247)
T d1ixza_         148 IVVMAATNR---PDILDPALLRPGRFD---RQIAIDAPDVKGREQILRIHARGKPLA---EDVDLALLAK---RTPGFVG  215 (247)
T ss_dssp             EEEEEEESC---GGGSCGGGGSTTSSC---EEEECCSCCHHHHHHHHHHHHTTSCBC---TTCCHHHHHH---TCTTCCH
T ss_pred             EEEEEeCCC---ccccCHhHcCCCCCc---EEEEECCcCHHHHHHHHHHHhcccCCc---cccCHHHHHH---HCCCCCH
Confidence            999999984   456667776  3776   589999999999999999988765222   2334677776   3334 34


Q ss_pred             HHHHHHHHHHHHHHHhccccCCcccccCHHHHHHHH
Q psy200          409 RKAIDITNHLIDLTYDNVKENGEVTGIGLKEVLGVI  444 (490)
Q Consensus       409 r~ai~ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~  444 (490)
                      +.+-++|+.|...|..++     ...|+.+||.+|+
T Consensus       216 ~di~~lv~~A~l~a~~~~-----~~~i~~~d~~~A~  246 (247)
T d1ixza_         216 ADLENLLNEAALLAAREG-----RRKITMKDLEEAA  246 (247)
T ss_dssp             HHHHHHHHHHHHHHHHTT-----CSSBCHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHcC-----CCCcCHHHHHHhh
Confidence            455568899988888887     6789999999986

>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=99.87  E-value=2.1e-22  Score=189.88  Aligned_cols=235  Identities=14%  Similarity=0.181  Sum_probs=164.7

Q ss_pred             cCCCCcchHHHhhcCCCCCCChHHHHHHHHHHHHhhhc-------------cCCCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          178 LFSEDKPKVEEKAKDSCELPGREVQLEGIRQFLLGHVN-------------NETSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       178 ~~~~~~~~~~~~~l~~~~lvgre~~~~~l~~~L~~~~~-------------~~~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      ..|.++|+|...    ++++|.++.+++|..||..+..             .+..++++|+||||||||++|+++++++.
T Consensus         2 ~lW~eky~P~~~----~dlig~~~~~~~L~~~l~~~~~~~~~~~~~~~~~~~~~~~~lll~GPpG~GKTt~a~~la~~~~   77 (253)
T d1sxja2           2 KLWTVKYAPTNL----QQVCGNKGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAAHLVAQELG   77 (253)
T ss_dssp             CCHHHHTCCSSG----GGCCSCHHHHHHHHHHHHTHHHHHHTTTCCCCTTSTTSCSEEEEECSTTSSHHHHHHHHHHHTT
T ss_pred             CccccCcCCCCH----HHhcCCHHHHHHHHHHHHhhhhcchhhhhhhcccCCCCCceEEEECCCCCCHHHHHHHHHHHHH
Confidence            378999999988    9999999999999999976431             22456899999999999999999999976


Q ss_pred             hcCCceEEEEeccCCCCHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCHHHHHHhHhC
Q psy200          245 IKDAFKTIYINCNSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEW  324 (490)
Q Consensus       245 ~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~  324 (490)
                          +.++++++....+...+...+-..+.........    ..........++..+|++||++.+....+..+..++++
T Consensus        78 ----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~vi~ide~~~~~~~~~~~~~~~~~~  149 (253)
T d1sxja2          78 ----YDILEQNASDVRSKTLLNAGVKNALDNMSVVGYF----KHNEEAQNLNGKHFVIIMDEVDGMSGGDRGGVGQLAQF  149 (253)
T ss_dssp             ----CEEEEECTTSCCCHHHHHHTGGGGTTBCCSTTTT----TC----CCSSTTSEEEEECSGGGCCTTSTTHHHHHHHH
T ss_pred             ----hhhhccccccchhhHHHHHHHHHHhhcchhhhhh----hhhhhcccccccceEEEeeeccccccchhhhhHHHhhh
Confidence                6788999988776554433221111111000000    00011122235678999999999998887766666654


Q ss_pred             CCCCCCcEEEEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHh
Q psy200          325 PSIPGSKLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAV  404 (490)
Q Consensus       325 ~~~~~~~vilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~  404 (490)
                      .......+++++.++....    ...+++|+.    .+.|.+++.+++..++...+..++  ..+++++++.|++   .+
T Consensus       150 ~~~~~~~ii~i~~~~~~~~----~~~l~~~~~----~i~f~~~~~~~i~~~l~~i~~~e~--i~i~~~~l~~i~~---~s  216 (253)
T d1sxja2         150 CRKTSTPLILICNERNLPK----MRPFDRVCL----DIQFRRPDANSIKSRLMTIAIREK--FKLDPNVIDRLIQ---TT  216 (253)
T ss_dssp             HHHCSSCEEEEESCTTSST----TGGGTTTSE----EEECCCCCHHHHHHHHHHHHHHHT--CCCCTTHHHHHHH---HT
T ss_pred             hcccccccccccccccccc----cccccceee----eeeccccchhHHHHHHHHHHHHhC--CCCCHHHHHHHHH---hC
Confidence            4334456777766553332    334666663    899999999999999999998763  4578899999987   67


Q ss_pred             hCCHHHHHHHHHHHHHHHHhccccCCcccccCHHHHHHHHHHh
Q psy200          405 SGDIRKAIDITNHLIDLTYDNVKENGEVTGIGLKEVLGVISSV  447 (490)
Q Consensus       405 ~Gd~r~ai~ll~~a~~~a~~~~~~~~~~~~It~~~v~~a~~~~  447 (490)
                      .||+|.+|+.|+.+..   ..       ..|+.+++.++....
T Consensus       217 ~GDiR~ai~~L~~~~~---~~-------~~i~~~~~~~~~~~~  249 (253)
T d1sxja2         217 RGDIRQVINLLSTIST---TT-------KTINHENINEISKAW  249 (253)
T ss_dssp             TTCHHHHHHHHTHHHH---HS-------SCCCTTHHHHHHHHH
T ss_pred             CCcHHHHHHHHHHHHH---cC-------CCCCHHHHHHHhchh
Confidence            8999999998865432   12       257777766655443

>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=99.85  E-value=3.3e-20  Score=173.22  Aligned_cols=212  Identities=16%  Similarity=0.202  Sum_probs=158.3

Q ss_pred             CCCCChHHHHHHHHHHHHhhhcc-CCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVNN-ETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNE  272 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~-~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~  272 (490)
                      ++++|+++.++.|..|+...... ...++++|+||||||||++|+.+++++.    +.+..+++......          
T Consensus         9 ddivGq~~~~~~L~~~i~~~~~~~~~~~~~Ll~GPpG~GKTtla~~la~~~~----~~~~~~~~~~~~~~----------   74 (239)
T d1ixsb2           9 DEYIGQERLKQKLRVYLEAAKARKEPLEHLLLFGPPGLGKTTLAHVIAHELG----VNLRVTSGPAIEKP----------   74 (239)
T ss_dssp             GGSCSCHHHHHHHHHHHHHHTTSSSCCCCEEEECCTTSCHHHHHHHHHHHHT----CCEEEEETTTCCSH----------
T ss_pred             HHhCCHHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHHHHHhC----CCeEeccCCccccc----------
Confidence            78999999999999999765432 3568999999999999999999999986    56777776655332          


Q ss_pred             hcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCHHHHHHhHhCC---------------CCCCCcEEEEEe
Q psy200          273 LKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWP---------------SIPGSKLVLVGV  337 (490)
Q Consensus       273 l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~---------------~~~~~~vilI~~  337 (490)
                                ......+...+   ....+++|||+|.+....++.+...++-.               .....+++++++
T Consensus        75 ----------~~~~~~~~~~~---~~~~i~~iDe~~~~~~~~~~~l~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~i~~  141 (239)
T d1ixsb2          75 ----------GDLAAILANSL---EEGDILFIDEIHRLSRQAEEHLYPAMEDFVMDIVIGQGPAARTIRLELPRFTLIGA  141 (239)
T ss_dssp             ----------HHHHHHHHTTC---CTTCEEEEETGGGCCHHHHHHHHHHHHHSEEEEECSCTTCCCEEEEECCCCEEEEE
T ss_pred             ----------hhhHHHHHhhc---cCCCeeeeecccccchhHHHhhhhhhhhhhhhhhhccchhhhhcccCCCCEEEEee
Confidence                      11222222212   23459999999999888777777655321               012456778888


Q ss_pred             cCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHHHHHH
Q psy200          338 ANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITNH  417 (490)
Q Consensus       338 tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll~~  417 (490)
                      ++.....  ..+.+++++    ..+.|.+++.+++..++...+..+  ...++++.++.+++   ...||+|.++++++.
T Consensus       142 ~~~~~~~--~~~~l~~~~----~~~~~~~~~~~~~~~i~~~~~~~~--~i~~~~~~l~~ia~---~s~gd~R~a~~~l~~  210 (239)
T d1ixsb2         142 TTRPGLI--TAPLLSRFG----IVEHLEYYTPEELAQGVMRDARLL--GVRITEEAALEIGR---RSRGTMRVAKRLFRR  210 (239)
T ss_dssp             ESCCSSC--SCGGGGGCS----EEEECCCCCHHHHHHHHHHHHGGG--CCCBCHHHHHHHHH---HTTSSHHHHHHHHHH
T ss_pred             ccCcccc--cchhhcccc----eeeEeeccChhhhhHHHHHHHHHh--CCccchHHHHHHHH---HcCCCHHHHHHHHHH
Confidence            8743221  123344443    389999999999999999999887  46789999999987   778999999999999


Q ss_pred             HHHHHHhccccCCcccccCHHHHHHHHHHhc
Q psy200          418 LIDLTYDNVKENGEVTGIGLKEVLGVISSVY  448 (490)
Q Consensus       418 a~~~a~~~~~~~~~~~~It~~~v~~a~~~~~  448 (490)
                      +...+...+     ...|+.+++.+++..+.
T Consensus       211 ~~~~a~~~~-----~~~It~~~~~~~l~~l~  236 (239)
T d1ixsb2         211 VRDFAQVAG-----EEVITRERALEALAALG  236 (239)
T ss_dssp             HHHHHTTSC-----CSCBCHHHHHHHHHHHT
T ss_pred             HHHHHHHhC-----CCCcCHHHHHHHHhhhC
Confidence            988887777     56899999999987553

>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=99.84  E-value=2.3e-20  Score=176.12  Aligned_cols=219  Identities=16%  Similarity=0.213  Sum_probs=151.3

Q ss_pred             CCCCChHHHHHHHHHHHHhhhc---------cCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVN---------NETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAAS  264 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~---------~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~  264 (490)
                      ++++|.++.++.|.+.+...+.         ...++++|||||||||||++++++++++.    ..++.+++..+.+   
T Consensus         4 ~dv~G~~~~k~~l~~~i~~~l~~~~~~~~~g~~~~~giLL~GppGtGKT~l~~ala~~~~----~~~~~i~~~~l~~---   76 (258)
T d1e32a2           4 DDVGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANETG----AFFFLINGPEIMS---   76 (258)
T ss_dssp             GGCCSCSHHHHHHHHHHHHHHHCHHHHHHCCCCCCCEEEEECCTTSSHHHHHHHHHHHTT----CEEEEECHHHHTT---
T ss_pred             hhhccHHHHHHHHHHHHHHHhcCHHHHHhCCCCCCceeEEecCCCCCchHHHHHHHHHhC----CeEEEEEchhhcc---
Confidence            5799999999999998654322         12567899999999999999999999875    7788887665422   


Q ss_pred             HHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCH-----------HHHHHhHhCCCCCCCcEE
Q psy200          265 VYETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQ-----------TILYTIFEWPSIPGSKLV  333 (490)
Q Consensus       265 l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~-----------~~L~~l~~~~~~~~~~vi  333 (490)
                                 .+.+.....+...|..+..  ..|+||||||+|.+.....           ..+...+.. .....+++
T Consensus        77 -----------~~~g~~~~~l~~~f~~A~~--~~p~il~iDeid~l~~~r~~~~~~~~~~~~~~~~~~~~~-~~~~~~vl  142 (258)
T d1e32a2          77 -----------KLAGESESNLRKAFEEAEK--NAPAIIFIDELDAIAPKREKTHGEVERRIVSQLLTLMDG-LKQRAHVI  142 (258)
T ss_dssp             -----------SCTTHHHHHHHHHHHHHHH--TCSEEEEESSGGGTCCHHHHCCCTTHHHHHHHHHHHHHT-CCCSSCEE
T ss_pred             -----------cccccHHHHHHHHHHHHHh--cCCeEEEehhhhhhccCCCCCCCchHHHHHHHhcccccc-ccccCCcc
Confidence                       4455556666666666554  5689999999999975421           122222322 34566799


Q ss_pred             EEEecCCCChhHhhhHHhhh--ccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhC-CHHH
Q psy200          334 LVGVANALDLTDRMLPRLQA--NVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSG-DIRK  410 (490)
Q Consensus       334 lI~~tn~~~~~~~l~~~l~~--R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~G-d~r~  410 (490)
                      +|++||.   ++.+++.+.+  ||.   ..|.|++++.++...|+...+....  . -.+..++.|++   .+.| ..+.
T Consensus       143 vi~tTn~---~~~ld~al~r~gRfd---~~i~~~~P~~~~R~~il~~~l~~~~--~-~~~~~~~~la~---~t~G~s~ad  210 (258)
T d1e32a2         143 VMAATNR---PNSIDPALRRFGRFD---REVDIGIPDATGRLEILQIHTKNMK--L-ADDVDLEQVAN---ETHGHVGAD  210 (258)
T ss_dssp             EEEEESC---GGGSCGGGTSTTSSC---EEEECCCCCHHHHHHHHHHTTTTSC--B-CTTCCHHHHHH---HCTTCCHHH
T ss_pred             EEEeCCC---ccccchhhhhccccc---ceeECCCCCHHHHHHHhhhhccCcc--c-ccccchhhhhh---cccCCCHHH
Confidence            9999994   4556667765  676   6899999999999999998886542  1 12234777877   3334 3344


Q ss_pred             HHHHHHHHHHHHHhccccC------------CcccccCHHHHHHHHH
Q psy200          411 AIDITNHLIDLTYDNVKEN------------GEVTGIGLKEVLGVIS  445 (490)
Q Consensus       411 ai~ll~~a~~~a~~~~~~~------------~~~~~It~~~v~~a~~  445 (490)
                      +-++++.|...|..+....            .....|+++||..|+.
T Consensus       211 l~~lv~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~it~~Df~~AL~  257 (258)
T d1e32a2         211 LAALCSEAALQAIRKKMDLIDLEDETIDAEVMNSLAVTMDDFRWALS  257 (258)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHCCCSSCCBHHHHHHCCBCHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHhhccccchhhhhhhhhhhccCccCHHHHHHHhC
Confidence            4457777766665443110            1134589999999875

>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=99.83  E-value=1.2e-20  Score=177.41  Aligned_cols=219  Identities=15%  Similarity=0.151  Sum_probs=139.3

Q ss_pred             CCCcchHHHhhcCCCCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCC
Q psy200          180 SEDKPKVEEKAKDSCELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSV  259 (490)
Q Consensus       180 ~~~~~~~~~~~l~~~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~  259 (490)
                      |.++|+|...    ++++|+++..+.|..++..   .....+++|+||+|+|||++|+++++++... ......+++...
T Consensus         1 W~eky~P~~~----~diig~~~~~~~L~~~~~~---~~~~~~lll~Gp~G~GKTt~~~~la~~l~~~-~~~~~~~~~~~~   72 (252)
T d1sxje2           1 WVDKYRPKSL----NALSHNEELTNFLKSLSDQ---PRDLPHLLLYGPNGTGKKTRCMALLESIFGP-GVYRLKIDVRQF   72 (252)
T ss_dssp             CTTTTCCCSG----GGCCSCHHHHHHHHTTTTC---TTCCCCEEEECSTTSSHHHHHHTHHHHHSCT-TCCC--------
T ss_pred             CCcccCCCCH----HHccCcHHHHHHHHHHHHc---CCCCCeEEEECCCCCCHHHHHHHHHHhhcCc-cccccccccccc
Confidence            8889999988    9999999988888777653   3456689999999999999999999987321 111111111111


Q ss_pred             CCHHHHHHHHHHH-------hcCCCCCC-cHHHHHHHHHHHH------------hcCCCeEEEEEecCccccccCHHHHH
Q psy200          260 RNAASVYETIVNE-------LKLKPGGK-SERHQLGAILKYF------------DTKHKSILLILDEIDALESRKQTILY  319 (490)
Q Consensus       260 ~~~~~l~~~i~~~-------l~~~~~~~-s~~~~~~~l~~~l------------~~~~~~~vI~IDEid~l~~~~~~~L~  319 (490)
                      .........+...       +.....+. ........+....            ...+...+|+|||+|.+....+..|.
T Consensus        73 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iiiide~d~l~~~~~~~l~  152 (252)
T d1sxje2          73 VTASNRKLELNVVSSPYHLEITPSDMGNNDRIVIQELLKEVAQMEQVDFQDSKDGLAHRYKCVIINEANSLTKDAQAALR  152 (252)
T ss_dssp             ----------CCEECSSEEEECCC----CCHHHHHHHHHHHTTTTC------------CCEEEEEECTTSSCHHHHHHHH
T ss_pred             cccccchhhhhhccCCccceeeecccccCCcceeeehhhhhhhhhhhhhhhcccccCCCceEEEeccccccccccchhhh
Confidence            1100000000000       00000000 1111111111110            01134569999999999888888888


Q ss_pred             HhHhCCCCCCCcEEEEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHH
Q psy200          320 TIFEWPSIPGSKLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAG  399 (490)
Q Consensus       320 ~l~~~~~~~~~~vilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~  399 (490)
                      .+++..   ..++.+|++||..   +.+.+.+++||.    .++|++++.+++.+++...+..++.. ..++++++.|+.
T Consensus       153 ~~~e~~---~~~~~~Il~tn~~---~~i~~~l~sR~~----~i~~~~~~~~~~~~~l~~i~~~e~~~-~~~~~~l~~i~~  221 (252)
T d1sxje2         153 RTMEKY---SKNIRLIMVCDSM---SPIIAPIKSQCL----LIRCPAPSDSEISTILSDVVTNERIQ-LETKDILKRIAQ  221 (252)
T ss_dssp             HHHHHS---TTTEEEEEEESCS---CSSCHHHHTTSE----EEECCCCCHHHHHHHHHHHHHHHTCE-ECCSHHHHHHHH
T ss_pred             cccccc---cccccceeeeccc---cchhhhhhcchh----eeeecccchhhHHHHHHHHHHHcCCC-CCcHHHHHHHHH
Confidence            887743   3456677778753   556788999984    79999999999999999988876322 235678888887


Q ss_pred             HHHHhhCCHHHHHHHHHHHHH
Q psy200          400 KVAAVSGDIRKAIDITNHLID  420 (490)
Q Consensus       400 ~i~~~~Gd~r~ai~ll~~a~~  420 (490)
                         .+.||+|.+|++|+.+..
T Consensus       222 ---~s~Gd~R~ai~~Lq~~~~  239 (252)
T d1sxje2         222 ---ASNGNLRVSLLMLESMAL  239 (252)
T ss_dssp             ---HHTTCHHHHHHHHTHHHH
T ss_pred             ---HcCCcHHHHHHHHHHHHH
Confidence               678999999999987654

>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=99.78  E-value=1.1e-17  Score=156.45  Aligned_cols=231  Identities=17%  Similarity=0.174  Sum_probs=163.9

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhc------CCceEEEEeccCCCCHHHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIK------DAFKTIYINCNSVRNAASVYE  267 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~------~~~~~~~v~~~~~~~~~~l~~  267 (490)
                      +.++||+++++++.+.|..    ....+++|+|+||+|||++++.+++.+...      .+..++.+++..+..      
T Consensus        18 d~~igRd~Ei~~l~~iL~r----~~k~n~lLVG~~GvGKTalv~~la~ri~~~~vp~~l~~~~i~~l~~~~lia------   87 (268)
T d1r6bx2          18 DPLIGREKELERAIQVLCR----RRKNNPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYSLDIGSLLA------   87 (268)
T ss_dssp             CCCCSCHHHHHHHHHHHTS----SSSCEEEEECCTTSSHHHHHHHHHHHHHHTCSCGGGTTCEEEECCCC---C------
T ss_pred             CcccChHHHHHHHHHHHhc----CccCCcEEECCCCCcHHHHHHHHHHHHHhCCcccccccceeEEeeechHhc------
Confidence            6789999999999999953    556789999999999999999999987532      234677777665522      


Q ss_pred             HHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccC-----HHHHHHhHhCCCCCCCcEEEEEecCCCC
Q psy200          268 TIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRK-----QTILYTIFEWPSIPGSKLVLVGVANALD  342 (490)
Q Consensus       268 ~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~-----~~~L~~l~~~~~~~~~~vilI~~tn~~~  342 (490)
                            +..+.|.-...+...+.+ +.. ...+||||||+|.|...+     ..-+..++. +......+.+||+|+..+
T Consensus        88 ------g~~~~g~~e~r~~~i~~~-~~~-~~~iIlfiDeih~l~~~g~~~g~~~d~a~~Lk-p~L~rg~i~vIgatT~ee  158 (268)
T d1r6bx2          88 ------GTKYRGDFEKRFKALLKQ-LEQ-DTNSILFIDEIHTIIGAGAASGGQVDAANLIK-PLLSSGKIRVIGSTTYQE  158 (268)
T ss_dssp             ------CCCCSSCHHHHHHHHHHH-HSS-SSCEEEEETTTTTTTTSCCSSSCHHHHHHHHS-SCSSSCCCEEEEEECHHH
T ss_pred             ------cCccchhHHHHHHHHHHH-hhc-cCCceEEecchHHHhcCCCCCCccccHHHHhh-HHHhCCCCeEEEeCCHHH
Confidence                  224444444444444444 333 457899999999997542     223445553 455677899999998554


Q ss_pred             hhHhh--hHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhcc--CCCCCCCHHHHHHHHHHHHHhhC---CHHHHHHHH
Q psy200          343 LTDRM--LPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQT--DKFNMFNASALQLLAGKVAAVSG---DIRKAIDIT  415 (490)
Q Consensus       343 ~~~~l--~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~--~~~~~~~~~~i~~i~~~i~~~~G---d~r~ai~ll  415 (490)
                      +...+  ++.|.+||.    .+.+.+++.++...||.......  .....+++++++.+.+....+-.   -+.++|++|
T Consensus       159 y~~~~e~d~al~rrF~----~I~V~Eps~e~t~~IL~~~~~~~e~~h~v~~~~~al~~~v~ls~ryi~~~~~PdKAIdll  234 (268)
T d1r6bx2         159 FSNIFEKDRALARRFQ----KIDITEPSIEETVQIINGLKPKYEAHHDVRYTAKAVRAAVELAVKYINDRHLPDKAIDVI  234 (268)
T ss_dssp             HHCCCCCTTSSGGGEE----EEECCCCCHHHHHHHHHHHHHHHHHHHTCCCCHHHHHHHHHHHHHHCTTSCTTHHHHHHH
T ss_pred             HHHHHhhcHHHHhhhc----ccccCCCCHHHHHHHHHHhhHHHhccCCEEeChHHHHHHHHHHHhhccCCCCCcHHHHHH
Confidence            43322  578899996    89999999999999987644332  24577999999998876655444   377999999


Q ss_pred             HHHHHHHHhccccCCcccccCHHHHHHHHHHhc
Q psy200          416 NHLIDLTYDNVKENGEVTGIGLKEVLGVISSVY  448 (490)
Q Consensus       416 ~~a~~~a~~~~~~~~~~~~It~~~v~~a~~~~~  448 (490)
                      +.|+..+...... .....|+.+|+...+.++.
T Consensus       235 Dea~a~~~~~~~~-~~~~~i~~~di~~~i~~~~  266 (268)
T d1r6bx2         235 DEAGARARLMPVS-KRKKTVNVADIESVVARIA  266 (268)
T ss_dssp             HHHHHHHHHSSSC-CCCCSCCHHHHHHHHHHHS
T ss_pred             HHHHHHHHhhccc-cCcccCCHHHHHHHHHHHh
Confidence            9998777643211 1134689999999888764

>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=99.73  E-value=5.2e-18  Score=160.29  Aligned_cols=202  Identities=16%  Similarity=0.216  Sum_probs=134.4

Q ss_pred             CCCCChHHHHHHHHHHHHhhhc---------cCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVN---------NETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAAS  264 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~---------~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~  264 (490)
                      ++++|.++.+++|.+++...+.         -..++++|||||||||||+++++++.+++    ..++++++..+     
T Consensus         7 ~di~G~~~~k~~l~~~i~~~l~~~~~~~~~g~~~~~giLL~Gp~GtGKT~l~~ala~~~~----~~~~~~~~~~l-----   77 (265)
T d1r7ra3           7 EDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANECQ----ANFISIKGPEL-----   77 (265)
T ss_dssp             SSCSSSSCCCCHHHHHTHHHHHCHHHHHHCCCCCCCEEEEBCCTTSSHHHHHHHHHHHTT----CEEEEECHHHH-----
T ss_pred             HHhcCHHHHHHHHHHHHHHHhhCHHHHHhCCCCCCCeEEEECCCCCcchhHHHHHHHHhC----CcEEEEEHHHh-----
Confidence            5678887777777776653322         12467899999999999999999999986    77888875443     


Q ss_pred             HHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccC-----------HHHHHHhHhCCC--CCCCc
Q psy200          265 VYETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRK-----------QTILYTIFEWPS--IPGSK  331 (490)
Q Consensus       265 l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~-----------~~~L~~l~~~~~--~~~~~  331 (490)
                               ...+.+.....+...|..+..  ..|+||+|||+|.+....           ...+..++.+..  ....+
T Consensus        78 ---------~~~~~~~~~~~l~~~f~~A~~--~~p~il~ideid~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~  146 (265)
T d1r7ra3          78 ---------LTMWFGESEANVREIFDKARQ--AAPCVLFFDELDSIAKARGGNIGDGGGAADRVINQILTEMDGMSTKKN  146 (265)
T ss_dssp             ---------HTSCTTTHHHHHHHHHHHHHH--TCSEEEEESSGGGTCCHHHHCCCTTHHHHHHHHHHHHHTCC------C
T ss_pred             ---------hhccccchHHHHHHHHHHHHh--cCCcceeHHhhhhccccCCCcCCCCcHHHHHHHHHHHHHhhCcCCCCC
Confidence                     224555666667677766554  568999999999997541           112333333321  23456


Q ss_pred             EEEEEecCCCChhHhhhHHhhh--ccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHH
Q psy200          332 LVLVGVANALDLTDRMLPRLQA--NVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIR  409 (490)
Q Consensus       332 vilI~~tn~~~~~~~l~~~l~~--R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r  409 (490)
                      +++|++||..   +.+++.+.+  ||.   ..|.|++++.++..+||+..+.....   ..+..++.+++...+.  ...
T Consensus       147 v~vi~ttn~~---~~ld~al~r~gRf~---~~i~~~~p~~~~R~~il~~~l~~~~~---~~~~~l~~la~~t~g~--s~~  215 (265)
T d1r7ra3         147 VFIIGATNRP---DIIDPAILRPGRLD---QLIYIPLPDEKSRVAILKANLRKSPV---AKDVDLEFLAKMTNGF--SGA  215 (265)
T ss_dssp             CEEEECCBSC---TTTSCGGGSSTTSE---EEEECCCCCCHHHHHHHHHHTTCC-------CCCCHHHHHHHCSS--CCH
T ss_pred             EEEEEeCCCc---hhCCHHHhCCCCcc---EEEEecchHHHHHHHHHHHHhccCCc---hhhhhHHHHHhcCCCC--CHH
Confidence            8999999854   445566654  676   58999999999999999987765411   1222356676633322  234


Q ss_pred             HHHHHHHHHHHHHHhcc
Q psy200          410 KAIDITNHLIDLTYDNV  426 (490)
Q Consensus       410 ~ai~ll~~a~~~a~~~~  426 (490)
                      .+-++|++|...|.++.
T Consensus       216 di~~lv~~A~~~A~~~~  232 (265)
T d1r7ra3         216 DLTEICQRACKLAIRES  232 (265)
T ss_dssp             HHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHHH
Confidence            44567888887777554

>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=99.70  E-value=4.6e-16  Score=141.27  Aligned_cols=195  Identities=13%  Similarity=0.121  Sum_probs=128.9

Q ss_pred             CChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhc--
Q psy200          197 PGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELK--  274 (490)
Q Consensus       197 vgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~--  274 (490)
                      ..+++.+++|...+..   +..++.++|+||+|+|||++|+.+++.+......  ..-.|....+...+.......+.  
T Consensus         5 Pw~~~~~~~l~~~~~~---~~l~h~lLl~Gp~G~GKtt~a~~~a~~l~~~~~~--~~~~~~~~~~~~~i~~~~~~~~~~~   79 (207)
T d1a5ta2           5 PWLRPDFEKLVASYQA---GRGHHALLIQALPGMGDDALIYALSRYLLCQQPQ--GHKSCGHCRGCQLMQAGTHPDYYTL   79 (207)
T ss_dssp             GGGHHHHHHHHHHHHT---TCCCSEEEEECCTTSCHHHHHHHHHHHHTCSSCB--TTBCCSCSHHHHHHHHTCCTTEEEE
T ss_pred             cccHHHHHHHHHHHHc---CCcCeEEEEECCCCCcHHHHHHHHHHhccccccc--ccccccccchhhhhhhccccccchh
Confidence            4566777777777763   3456679999999999999999999987421110  00011111111111110000000  


Q ss_pred             ---CCCCCCcHHHHHHHHHHHHh--cCCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEEEecCCCChhHhhhH
Q psy200          275 ---LKPGGKSERHQLGAILKYFD--TKHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVANALDLTDRMLP  349 (490)
Q Consensus       275 ---~~~~~~s~~~~~~~l~~~l~--~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI~~tn~~~~~~~l~~  349 (490)
                         ........+.+++.......  ..++..||||||+|.|....+..|+.+++.+   ..++++|.+|+.   ..++++
T Consensus        80 ~~~~~~~~i~~~~ir~l~~~~~~~~~~~~~kviIide~d~l~~~a~n~Llk~lEep---~~~~~fIl~t~~---~~~ll~  153 (207)
T d1a5ta2          80 APEKGKNTLGVDAVREVTEKLNEHARLGGAKVVWVTDAALLTDAAANALLKTLEEP---PAETWFFLATRE---PERLLA  153 (207)
T ss_dssp             CCCTTCSSBCHHHHHHHHHHTTSCCTTSSCEEEEESCGGGBCHHHHHHHHHHHTSC---CTTEEEEEEESC---GGGSCH
T ss_pred             hhhhcccccccchhhHHhhhhhhccccCccceEEechhhhhhhhhhHHHHHHHHhh---cccceeeeeecC---hhhhhh
Confidence               00111234444444333221  1356779999999999999999999998854   456777777763   467899


Q ss_pred             HhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHHHHH
Q psy200          350 RLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITN  416 (490)
Q Consensus       350 ~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll~  416 (490)
                      .+++||.    .+.|.+++.+++..+|...       ..+++++++.+++   ...|++|.||++++
T Consensus       154 tI~SRc~----~i~~~~~~~~~~~~~L~~~-------~~~~~~~~~~i~~---~s~Gs~r~al~~le  206 (207)
T d1a5ta2         154 TLRSRCR----LHYLAPPPEQYAVTWLSRE-------VTMSQDALLAALR---LSAGSPGAALALFQ  206 (207)
T ss_dssp             HHHTTSE----EEECCCCCHHHHHHHHHHH-------CCCCHHHHHHHHH---HTTTCHHHHHHTTS
T ss_pred             hhcceeE----EEecCCCCHHHHHHHHHHc-------CCCCHHHHHHHHH---HcCCCHHHHHHHhC
Confidence            9999995    8999999999999988753       3368899999987   67799999998764

>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=99.68  E-value=1.4e-15  Score=141.66  Aligned_cols=190  Identities=16%  Similarity=0.174  Sum_probs=116.6

Q ss_pred             CCCCChHHHHHHHHHHHHhhh------ccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHV------NNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYE  267 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~------~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~  267 (490)
                      +.++|..+.++.+.+-+...+      ...+.+++||+||||||||++|++++++++    +.++.++++....      
T Consensus         9 ~~~i~~~~~i~~i~~~~~~~~~~~~~~~~~p~~~vLL~GppGtGKT~la~alA~~~~----~~~~~i~~~~~~~------   78 (246)
T d1d2na_           9 NGIIKWGDPVTRVLDDGELLVQQTKNSDRTPLVSVLLEGPPHSGKTALAAKIAEESN----FPFIKICSPDKMI------   78 (246)
T ss_dssp             TCCCCCSHHHHHHHHHHHHHHHHHHHCSSCSEEEEEEECSTTSSHHHHHHHHHHHHT----CSEEEEECGGGCT------
T ss_pred             cCCcCcCHHHHHHHHHHHHHHHHHhccCCCCCeEEEEECcCCCCHHHHHHHHhhccc----ccccccccccccc------
Confidence            567777666655555443222      122457899999999999999999999976    7888888765311      


Q ss_pred             HHHHHhcCCCCCCc-HHHHHHHHHHHHhcCCCeEEEEEecCccccccC-------H---HHHHHhHhCCCCCCCcEEEEE
Q psy200          268 TIVNELKLKPGGKS-ERHQLGAILKYFDTKHKSILLILDEIDALESRK-------Q---TILYTIFEWPSIPGSKLVLVG  336 (490)
Q Consensus       268 ~i~~~l~~~~~~~s-~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~-------~---~~L~~l~~~~~~~~~~vilI~  336 (490)
                              ...+.+ ...+...|..+..  ..|+||||||||.+....       .   ..|..+++.......+++||+
T Consensus        79 --------g~~~~~~~~~i~~if~~A~~--~~p~il~iDEid~l~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~v~vi~  148 (246)
T d1d2na_          79 --------GFSETAKCQAMKKIFDDAYK--SQLSCVVVDDIERLLDYVPIGPRFSNLVLQALLVLLKKAPPQGRKLLIIG  148 (246)
T ss_dssp             --------TCCHHHHHHHHHHHHHHHHT--SSEEEEEECCHHHHTTCBTTTTBCCHHHHHHHHHHTTCCCSTTCEEEEEE
T ss_pred             --------cccccchhhhhhhhhhhhhh--cccceeehhhhhhHhhhcccccchhHHHHHHHHHHhcCCCccccceeeee
Confidence                    111111 1223344544443  568999999999985431       2   233344443334556899999


Q ss_pred             ecCCCChhHhhhH-HhhhccCCCCeeEEeCCCC-HHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhC--CHHHHH
Q psy200          337 VANALDLTDRMLP-RLQANVTLQPTLMNFAPYS-REQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSG--DIRKAI  412 (490)
Q Consensus       337 ~tn~~~~~~~l~~-~l~~R~~~~~~~i~~~pls-~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~G--d~r~ai  412 (490)
                      +||..   +.+++ .+.+||.   ..|.|+.+. .+++.+++...       ..+.+..+..+++.+.+..+  +++.++
T Consensus       149 tTn~~---~~ld~~~~~~rF~---~~i~~P~~~~r~~il~~l~~~-------~~~~~~~~~~i~~~~~g~~~~~~ik~ll  215 (246)
T d1d2na_         149 TTSRK---DVLQEMEMLNAFS---TTIHVPNIATGEQLLEALELL-------GNFKDKERTTIAQQVKGKKVWIGIKKLL  215 (246)
T ss_dssp             EESCH---HHHHHTTCTTTSS---EEEECCCEEEHHHHHHHHHHH-------TCSCHHHHHHHHHHHTTSEEEECHHHHH
T ss_pred             ccCCh---hhccchhhcCccc---eEEecCCchhHHHHHHHHHhc-------cCCChHHHHHHHHHcCCCccchhHHHHH
Confidence            99953   44443 3667886   468885554 55666655432       23577777888874433222  466666


Q ss_pred             HHHH
Q psy200          413 DITN  416 (490)
Q Consensus       413 ~ll~  416 (490)
                      .+++
T Consensus       216 ~~ie  219 (246)
T d1d2na_         216 MLIE  219 (246)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            5543

>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=99.65  E-value=1e-15  Score=151.01  Aligned_cols=210  Identities=18%  Similarity=0.206  Sum_probs=136.9

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhc------CCceEEEEeccCCCCHHHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIK------DAFKTIYINCNSVRNAASVYE  267 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~------~~~~~~~v~~~~~~~~~~l~~  267 (490)
                      +.++||+++++++.+.|..    ....+++|+|+||+|||+++..+++.+...      .+..++.++...+..      
T Consensus        22 d~~~gr~~ei~~~~~~L~r----~~k~n~llvG~~GvGKtaiv~~la~~i~~~~vp~~l~~~~i~~ld~~~l~a------   91 (387)
T d1qvra2          22 DPVIGRDEEIRRVIQILLR----RTKNNPVLIGEPGVGKTAIVEGLAQRIVKGDVPEGLKGKRIVSLQMGSLLA------   91 (387)
T ss_dssp             CCCCSCHHHHHHHHHHHHC----SSCCCCEEEECTTSCHHHHHHHHHHHHHHTCSCTTSTTCEEEEECC-----------
T ss_pred             CCCcCcHHHHHHHHHHHhc----CCCCCCeEECCCCCCHHHHHHHHHHHHHhCCCCHHHcCceEEEeeHhhhhc------
Confidence            7899999999999999964    456677888999999999999999887532      134677887766522      


Q ss_pred             HHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCHH----HHHHhHhCCCCCCCcEEEEEecCCCCh
Q psy200          268 TIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQT----ILYTIFEWPSIPGSKLVLVGVANALDL  343 (490)
Q Consensus       268 ~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~~----~L~~l~~~~~~~~~~vilI~~tn~~~~  343 (490)
                            +..+.|.-...+...+.+... ...++||||||+|.+.+.+..    -+.+++. +....+.+-+||+|+..++
T Consensus        92 ------g~~~~g~~e~r~~~i~~~~~~-~~~~~ilfide~h~l~~~g~~~g~~d~a~~Lk-p~L~rg~~~~I~~tT~~ey  163 (387)
T d1qvra2          92 ------GAKYRGEFEERLKAVIQEVVQ-SQGEVILFIDELHTVVGAGKAEGAVDAGNMLK-PALARGELRLIGATTLDEY  163 (387)
T ss_dssp             ------------CHHHHHHHHHHHHHT-TCSSEEEEECCC-------------------H-HHHHTTCCCEEEEECHHHH
T ss_pred             ------ccCcchhHHHHHHHHHHHhcc-CCCceEEEeccHHHHhcCCCCCCcccHHHHHH-HHHhCCCcceeeecCHHHH
Confidence                  123344444455455544333 345789999999999764311    1122221 2224567888888885554


Q ss_pred             hHhh--hHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhcc--CCCCCCCHHHHHHHHHHHHHhh---CCHHHHHHHHH
Q psy200          344 TDRM--LPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQT--DKFNMFNASALQLLAGKVAAVS---GDIRKAIDITN  416 (490)
Q Consensus       344 ~~~l--~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~--~~~~~~~~~~i~~i~~~i~~~~---Gd~r~ai~ll~  416 (490)
                      . .+  ++.|.+||.    .+.+.+++.++...||+......  .+...++++++..+.+....+-   .-+.+||++|.
T Consensus       164 ~-~~e~d~al~rrF~----~v~v~ep~~~~~~~il~~~~~~~e~~h~v~~~~~ai~~~v~ls~ryi~~r~~PdKAidlld  238 (387)
T d1qvra2         164 R-EIEKDPALERRFQ----PVYVDEPTVEETISILRGLKEKYEVHHGVRISDSAIIAAATLSHRYITERRLPDKAIDLID  238 (387)
T ss_dssp             H-HHTTCTTTCSCCC----CEEECCCCHHHHHHHHHHHHHHHHHHTTCEECHHHHHHHHHHHHHHCCSSCTHHHHHHHHH
T ss_pred             H-HhcccHHHHHhcc----cccCCCCcHHHHHHHHHHHHHHHHhccCCcccHHHHHHHHHhcccccccccChhhHHHHHH
Confidence            2 23  568889996    89999999999999988655443  2467799999999887655544   34889999999


Q ss_pred             HHHHHHHhcc
Q psy200          417 HLIDLTYDNV  426 (490)
Q Consensus       417 ~a~~~a~~~~  426 (490)
                      .|+..+....
T Consensus       239 ~a~a~~~i~~  248 (387)
T d1qvra2         239 EAAARLRMAL  248 (387)
T ss_dssp             HHHHHHHHTT
T ss_pred             HHHHHHHhhc
Confidence            9987766543

>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=99.61  E-value=2.4e-14  Score=130.15  Aligned_cols=196  Identities=19%  Similarity=0.279  Sum_probs=127.8

Q ss_pred             CCCCCh--HHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHH
Q psy200          194 CELPGR--EVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVN  271 (490)
Q Consensus       194 ~~lvgr--e~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~  271 (490)
                      +.++|.  +.....+.++++.  .+...+.++|||++|+|||+|++++++++.. .+..++|+++      ..+...+..
T Consensus        11 nF~vg~~N~~a~~~~~~~~~~--~~~~~n~l~l~G~~G~GKTHLl~A~~~~~~~-~~~~~~~~~~------~~~~~~~~~   81 (213)
T d1l8qa2          11 NFIVGEGNRLAYEVVKEALEN--LGSLYNPIFIYGSVGTGKTHLLQAAGNEAKK-RGYRVIYSSA------DDFAQAMVE   81 (213)
T ss_dssp             SCCCCTTTHHHHHHHHHHHHT--TTTSCSSEEEECSSSSSHHHHHHHHHHHHHH-TTCCEEEEEH------HHHHHHHHH
T ss_pred             hccCCCcHHHHHHHHHHHHhC--cCCCCCcEEEECCCCCcHHHHHHHHHHHhcc-CccceEEech------HHHHHHHHH
Confidence            445664  3334444555543  1233456999999999999999999999863 3456778743      444444444


Q ss_pred             HhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCcccccc--CHHHHHHhHhCCCCCCCcEEEEEecCCCChhHhhhH
Q psy200          272 ELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESR--KQTILYTIFEWPSIPGSKLVLVGVANALDLTDRMLP  349 (490)
Q Consensus       272 ~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~--~~~~L~~l~~~~~~~~~~vilI~~tn~~~~~~~l~~  349 (490)
                      .+...    ...++.+    .+..   .-+|+|||+|.+...  .+..|+.+++.....+..+++.+.....++ ..+.+
T Consensus        82 ~~~~~----~~~~~~~----~~~~---~dll~iDDi~~i~~~~~~~~~lf~lin~~~~~~~~iiits~~~p~~l-~~~~~  149 (213)
T d1l8qa2          82 HLKKG----TINEFRN----MYKS---VDLLLLDDVQFLSGKERTQIEFFHIFNTLYLLEKQIILASDRHPQKL-DGVSD  149 (213)
T ss_dssp             HHHHT----CHHHHHH----HHHT---CSEEEEECGGGGTTCHHHHHHHHHHHHHHHHTTCEEEEEESSCGGGC-TTSCH
T ss_pred             HHHcc----chhhHHH----HHhh---ccchhhhhhhhhcCchHHHHHHHHHHHHHhhccceEEEecCCcchhc-cccch
Confidence            43221    1222222    2322   239999999999765  467788888765545555555443333333 34568


Q ss_pred             HhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHHHHHHH
Q psy200          350 RLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITNHL  418 (490)
Q Consensus       350 ~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll~~a  418 (490)
                      ++++|+..+ ..+.+. ++.++..+++++++...  ...+++++++.|++    ...++|.+..++...
T Consensus       150 dL~SRL~~g-~~~~i~-p~d~~~~~iL~~~a~~r--gl~l~~~v~~yl~~----~~~~~R~L~~~l~~l  210 (213)
T d1l8qa2         150 RLVSRFEGG-ILVEIE-LDNKTRFKIIKEKLKEF--NLELRKEVIDYLLE----NTKNVREIEGKIKLI  210 (213)
T ss_dssp             HHHHHHHTS-EEEECC-CCHHHHHHHHHHHHHHT--TCCCCHHHHHHHHH----HCSSHHHHHHHHHHH
T ss_pred             HHHHHhhCc-eEEEEC-CCcHHHHHHHHHHHHHc--CCCCCHHHHHHHHH----hcCcHHHHHHHHHHh
Confidence            888888654 357775 57788999999998776  57799999999997    346888876666543

>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=99.57  E-value=3.1e-15  Score=132.11  Aligned_cols=157  Identities=18%  Similarity=0.250  Sum_probs=107.4

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhc------CCceEEEEeccCCCCHHHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIK------DAFKTIYINCNSVRNAASVYE  267 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~------~~~~~~~v~~~~~~~~~~l~~  267 (490)
                      +.++||+++++++.+.|..    ....+++|+|+||+|||++++.+++.+...      .+..++.++...+-.      
T Consensus        22 d~~igRd~Ei~~l~~iL~r----~~k~n~lLvG~pGVGKTalv~~LA~ri~~~~vp~~L~~~~i~~ld~~~LiA------   91 (195)
T d1jbka_          22 DPVIGRDEEIRRTIQVLQR----RTKNNPVLIGEPGVGKTAIVEGLAQRIINGEVPEGLKGRRVLALDMGALVA------   91 (195)
T ss_dssp             CCCCSCHHHHHHHHHHHTS----SSSCEEEEECCTTSCHHHHHHHHHHHHHHTCSCGGGTTCEEEEECHHHHHT------
T ss_pred             CCCcCcHHHHHHHHHHHhc----cCCCCeEEEecCCcccHHHHHHHHHHHHhCCCCHHHcCceEEEeeHHHHhc------
Confidence            7899999999999999864    456789999999999999999999988532      245677776543311      


Q ss_pred             HHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCH--------HHHHHhHhCCCCCCCcEEEEEecC
Q psy200          268 TIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQ--------TILYTIFEWPSIPGSKLVLVGVAN  339 (490)
Q Consensus       268 ~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~--------~~L~~l~~~~~~~~~~vilI~~tn  339 (490)
                            +..+.|.-.+.+...+.+..+ ....+||||||+|.+.....        +.|.-.+.     ...+.+|++|+
T Consensus        92 ------g~~~rG~~E~rl~~il~e~~~-~~~~iILfIDeih~l~~~g~~~g~~d~~~~Lkp~L~-----rg~l~~IgatT  159 (195)
T d1jbka_          92 ------GAKYRGEFEERLKGVLNDLAK-QEGNVILFIDELHTMVGAGKADGAMDAGNMLKPALA-----RGELHCVGATT  159 (195)
T ss_dssp             ------TTCSHHHHHHHHHHHHHHHHH-STTTEEEEEETGGGGTT------CCCCHHHHHHHHH-----TTSCCEEEEEC
T ss_pred             ------cCCccHHHHHHHHHHHHHHhc-CCCcEEEEcchHHHHhcCCCCCCcccHHHHHHHHHh-----CCCceEEecCC
Confidence                  111111222333334444322 24478999999999976532        34443333     45688888887


Q ss_pred             CCChhHhh--hHHhhhccCCCCeeEEeCCCCHHHHHHHH
Q psy200          340 ALDLTDRM--LPRLQANVTLQPTLMNFAPYSREQILEII  376 (490)
Q Consensus       340 ~~~~~~~l--~~~l~~R~~~~~~~i~~~pls~~e~~~il  376 (490)
                      ..++...+  ++.|.+||.    .|.+.+++.++...||
T Consensus       160 ~eey~~~~e~d~aL~rrF~----~I~V~Ep~~e~t~~IL  194 (195)
T d1jbka_         160 LDEYRQYIEKDAALERRFQ----KVFVAEPSVEDTIAIL  194 (195)
T ss_dssp             HHHHHHHTTTCHHHHTTEE----EEECCCCCHHHHHTTC
T ss_pred             HHHHHHHHHcCHHHHhcCC----EeecCCCCHHHHHHHh
Confidence            55544333  678999996    8999999999988765

>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=99.56  E-value=7.8e-14  Score=134.24  Aligned_cols=236  Identities=15%  Similarity=0.208  Sum_probs=136.8

Q ss_pred             CCCCChHHHHHHHHHHHHhhhc----------cCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVN----------NETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAA  263 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~----------~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~  263 (490)
                      ..++|+++.++.|...+.+.+.          ..+++++||+||||||||.||+++++.+.    ..++.++++.+....
T Consensus        14 ~~ViGQd~A~~~l~~av~~~~~r~~~~~~~~~~~~~~~iLl~GPpG~GKT~lAkalA~~~~----~~~~~i~~s~~~~~~   89 (309)
T d1ofha_          14 QHIIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAKLAN----APFIKVEATKFTEVG   89 (309)
T ss_dssp             TTCCSCHHHHHHHHHHHHHHHHTTSSCHHHHHHCCCCCEEEECCTTSSHHHHHHHHHHHHT----CCEEEEEGGGGSSCC
T ss_pred             CcccChHHHHHHHHHHHHHHHHHhccCCCCccCCCCceEEEECCCCCCHHHHHHHHhhccc----cchhcccccccccce
Confidence            7799999999999887743211          12578999999999999999999999975    567888887764211


Q ss_pred             HHHHHHHHHhcCCCCCCcHHHHHHHHHHHHh---cCCCeEEEEEecCccccccCH------------HHHHHhHhCCCC-
Q psy200          264 SVYETIVNELKLKPGGKSERHQLGAILKYFD---TKHKSILLILDEIDALESRKQ------------TILYTIFEWPSI-  327 (490)
Q Consensus       264 ~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~---~~~~~~vI~IDEid~l~~~~~------------~~L~~l~~~~~~-  327 (490)
                                  .+.+.....+...+..+..   ...+++||||||||.+.....            ..|..+++-... 
T Consensus        90 ------------~~~~~~~~~~~~~f~~a~~~~~~~~~~~IIf~DEIdki~~~~~~~~~~~~~~gv~~~LL~~~dg~~~~  157 (309)
T d1ofha_          90 ------------YVGKEVDSIIRDLTDSAGGAIDAVEQNGIVFIDEIDKICKKGEYSGADVSREGVQRDLLPLVEGSTVS  157 (309)
T ss_dssp             ------------SGGGSTTHHHHHHHHTTTTCHHHHHHHCEEEEECGGGGSCCSSCCSSHHHHHHHHHHHHHHHHCCEEE
T ss_pred             ------------eEeeeccccccccchhhhcccccccCCceEEehhhhhhhhhccCcccchhhhHHHHHhhHHhcCCEEe
Confidence                        1122233333333322110   012368999999999975521            123333331100 


Q ss_pred             ------CCCcEEEEEecC-CCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHH-----------hccCCCCCC
Q psy200          328 ------PGSKLVLVGVAN-ALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKL-----------KQTDKFNMF  389 (490)
Q Consensus       328 ------~~~~vilI~~tn-~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l-----------~~~~~~~~~  389 (490)
                            ...++++|++.+ .......+.+.+..||.   ..+.|.+++..++.+|+....           ...+....+
T Consensus       158 ~~~~~i~~s~ilfi~~ga~~~~~~~~~~p~l~~R~~---~~i~~~~~~~~~~~~Il~~~~~~l~~~~~~~~~~~~~~~~~  234 (309)
T d1ofha_         158 TKHGMVKTDHILFIASGAFQVARPSDLIPELQGRLP---IRVELTALSAADFERILTEPHASLTEQYKALMATEGVNIAF  234 (309)
T ss_dssp             ETTEEEECTTCEEEEEECCSSSCGGGSCHHHHHTCC---EEEECCCCCHHHHHHHHHSSTTCHHHHHHHHHHHTTCEEEE
T ss_pred             cCCeEEEccceeEEeccchhhcCcccchhhhhhhhh---eeeeccCCCHHHHHHHHHHHHHHHHHHHHHHHhhcCCcccc
Confidence                  123455665432 12235667888999997   589999999999999864321           111233445


Q ss_pred             CHHHHHHHHHHHHHh---h--CCHHHHHHHHHHHHHHH-HhccccCCcccccCHHHHHHHHHHhc
Q psy200          390 NASALQLLAGKVAAV---S--GDIRKAIDITNHLIDLT-YDNVKENGEVTGIGLKEVLGVISSVY  448 (490)
Q Consensus       390 ~~~~i~~i~~~i~~~---~--Gd~r~ai~ll~~a~~~a-~~~~~~~~~~~~It~~~v~~a~~~~~  448 (490)
                      ++.+....+......   +  -+.|.+..+++..+... ..........-.|+.+.+.+++.++.
T Consensus       235 ~~~~~~~~~~~~~~~~~~~~~~GaR~L~~~ie~i~~~~~~~~~~~~~~~v~i~~~~v~~~l~~~~  299 (309)
T d1ofha_         235 TTDAVKKIAEAAFRVNEKTENIGARRLHTVMERLMDKISFSASDMNGQTVNIDAAYVADALGEVV  299 (309)
T ss_dssp             CHHHHHHHHHHHHHHHHHSCCCTTHHHHHHHHHHSHHHHHHGGGCTTCEEEECHHHHHHHTCSSS
T ss_pred             chHHHHHHHHHHHHHhhcchhcCchHHHHHHHHHHHHHHccccccCCCEEEECHHHHHHhcCCcc
Confidence            666666555433221   1  24555555555443221 11111111123567777777766543

>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=99.56  E-value=1.1e-14  Score=135.54  Aligned_cols=225  Identities=18%  Similarity=0.173  Sum_probs=148.8

Q ss_pred             CCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhc
Q psy200          195 ELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELK  274 (490)
Q Consensus       195 ~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~  274 (490)
                      ++||....++++.+.+...  .....+|+|+|++||||+++|++++... ......++.++|... +...+...++..-.
T Consensus         1 ~~v~~S~~~~~~~~~~~~~--a~~~~pvlI~Ge~GtGK~~~A~~ih~~s-~~~~~~~~~~~~~~~-~~~~~~~~lfg~~~   76 (247)
T d1ny5a2           1 EYVFESPKMKEILEKIKKI--SCAECPVLITGESGVGKEVVARLIHKLS-DRSKEPFVALNVASI-PRDIFEAELFGYEK   76 (247)
T ss_dssp             CCCCCSHHHHHHHHHHHHH--TTCCSCEEEECSTTSSHHHHHHHHHHHS-TTTTSCEEEEETTTS-CHHHHHHHHHCBCT
T ss_pred             CeEecCHHHHHHHHHHHHH--hCCCCCEEEECCCCcCHHHHHHHHHHhc-CCcccccccchhhhh-hhcccHHHhcCccc
Confidence            5789989999999888874  3456689999999999999999997643 334457888888877 44444444433221


Q ss_pred             CCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCHHHHHHhHhCCCC--------CCCcEEEEEecCCCChhH-
Q psy200          275 LKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPSI--------PGSKLVLVGVANALDLTD-  345 (490)
Q Consensus       275 ~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~--------~~~~vilI~~tn~~~~~~-  345 (490)
                      ....+.. ......|.. .. +|   +|||||||.|....|..|..+++....        ....+.+|++++.. +.+ 
T Consensus        77 ~~~~~~~-~~~~g~l~~-a~-gG---tL~l~~i~~L~~~~Q~~L~~~l~~~~~~~~~~~~~~~~~~RlI~~s~~~-l~~l  149 (247)
T d1ny5a2          77 GAFTGAV-SSKEGFFEL-AD-GG---TLFLDEIGELSLEAQAKLLRVIESGKFYRLGGRKEIEVNVRILAATNRN-IKEL  149 (247)
T ss_dssp             TSSTTCC-SCBCCHHHH-TT-TS---EEEEESGGGCCHHHHHHHHHHHHHSEECCBTCCSBEECCCEEEEEESSC-HHHH
T ss_pred             CCcCCcc-cccCCHHHc-cC-CC---EEEEeChHhCCHHHHHHHHHHHHhCCEEECCCCCceecCeEEEEecCCC-HHHH
Confidence            1111100 000111221 11 12   899999999999999998888753210        11245566666531 211 


Q ss_pred             ----hhhHHhhhccCCCCeeEEeCCCC--HHHHHHHHHHHHhcc----CCC-CCCCHHHHHHHHHHHHHhhCCHHHHHHH
Q psy200          346 ----RMLPRLQANVTLQPTLMNFAPYS--REQILEIISQKLKQT----DKF-NMFNASALQLLAGKVAAVSGDIRKAIDI  414 (490)
Q Consensus       346 ----~l~~~l~~R~~~~~~~i~~~pls--~~e~~~il~~~l~~~----~~~-~~~~~~~i~~i~~~i~~~~Gd~r~ai~l  414 (490)
                          .+.+.+..|+..  ..|.++|+.  .+++..++...+...    +.. ..+++++++.+..  +.|.||++++.++
T Consensus       150 ~~~~~f~~~L~~~l~~--~~i~lPpLreR~~Di~~l~~~~l~~~~~~~~~~~~~ls~~al~~L~~--~~WPGNl~EL~~~  225 (247)
T d1ny5a2         150 VKEGKFREDLYYRLGV--IEIEIPPLRERKEDIIPLANHFLKKFSRKYAKEVEGFTKSAQELLLS--YPWYGNVRELKNV  225 (247)
T ss_dssp             HHTTSSCHHHHHHHTT--EEEECCCGGGCHHHHHHHHHHHHHHHHHHTTCCCCEECHHHHHHHHH--SCCTTHHHHHHHH
T ss_pred             HHcCCCcHHHHhhcCe--eeecCCChhhchhhHhhhhhhhhhhhhhhcCCCCCCCCHHHHHHHHh--CCCCCHHHHHHHH
Confidence                234556666543  478999996  578877776665543    222 3489999999987  8899999999999


Q ss_pred             HHHHHHHHHhccccCCcccccCHHHHHH
Q psy200          415 TNHLIDLTYDNVKENGEVTGIGLKEVLG  442 (490)
Q Consensus       415 l~~a~~~a~~~~~~~~~~~~It~~~v~~  442 (490)
                      +++|+..+.  +      ..|+.+|+..
T Consensus       226 l~~a~~~~~--~------~~I~~~dl~~  245 (247)
T d1ny5a2         226 IERAVLFSE--G------KFIDRGELSC  245 (247)
T ss_dssp             HHHHHHHCC--S------SEECHHHHHH
T ss_pred             HHHHHHhCC--C------CeECHHHccc
Confidence            999986553  3      4689998865

>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=99.52  E-value=5.4e-14  Score=135.56  Aligned_cols=217  Identities=18%  Similarity=0.200  Sum_probs=144.5

Q ss_pred             hHHHhhcCCCCCCChHHHHHHHHHHHHhhhcc----C-CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCC
Q psy200          185 KVEEKAKDSCELPGREVQLEGIRQFLLGHVNN----E-TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSV  259 (490)
Q Consensus       185 ~~~~~~l~~~~lvgre~~~~~l~~~L~~~~~~----~-~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~  259 (490)
                      ......|. ..++|+++.++.|...+..+..+    . +...++++||+|+|||.||+.+++.+.    .+++.++++.+
T Consensus        14 ~~l~~~L~-~~viGQ~~a~~~v~~~v~~~~~~l~~~~~p~~~~lf~Gp~GvGKT~lak~la~~l~----~~~i~~d~s~~   88 (315)
T d1r6bx3          14 KNLGDRLK-MLVFGQDKAIEALTEAIKMARAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSKALG----IELLRFDMSEY   88 (315)
T ss_dssp             HHHHHHHT-TTSCSCHHHHHHHHHHHHHHHTTCSCTTSCSEEEEEECSTTSSHHHHHHHHHHHHT----CEEEEEEGGGC
T ss_pred             HHHHHHhC-CeecChHHHHHHHHHHHHHHHccCCCCCCCceEEEEECCCcchhHHHHHHHHhhcc----CCeeEeccccc
Confidence            33444444 89999999999999988654321    2 234788999999999999999999875    57899999887


Q ss_pred             CCHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCHHHHHHhHhCCC--------CCCCc
Q psy200          260 RNAASVYETIVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPS--------IPGSK  331 (490)
Q Consensus       260 ~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~--------~~~~~  331 (490)
                      ......     ..|.+...|.........+...+.. ....||++||++.+...-++.|.++++...        ..-.+
T Consensus        89 ~~~~~~-----~~l~g~~~gy~g~~~~~~l~~~~~~-~~~~vvl~DeieKa~~~V~~~lLqild~G~ltd~~Gr~vdf~n  162 (315)
T d1r6bx3          89 MERHTV-----SRLIGAPPGYVGFDQGGLLTDAVIK-HPHAVLLLDEIEKAHPDVFNILLQVMDNGTLTDNNGRKADFRN  162 (315)
T ss_dssp             SSSSCC-----SSSCCCCSCSHHHHHTTHHHHHHHH-CSSEEEEEETGGGSCHHHHHHHHHHHHHSEEEETTTEEEECTT
T ss_pred             cchhhh-----hhhcccCCCccccccCChhhHHHHh-CccchhhhcccccccchHhhhhHHhhccceecCCCCCccCccc
Confidence            543211     1111222222222222233444443 446799999999998888888888876431        13456


Q ss_pred             EEEEEecCCC--C--------------------hhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhcc------
Q psy200          332 LVLVGVANAL--D--------------------LTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQT------  383 (490)
Q Consensus       332 vilI~~tn~~--~--------------------~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~------  383 (490)
                      .++|+++|.-  +                    +...+.+.+..|+.   ..+.|.|++.+++.+|+...+...      
T Consensus       163 ~iiI~Tsnig~~~i~~~~~~~~~~~~~~~~~~~l~~~f~pEflnRid---~ii~f~~l~~~~~~~I~~~~l~~~~~~l~~  239 (315)
T d1r6bx3         163 VVLVMTTNAGVRETERKSIGLIHQDNSTDAMEEIKKIFTPEFRNRLD---NIIWFDHLSTDVIHQVVDKFIVELQVQLDQ  239 (315)
T ss_dssp             EEEEEEECSSCC-----------------CHHHHHHHSCHHHHTTCS---EEEECCCCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             eEEEeccchhhHHHHhhhccchhhhhhHhHHHHHHHhcCHHHHhhhh---hhhcccchhhhHHHHHHHHHHHHHHHHHHh
Confidence            7888888821  0                    11234567888887   589999999999998876655433      


Q ss_pred             -CCCCCCCHHHHHHHHHHHHHhhCCHHHHHHHH
Q psy200          384 -DKFNMFNASALQLLAGKVAAVSGDIRKAIDIT  415 (490)
Q Consensus       384 -~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll  415 (490)
                       +....+++++++.|++..+....+.|.+-..+
T Consensus       240 ~~i~l~~~~~a~~~l~~~~yd~~~GaR~L~r~I  272 (315)
T d1r6bx3         240 KGVSLEVSQEARNWLAEKGYDRAMGARPMARVI  272 (315)
T ss_dssp             TTEEEEECHHHHHHHHHHHCBTTTBTTTHHHHH
T ss_pred             cCcchhhHHHHHHHHHHhCCCCCCChhhHHHHH
Confidence             44567899999999986544444444443333

>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=99.48  E-value=1.7e-12  Score=122.71  Aligned_cols=198  Identities=9%  Similarity=0.066  Sum_probs=120.6

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhh--hcCCc-eEEEEeccCCCCHHHHHHHH-
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAE--IKDAF-KTIYINCNSVRNAASVYETI-  269 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~--~~~~~-~~~~v~~~~~~~~~~l~~~i-  269 (490)
                      ..++||+.++++|.++|... .......|.|+|++|+||||||+.++++..  ....| .++|++.....+...+...+ 
T Consensus        20 ~~~~gR~~~~~~i~~~L~~~-~~~~~~~v~I~GmgGiGKTtLA~~v~~~~~~~~~~~f~~~~Wv~vs~~~~~~~l~~~~~   98 (277)
T d2a5yb3          20 MTCYIREYHVDRVIKKLDEM-CDLDSFFLFLHGRAGSGKSVIASQALSKSDQLIGINYDSIVWLKDSGTAPKSTFDLFTD   98 (277)
T ss_dssp             CCSCCCHHHHHHHHHHHHHH-TTSSSEEEEEECSTTSSHHHHHHHHHHHCSSTBTTTBSEEEEEECCCCSTTHHHHHHHH
T ss_pred             CceeCcHHHHHHHHHHHHhc-cCCCceEEEEECCCCCCHHHHHHHHHHhhhhhhhhcCceEEEEEecCCCCHHHHHHHHH
Confidence            67889999999999999752 233456888999999999999999998743  22334 56788877766655554443 


Q ss_pred             --HHHhcCCC------C-CCcHHHHH-HHHHHHHhcCCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEEEecC
Q psy200          270 --VNELKLKP------G-GKSERHQL-GAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVAN  339 (490)
Q Consensus       270 --~~~l~~~~------~-~~s~~~~~-~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI~~tn  339 (490)
                        +..++...      . ........ ..+.+.+.  +++++|||||+|...     .+..+..    .++++++  +|.
T Consensus        99 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~--~kr~LlVLDDv~~~~-----~~~~~~~----~~srilv--TTR  165 (277)
T d2a5yb3          99 ILLMLKSEDDLLNFPSVEHVTSVVLKRMICNALID--RPNTLFVFDDVVQEE-----TIRWAQE----LRLRCLV--TTR  165 (277)
T ss_dssp             HHHHHTTTSCCTTCCCCTTCCHHHHHHHHHHHHTT--STTEEEEEEEECCHH-----HHHHHHH----TTCEEEE--EES
T ss_pred             HHHHHhcchhhcCCccchhhhhHHHHHHHHHHHhc--cCCeeEecchhhHHh-----hhhhhcc----cCceEEE--Eee
Confidence              33333211      1 11112222 22333333  568999999999742     2222221    2344433  343


Q ss_pred             CCChhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHhhCCHHHHHHHHHHH
Q psy200          340 ALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDITNHL  418 (490)
Q Consensus       340 ~~~~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~~~i~~i~~~i~~~~Gd~r~ai~ll~~a  418 (490)
                      ..++...    +...    ...+.+++++.++.+++|..+....   ..  .+..+.++++++..||+.+.||.++...
T Consensus       166 ~~~v~~~----~~~~----~~~~~l~~L~~~ea~~Lf~~~~~~~---~~--~~~~~~~~~~iv~~c~GlPLAl~~ig~~  231 (277)
T d2a5yb3         166 DVEISNA----ASQT----CEFIEVTSLEIDECYDFLEAYGMPM---PV--GEKEEDVLNKTIELSSGNPATLMMFFKS  231 (277)
T ss_dssp             BGGGGGG----CCSC----EEEEECCCCCHHHHHHHHHHTSCCC---C----CHHHHHHHHHHHHHTTCHHHHHHHHTT
T ss_pred             hHHHHHh----cCCC----CceEECCCCCHHHHHHHHHHHhCCc---cC--chhhHHHHHHHHHHhCCCHHHHHHHHHH
Confidence            2222221    1111    1368999999999999997653322   11  1223556666777999999999887443

>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=99.47  E-value=9.9e-14  Score=133.47  Aligned_cols=214  Identities=17%  Similarity=0.208  Sum_probs=139.5

Q ss_pred             CCCCChHHHHHHHHHHHHhhhcc----CCC-CeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVNN----ETS-GSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYET  268 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~----~~~-~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~  268 (490)
                      ..++|+++.++.|...+..+..+    ..+ ..++++||+|+|||.+|+.+++.+. .....++.++++.+....... .
T Consensus        23 ~~v~GQ~~ai~~v~~~i~~~~~~l~~~~kp~~~~lf~Gp~G~GKt~lak~la~~l~-~~~~~~~~~~~~~~~~~~~~~-~  100 (315)
T d1qvra3          23 KRVVGQDEAIRAVADAIRRARAGLKDPNRPIGSFLFLGPTGVGKTELAKTLAATLF-DTEEAMIRIDMTEYMEKHAVS-R  100 (315)
T ss_dssp             HHSCSCHHHHHHHHHHHHHHGGGCSCSSSCSEEEEEBSCSSSSHHHHHHHHHHHHH-SSGGGEEEECTTTCCSSGGGG-G
T ss_pred             CeEeCHHHHHHHHHHHHHHHhcCCCCCCCCceEEEEECCCcchHHHHHHHHHHHhc-CCCcceEEEeccccccchhhh-h
Confidence            78999999999999988765321    123 3678999999999999999999873 233578889988875432211 0


Q ss_pred             HHHHhcCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCHHHHHHhHhCCC--------CCCCcEEEEEecCC
Q psy200          269 IVNELKLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPS--------IPGSKLVLVGVANA  340 (490)
Q Consensus       269 i~~~l~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~--------~~~~~vilI~~tn~  340 (490)
                          |-+...|.........|.+++.. ....||++|||+.+...-++.|..+++...        ..-.++++|+++|-
T Consensus       101 ----L~g~~~gyvG~~~~~~l~~~~~~-~p~~Vvl~DEieK~~~~v~~~ll~~l~~g~~~~~~gr~v~~~~~i~i~tsnl  175 (315)
T d1qvra3         101 ----LIGAPPGYVGYEEGGQLTEAVRR-RPYSVILFDEIEKAHPDVFNILLQILDDGRLTDSHGRTVDFRNTVIILTSNL  175 (315)
T ss_dssp             ----C--------------CHHHHHHH-CSSEEEEESSGGGSCHHHHHHHHHHHTTTEECCSSSCCEECTTEEEEEECCT
T ss_pred             ----hcCCCCCCcCcccCChHHHHHHh-CCCcEEEEehHhhcCHHHHHHHHHHhccCceeCCCCcEecCcceEEEEeccc
Confidence                10111111011111233444444 346799999999999888888988886531        22356789999982


Q ss_pred             CC-----------------------hhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhcc-------CCCCCCC
Q psy200          341 LD-----------------------LTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQT-------DKFNMFN  390 (490)
Q Consensus       341 ~~-----------------------~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~-------~~~~~~~  390 (490)
                      -.                       +...+.+.+..|+.   ..+.|.|++.+++.+|+...+...       +....++
T Consensus       176 G~~~i~~~~~~~~~~~~~~~~~~~~l~~~f~pEflnRid---~Ii~F~~L~~~~~~~I~~~~l~~l~~rl~~~~i~l~i~  252 (315)
T d1qvra3         176 GSPLILEGLQKGWPYERIRDEVFKVLQQHFRPEFLNRLD---EIVVFRPLTKEQIRQIVEIQLSYLRARLAEKRISLELT  252 (315)
T ss_dssp             THHHHHHHHHTTCCHHHHHHHHHHHHHTTSCHHHHHTCS---BCCBCCCCCHHHHHHHHHHHHHHHHHHHHTTTCEEEEC
T ss_pred             ChHHHhhhcccccchhhhhHHHHHHHHhhcCHHHHhcCC---eeeeccchhhhhhHHHHHHHHHHHHHHHHhcccccccc
Confidence            10                       11224567888887   478999999999999876554433       4556789


Q ss_pred             HHHHHHHHHHHHHhhCCHHHHHHHHHH
Q psy200          391 ASALQLLAGKVAAVSGDIRKAIDITNH  417 (490)
Q Consensus       391 ~~~i~~i~~~i~~~~Gd~r~ai~ll~~  417 (490)
                      +++++.|+++.+...-+.|.+-..+++
T Consensus       253 ~~~~~~L~~~~y~~~~GAR~L~r~Ie~  279 (315)
T d1qvra3         253 EAAKDFLAERGYDPVFGARPLRRVIQR  279 (315)
T ss_dssp             HHHHHHHHHHHCBTTTBTSTHHHHHHH
T ss_pred             HHHHHHHHHhCCCCCCCcchHHHHHHH
Confidence            999999998654444444444444433

>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=99.45  E-value=1.9e-13  Score=128.84  Aligned_cols=195  Identities=14%  Similarity=0.243  Sum_probs=113.0

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCC-----CHHHHHHH
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVR-----NAASVYET  268 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~-----~~~~l~~~  268 (490)
                      ++|+||++++++|.+.        ..++++|+||+|+|||+|++.+++.+.    ..+.++++....     ....++..
T Consensus        12 ~~f~GR~~el~~l~~~--------~~~~i~i~G~~G~GKTsLl~~~~~~~~----~~~~~i~~~~~~~~~~~~~~~~~~~   79 (283)
T d2fnaa2          12 KDFFDREKEIEKLKGL--------RAPITLVLGLRRTGKSSIIKIGINELN----LPYIYLDLRKFEERNYISYKDFLLE   79 (283)
T ss_dssp             GGSCCCHHHHHHHHHT--------CSSEEEEEESTTSSHHHHHHHHHHHHT----CCEEEEEGGGGTTCSCCCHHHHHHH
T ss_pred             hhCCChHHHHHHHHhc--------cCCEEEEEcCCCCcHHHHHHHHHHHCC----CCeEEEEeccccccccccHHHHHHH
Confidence            7899999999887652        357899999999999999999998875    344555554332     23444444


Q ss_pred             HHHHhcC---------------------------CCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCccccccCH----HH
Q psy200          269 IVNELKL---------------------------KPGGKSERHQLGAILKYFDTKHKSILLILDEIDALESRKQ----TI  317 (490)
Q Consensus       269 i~~~l~~---------------------------~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~----~~  317 (490)
                      +...+..                           .........+.+.+.......+++++|++||++.+.....    ..
T Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~~~~~~~i~id~~~~~~~~~~~~~~~~  159 (283)
T d2fnaa2          80 LQKEINKLVKRLPSLLKALKNIQGIVIMGNEIKFNWNRKDRLSFANLLESFEQASKDNVIIVLDEAQELVKLRGVNLLPA  159 (283)
T ss_dssp             HHHHHHHHHHHCTTHHHHTTTSTTEEECSSSEEEC-----CCCHHHHHHHHHHTCSSCEEEEEETGGGGGGCTTCCCHHH
T ss_pred             HHHHhhhhhhhhHHHHHHHHhhhcccccccccccccchhhhhHHHHHHHHHHhhcccccccccchhhhhcccchHHHHHH
Confidence            4333210                           0000112223344444444557789999999999866532    23


Q ss_pred             HHHhHhCCCCCCCcEEEEEecCCCChhHhhhH------HhhhccCCCCeeEEeCCCCHHHHHHHHHHHHhccCCCCCCCH
Q psy200          318 LYTIFEWPSIPGSKLVLVGVANALDLTDRMLP------RLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNA  391 (490)
Q Consensus       318 L~~l~~~~~~~~~~vilI~~tn~~~~~~~l~~------~l~~R~~~~~~~i~~~pls~~e~~~il~~~l~~~~~~~~~~~  391 (490)
                      +..++..    ...+.++.+.........+..      .+..|+   ...+.+.|++.+++.+++.+.+...+    ++.
T Consensus       160 l~~~~~~----~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~i~L~~l~~~e~~~~l~~~~~~~~----~~~  228 (283)
T d2fnaa2         160 LAYAYDN----LKRIKFIMSGSEMGLLYDYLRVEDPESPLFGRA---FSTVELKPFSREEAIEFLRRGFQEAD----IDF  228 (283)
T ss_dssp             HHHHHHH----CTTEEEEEEESSHHHHHHHTTTTCTTSTTTTCC---CEEEEECCCCHHHHHHHHHHHHHHHT----CCC
T ss_pred             HHHHHHh----hhhhhhhhccccchHHHHHHHhhhhcchhcccc---eeEEeeCCCCHHHHHHHHHhhhhhcC----CCH
Confidence            3333221    123333333322112222211      111122   24799999999999999998887653    333


Q ss_pred             HHHHHHHHHHHHhhCCHHHHHHHH
Q psy200          392 SALQLLAGKVAAVSGDIRKAIDIT  415 (490)
Q Consensus       392 ~~i~~i~~~i~~~~Gd~r~ai~ll  415 (490)
                      +.++.+.+    .+|+.+..++++
T Consensus       229 ~~~~~i~~----~~~G~P~~L~~~  248 (283)
T d2fnaa2         229 KDYEVVYE----KIGGIPGWLTYF  248 (283)
T ss_dssp             CCHHHHHH----HHCSCHHHHHHH
T ss_pred             HHHHHHHH----HhCCCHHHHHHH
Confidence            34566665    555556666644

>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=99.42  E-value=1.7e-14  Score=137.66  Aligned_cols=139  Identities=8%  Similarity=0.096  Sum_probs=97.5

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHhcCC
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKPGGKSERHQLGAILKYFDTKH  297 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~~~s~~~~~~~l~~~l~~~~  297 (490)
                      +.++++|+||||||||.+|++++.+++  .++.++.++++.+.+              .+.|.....+++.|.++..   
T Consensus       122 ~~g~~l~~G~pG~GKT~la~ala~~~~--~~~~~~~~~~~~~~~--------------~~~G~~e~~~~~~f~~a~~---  182 (321)
T d1w44a_         122 ASGMVIVTGKGNSGKTPLVHALGEALG--GKDKYATVRFGEPLS--------------GYNTDFNVFVDDIARAMLQ---  182 (321)
T ss_dssp             ESEEEEEECSSSSCHHHHHHHHHHHHH--TTSCCEEEEBSCSST--------------TCBCCHHHHHHHHHHHHHH---
T ss_pred             CCceEEEECCCCccHHHHHHHHHHHhc--CCCCeEEEEhhHhhh--------------cccchHHHHHHHHHHHHhh---
Confidence            344566799999999999999999986  445677888877644              6888889999888887754   


Q ss_pred             CeEEEEEecCccccccCH---------HHHHHhHh-CC-CCCCCcEEEEEecCCCChhHhhhHHhh--hccCCCCeeEEe
Q psy200          298 KSILLILDEIDALESRKQ---------TILYTIFE-WP-SIPGSKLVLVGVANALDLTDRMLPRLQ--ANVTLQPTLMNF  364 (490)
Q Consensus       298 ~~~vI~IDEid~l~~~~~---------~~L~~l~~-~~-~~~~~~vilI~~tn~~~~~~~l~~~l~--~R~~~~~~~i~~  364 (490)
                       ++||||||||.+...+.         ..+.+++. +. ......|+||++||+.++.+.+++.+.  .||.   ..+.+
T Consensus       183 -~~ilf~DEid~~~~~r~~~~~~~~~~r~v~~lL~e~dg~~~~~~v~viaatN~~~~~~~i~~~~~r~~Rf~---~~v~v  258 (321)
T d1w44a_         183 -HRVIVIDSLKNVIGAAGGNTTSGGISRGAFDLLSDIGAMAASRGCVVIASLNPTSNDDKIVELVKEASRSN---STSLV  258 (321)
T ss_dssp             -CSEEEEECCTTTC-----------CCHHHHHHHHHHHHHHHHHTCEEEEECCCCCCCHHHHHHHHHHHHHS---CSEEE
T ss_pred             -ccEEEeehhhhhccccccCCCCCcchhhhhhhhhhccccccCCCeEEEEeCCCcccccchhhhhhccCccc---ceeec
Confidence             56999999999976531         23333321 11 112346999999998766666654332  3565   36888


Q ss_pred             CCCCHHHHHHHHHHH
Q psy200          365 APYSREQILEIISQK  379 (490)
Q Consensus       365 ~pls~~e~~~il~~~  379 (490)
                      .+++.++.++||...
T Consensus       259 ~~pd~~~r~~il~~~  273 (321)
T d1w44a_         259 ISTDVDGEWQVLTRT  273 (321)
T ss_dssp             EECSSTTEEEEEEEC
T ss_pred             CCCChHHHHHHHHHh
Confidence            888888877777644

>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=99.39  E-value=2.2e-12  Score=126.12  Aligned_cols=208  Identities=17%  Similarity=0.237  Sum_probs=131.1

Q ss_pred             CCCCChHHHHHHHHHHHHhhhc--------------------------cCCCCeEEEECCCCCcHHHHHHHHHHHhhhcC
Q psy200          194 CELPGREVQLEGIRQFLLGHVN--------------------------NETSGSMYISGPPGTGKSASLNLLVSRAEIKD  247 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~--------------------------~~~~~~ill~GppGtGKTtla~~l~~~l~~~~  247 (490)
                      ..++|++++++.+..++.+.+.                          ..+.+++|+.||+|||||-+|+++++.+.   
T Consensus        17 ~~ViGQd~Akkava~Avrn~~rR~~~~~~~r~~~~~~~~~~~~~~~~~~~p~~niLfiGPTGvGKTElAk~LA~~~~---   93 (364)
T d1um8a_          17 NYVIGQEQAKKVFSVAVYNHYKRLSFKEKLKKQDNQDSNVELEHLEEVELSKSNILLIGPTGSGKTLMAQTLAKHLD---   93 (364)
T ss_dssp             TTCCSCHHHHHHHHHHHHHHHHHHHHHHHHHHHCSHHHHHHHHHHHHTTCCCCCEEEECCTTSSHHHHHHHHHHHTT---
T ss_pred             CeecChHHHHHHHHHHHHHHHHHHHHHHHhhccccccccccccccccccCCCcceeeeCCCCccHHHHHHHHHhhcc---
Confidence            7899999999999877743211                          23678899999999999999999998763   


Q ss_pred             CceEEEEeccCCCCHHHHHHHHHHHhcCCCCCCcHHH-HHHHHHHH---HhcCCCeEEEEEecCcccccc----------
Q psy200          248 AFKTIYINCNSVRNAASVYETIVNELKLKPGGKSERH-QLGAILKY---FDTKHKSILLILDEIDALESR----------  313 (490)
Q Consensus       248 ~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~~~s~~~-~~~~l~~~---l~~~~~~~vI~IDEid~l~~~----------  313 (490)
                       ..++.++++.+.....             .|..... +.+.+...   ... ....++++||++.....          
T Consensus        94 -~~~ir~D~s~~~e~gy-------------vg~dv~~~i~~l~~~~~~~v~~-~~~~iv~lDEieK~~~~s~~~~~~~d~  158 (364)
T d1um8a_          94 -IPIAISDATSLTEAGY-------------VGEDVENILTRLLQASDWNVQK-AQKGIVFIDEIDKISRLSENRSITRDV  158 (364)
T ss_dssp             -CCEEEEEGGGCC---------------------CTHHHHHHHHHTTTCHHH-HTTSEEEEETGGGC-------------
T ss_pred             -cceeehhhhhcccchh-------------hHhhhccchhhhhhhchhHHHH-hhcccchhhhhhhhccccccccccccc
Confidence             5688888888754211             1111111 22222111   111 22459999999996532          


Q ss_pred             ----CHHHHHHhHhCCC--C--------CCCcEEEEEecCC--------C------------------------------
Q psy200          314 ----KQTILYTIFEWPS--I--------PGSKLVLVGVANA--------L------------------------------  341 (490)
Q Consensus       314 ----~~~~L~~l~~~~~--~--------~~~~vilI~~tn~--------~------------------------------  341 (490)
                          -++.|+++++-..  .        ...+.+++.++|-        .                              
T Consensus       159 a~~~V~~~lLqild~~~~~~~~~~gr~~~~~~~i~i~t~~i~~~~~ga~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  238 (364)
T d1um8a_         159 SGEGVQQALLKIVEGSLVNIPPKGGRKHPEGNFIQIDTSDILFICAGAFDGLAEIIKKRTTQNVLGFTQEKMSKKEQEAI  238 (364)
T ss_dssp             -CHHHHHHHHHHHHCCEEC---------------CEECTTCEEEEEECCTTHHHHTTTSCSSCCCSCCCSSCCTTTTTTS
T ss_pred             cchHHHHhhhhhhcCceeccCCCCCCcCCcceeEEEeehhhhhhhcccchhhhhhhhhhcccccccccccccchhhhhhh
Confidence                2667777776211  0        1122333333331        0                              


Q ss_pred             -------C-hhHhhhHHhhhccCCCCeeEEeCCCCHHHHHHHHHH-----------HHhccCCCCCCCHHHHHHHHHHHH
Q psy200          342 -------D-LTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQ-----------KLKQTDKFNMFNASALQLLAGKVA  402 (490)
Q Consensus       342 -------~-~~~~l~~~l~~R~~~~~~~i~~~pls~~e~~~il~~-----------~l~~~~~~~~~~~~~i~~i~~~i~  402 (490)
                             + +...+.|.|..|+.   .++.|++++.+++.+|+..           .+...+....+++++++.|+++.+
T Consensus       239 ~~~~~~~~~~~~~f~PEf~gRi~---~iv~f~~L~~~~l~~Il~~~~~~l~kq~~~~l~~~gi~L~~td~a~~~la~~g~  315 (364)
T d1um8a_         239 LHLVQTHDLVTYGLIPELIGRLP---VLSTLDSISLEAMVDILQKPKNALIKQYQQLFKMDEVDLIFEEEAIKEIAQLAL  315 (364)
T ss_dssp             GGGCCHHHHHHTTCCHHHHTTCC---EEEECCCCCHHHHHHHHHSSTTCHHHHHHHHHHTTTCEEEECHHHHHHHHHHHH
T ss_pred             hccccHHHHhhhhhHHHHHHHhc---chhhHhhhhHHHHHHHHHHHHHHHHHHHHHHHHhCCcEEEECHHHHHHHHHhcc
Confidence                   0 01124577888887   5899999999999999852           233335567799999999999888


Q ss_pred             HhhCCHHHHHHHHHHHHHHH
Q psy200          403 AVSGDIRKAIDITNHLIDLT  422 (490)
Q Consensus       403 ~~~Gd~r~ai~ll~~a~~~a  422 (490)
                      ...-+.|.+-.++++.+.-.
T Consensus       316 d~~~GAR~L~riie~~l~~~  335 (364)
T d1um8a_         316 ERKTGARGLRAIIEDFCLDI  335 (364)
T ss_dssp             HTTCTGGGHHHHHHHHHHHH
T ss_pred             CCCCCchHHHHHHHHHHHHH
Confidence            87788887777777766443

>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=99.37  E-value=2.7e-12  Score=124.81  Aligned_cols=226  Identities=16%  Similarity=0.161  Sum_probs=140.1

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEE--------------------
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIY--------------------  253 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~--------------------  253 (490)
                      .+++|++..+..|.-.+.    ....+++||+|+||||||++|+.++.-+.   ....+.                    
T Consensus         7 ~~I~Gq~~~kral~laa~----~~~~h~vLl~G~pG~GKT~lar~~~~iLp---~~~~~~~~~~~~~~~~~~~~~~~~~~   79 (333)
T d1g8pa_           7 SAIVGQEDMKLALLLTAV----DPGIGGVLVFGDRGTGKSTAVRALAALLP---EIEAVEGCPVSSPNVEMIPDWATVLS   79 (333)
T ss_dssp             GGSCSCHHHHHHHHHHHH----CGGGCCEEEECCGGGCTTHHHHHHHHHSC---CEEEETTCTTCCSSGGGSCTTCCCSC
T ss_pred             hhccCcHHHHHHHHHHHh----ccCCCeEEEECCCCccHHHHHHHHHHhCC---CchhhccCccccCccccccchhhccc
Confidence            578999988776554332    12346899999999999999999998652   111110                    


Q ss_pred             ----------EeccCCCCHHHHHHHHHHHhcCCCCCCcHHHHHH---------HHHHHHhcCCCeEEEEEecCccccccC
Q psy200          254 ----------INCNSVRNAASVYETIVNELKLKPGGKSERHQLG---------AILKYFDTKHKSILLILDEIDALESRK  314 (490)
Q Consensus       254 ----------v~~~~~~~~~~l~~~i~~~l~~~~~~~s~~~~~~---------~l~~~l~~~~~~~vI~IDEid~l~~~~  314 (490)
                                +......+...++..           ........         .+..+   .  .-|+||||++.+....
T Consensus        80 ~~~~~~~~~~~~~~~~~~~~~l~G~-----------~d~~~~~~~g~~~~~~G~l~~A---~--~gvl~iDEi~~~~~~~  143 (333)
T d1g8pa_          80 TNVIRKPTPVVDLPLGVSEDRVVGA-----------LDIERAISKGEKAFEPGLLARA---N--RGYLYIDECNLLEDHI  143 (333)
T ss_dssp             CCEEEECCCEEEECTTCCHHHHHCE-----------ECHHHHHHHCGGGEECCHHHHH---T--TEEEEETTGGGSCHHH
T ss_pred             cCcccccCceeeccCCCCcccccCc-----------chhhhccccCcceeeccccccc---c--ccEeecccHHHHHHHH
Confidence                      001111111111100           00000000         01111   1  2399999999999999


Q ss_pred             HHHHHHhHhCCCC----------CCCcEEEEEecCCCChhHhhhHHhhhccCCCCeeEEeCCCC-HHHHHHHHHHHHhc-
Q psy200          315 QTILYTIFEWPSI----------PGSKLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYS-REQILEIISQKLKQ-  382 (490)
Q Consensus       315 ~~~L~~l~~~~~~----------~~~~vilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~pls-~~e~~~il~~~l~~-  382 (490)
                      ++.|...++....          ...++++++++|..+  ..+.+.+.+||.+   .+.+..+. .++...++...... 
T Consensus       144 ~~aLl~~me~~~v~i~r~g~~~~~p~~f~liaa~Np~~--~~l~~~llDRf~~---~i~v~~~~~~~~~~~~~~~~~~~~  218 (333)
T d1g8pa_         144 VDLLLDVAQSGENVVERDGLSIRHPARFVLVGSGNPEE--GDLRPQLLDRFGL---SVEVLSPRDVETRVEVIRRRDTYD  218 (333)
T ss_dssp             HHHHHHHHHHSEEEECCTTCCEEEECCEEEEEEECSCS--CCCCHHHHTTCSE---EEECCCCCSHHHHHHHHHHHHHHH
T ss_pred             HHHHhhhhcCCeEEecccCceecCCCCEEEEEecCccc--cccccchhhhhcc---eeeccCcchhhHHHHHHHhhhhcc
Confidence            9999988864321          135788999999654  4567788899974   56666553 33332222211100 


Q ss_pred             --------------------------cCCCCCCCHHHHHHHHHHHHHhhC-CHHHHHHHHHHHHHHHHhccccCCccccc
Q psy200          383 --------------------------TDKFNMFNASALQLLAGKVAAVSG-DIRKAIDITNHLIDLTYDNVKENGEVTGI  435 (490)
Q Consensus       383 --------------------------~~~~~~~~~~~i~~i~~~i~~~~G-d~r~ai~ll~~a~~~a~~~~~~~~~~~~I  435 (490)
                                                ......+.++....+......... ++|..+.+++.|..+|..++     ...|
T Consensus       219 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~v~~~~~~~~~~~~~~~~~~~~S~R~~~~llrvArtiA~L~g-----r~~V  293 (333)
T d1g8pa_         219 ADPKAFLEEWRPKDMDIRNQILEARERLPKVEAPNTALYDCAALCIALGSDGLRGELTLLRSARALAALEG-----ATAV  293 (333)
T ss_dssp             HCHHHHHHHHHHHHHHHHHHHHHHHHHGGGCBCCHHHHHHHHHHHHHSSSCSHHHHHHHHHHHHHHHHHTT-----CSBC
T ss_pred             cChHHHHHHHHHHHHHHHHHHHHHhhcccceecCHHHHHHHHHHHHHcCCCChHHHHHHHHHHHHHHHHcC-----CCCC
Confidence                                      012344667777777665544444 78988899999999999999     7899


Q ss_pred             CHHHHHHHHHHhccCcc
Q psy200          436 GLKEVLGVISSVYCTSQ  452 (490)
Q Consensus       436 t~~~v~~a~~~~~~~~~  452 (490)
                      +.+||.+|+.-+...+.
T Consensus       294 ~~~di~~a~~lvL~hR~  310 (333)
T d1g8pa_         294 GRDHLKRVATMALSHRL  310 (333)
T ss_dssp             CHHHHHHHHHHHHGGGC
T ss_pred             CHHHHHHHHHHHHHhhc
Confidence            99999999988876655

>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=99.28  E-value=2.3e-11  Score=108.64  Aligned_cols=134  Identities=13%  Similarity=0.044  Sum_probs=94.0

Q ss_pred             HHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhc--CCceEEEEeccCCCCHHHHHHHHHHHhcCCCCC
Q psy200          202 QLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIK--DAFKTIYINCNSVRNAASVYETIVNELKLKPGG  279 (490)
Q Consensus       202 ~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~--~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~~~  279 (490)
                      +++-|..+++    .+.+..++|+|++|+|||++|..+++.+...  .+..++++.....                   .
T Consensus         2 ~~~~l~~~i~----~~~~~~~l~~G~~g~gk~~~a~~l~~~i~~~~~~h~D~~~i~~~~~-------------------~   58 (198)
T d2gnoa2           2 QLETLKRIIE----KSEGISILINGEDLSYPREVSLELPEYVEKFPPKASDVLEIDPEGE-------------------N   58 (198)
T ss_dssp             HHHHHHHHHH----TCSSEEEEEECSSSSHHHHHHHHHHHHHHTSCCCTTTEEEECCSSS-------------------C
T ss_pred             HHHHHHHHHh----cCCCceEEEECCCCCCHHHHHHHHHHHHhccccCCCCEEEEeCCcC-------------------C
Confidence            3445555554    4678899999999999999999999887522  1224666653221                   1


Q ss_pred             CcHHHHHHHHHHHHhc--CCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEEEecCCCChhHhhhHHhhhccCC
Q psy200          280 KSERHQLGAILKYFDT--KHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVANALDLTDRMLPRLQANVTL  357 (490)
Q Consensus       280 ~s~~~~~~~l~~~l~~--~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI~~tn~~~~~~~l~~~l~~R~~~  357 (490)
                      .+.+++++....+...  .++..|+||||+|.|....+++|+..++.+   ....++|.+|+.   ...+.+.+++||. 
T Consensus        59 I~Id~IR~i~~~~~~~~~~~~~KviIId~ad~l~~~aqNaLLK~LEEP---p~~t~fiLit~~---~~~ll~TI~SRC~-  131 (198)
T d2gnoa2          59 IGIDDIRTIKDFLNYSPELYTRKYVIVHDCERMTQQAANAFLKALEEP---PEYAVIVLNTRR---WHYLLPTIKSRVF-  131 (198)
T ss_dssp             BCHHHHHHHHHHHTSCCSSSSSEEEEETTGGGBCHHHHHHTHHHHHSC---CTTEEEEEEESC---GGGSCHHHHTTSE-
T ss_pred             CCHHHHHHHHHHHhhCcccCCCEEEEEeCccccchhhhhHHHHHHhCC---CCCceeeeccCC---hhhCHHHHhcceE-
Confidence            2455666543332222  255679999999999999999999999853   345556656663   5678999999995 


Q ss_pred             CCeeEEeCCCC
Q psy200          358 QPTLMNFAPYS  368 (490)
Q Consensus       358 ~~~~i~~~pls  368 (490)
                         .+.|.++.
T Consensus       132 ---~i~~~~p~  139 (198)
T d2gnoa2         132 ---RVVVNVPK  139 (198)
T ss_dssp             ---EEECCCCH
T ss_pred             ---EEeCCCch
Confidence               79998765

>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=99.17  E-value=6.7e-10  Score=110.90  Aligned_cols=146  Identities=16%  Similarity=0.245  Sum_probs=90.8

Q ss_pred             EEEEecCccccccC------------HHHHHHhHhCC-------CCCCCcEEEEEecCCCC-hhHhhhHHhhhccCCCCe
Q psy200          301 LLILDEIDALESRK------------QTILYTIFEWP-------SIPGSKLVLVGVANALD-LTDRMLPRLQANVTLQPT  360 (490)
Q Consensus       301 vI~IDEid~l~~~~------------~~~L~~l~~~~-------~~~~~~vilI~~tn~~~-~~~~l~~~l~~R~~~~~~  360 (490)
                      ++++||++......            +..+..+++-.       ......+.+|+.....+ ....+.|.|..||.   .
T Consensus       252 ~~~~dei~k~~~~~~~~g~d~~~eg~~~~ll~~~e~~~v~~~~~~~~~~~~l~i~~~~~~~~~~~gliPEliGRlP---i  328 (443)
T d1g41a_         252 IVFIDEIDKICKKGEYSGADVSREGVQRDLLPLVEGSTVSTKHGMVKTDHILFIASGAFQVARPSDLIPELQGRLP---I  328 (443)
T ss_dssp             EEEEETGGGGSCCSSCSSSHHHHHHHHHHHHHHHHCCEEEETTEEEECTTCEEEEEECCSSCCGGGSCHHHHTTCC---E
T ss_pred             ccccchhhhhhhcccCCCCCcccchhhhhhhhhccccccccccccccccchhhccccchhhcccccchhhhccceE---E
Confidence            89999999886432            22233332211       11233445555543221 23456789999988   4


Q ss_pred             eEEeCCCCHHHHHHHHHH-----------HHhccCCCCCCCHHHHHHHHHHHHHh-----hCCHHHHHHHHHHHHHHHHh
Q psy200          361 LMNFAPYSREQILEIISQ-----------KLKQTDKFNMFNASALQLLAGKVAAV-----SGDIRKAIDITNHLIDLTYD  424 (490)
Q Consensus       361 ~i~~~pls~~e~~~il~~-----------~l~~~~~~~~~~~~~i~~i~~~i~~~-----~Gd~r~ai~ll~~a~~~a~~  424 (490)
                      +..|.+++.+++..||..           .+...+.+..|++++++.|+++....     .-+.|.+-.++++.+.-+.-
T Consensus       329 ~v~L~~L~~~dL~rILtEPknsLikQy~~lf~~~gv~L~ft~~al~~iA~~A~~~n~~~~~~GAR~Lr~i~E~~l~~~~f  408 (443)
T d1g41a_         329 RVELTALSAADFERILTEPHASLTEQYKALMATEGVNIAFTTDAVKKIAEAAFRVNEKTENIGARRLHTVMERLMDKISF  408 (443)
T ss_dssp             EEECCCCCHHHHHHHHHSSTTCHHHHHHHHHHTTTCEEEECHHHHHHHHHHHHHHHHHSCCCGGGHHHHHHHHHHHHHHH
T ss_pred             EEEccCccHHHHHHHHHhhhhhHHHHHHHHHhhcCcEEEEcHHHHHHHHHHHHHhhhhcccCCchHHHHHHHHHHHHHhc
Confidence            899999999999998742           22333566778999999999876542     12567666667766554432


Q ss_pred             cccc-CCcccccCHHHHHHHHHHhcc
Q psy200          425 NVKE-NGEVTGIGLKEVLGVISSVYC  449 (490)
Q Consensus       425 ~~~~-~~~~~~It~~~v~~a~~~~~~  449 (490)
                      +... ....-.|+.+.|.+.+..+..
T Consensus       409 ~~p~~~~~~v~Id~~~v~~~l~~~~~  434 (443)
T d1g41a_         409 SASDMNGQTVNIDAAYVADALGEVVE  434 (443)
T ss_dssp             HGGGCTTCEEEECHHHHHHHHTTTTT
T ss_pred             cCCCCCCCEEEECHHHHHhhhhchhh
Confidence            2211 112346889999888876653

>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=98.81  E-value=3.6e-09  Score=102.77  Aligned_cols=60  Identities=25%  Similarity=0.306  Sum_probs=42.2

Q ss_pred             CCCCChHHHHHHHHHHHHhhhcc-CCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCC
Q psy200          194 CELPGREVQLEGIRQFLLGHVNN-ETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVR  260 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~-~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~  260 (490)
                      ..+.+.+..+   .++|...+.+ ...++++|+||||||||++++++++.++    ..++.+|++...
T Consensus       131 ~~~~~~~~~i---~~~l~~~~~~~~~~~~~~~~g~~~~gk~~~~~~~~~~~~----~~~i~in~s~~r  191 (362)
T d1svma_         131 CLLPKMDSVV---YDFLKCMVYNIPKKRYWLFKGPIDSGKTTLAAALLELCG----GKALNVNLPLDR  191 (362)
T ss_dssp             TTSTTHHHHH---HHHHHHHHHCCTTCCEEEEECSTTSSHHHHHHHHHHHHC----CEEECCSSCTTT
T ss_pred             hcccchHHHH---HHHHHHHHhCCCCcCeEEEECCCCCCHHHHHHHHHHHcC----CCEEEEECcchh
Confidence            3355544443   3344333222 3456999999999999999999999987    678888887654

>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=98.39  E-value=1.2e-06  Score=75.51  Aligned_cols=24  Identities=33%  Similarity=0.654  Sum_probs=22.4

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHhh
Q psy200          221 SMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      .|+|+||+|+|||||++.++..+.
T Consensus         2 ki~I~G~~G~GKSTLl~~i~~~l~   25 (178)
T d1ye8a1           2 KIIITGEPGVGKTTLVKKIVERLG   25 (178)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHG
T ss_pred             EEEEECCCCcHHHHHHHHHHhcCC
Confidence            489999999999999999999886

>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=98.14  E-value=8e-07  Score=82.16  Aligned_cols=40  Identities=20%  Similarity=0.422  Sum_probs=32.1

Q ss_pred             cCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCC
Q psy200          216 NETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSV  259 (490)
Q Consensus       216 ~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~  259 (490)
                      ...+.+++|+||||||||++|++++.++.    ..++.+++..+
T Consensus        29 ~~~P~~ilL~GpPGtGKT~la~~la~~~~----~~~~~i~~d~~   68 (273)
T d1gvnb_          29 VESPTAFLLGGQPGSGKTSLRSAIFEETQ----GNVIVIDNDTF   68 (273)
T ss_dssp             CSSCEEEEEECCTTSCTHHHHHHHHHHTT----TCCEEECTHHH
T ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHHHhh----cceEEEecHHH
Confidence            34667899999999999999999999975    45677776443

>d1a1va1 c.37.1.14 (A:190-325) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: HCV helicase domain
species: Human hepatitis C virus (HCV), different isolates [TaxId: 11103]

Probab=97.81  E-value=1.4e-05  Score=65.57  Aligned_cols=100  Identities=15%  Similarity=0.141  Sum_probs=51.6

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCCC----CC--------C---cH
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKP----GG--------K---SE  282 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~----~~--------~---s~  282 (490)
                      ..+..+|.+|.|+|||+++-.++.+.    +..++++ +....-..++...+...+....    .+        .   ..
T Consensus         7 ~~~~~ll~apTGsGKT~~~~~~~~~~----~~~vli~-~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   81 (136)
T d1a1va1           7 SFQVAHLHAPTGSGKSTKVPAAYAAQ----GYKVLVL-NPSVAATLGFGAYMSKAHGVDPNIRTGVRTITTGSPITYSTY   81 (136)
T ss_dssp             SCEEEEEECCTTSCTTTHHHHHHHTT----TCCEEEE-ESCHHHHHHHHHHHHHHHSCCCEEECSSCEECCCCSEEEEEH
T ss_pred             CCCEEEEEeCCCCCHHHHHHHHHHHc----CCcEEEE-cChHHHHHHHHHHHHHHhhccccccccccccccccceEEEee
Confidence            45788999999999999886555433    2344444 3322223344444444443210    00        0   11


Q ss_pred             HHHHHHHHHHHhcCCCeEEEEEecCccccccCHHHHHHhHhCC
Q psy200          283 RHQLGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWP  325 (490)
Q Consensus       283 ~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~  325 (490)
                      ........   ....+.-+|||||+|.+.......+..+++..
T Consensus        82 ~~~~~~~~---~~~~~~~~vIiDE~H~~~~~~~~~~~~~l~~~  121 (136)
T d1a1va1          82 GKFLADGG---CSGGAYDIIICDECHSTDATSILGIGTVLDQA  121 (136)
T ss_dssp             HHHHHTTG---GGGCCCSEEEEETTTCCSHHHHHHHHHHHHHT
T ss_pred             eeeccccc---hhhhcCCEEEEecccccCHHHHHHHHHHHHHH
Confidence            11111111   11133459999999998654444454555443

>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=97.77  E-value=7.7e-05  Score=65.58  Aligned_cols=96  Identities=14%  Similarity=0.191  Sum_probs=60.6

Q ss_pred             cCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCC-HHHHHHHHHHHhcCCC----CCCcHHHHHHHHH
Q psy200          216 NETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRN-AASVYETIVNELKLKP----GGKSERHQLGAIL  290 (490)
Q Consensus       216 ~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~-~~~l~~~i~~~l~~~~----~~~s~~~~~~~l~  290 (490)
                      ...+..++|+||+|+||||++-.++..+. ..+..+..+.+-.++. ..+-+..+.+.++.+.    .+.....+.....
T Consensus         6 ~~~p~vi~lvGptGvGKTTTiAKLA~~~~-~~g~kV~lit~Dt~R~gA~eQL~~~a~~l~v~~~~~~~~~d~~~~l~~~~   84 (211)
T d2qy9a2           6 GKAPFVILMVGVNGVGKTTTIGKLARQFE-QQGKSVMLAAGDTFRAAAVEQLQVWGQRNNIPVIAQHTGADSASVIFDAI   84 (211)
T ss_dssp             SCTTEEEEEECCTTSCHHHHHHHHHHHHH-TTTCCEEEECCCTTCHHHHHHHHHHHHHTTCCEECCSTTCCHHHHHHHHH
T ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHHHHH-HCCCcEEEEecccccccchhhhhhhhhhcCCcccccccCCCHHHHHHHHH
Confidence            34567888999999999999999998876 3445777777766653 2445667777777642    2223333332222


Q ss_pred             HHHhcCCCeEEEEEecCcccccc
Q psy200          291 KYFDTKHKSILLILDEIDALESR  313 (490)
Q Consensus       291 ~~l~~~~~~~vI~IDEid~l~~~  313 (490)
                      +.... ...-+||||=..+....
T Consensus        85 ~~a~~-~~~d~ilIDTaGr~~~d  106 (211)
T d2qy9a2          85 QAAKA-RNIDVLIADTAGRLQNK  106 (211)
T ss_dssp             HHHHH-TTCSEEEECCCCCGGGH
T ss_pred             HHHHH-cCCCEEEeccCCCcccc
Confidence            22211 22349999998876543

>d1w36d1 c.37.1.19 (D:2-360) Exodeoxyribonuclease V alpha chain (RecD) {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Exodeoxyribonuclease V alpha chain (RecD)
species: Escherichia coli [TaxId: 562]

Probab=97.76  E-value=2.1e-05  Score=75.60  Aligned_cols=128  Identities=16%  Similarity=0.207  Sum_probs=63.0

Q ss_pred             HHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhh---cCCceEEEEeccCCCCHHHHHHHHHHH---h
Q psy200          200 EVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEI---KDAFKTIYINCNSVRNAASVYETIVNE---L  273 (490)
Q Consensus       200 e~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~---~~~~~~~~v~~~~~~~~~~l~~~i~~~---l  273 (490)
                      +.+...+...+.       .+.++|+|+||||||+++..+...+..   ..+.. +.+..+.......+.+.+...   +
T Consensus       151 ~~Q~~A~~~al~-------~~~~vI~G~pGTGKTt~i~~~l~~l~~~~~~~~~~-I~l~ApTgkAA~~L~e~~~~~~~~~  222 (359)
T d1w36d1         151 NWQKVAAAVALT-------RRISVISGGPGTGKTTTVAKLLAALIQMADGERCR-IRLAAPTGKAAARLTESLGKALRQL  222 (359)
T ss_dssp             CHHHHHHHHHHT-------BSEEEEECCTTSTHHHHHHHHHHHHHHTCSSCCCC-EEEEBSSHHHHHHHHHHHTHHHHHS
T ss_pred             cHHHHHHHHHHc-------CCeEEEEcCCCCCceehHHHHHHHHHHHHhccCCe-EEEecCcHHHHHHHHHHHHHHHhhc
Confidence            345555555542       468999999999999998776655531   22233 333333332233333333222   1


Q ss_pred             cCC--------CCCCcHHHH------HHHHHHHHhcCCCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEEEecC
Q psy200          274 KLK--------PGGKSERHQ------LGAILKYFDTKHKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVAN  339 (490)
Q Consensus       274 ~~~--------~~~~s~~~~------~~~l~~~l~~~~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI~~tn  339 (490)
                      ...        ....+...+      ...+..........-+|||||+-.+..   ..+..++... ..+.++|++|-.+
T Consensus       223 ~~~~~~~~~~~~~~~t~~~ll~~~~~~~~~~~~~~~~l~~d~lIIDEaSmv~~---~l~~~ll~~~-~~~~~lILvGD~~  298 (359)
T d1w36d1         223 PLTDEQKKRIPEDASTLHRLLGAQPGSQRLRHHAGNPLHLDVLVVDEASMIDL---PMMSRLIDAL-PDHARVIFLGDRD  298 (359)
T ss_dssp             SCCSCCCCSCSCCCBTTTSCC-----------CTTSCCSCSEEEECSGGGCBH---HHHHHHHHTC-CTTCEEEEEECTT
T ss_pred             CchhhhhhhhhhhhhHHHHHHhhhhcchHHHHhhhcccccceeeehhhhccCH---HHHHHHHHHh-cCCCEEEEECChh
Confidence            110        000011110      111111111112345999999999864   3344454433 2567899988654

>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=97.74  E-value=8.5e-05  Score=65.40  Aligned_cols=152  Identities=13%  Similarity=0.117  Sum_probs=77.6

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCC-HHHHHHHHHHHhcCCCC----CCc-HHHHHHHHH
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRN-AASVYETIVNELKLKPG----GKS-ERHQLGAIL  290 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~-~~~l~~~i~~~l~~~~~----~~s-~~~~~~~l~  290 (490)
                      ..+..++|+||+|+||||++-.++..+.. .+.++..+.+-.++. ..+-+..+...++.+..    ... ...+.+.+.
T Consensus        10 k~p~vi~lvGptGvGKTTTiAKLA~~~~~-~g~kV~lit~Dt~R~ga~eQL~~~a~~l~v~~~~~~~~~~~~~~~~~a~~   88 (211)
T d1j8yf2          10 KIPYVIMLVGVQGTGKATTAGKLAYFYKK-KGFKVGLVGADVYRPAALEQLQQLGQQIGVPVYGEPGEKDVVGIAKRGVE   88 (211)
T ss_dssp             SSSEEEEEECSCCC----HHHHHHHHHHH-TTCCEEEEECCCSSHHHHHHHHHHHHHHTCCEECCTTCCCHHHHHHHHHH
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHHHH-CCCceEEEEeeccccchhHHHHHhccccCcceeecccchhhhHHHHHHHH
Confidence            45678889999999999999999988763 345677777766653 33456666777765421    122 222333333


Q ss_pred             HHHhcCCCeEEEEEecCccccccCH----HHHHHhHhCCCCCCCcEEEEEecCCCChhHhhhHHhhhccCCCCeeEEeCC
Q psy200          291 KYFDTKHKSILLILDEIDALESRKQ----TILYTIFEWPSIPGSKLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAP  366 (490)
Q Consensus       291 ~~l~~~~~~~vI~IDEid~l~~~~~----~~L~~l~~~~~~~~~~vilI~~tn~~~~~~~l~~~l~~R~~~~~~~i~~~p  366 (490)
                      .+...  ..-+||||=.........    +.+..+.+... ....++++.++...+..+.+.. ....++.  ..+-|..
T Consensus        89 ~~~~~--~~d~IlIDTaGr~~~~~~~~~~~el~~~~~~~~-~~~~~LVl~a~~~~~~~~~~~~-~~~~~~~--~~lI~TK  162 (211)
T d1j8yf2          89 KFLSE--KMEIIIVDTAGRHGYGEEAALLEEMKNIYEAIK-PDEVTLVIDASIGQKAYDLASK-FNQASKI--GTIIITK  162 (211)
T ss_dssp             HHHHT--TCSEEEEECCCSCCTTCHHHHHHHHHHHHHHHC-CSEEEEEEEGGGGGGHHHHHHH-HHHHCTT--EEEEEEC
T ss_pred             Hhhcc--CCceEEEecCCcCccchhhHHHHHHHHHHhhcC-CceEEEEEecccCcchHHHHhh-hhcccCc--ceEEEec
Confidence            33322  234999998876433221    22333333211 2223344444433333333222 2223333  4577888


Q ss_pred             CCHHHHHHH
Q psy200          367 YSREQILEI  375 (490)
Q Consensus       367 ls~~e~~~i  375 (490)
                      ++.....--
T Consensus       163 lDet~~~G~  171 (211)
T d1j8yf2         163 MDGTAKGGG  171 (211)
T ss_dssp             TTSCSCHHH
T ss_pred             ccCCCcccH
Confidence            876544433

>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=97.73  E-value=0.0011  Score=57.98  Aligned_cols=94  Identities=15%  Similarity=0.183  Sum_probs=62.0

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCC-CHHHHHHHHHHHhcCCC----CCCcHHHHH-HHHH
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVR-NAASVYETIVNELKLKP----GGKSERHQL-GAIL  290 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~-~~~~l~~~i~~~l~~~~----~~~s~~~~~-~~l~  290 (490)
                      ..++.++|+||+|+||||++-.++..+... +.++..+.+-.++ ...+-+..+.+.++.+.    .+....... +.+.
T Consensus         4 ~~~~vi~lvGptGvGKTTTiaKLA~~~~~~-g~kV~lit~Dt~R~gA~eQL~~~a~~l~i~~~~~~~~~d~~~~~~~~~~   82 (207)
T d1okkd2           4 PKGRVVLVVGVNGVGKTTTIAKLGRYYQNL-GKKVMFCAGDTFRAAGGTQLSEWGKRLSIPVIQGPEGTDPAALAYDAVQ   82 (207)
T ss_dssp             CSSSEEEEECSTTSSHHHHHHHHHHHHHTT-TCCEEEECCCCSSTTHHHHHHHHHHHHTCCEECCCTTCCHHHHHHHHHH
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHHHHC-CCcEEEEEeccccccchhhHhhcccccCceEEeccCCccHHHHHHHHHH
Confidence            356789999999999999999999887633 4577777777765 34566777788777643    222333332 2222


Q ss_pred             HHHhcCCCeEEEEEecCcccccc
Q psy200          291 KYFDTKHKSILLILDEIDALESR  313 (490)
Q Consensus       291 ~~l~~~~~~~vI~IDEid~l~~~  313 (490)
                      .....  ..-+||||=.......
T Consensus        83 ~~~~~--~~d~ilIDTaGr~~~d  103 (207)
T d1okkd2          83 AMKAR--GYDLLFVDTAGRLHTK  103 (207)
T ss_dssp             HHHHH--TCSEEEECCCCCCTTC
T ss_pred             HHHHC--CCCEEEcCccccchhh
Confidence            22221  1349999998876544

>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=97.73  E-value=9.6e-05  Score=65.15  Aligned_cols=96  Identities=15%  Similarity=0.135  Sum_probs=60.1

Q ss_pred             cCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCC-HHHHHHHHHHHhcCCC----CCCcHHHHHHHHH
Q psy200          216 NETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRN-AASVYETIVNELKLKP----GGKSERHQLGAIL  290 (490)
Q Consensus       216 ~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~-~~~l~~~i~~~l~~~~----~~~s~~~~~~~l~  290 (490)
                      ...+..++++||+|+||||++-.++..+. ..+.++..+.+-.++- ..+-+..+.+.++.+.    .+.....+.....
T Consensus         8 ~~~p~vi~lvGptGvGKTTTiAKLAa~~~-~~~~kV~lit~Dt~R~gA~eQL~~~a~~l~i~~~~~~~~~d~~~~~~~~~   86 (213)
T d1vmaa2           8 PEPPFVIMVVGVNGTGKTTSCGKLAKMFV-DEGKSVVLAAADTFRAAAIEQLKIWGERVGATVISHSEGADPAAVAFDAV   86 (213)
T ss_dssp             SSSCEEEEEECCTTSSHHHHHHHHHHHHH-HTTCCEEEEEECTTCHHHHHHHHHHHHHHTCEEECCSTTCCHHHHHHHHH
T ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHHHHH-HCCCceEEEeecccccchhHHHHHHhhhcCccccccCCCCcHHHHHHHHH
Confidence            35667889999999999999999998885 3345666777666653 3445666677776532    2223333332222


Q ss_pred             HHHhcCCCeEEEEEecCcccccc
Q psy200          291 KYFDTKHKSILLILDEIDALESR  313 (490)
Q Consensus       291 ~~l~~~~~~~vI~IDEid~l~~~  313 (490)
                      ..... ...-+|+||=.......
T Consensus        87 ~~~~~-~~~d~ilIDTaGr~~~d  108 (213)
T d1vmaa2          87 AHALA-RNKDVVIIDTAGRLHTK  108 (213)
T ss_dssp             HHHHH-TTCSEEEEEECCCCSCH
T ss_pred             HHHHH-cCCCEEEEeccccccch
Confidence            22111 22349999988876544

>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=97.66  E-value=0.00031  Score=57.93  Aligned_cols=24  Identities=25%  Similarity=0.426  Sum_probs=20.9

Q ss_pred             CeEEEECCCCCcHHHHHHHHHHHh
Q psy200          220 GSMYISGPPGTGKSASLNLLVSRA  243 (490)
Q Consensus       220 ~~ill~GppGtGKTtla~~l~~~l  243 (490)
                      +.|+|+|+||+||||+|+.++...
T Consensus         3 klIii~G~pGsGKTTla~~L~~~~   26 (152)
T d1ly1a_           3 KIILTIGCPGSGKSTWAREFIAKN   26 (152)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHHHhC
Confidence            468899999999999999987654

>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=97.63  E-value=0.00052  Score=60.08  Aligned_cols=94  Identities=13%  Similarity=0.174  Sum_probs=59.5

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCC-HHHHHHHHHHHhcCCC----CCCcHHHHHHHHHHH
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRN-AASVYETIVNELKLKP----GGKSERHQLGAILKY  292 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~-~~~l~~~i~~~l~~~~----~~~s~~~~~~~l~~~  292 (490)
                      ..+.++|+||+|+||||++-.++..+.. .+..+..+.+-.++. ..+-+..+.+.++.+.    ...............
T Consensus         9 ~~~vi~lvGp~GvGKTTTiaKLA~~~~~-~g~kV~lit~Dt~R~gA~eQL~~~a~~l~v~~~~~~~~~~~~~~~~~~~~~   87 (207)
T d1ls1a2           9 DRNLWFLVGLQGSGKTTTAAKLALYYKG-KGRRPLLVAADTQRPAAREQLRLLGEKVGVPVLEVMDGESPESIRRRVEEK   87 (207)
T ss_dssp             SSEEEEEECCTTTTHHHHHHHHHHHHHH-TTCCEEEEECCSSCHHHHHHHHHHHHHHTCCEEECCTTCCHHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHHH-CCCcEEEEecccccchHHHHHHHHHHhcCCccccccccchhhHHHHHHHHH
Confidence            3467789999999999999999998863 355777777776653 3455666777776542    223344433322222


Q ss_pred             HhcCCCeEEEEEecCcccccc
Q psy200          293 FDTKHKSILLILDEIDALESR  313 (490)
Q Consensus       293 l~~~~~~~vI~IDEid~l~~~  313 (490)
                      ... ...-+|+||=+.+....
T Consensus        88 ~~~-~~~d~vlIDTaGr~~~d  107 (207)
T d1ls1a2          88 ARL-EARDLILVDTAGRLQID  107 (207)
T ss_dssp             HHH-HTCCEEEEECCCCSSCC
T ss_pred             Hhh-ccCcceeecccccchhh
Confidence            111 12338999988876543

>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=97.63  E-value=6.3e-05  Score=64.29  Aligned_cols=27  Identities=26%  Similarity=0.329  Sum_probs=23.2

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHh
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRA  243 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l  243 (490)
                      ..+..|+++|+||+||||+++.++...
T Consensus        12 ~~p~liil~G~pGsGKST~a~~l~~~~   38 (172)
T d1yj5a2          12 PNPEVVVAVGFPGAGKSTFIQEHLVSA   38 (172)
T ss_dssp             SSCCEEEEECCTTSSHHHHHHHHTGGG
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHhc
Confidence            467789999999999999999887654

>d1kaga_ c.37.1.2 (A:) Shikimate kinase (AroK) {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Escherichia coli [TaxId: 562]

Probab=97.61  E-value=1.9e-05  Score=66.24  Aligned_cols=25  Identities=28%  Similarity=0.519  Sum_probs=23.1

Q ss_pred             CeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          220 GSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       220 ~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      ++|+|+|++|+||||+++.+++.++
T Consensus         3 k~I~l~G~~GsGKSTvak~La~~L~   27 (169)
T d1kaga_           3 RNIFLVGPMGAGKSTIGRQLAQQLN   27 (169)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHHHTT
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHhC
Confidence            5789999999999999999999985

>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=97.60  E-value=2.1e-05  Score=67.31  Aligned_cols=26  Identities=23%  Similarity=0.566  Sum_probs=24.0

Q ss_pred             CeEEEECCCCCcHHHHHHHHHHHhhh
Q psy200          220 GSMYISGPPGTGKSASLNLLVSRAEI  245 (490)
Q Consensus       220 ~~ill~GppGtGKTtla~~l~~~l~~  245 (490)
                      ++|+|+||||+|||||++.++..+..
T Consensus         2 k~v~ItG~~GtGKTtl~~~i~~~l~~   27 (189)
T d2i3ba1           2 RHVFLTGPPGVGKTTLIHKASEVLKS   27 (189)
T ss_dssp             CCEEEESCCSSCHHHHHHHHHHHHHH
T ss_pred             cEEEEECCCCCcHHHHHHHHHHHHHH
Confidence            68999999999999999999999863

>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=97.60  E-value=0.00016  Score=64.92  Aligned_cols=91  Identities=18%  Similarity=0.269  Sum_probs=56.9

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCC----------------CCCCc
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLK----------------PGGKS  281 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~----------------~~~~s  281 (490)
                      .+..++|+|+||+|||+++..++..... .+..++|+....  +...+.... ..++..                .....
T Consensus        25 ~gsl~li~G~pGsGKT~l~~qia~~~~~-~~~~~~~is~e~--~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~  100 (242)
T d1tf7a2          25 KDSIILATGATGTGKTLLVSRFVENACA-NKERAILFAYEE--SRAQLLRNA-YSWGMDFEEMERQNLLKIVCAYPESAG  100 (242)
T ss_dssp             SSCEEEEEECTTSSHHHHHHHHHHHHHT-TTCCEEEEESSS--CHHHHHHHH-HTTSCCHHHHHHTTSEEECCCCGGGSC
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHHHHH-hccccceeeccC--CHHHHHHHH-HHcCCChHHHhhcCceEEEEeecchhh
Confidence            5678999999999999999999998642 334566665432  344443322 222110                11123


Q ss_pred             HHHHHHHHHHHHhcCCCeEEEEEecCcccccc
Q psy200          282 ERHQLGAILKYFDTKHKSILLILDEIDALESR  313 (490)
Q Consensus       282 ~~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~  313 (490)
                      ..+..+.+...+.. .++.+++||.++.+...
T Consensus       101 ~~~~~~~i~~~i~~-~~~~~vviDs~~~~~~~  131 (242)
T d1tf7a2         101 LEDHLQIIKSEIND-FKPARIAIDSLSALARG  131 (242)
T ss_dssp             HHHHHHHHHHHHHT-TCCSEEEEECHHHHTSS
T ss_pred             HHHHHHHHHHHHHh-cCCceeeeecchhhhcC
Confidence            44555555555554 45679999999988654

>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=97.49  E-value=3e-05  Score=66.44  Aligned_cols=27  Identities=26%  Similarity=0.277  Sum_probs=24.4

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      -.+.|+|.|++|+||||+|++|++.++
T Consensus         6 ~~K~I~i~G~~GsGKTTla~~La~~~~   32 (192)
T d1lw7a2           6 FAKTVAILGGESSGKSVLVNKLAAVFN   32 (192)
T ss_dssp             TCEEEEEECCTTSHHHHHHHHHHHHTT
T ss_pred             cceEEEEECCCCCCHHHHHHHHHHHhC
Confidence            357899999999999999999999875

>d1yksa1 c.37.1.14 (A:185-324) YFV helicase domain {Yellow fever virus [TaxId: 11089]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: YFV helicase domain
species: Yellow fever virus [TaxId: 11089]

Probab=97.49  E-value=6.9e-05  Score=60.88  Aligned_cols=50  Identities=12%  Similarity=0.264  Sum_probs=30.0

Q ss_pred             CCCeEEEECCCCCcHHHHHH-HHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHh
Q psy200          218 TSGSMYISGPPGTGKSASLN-LLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNEL  273 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~-~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l  273 (490)
                      ++..++|++|+|+|||..+- .+.+... ..+..++.+...     ..++.+..+.+
T Consensus         6 ~~~~~il~~~tGsGKT~~~~~~~~~~~~-~~~~~vli~~p~-----~~l~~q~~~~~   56 (140)
T d1yksa1           6 KGMTTVLDFHPGAGKTRRFLPQILAECA-RRRLRTLVLAPT-----RVVLSEMKEAF   56 (140)
T ss_dssp             TTCEEEECCCTTSSTTTTHHHHHHHHHH-HTTCCEEEEESS-----HHHHHHHHHHT
T ss_pred             cCCcEEEEcCCCCChhHHHHHHHHHHhh-hcCceeeeeecc-----hhHHHHHHHHh
Confidence            46789999999999996663 4444443 233444554322     34455555544

>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=97.45  E-value=4.2e-05  Score=64.78  Aligned_cols=25  Identities=28%  Similarity=0.530  Sum_probs=22.7

Q ss_pred             CeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          220 GSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       220 ~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      ..|+|+|+||+||||+++.+++.++
T Consensus         5 ~~I~i~G~pGsGKTTia~~La~~l~   29 (173)
T d1rkba_           5 PNILLTGTPGVGKTTLGKELASKSG   29 (173)
T ss_dssp             CCEEEECSTTSSHHHHHHHHHHHHC
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHC
Confidence            4688999999999999999999875

>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=97.43  E-value=5.7e-05  Score=64.29  Aligned_cols=29  Identities=17%  Similarity=0.225  Sum_probs=25.4

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHhhh
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRAEI  245 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l~~  245 (490)
                      ..+..|+|+|+||+||||++++|++.+..
T Consensus         4 ~~g~~I~l~G~~GsGKTTia~~La~~L~~   32 (183)
T d1m8pa3           4 TQGFTIFLTGYMNSGKDAIARALQVTLNQ   32 (183)
T ss_dssp             TCCEEEEEECSTTSSHHHHHHHHHHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHHhh
Confidence            35667889999999999999999999863

>d1zp6a1 c.37.1.25 (A:6-181) Hypothetical protein Atu3015 {Agrobacterium tumefaciens [TaxId: 358]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Atu3015-like
domain: Hypothetical protein Atu3015
species: Agrobacterium tumefaciens [TaxId: 358]

Probab=97.40  E-value=3.4e-05  Score=65.63  Aligned_cols=34  Identities=24%  Similarity=0.405  Sum_probs=27.9

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEe
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYIN  255 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~  255 (490)
                      .++.|+|.|+||+||||+++.+++.++    +.+++++
T Consensus         3 ~g~iI~l~G~~GsGKSTia~~La~~lg----~~~~~~~   36 (176)
T d1zp6a1           3 GGNILLLSGHPGSGKSTIAEALANLPG----VPKVHFH   36 (176)
T ss_dssp             TTEEEEEEECTTSCHHHHHHHHHTCSS----SCEEEEC
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHhC----CCEEEec
Confidence            356899999999999999999988764    5666664

>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=97.34  E-value=8e-05  Score=62.97  Aligned_cols=28  Identities=21%  Similarity=0.277  Sum_probs=25.0

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      ..++.++|+|++|+||||+++.+++.++
T Consensus         4 ~~~~iivl~G~~GsGKsT~a~~La~~l~   31 (171)
T d1knqa_           4 HDHHIYVLMGVSGSGKSAVASEVAHQLH   31 (171)
T ss_dssp             TTSEEEEEECSTTSCHHHHHHHHHHHHT
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHhC
Confidence            4567888999999999999999999875

>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=97.33  E-value=0.0012  Score=60.15  Aligned_cols=88  Identities=15%  Similarity=0.201  Sum_probs=63.0

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCCC------CCCcHHHHHHHHHH
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKP------GGKSERHQLGAILK  291 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~------~~~s~~~~~~~l~~  291 (490)
                      .++...|+|++|+|||+++..++..... .+..++|++.-...++.     +++.++...      .-.+.++..+.+..
T Consensus        56 ~g~itei~G~~~sGKT~l~l~~~~~aqk-~g~~v~yiDtE~~~~~~-----~a~~~Gvd~d~i~~~~~~~~E~~~~~~~~  129 (268)
T d1xp8a1          56 RGRITEIYGPESGGKTTLALAIVAQAQK-AGGTCAFIDAEHALDPV-----YARALGVNTDELLVSQPDNGEQALEIMEL  129 (268)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHHHH-TTCCEEEEESSCCCCHH-----HHHHTTCCGGGCEEECCSSHHHHHHHHHH
T ss_pred             CceEEEEecCCccchHHHHHHHHHHHHh-CCCEEEEEECCccCCHH-----HHHHhCCCchhEEEEcCCCHHHHHHHHHH
Confidence            5668889999999999999999888763 44678999877655553     445555421      12356667777766


Q ss_pred             HHhcCCCeEEEEEecCccccc
Q psy200          292 YFDTKHKSILLILDEIDALES  312 (490)
Q Consensus       292 ~l~~~~~~~vI~IDEid~l~~  312 (490)
                      +.+. +...+||||-+..+..
T Consensus       130 l~~~-~~~~liIiDSi~al~~  149 (268)
T d1xp8a1         130 LVRS-GAIDVVVVDSVAALTP  149 (268)
T ss_dssp             HHTT-TCCSEEEEECTTTCCC
T ss_pred             HHhc-CCCcEEEEeccccccc
Confidence            5544 5577999999999873

>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=97.32  E-value=0.00075  Score=61.77  Aligned_cols=51  Identities=12%  Similarity=0.070  Sum_probs=36.6

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHH
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIV  270 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~  270 (490)
                      ++..++|.|+||+|||+++..++..+....+.+++++++-.  +...+...++
T Consensus        34 ~G~l~vi~G~~G~GKT~~~~~la~~~a~~~g~~v~~~s~E~--~~~~~~~r~~   84 (277)
T d1cr2a_          34 GGEVIMVTSGSGMGKSTFVRQQALQWGTAMGKKVGLAMLEE--SVEETAEDLI   84 (277)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHHHHHHHTSCCCEEEEESSS--CHHHHHHHHH
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHhhhhhcccceeEeeecc--chhhHHhHHH
Confidence            56789999999999999999998776545567777776442  4444444333

>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=97.30  E-value=9.5e-05  Score=62.63  Aligned_cols=26  Identities=23%  Similarity=0.300  Sum_probs=24.0

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      .+.|+|+|++|+||||+++.|++.++
T Consensus         3 ~kiI~l~G~~GsGKsTva~~L~~~l~   28 (178)
T d1qhxa_           3 TRMIILNGGSSAGKSGIVRCLQSVLP   28 (178)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHSS
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHcC
Confidence            56899999999999999999999975

>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=97.28  E-value=5.5e-05  Score=63.92  Aligned_cols=25  Identities=32%  Similarity=0.559  Sum_probs=22.8

Q ss_pred             CeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          220 GSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       220 ~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      +.|+|+|+||+||||+|+.+++.+.
T Consensus         3 klI~i~G~~GsGKTTva~~L~~~~~   27 (176)
T d2bdta1           3 KLYIITGPAGVGKSTTCKRLAAQLD   27 (176)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHSS
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHcC
Confidence            4689999999999999999999874

>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=97.28  E-value=7.2e-05  Score=63.42  Aligned_cols=28  Identities=25%  Similarity=0.563  Sum_probs=24.5

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      ..+..|+|+|+||+||||+++.+++.+.
T Consensus         3 pk~~~I~i~G~~GsGKTT~~~~La~~l~   30 (174)
T d1y63a_           3 PKGINILITGTPGTGKTSMAEMIAAELD   30 (174)
T ss_dssp             CSSCEEEEECSTTSSHHHHHHHHHHHST
T ss_pred             CCCCEEEEEeCCCCCHHHHHHHHHHHhC
Confidence            3456799999999999999999999873

>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=97.25  E-value=0.00078  Score=61.27  Aligned_cols=87  Identities=14%  Similarity=0.200  Sum_probs=60.7

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCCC------CCCcHHHHHHHHHH
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKP------GGKSERHQLGAILK  291 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~------~~~s~~~~~~~l~~  291 (490)
                      .++.+.|+|++|+|||+++-.++..... .+..++|++.-...+..     .+..++...      .-.+.++..+.+..
T Consensus        53 ~g~itei~G~~gsGKTtl~l~~~~~~q~-~g~~~vyidtE~~~~~~-----~a~~~Gvd~d~v~~~~~~~~E~~~~~i~~  126 (263)
T d1u94a1          53 MGRIVEIYGPESSGKTTLTLQVIAAAQR-EGKTCAFIDAEHALDPI-----YARKLGVDIDNLLCSQPDTGEQALEICDA  126 (263)
T ss_dssp             TTSEEEEECSTTSSHHHHHHHHHHHHHH-TTCCEEEEESSCCCCHH-----HHHHTTCCGGGCEEECCSSHHHHHHHHHH
T ss_pred             CceEEEEecCCCcHHHHHHHHHHHHHHc-CCCEEEEEccccccCHH-----HHHHhCCCHHHEEEecCCCHHHHHHHHHH
Confidence            5678999999999999999999988763 34567899877655542     234444321      11345666666666


Q ss_pred             HHhcCCCeEEEEEecCcccc
Q psy200          292 YFDTKHKSILLILDEIDALE  311 (490)
Q Consensus       292 ~l~~~~~~~vI~IDEid~l~  311 (490)
                      ..+. +...+||||-+..+.
T Consensus       127 l~~~-~~~~liViDSi~al~  145 (263)
T d1u94a1         127 LARS-GAVDVIVVDSVAALT  145 (263)
T ss_dssp             HHHH-TCCSEEEEECGGGCC
T ss_pred             HHhc-CCCCEEEEECccccc
Confidence            5554 456689999998886

>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=97.24  E-value=9.4e-05  Score=64.24  Aligned_cols=29  Identities=21%  Similarity=0.439  Sum_probs=25.5

Q ss_pred             cCCCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          216 NETSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       216 ~~~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      ...+..|+|.||||+||||+++.|+++++
T Consensus         3 ~~kp~iI~i~G~pGSGKsT~a~~La~~~g   31 (194)
T d1qf9a_           3 KSKPNVVFVLGGPGSGKGTQCANIVRDFG   31 (194)
T ss_dssp             CCCCEEEEEEESTTSSHHHHHHHHHHHHC
T ss_pred             CCCCcEEEEECCCCCCHHHHHHHHHHHHC
Confidence            35677899999999999999999999874

>d1wp9a1 c.37.1.19 (A:1-200) putative ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase PF2015
species: Pyrococcus furiosus [TaxId: 2261]

Probab=97.24  E-value=0.00039  Score=60.36  Aligned_cols=35  Identities=20%  Similarity=0.198  Sum_probs=23.6

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEe
Q psy200          221 SMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYIN  255 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~  255 (490)
                      +++|++|.|+|||.++-.++.......+..++++.
T Consensus        25 n~lv~~pTGsGKT~i~~~~~~~~~~~~~~~il~i~   59 (200)
T d1wp9a1          25 NCLIVLPTGLGKTLIAMMIAEYRLTKYGGKVLMLA   59 (200)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHHHHHSCSCEEEEC
T ss_pred             CeEEEeCCCCcHHHHHHHHHHHHHHhcCCcEEEEc
Confidence            57899999999998766665544323334566663

>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=97.23  E-value=0.00011  Score=62.04  Aligned_cols=24  Identities=25%  Similarity=0.332  Sum_probs=22.3

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHhh
Q psy200          221 SMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      +|+|.|+||+||||+++.+++.++
T Consensus         2 ~I~liG~~GsGKsTi~k~La~~l~   25 (161)
T d1viaa_           2 NIVFIGFMGSGKSTLARALAKDLD   25 (161)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHHT
T ss_pred             cEEEECCCCCCHHHHHHHHHHHhC
Confidence            588889999999999999999986

>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=97.21  E-value=8.4e-05  Score=64.25  Aligned_cols=27  Identities=19%  Similarity=0.303  Sum_probs=24.2

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      .+..|+|+|+||+||||+++.|+..+.
T Consensus        18 ~g~vI~L~G~pGSGKTTiAk~La~~l~   44 (195)
T d1x6va3          18 RGCTVWLTGLSGAGKTTVSMALEEYLV   44 (195)
T ss_dssp             CCEEEEEESSCHHHHHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHH
Confidence            456788999999999999999999886

>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=97.21  E-value=0.00012  Score=62.14  Aligned_cols=25  Identities=16%  Similarity=0.288  Sum_probs=23.0

Q ss_pred             CeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          220 GSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       220 ~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      +.|+|.|++|+||||+++.+++.++
T Consensus         3 ~~Iil~G~~GsGKSTia~~LA~~Lg   27 (170)
T d1e6ca_           3 EPIFMVGARGCGMTTVGRELARALG   27 (170)
T ss_dssp             CCEEEESCTTSSHHHHHHHHHHHHT
T ss_pred             CCEEEECCCCCCHHHHHHHHHHHhC
Confidence            4678899999999999999999986

>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=97.18  E-value=0.0015  Score=59.48  Aligned_cols=88  Identities=15%  Similarity=0.203  Sum_probs=61.7

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcCCC------CCCcHHHHHHHHHH
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLKP------GGKSERHQLGAILK  291 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~~------~~~s~~~~~~~l~~  291 (490)
                      .++...|+|++|+|||+++..++..... .+..++|++.-...+.. .    +..++...      ...+.+++.+.+..
T Consensus        59 ~g~i~e~~G~~~~GKT~l~l~~~~~~q~-~g~~~vyIDtE~~~~~e-~----a~~~GvD~d~il~~~~~~~E~~~~~~~~  132 (269)
T d1mo6a1          59 RGRVIEIYGPESSGKTTVALHAVANAQA-AGGVAAFIDAEHALDPD-Y----AKKLGVDTDSLLVSQPDTGEQALEIADM  132 (269)
T ss_dssp             SSSEEEEECSSSSSHHHHHHHHHHHHHH-TTCEEEEEESSCCCCHH-H----HHHHTCCGGGCEEECCSSHHHHHHHHHH
T ss_pred             cceeEEEecCCCcHHHHHHHHHHHHHhc-CCCEEEEEECCccCCHH-H----HHHhCCCHHHeEEecCCCHHHHHHHHHH
Confidence            5678889999999999999888776643 44578999877765543 2    33344321      12356777776666


Q ss_pred             HHhcCCCeEEEEEecCccccc
Q psy200          292 YFDTKHKSILLILDEIDALES  312 (490)
Q Consensus       292 ~l~~~~~~~vI~IDEid~l~~  312 (490)
                      .... +...+||||-+..+..
T Consensus       133 l~~~-~~~~liIiDSi~al~~  152 (269)
T d1mo6a1         133 LIRS-GALDIVVIDSVAALVP  152 (269)
T ss_dssp             HHHT-TCEEEEEEECSTTCCC
T ss_pred             HHhc-CCCCEEEEeccccccc
Confidence            5543 6688999999999874

>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=97.13  E-value=0.00047  Score=59.41  Aligned_cols=26  Identities=27%  Similarity=0.396  Sum_probs=22.2

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      +..|+|.||||+||||+++.|++.++
T Consensus         3 ~~riil~G~pGSGKsT~a~~La~~~g   28 (190)
T d1ak2a1           3 GVRAVLLGPPGAGKGTQAPKLAKNFC   28 (190)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHHT
T ss_pred             ccEEEEECCCCCCHHHHHHHHHHHhC
Confidence            34566789999999999999999874

>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=97.07  E-value=0.0011  Score=58.61  Aligned_cols=40  Identities=20%  Similarity=0.247  Sum_probs=28.6

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEecc
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCN  257 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~  257 (490)
                      .+..++|+|+||+|||+++..++..........+.|+...
T Consensus        25 ~G~~~~I~G~~G~GKT~la~~~~~~~~~~~~~~~~~~s~e   64 (242)
T d1tf7a1          25 IGRSTLVSGTSGTGKTLFSIQFLYNGIIEFDEPGVFVTFE   64 (242)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHHHHHHCCCEEEEESS
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHHHHHhcCCCccccccc
Confidence            6778999999999999999876654333333456666543

>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=97.06  E-value=0.00019  Score=60.61  Aligned_cols=24  Identities=29%  Similarity=0.365  Sum_probs=21.2

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHhh
Q psy200          221 SMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      .++|.|++|+||||+++.+++.++
T Consensus         3 ~IvliG~~G~GKSTig~~La~~l~   26 (165)
T d2iyva1           3 KAVLVGLPGSGKSTIGRRLAKALG   26 (165)
T ss_dssp             SEEEECSTTSSHHHHHHHHHHHHT
T ss_pred             cEEEECCCCCCHHHHHHHHHHHhC
Confidence            355669999999999999999986

>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=97.04  E-value=0.0053  Score=52.39  Aligned_cols=25  Identities=44%  Similarity=0.624  Sum_probs=22.6

Q ss_pred             CeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          220 GSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       220 ~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      +.|+|+||+|+|||||++.++++..
T Consensus         2 rpIvl~GpsG~GK~tl~~~L~~~~~   26 (186)
T d1gkya_           2 RPIVISGPSGTGKSTLLKKLFAEYP   26 (186)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHCT
T ss_pred             CeEEEECCCCCCHHHHHHHHHHhCC
Confidence            5689999999999999999998864

>d2fz4a1 c.37.1.19 (A:24-229) DNA repair protein RAD25 {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DNA repair protein RAD25
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=97.03  E-value=0.0023  Score=55.82  Aligned_cols=44  Identities=20%  Similarity=0.317  Sum_probs=31.1

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      ..+--|+-+.+.+..++.       .+..+|.+|+|+|||.++-.++.++.
T Consensus        67 ~~~~Lr~yQ~eav~~~~~-------~~~~ll~~~tG~GKT~~a~~~~~~~~  110 (206)
T d2fz4a1          67 AEISLRDYQEKALERWLV-------DKRGCIVLPTGSGKTHVAMAAINELS  110 (206)
T ss_dssp             CCCCCCHHHHHHHHHHTT-------TSEEEEEESSSTTHHHHHHHHHHHSC
T ss_pred             CCCCcCHHHHHHHHHHHh-------CCCcEEEeCCCCCceehHHhHHHHhc
Confidence            345556666666665542       23556889999999999988887764

>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=97.00  E-value=0.0013  Score=59.94  Aligned_cols=40  Identities=20%  Similarity=0.180  Sum_probs=29.9

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHhhhc---------CCceEEEEeccC
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRAEIK---------DAFKTIYINCNS  258 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l~~~---------~~~~~~~v~~~~  258 (490)
                      +...+|+|++|+|||+++-.++..+...         ....++|+++-.
T Consensus        29 g~~~~i~G~~G~GKS~l~l~la~~ia~g~~~~~~~~~~~~~vl~~~~E~   77 (274)
T d1nlfa_          29 GTVGALVSPGGAGKSMLALQLAAQIAGGPDLLEVGELPTGPVIYLPAED   77 (274)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHHHHHTCCCTTCCCCCCCCCEEEEESSS
T ss_pred             CcEEEEEeCCCCCHHHHHHHHHHHHHcCCCcccccccCCCceEEEeccc
Confidence            5688899999999999999998876422         123577776544

>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=96.97  E-value=0.00038  Score=59.93  Aligned_cols=43  Identities=16%  Similarity=0.198  Sum_probs=30.1

Q ss_pred             HHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          201 VQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       201 ~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      +.++.|...+.. ++...+-.|.|.|++|+||||+|+.+.+.+.
T Consensus         5 ~~~~~~~~~~~~-~~~~~~~iIgI~G~~GSGKSTla~~L~~~l~   47 (198)
T d1rz3a_           5 DRIDFLCKTILA-IKTAGRLVLGIDGLSRSGKTTLANQLSQTLR   47 (198)
T ss_dssp             HHHHHHHHHHHT-SCCSSSEEEEEEECTTSSHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHh-ccCCCCEEEEEECCCCCCHHHHHHHHHHHhc
Confidence            345555555533 2333334566999999999999999998876

>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=96.96  E-value=0.00039  Score=58.27  Aligned_cols=25  Identities=24%  Similarity=0.258  Sum_probs=23.0

Q ss_pred             CeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          220 GSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       220 ~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      +.+.|+|++|+|||||++.+++++.
T Consensus         3 Pvi~itG~~GSGKTTL~~~L~~~l~   27 (170)
T d1np6a_           3 PLLAFAAWSGTGKTTLLKKLIPALC   27 (170)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHHH
T ss_pred             CEEEEEcCCCCCHHHHHHHHHHHHH
Confidence            4788999999999999999999875

>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=96.94  E-value=0.00035  Score=61.62  Aligned_cols=41  Identities=17%  Similarity=0.395  Sum_probs=32.1

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHH
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVN  271 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~  271 (490)
                      .+.|.|.||||+||+|+++.|+++++      +.++      +..++++.+..
T Consensus         3 ~piI~I~GppGSGKgT~ak~La~~~g------l~~i------StGdLlR~~a~   43 (225)
T d1ckea_           3 APVITIDGPSGAGKGTLCKAMAEALQ------WHLL------DSGAIYRVLAL   43 (225)
T ss_dssp             SCEEEEECCTTSSHHHHHHHHHHHHT------CEEE------EHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHhC------CcEE------CHHHHHHHHHH
Confidence            35788999999999999999999975      3444      56677776554

>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=96.94  E-value=0.00022  Score=61.62  Aligned_cols=26  Identities=27%  Similarity=0.506  Sum_probs=23.2

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      +..|+|.||||+||||+++.+++.++
T Consensus         3 Pm~I~i~GppGsGKsT~a~~La~~~~   28 (189)
T d1zaka1           3 PLKVMISGAPASGKGTQCELIKTKYQ   28 (189)
T ss_dssp             SCCEEEEESTTSSHHHHHHHHHHHHC
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHC
Confidence            45688999999999999999999874

>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=96.94  E-value=0.00024  Score=60.55  Aligned_cols=26  Identities=23%  Similarity=0.474  Sum_probs=23.8

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      ++.|+|.|++|+||||+++.+++.+.
T Consensus         1 ~kiI~i~G~~GsGKsT~~~~L~~~l~   26 (190)
T d1khta_           1 NKVVVVTGVPGVGSTTSSQLAMDNLR   26 (190)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHHH
Confidence            36799999999999999999999886

>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=96.92  E-value=0.00029  Score=61.07  Aligned_cols=28  Identities=25%  Similarity=0.513  Sum_probs=24.6

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      .....|+|.||||+||||+|+.|++.++
T Consensus         6 ~~~~iI~i~GppGSGKsT~a~~La~~~g   33 (196)
T d1ukza_           6 DQVSVIFVLGGPGAGKGTQCEKLVKDYS   33 (196)
T ss_dssp             TTCEEEEEECSTTSSHHHHHHHHHHHSS
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHHhC
Confidence            4567889999999999999999999864

>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=96.90  E-value=0.0013  Score=54.58  Aligned_cols=46  Identities=15%  Similarity=0.186  Sum_probs=33.2

Q ss_pred             HHHHHHHHHHHHhhhc---cCCCCeEEEECCCCCcHHHHHHHHHHHhhh
Q psy200          200 EVQLEGIRQFLLGHVN---NETSGSMYISGPPGTGKSASLNLLVSRAEI  245 (490)
Q Consensus       200 e~~~~~l~~~L~~~~~---~~~~~~ill~GppGtGKTtla~~l~~~l~~  245 (490)
                      +.+..++.+.|...+.   ..++-.++|.|+=|+||||+++.+++.++.
T Consensus        11 e~~t~~lg~~la~~l~~~~~~~g~ii~L~G~LGaGKTtfvr~~~~~lg~   59 (158)
T d1htwa_          11 EFSMLRFGKKFAEILLKLHTEKAIMVYLNGDLGAGKTTLTRGMLQGIGH   59 (158)
T ss_dssp             HHHHHHHHHHHHHHHHHHCCSSCEEEEEECSTTSSHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHHHHHhccCCCCeEEEEecCCCccHHHHHHHHHhhccc
Confidence            4445555555554432   234457889999999999999999999973

>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=96.88  E-value=0.00031  Score=61.79  Aligned_cols=42  Identities=14%  Similarity=0.195  Sum_probs=32.9

Q ss_pred             ccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEec
Q psy200          215 NNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINC  256 (490)
Q Consensus       215 ~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~  256 (490)
                      ....+..|+|+|.||+||||+++.+++.+.......+++++.
T Consensus        20 ~~~kg~vIwltGlsGsGKTTia~~L~~~l~~~~~~~~~~ldg   61 (208)
T d1m7ga_          20 RNQRGLTIWLTGLSASGKSTLAVELEHQLVRDRRVHAYRLDG   61 (208)
T ss_dssp             HTSSCEEEEEECSTTSSHHHHHHHHHHHHHHHHCCCEEEECH
T ss_pred             hCCCCeEEEEECCCCCCHHHHHHHHHHHHHHhcCceEEEEcc
Confidence            346788999999999999999999998875333456666654

>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=96.86  E-value=0.00035  Score=60.54  Aligned_cols=27  Identities=26%  Similarity=0.546  Sum_probs=24.1

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      .++.|+|.||||+||||+++.|++.++
T Consensus         7 ~~~iI~l~G~pGSGKsT~a~~La~~~g   33 (194)
T d3adka_           7 KSKIIFVVGGPGSGKGTQCEKIVQKYG   33 (194)
T ss_dssp             TSCEEEEEECTTSSHHHHHHHHHHHTC
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHhC
Confidence            467899999999999999999999864

>d1zina1 c.37.1.1 (A:1-125,A:161-217) Adenylate kinase {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=96.85  E-value=0.00037  Score=59.44  Aligned_cols=24  Identities=25%  Similarity=0.493  Sum_probs=21.9

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHhh
Q psy200          221 SMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      .|+|.||||+||||+++.|++.++
T Consensus         2 ~I~i~G~pGSGKsT~a~~La~~~~   25 (182)
T d1zina1           2 NLVLMGLPGAGKGTQAEKIVAAYG   25 (182)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHC
Confidence            478999999999999999999874

>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=96.82  E-value=0.00038  Score=60.13  Aligned_cols=25  Identities=24%  Similarity=0.470  Sum_probs=22.7

Q ss_pred             CeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          220 GSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       220 ~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      ..|+|.||||+||||.|+.|++.++
T Consensus         2 ~iI~i~GppGSGKsT~a~~La~~~g   26 (194)
T d1teva_           2 LVVFVLGGPGAGKGTQCARIVEKYG   26 (194)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHC
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHhC
Confidence            4688999999999999999999874

>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=96.82  E-value=0.0032  Score=57.07  Aligned_cols=98  Identities=15%  Similarity=0.279  Sum_probs=59.9

Q ss_pred             cCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCC-CHHHHHHHHHHHh--cCC-----------CCCCc
Q psy200          216 NETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVR-NAASVYETIVNEL--KLK-----------PGGKS  281 (490)
Q Consensus       216 ~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~-~~~~l~~~i~~~l--~~~-----------~~~~s  281 (490)
                      -..++-++|.|++|+|||+|+..+++..........+++-+..-. ...+++.++.+.-  ...           ....+
T Consensus        65 igkGQr~~If~~~g~GKt~l~~~i~~~~~~~~~~v~V~~~iGer~~ev~~~~~~~~~~~~~~~~~~~~~tvvv~~~s~~~  144 (276)
T d2jdid3          65 YAKGGKIGLFGGAGVGKTVLIMELINNVAKAHGGYSVFAGVGERTREGNDLYHEMIESGVINLKDATSKVALVYGQMNEP  144 (276)
T ss_dssp             EETTCEEEEEECTTSSHHHHHHHHHHHHTTTCSSEEEEEEESCCHHHHHHHHHHHHHHTSSCSSSSCCCEEEEEECTTSC
T ss_pred             ccCCCEEEeeCCCCCCHHHHHHHHHHHHHhhCCCeEEEEEeccChHHHHHHHHHHHhcCccccccccceEEEEEECCCCC
Confidence            356788999999999999999999887543333345666555432 3356666665531  100           00111


Q ss_pred             -HHHH-----HHHHHHHHh-cCCCeEEEEEecCcccccc
Q psy200          282 -ERHQ-----LGAILKYFD-TKHKSILLILDEIDALESR  313 (490)
Q Consensus       282 -~~~~-----~~~l~~~l~-~~~~~~vI~IDEid~l~~~  313 (490)
                       ...+     .-.+.+++. ..++.++|++|++-+....
T Consensus       145 ~~~r~~~~~~a~~iAEyf~~~~G~~VLv~~Dsltr~A~A  183 (276)
T d2jdid3         145 PGARARVALTGLTVAEYFRDQEGQDVLLFIDNIFRFTQA  183 (276)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHTTCSCEEEEEECTHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHhcCCCeEEEEEcchhHHHHH
Confidence             1111     123455665 4588999999999887543

>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=96.78  E-value=0.00043  Score=59.12  Aligned_cols=24  Identities=29%  Similarity=0.578  Sum_probs=21.9

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHhh
Q psy200          221 SMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      .|+|.||||+||||+++.+++.++
T Consensus         2 ~I~i~G~pGsGKsT~a~~La~~~g   25 (181)
T d2cdna1           2 RVLLLGPPGAGKGTQAVKLAEKLG   25 (181)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHC
Confidence            478899999999999999999975

>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=96.71  E-value=0.00063  Score=58.72  Aligned_cols=27  Identities=26%  Similarity=0.330  Sum_probs=22.9

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      +.-.|+|.||||+||||+++.+++.++
T Consensus         5 r~mrIiliG~PGSGKtT~a~~La~~~g   31 (189)
T d2ak3a1           5 RLLRAAIMGAPGSGKGTVSSRITKHFE   31 (189)
T ss_dssp             CCCEEEEECCTTSSHHHHHHHHHHHBC
T ss_pred             cceeEEEECCCCCCHHHHHHHHHHHHC
Confidence            345677889999999999999999864

>d1szpa2 c.37.1.11 (A:145-395) DNA repair protein Rad51, catalytic domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=96.68  E-value=0.004  Score=55.12  Aligned_cols=44  Identities=25%  Similarity=0.232  Sum_probs=32.2

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhh-----cCCceEEEEeccCCCC
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEI-----KDAFKTIYINCNSVRN  261 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~-----~~~~~~~~v~~~~~~~  261 (490)
                      .+..++|+|+||+|||+++..++.....     ..+..++|++......
T Consensus        33 ~G~~~li~G~pGsGKT~l~lq~~~~~~~~~~~~~~~~~~~~i~~~~~~~   81 (251)
T d1szpa2          33 TGSITELFGEFRTGKSQLCHTLAVTCQIPLDIGGGEGKCLYIDTEGTFR   81 (251)
T ss_dssp             SSSEEEEEESTTSSHHHHHHHHTTTTTSCTTTTCCSCEEEEEESSSCCC
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHhhhhhhhccCCceEEEEeecchHH
Confidence            5678999999999999999988765421     1234677887655543

>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=96.67  E-value=0.00055  Score=58.51  Aligned_cols=24  Identities=25%  Similarity=0.538  Sum_probs=21.8

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHhh
Q psy200          221 SMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      .|+|.||||+||||+++.|++.++
T Consensus         2 ~I~i~G~pGSGKsT~a~~La~~~g   25 (182)
T d1s3ga1           2 NIVLMGLPGAGKGTQADRIVEKYG   25 (182)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHC
Confidence            478899999999999999999974

>d2p6ra3 c.37.1.19 (A:1-202) Hel308 helicase {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Hel308 helicase
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=96.59  E-value=0.0029  Score=54.84  Aligned_cols=34  Identities=21%  Similarity=0.423  Sum_probs=22.5

Q ss_pred             CCeEEEECCCCCcHHHHHHH-HHHHhhhcCCceEEEE
Q psy200          219 SGSMYISGPPGTGKSASLNL-LVSRAEIKDAFKTIYI  254 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~-l~~~l~~~~~~~~~~v  254 (490)
                      ++.++|.+|+|+|||+++.. ++..+.  ....++++
T Consensus        40 ~~~~il~apTGsGKT~~a~l~i~~~~~--~~~~vl~l   74 (202)
T d2p6ra3          40 GKNLLLAMPTAAGKTLLAEMAMVREAI--KGGKSLYV   74 (202)
T ss_dssp             CSCEEEECSSHHHHHHHHHHHHHHHHH--TTCCEEEE
T ss_pred             CCCEEEEcCCCCchhHHHHHHHHHHhh--ccCcceee
Confidence            45789999999999988633 344443  22345555

>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=96.59  E-value=0.00056  Score=59.64  Aligned_cols=26  Identities=19%  Similarity=0.231  Sum_probs=23.1

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      +-.|+++|.||+||||+++++++.+.
T Consensus         2 p~li~l~GlpgsGKSTla~~L~~~l~   27 (213)
T d1bifa1           2 PTLIVMVGLPARGKTYISKKLTRYLN   27 (213)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHH
Confidence            34688999999999999999999876

>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=96.59  E-value=0.00077  Score=57.51  Aligned_cols=24  Identities=38%  Similarity=0.617  Sum_probs=21.3

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHhh
Q psy200          221 SMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      .|+|.||||+||||+++.|++.++
T Consensus         4 rIvl~G~pGSGKtT~a~~La~~~g   27 (180)
T d1akya1           4 RMVLIGPPGAGKGTQAPNLQERFH   27 (180)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhC
Confidence            467889999999999999999874

>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=96.58  E-value=0.00087  Score=57.12  Aligned_cols=35  Identities=26%  Similarity=0.327  Sum_probs=27.3

Q ss_pred             CeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEe
Q psy200          220 GSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYIN  255 (490)
Q Consensus       220 ~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~  255 (490)
                      +.++|.|++|+||||+++.+++.+.. .++.+..+.
T Consensus         2 kiivi~G~~GsGKTT~~~~La~~L~~-~~~~~~~~~   36 (194)
T d1nksa_           2 KIGIVTGIPGVGKSTVLAKVKEILDN-QGINNKIIN   36 (194)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHHHHHT-TTCCEEEEE
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHH-cCCCEEEEE
Confidence            46789999999999999999999862 244455443

>d1v5wa_ c.37.1.11 (A:) Meiotic recombination protein DMC1/LIM15 homolog {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Meiotic recombination protein DMC1/LIM15 homolog
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.54  E-value=0.011  Score=52.50  Aligned_cols=93  Identities=20%  Similarity=0.195  Sum_probs=51.7

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhc-----CCceEEEEeccCCCCHHHHHHHHHHHhcC-------------CCCC
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIK-----DAFKTIYINCNSVRNAASVYETIVNELKL-------------KPGG  279 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~-----~~~~~~~v~~~~~~~~~~l~~~i~~~l~~-------------~~~~  279 (490)
                      .+..++|+|+||+|||+++..++.+....     ....++++........ .....+......             ....
T Consensus        36 ~G~~~~i~G~~GsGKT~lalq~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  114 (258)
T d1v5wa_          36 SMAITEAFGEFRTGKTQLSHTLCVTAQLPGAGGYPGGKIIFIDTENTFRP-DRLRDIADRFNVDHDAVLDNVLYARAYTS  114 (258)
T ss_dssp             SSEEEEEECCTTCTHHHHHHHHHHHTTSCBTTTBCCCEEEEEESSSCCCH-HHHHHHHHHTTCCHHHHHHTEEEEECCST
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHHHhhhhcccccceEEEechHHHHHH-HHHHHHHhhhcccchhhhhcccccccCcH
Confidence            55689999999999999999998765321     2235666766554332 223333322211             1111


Q ss_pred             CcHHHHHHHHHHHH-hcCCCeEEEEEecCcccc
Q psy200          280 KSERHQLGAILKYF-DTKHKSILLILDEIDALE  311 (490)
Q Consensus       280 ~s~~~~~~~l~~~l-~~~~~~~vI~IDEid~l~  311 (490)
                      ....+..+.+.... .......++++|.+..+.
T Consensus       115 ~~~~~~~~~~~~~~~~~~~~~~~~vid~~~~~~  147 (258)
T d1v5wa_         115 EHQMELLDYVAAKFHEEAGIFKLLIIDSIMALF  147 (258)
T ss_dssp             THHHHHHHHHHHHHHHSCSSEEEEEEETSGGGH
T ss_pred             HHHHHHHHHHHHHhhhhccCceEEEeeehhhhh
Confidence            12222222222222 333456688889888774

>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=96.50  E-value=0.00092  Score=58.86  Aligned_cols=41  Identities=20%  Similarity=0.425  Sum_probs=31.4

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHh
Q psy200          221 SMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNEL  273 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l  273 (490)
                      .|.|.||||+||||+|+.|+++++      +.++      +..++|+.+....
T Consensus         5 ~IaIdGp~GsGKgT~ak~La~~lg------~~~i------stGdl~R~~a~~~   45 (223)
T d1q3ta_           5 QIAIDGPASSGKSTVAKIIAKDFG------FTYL------DTGAMYRAATYMA   45 (223)
T ss_dssp             EEEEECSSCSSHHHHHHHHHHHHC------CEEE------EHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhC------CcEE------CHHHHHHHHHHHH
Confidence            456889999999999999999975      3445      5677777765443

>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=96.49  E-value=0.00084  Score=57.11  Aligned_cols=24  Identities=17%  Similarity=0.430  Sum_probs=21.5

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHhh
Q psy200          221 SMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      .|+|.||||+||||+++.+++.++
T Consensus         2 ~I~i~G~pGSGKsT~~~~La~~~~   25 (179)
T d1e4va1           2 RIILLGAPVAGKGTQAQFIMEKYG   25 (179)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhC
Confidence            477899999999999999999864

>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=96.41  E-value=0.0065  Score=53.61  Aligned_cols=40  Identities=28%  Similarity=0.421  Sum_probs=28.1

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccC
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNS  258 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~  258 (490)
                      ..+..+.|.||.|+|||||++.++.-..  +.-.-++++...
T Consensus        29 ~~Ge~~~iiG~sGsGKSTLl~~i~gl~~--p~sG~I~~~g~~   68 (230)
T d1l2ta_          29 KEGEFVSIMGPSGSGKSTMLNIIGCLDK--PTEGEVYIDNIK   68 (230)
T ss_dssp             CTTCEEEEECSTTSSHHHHHHHHTTSSC--CSEEEEEETTEE
T ss_pred             cCCCEEEEECCCCCCcchhhHhccCCCC--CCcceeEECCEE
Confidence            3567899999999999999998876543  222334554433

>d2eyqa3 c.37.1.19 (A:546-778) Transcription-repair coupling factor, TRCF {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Transcription-repair coupling factor, TRCF
species: Escherichia coli [TaxId: 562]

Probab=96.41  E-value=0.016  Score=51.03  Aligned_cols=118  Identities=14%  Similarity=0.126  Sum_probs=68.0

Q ss_pred             ccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhcC---C----CCCCcHHHHHH
Q psy200          215 NNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKL---K----PGGKSERHQLG  287 (490)
Q Consensus       215 ~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~~---~----~~~~s~~~~~~  287 (490)
                      ....+...||+|..|+|||-++-..+...- ..+..++.+ ++...-..+.+..+-..+..   .    ....+..+-.+
T Consensus        72 ~~~~~~~~LL~GdvGsGKT~V~~~a~~~~~-~~g~qv~~l-~Pt~~La~Q~~~~~~~~~~~~~~~v~~l~~~~~~~~~~~  149 (233)
T d2eyqa3          72 CQPLAMDRLVCGDVGFGKTEVAMRAAFLAV-DNHKQVAVL-VPTTLLAQQHYDNFRDRFANWPVRIEMISRFRSAKEQTQ  149 (233)
T ss_dssp             HSSSCCEEEEECCCCTTTHHHHHHHHHHHH-TTTCEEEEE-CSSHHHHHHHHHHHHHHSTTTTCCEEEESTTSCHHHHHH
T ss_pred             hccCccCeEEEcCCCCCcHHHHHHHHHHHH-HcCCceEEE-ccHHHhHHHHHHHHHHHHhhCCCEEEeccCcccchhHHH
Confidence            446677889999999999999877776543 244455554 23332334555555554432   1    12234444444


Q ss_pred             HHHHHHhcC-----------------CCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEEEecC
Q psy200          288 AILKYFDTK-----------------HKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVGVAN  339 (490)
Q Consensus       288 ~l~~~l~~~-----------------~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI~~tn  339 (490)
                      .+.....+.                 .+--+|||||=|.+.-...+.+....     .+..+++..+|-
T Consensus       150 ~~~~~~~g~~~iviGths~l~~~~~f~~LgLiIiDEeH~fg~kQ~~~l~~~~-----~~~~~l~~SATP  213 (233)
T d2eyqa3         150 ILAEVAEGKIDILIGTHKLLQSDVKFKDLGLLIVDEEHRFGVRHKERIKAMR-----ANVDILTLTATP  213 (233)
T ss_dssp             HHHHHHTTCCSEEEECTHHHHSCCCCSSEEEEEEESGGGSCHHHHHHHHHHH-----TTSEEEEEESSC
T ss_pred             HHHHHhCCCCCEEEeehhhhccCCccccccceeeechhhhhhHHHHHHHhhC-----CCCCEEEEecch
Confidence            444433221                 23459999999997665545443322     245666666654

>d1xpua3 c.37.1.11 (A:129-417) Transcription termination factor Rho, ATPase domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Transcription termination factor Rho, ATPase domain
species: Escherichia coli [TaxId: 562]

Probab=96.39  E-value=0.0021  Score=58.68  Aligned_cols=95  Identities=15%  Similarity=0.151  Sum_probs=55.0

Q ss_pred             ccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcC-CceEEEEeccCCCCHHHHHHHHHHHhcC----CCCCCcH-H-----
Q psy200          215 NNETSGSMYISGPPGTGKSASLNLLVSRAEIKD-AFKTIYINCNSVRNAASVYETIVNELKL----KPGGKSE-R-----  283 (490)
Q Consensus       215 ~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~-~~~~~~v~~~~~~~~~~l~~~i~~~l~~----~~~~~s~-~-----  283 (490)
                      .-+.++-++|.|++|+|||+|+..+++...... .+.++..-+...   .+-+.++......    ....... .     
T Consensus        39 PigrGQr~~I~g~~g~GKT~l~~~i~~~~~~~~~~~v~~~~~iger---~~ev~~~~~~~~~~vv~~t~d~~~~~r~~~~  115 (289)
T d1xpua3          39 PIGRGQRGLIVAPPKAGKTMLLQNIAQSIAYNHPDCVLMVLLIDER---PEEVTEMQRLVKGEVVASTFDEPASRHVQVA  115 (289)
T ss_dssp             CCBTTCEEEEEECSSSSHHHHHHHHHHHHHHHCTTSEEEEEEEEEC---HHHHHHHHHHCSSEEEEEETTSCHHHHHHHH
T ss_pred             cccCCCeeeEeCCCCCCHHHHHHHHHHHHhhcCCCeEEEEEeecee---HHHHHhHHhhcceEEEeccCCCchhHHHHHH
Confidence            346788999999999999999999998775332 223232222221   2222333333221    0111111 1     


Q ss_pred             HHHHHHHHHHhcCCCeEEEEEecCccccc
Q psy200          284 HQLGAILKYFDTKHKSILLILDEIDALES  312 (490)
Q Consensus       284 ~~~~~l~~~l~~~~~~~vI~IDEid~l~~  312 (490)
                      ...-.+.+++...++.++|++|++-++..
T Consensus       116 ~~a~~iAEyfrd~G~dVLli~Dsltr~A~  144 (289)
T d1xpua3         116 EMVIEKAKRLVEHKKDVIILLDSITRLAR  144 (289)
T ss_dssp             HHHHHHHHHHHTTTCEEEEEESCHHHHHH
T ss_pred             HHHHHHHHHHHHhccCceeecCcHHHHHH
Confidence            12224555666678899999999877653

>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=96.38  E-value=0.012  Score=51.07  Aligned_cols=39  Identities=15%  Similarity=0.169  Sum_probs=29.3

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEecc
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCN  257 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~  257 (490)
                      ++..|.|.|+.|+||||+++.+++.+... ++.++.+..+
T Consensus         2 rG~lI~ieG~dGsGKsT~~~~L~~~L~~~-g~~v~~~~~p   40 (209)
T d1nn5a_           2 RGALIVLEGVDRAGKSTQSRKLVEALCAA-GHRAELLRFP   40 (209)
T ss_dssp             CCCEEEEEESTTSSHHHHHHHHHHHHHHT-TCCEEEEESS
T ss_pred             CeeEEEEECCCCCCHHHHHHHHHHHHHHC-CCcEEEEeCC
Confidence            35677888999999999999999988533 4455555444

>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=96.34  E-value=0.0079  Score=53.12  Aligned_cols=93  Identities=12%  Similarity=0.159  Sum_probs=52.6

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhc---------------CCceEEEEeccCCCCHHHHHHHHHHHhcCC------
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIK---------------DAFKTIYINCNSVRNAASVYETIVNELKLK------  276 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~---------------~~~~~~~v~~~~~~~~~~l~~~i~~~l~~~------  276 (490)
                      .+..++|+|+||+|||+++..++..+...               ....++|+.+....... ....+...+...      
T Consensus        33 ~G~l~~i~G~~G~GKT~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~e~~~~~~-~~~~~~~~~~~~~~~~~~  111 (258)
T d2i1qa2          33 SQSVTEFAGVFGSGKTQIMHQSCVNLQNPEFLFYDEEAVSKGEVAQPKAVYIDTEGTFRPE-RIMQMAEHAGIDGQTVLD  111 (258)
T ss_dssp             TTEEEEEEESTTSSHHHHHHHHHHHTTCGGGEECCTTTSCTTTTSSEEEEEEESSSCCCHH-HHHHHHHHHTCCHHHHHH
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHHHHhcCCCceEEeecccchhcCceEEEEEecCCcCHH-HHHHHHhhcchhhhhhhh
Confidence            56789999999999999999999876421               12256778765443332 223333332211      


Q ss_pred             ----CCCCcHHHHHH---HHHHHHhcCCCeEEEEEecCcccc
Q psy200          277 ----PGGKSERHQLG---AILKYFDTKHKSILLILDEIDALE  311 (490)
Q Consensus       277 ----~~~~s~~~~~~---~l~~~l~~~~~~~vI~IDEid~l~  311 (490)
                          ...........   .....+.......++++|.+..+.
T Consensus       112 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vid~i~~~~  153 (258)
T d2i1qa2         112 NTFVARAYNSDMQMLFAEKIEDLIQEGNNIKLVVIDSLTSTF  153 (258)
T ss_dssp             TEEEEECSSHHHHHHHHHTHHHHHHTTCEEEEEEEECSSHHH
T ss_pred             cceeeccCchhhHHHHHHHHHHHHHHhcccceeeeeEEEEee
Confidence                00111222222   222233334567788889887764

>d1p9ra_ c.37.1.11 (A:) Extracellular secretion NTPase EpsE {Vibrio cholerae [TaxId: 666]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Extracellular secretion NTPase EpsE
species: Vibrio cholerae [TaxId: 666]

Probab=96.32  E-value=0.0052  Score=59.30  Aligned_cols=103  Identities=14%  Similarity=0.221  Sum_probs=61.2

Q ss_pred             CCCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHh
Q psy200          194 CELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNEL  273 (490)
Q Consensus       194 ~~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l  273 (490)
                      +++--.+.+++.+.+++.     ...+.++|+||.|+||||++..+.+++.. ....++.+.-+-.......     .++
T Consensus       138 ~~LG~~~~~~~~l~~l~~-----~~~GliLvtGpTGSGKSTTl~~~l~~~~~-~~~~i~tiEdPiE~~~~~~-----~q~  206 (401)
T d1p9ra_         138 HSLGMTAHNHDNFRRLIK-----RPHGIILVTGPTGSGKSTTLYAGLQELNS-SERNILTVEDPIEFDIDGI-----GQT  206 (401)
T ss_dssp             GGSCCCHHHHHHHHHHHT-----SSSEEEEEECSTTSCHHHHHHHHHHHHCC-TTSCEEEEESSCCSCCSSS-----EEE
T ss_pred             hhhcccHHHHHHHHHHHh-----hhhceEEEEcCCCCCccHHHHHHhhhhcC-CCceEEEeccCcccccCCC-----Cee
Confidence            445555677777776663     56789999999999999999999998852 2234555532221100000     000


Q ss_pred             cCCCCCCcHHHHHHHHHHHHhcCCCeEEEEEecCcccc
Q psy200          274 KLKPGGKSERHQLGAILKYFDTKHKSILLILDEIDALE  311 (490)
Q Consensus       274 ~~~~~~~s~~~~~~~l~~~l~~~~~~~vI~IDEid~l~  311 (490)
                        .........+...+..++..  .|-||+|.|+-...
T Consensus       207 --~v~~~~~~~~~~~l~~~lR~--dPDvi~igEiRd~~  240 (401)
T d1p9ra_         207 --QVNPRVDMTFARGLRAILRQ--DPDVVMVGEIRDLE  240 (401)
T ss_dssp             --ECBGGGTBCHHHHHHHHGGG--CCSEEEESCCCSHH
T ss_pred             --eecCCcCCCHHHHHHHHHhh--cCCEEEecCcCChH
Confidence              00011122345556666654  37799999998754

>d1gm5a3 c.37.1.19 (A:286-549) RecG helicase domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: RecG helicase domain
species: Thermotoga maritima [TaxId: 2336]

Probab=96.30  E-value=0.029  Score=50.34  Aligned_cols=131  Identities=14%  Similarity=0.172  Sum_probs=66.8

Q ss_pred             HHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhc---CC-
Q psy200          201 VQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELK---LK-  276 (490)
Q Consensus       201 ~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~---~~-  276 (490)
                      ++.+.+.+...+ +..+.+..-||.|..|+|||-++-..+...- ..++.++.+ ++...-..+.+..+...+.   .. 
T Consensus        87 ~Q~~ai~ei~~d-~~~~~~m~rLL~GdvGSGKT~Va~~a~~~~~-~~g~q~~~m-~Pt~~La~Qh~~~~~~~f~~~~~~v  163 (264)
T d1gm5a3          87 AQKRAHQEIRND-MISEKPMNRLLQGDVGSGKTVVAQLAILDNY-EAGFQTAFM-VPTSILAIQHYRRTVESFSKFNIHV  163 (264)
T ss_dssp             HHHHHHHHHHHH-HHSSSCCCCEEECCSSSSHHHHHHHHHHHHH-HHTSCEEEE-CSCHHHHHHHHHHHHHHHTCSSCCE
T ss_pred             hHHHHHHHHHHH-hhccCcceeeeeccccccccHHHHHHHHHHH-hcccceeEE-eehHhhhHHHHHHHHHhhhhccccc
Confidence            344344443332 2345667789999999999999877765543 233455544 2222123445555555553   21 


Q ss_pred             ---CCCCcHHHHHHHHHHHHhcC-----------------CCeEEEEEecCccccccCHHHHHHhHhCCCCCCCcEEEEE
Q psy200          277 ---PGGKSERHQLGAILKYFDTK-----------------HKSILLILDEIDALESRKQTILYTIFEWPSIPGSKLVLVG  336 (490)
Q Consensus       277 ---~~~~s~~~~~~~l~~~l~~~-----------------~~~~vI~IDEid~l~~~~~~~L~~l~~~~~~~~~~vilI~  336 (490)
                         ..+.+..+-.+.+.....+.                 .+--+|||||=|.+.-...+.+     ........+++..
T Consensus       164 ~~l~~~~~~~~r~~~~~~~~~g~~~iiIGThsl~~~~~~f~~LglviiDEqH~fgv~Qr~~l-----~~~~~~~~~l~~S  238 (264)
T d1gm5a3         164 ALLIGATTPSEKEKIKSGLRNGQIDVVIGTHALIQEDVHFKNLGLVIIDEQHRFGVKQREAL-----MNKGKMVDTLVMS  238 (264)
T ss_dssp             EECCSSSCHHHHHHHHHHHHSSCCCEEEECTTHHHHCCCCSCCCEEEEESCCCC-----CCC-----CSSSSCCCEEEEE
T ss_pred             eeeccccchHHHHHHHHHHHCCCCCEEEeehHHhcCCCCccccceeeeccccccchhhHHHH-----HHhCcCCCEEEEE
Confidence               12334444444444432210                 2344899999888754433222     1122345666655


Q ss_pred             ecC
Q psy200          337 VAN  339 (490)
Q Consensus       337 ~tn  339 (490)
                      +|-
T Consensus       239 ATP  241 (264)
T d1gm5a3         239 ATP  241 (264)
T ss_dssp             SSC
T ss_pred             CCC
Confidence            554

>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=96.28  E-value=0.011  Score=51.28  Aligned_cols=28  Identities=32%  Similarity=0.427  Sum_probs=24.3

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHhhhc
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRAEIK  246 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l~~~  246 (490)
                      ++.|.|.|+.|+||||+++.+.+.+...
T Consensus         2 gkfIviEG~dGsGKsT~~~~L~~~L~~~   29 (210)
T d4tmka_           2 SKYIVIEGLEGAGKTTARNVVVETLEQL   29 (210)
T ss_dssp             CCEEEEEECTTSCHHHHHHHHHHHHHHT
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHHHhC
Confidence            5678899999999999999999988633

>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=96.24  E-value=0.0012  Score=56.86  Aligned_cols=25  Identities=36%  Similarity=0.587  Sum_probs=22.2

Q ss_pred             CeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          220 GSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       220 ~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      +.|+|+||+|+||||+++.+++...
T Consensus         1 rpIvl~GPsGsGK~tl~~~L~~~~~   25 (190)
T d1lvga_           1 RPVVLSGPSGAGKSTLLKKLFQEHS   25 (190)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHHT
T ss_pred             CeEEEECCCCCCHHHHHHHHHHhCC
Confidence            3588999999999999999998864

>d1g6oa_ c.37.1.11 (A:) Hexameric traffic ATPase, HP0525 {Helicobacter pylori [TaxId: 210]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Hexameric traffic ATPase, HP0525
species: Helicobacter pylori [TaxId: 210]

Probab=96.22  E-value=0.0025  Score=59.63  Aligned_cols=34  Identities=18%  Similarity=0.334  Sum_probs=27.5

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEE
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYI  254 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v  254 (490)
                      ..+++|+|++|+||||++++++..+.  .+.+++.+
T Consensus       166 ~~nili~G~tgSGKTT~l~al~~~i~--~~~rivti  199 (323)
T d1g6oa_         166 GKNVIVCGGTGSGKTTYIKSIMEFIP--KEERIISI  199 (323)
T ss_dssp             TCCEEEEESTTSSHHHHHHHHGGGSC--TTCCEEEE
T ss_pred             CCCEEEEeeccccchHHHHHHhhhcc--cccceeec
Confidence            45799999999999999999998875  44455555

>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=96.21  E-value=0.0041  Score=58.15  Aligned_cols=53  Identities=19%  Similarity=0.177  Sum_probs=33.1

Q ss_pred             cCCCCeEEEECCCCCcHHHHHHHHHHHhhhc-CCceEEEEeccCCCCHHHHHHH
Q psy200          216 NETSGSMYISGPPGTGKSASLNLLVSRAEIK-DAFKTIYINCNSVRNAASVYET  268 (490)
Q Consensus       216 ~~~~~~ill~GppGtGKTtla~~l~~~l~~~-~~~~~~~v~~~~~~~~~~l~~~  268 (490)
                      .++...|-|+|+||+|||||+..+...+... ..+.++.++.+...+...++..
T Consensus        51 ~~~~~~IgitG~pGaGKSTLi~~l~~~~~~~g~~vavlavDpss~~~ggailgd  104 (327)
T d2p67a1          51 CGNTLRLGVTGTPGAGKSTFLEAFGMLLIREGLKVAVIAVDPSSPVTGGSILGD  104 (327)
T ss_dssp             CSCSEEEEEEECTTSCHHHHHHHHHHHHHHTTCCEEEEEECCC-----------
T ss_pred             cCCceEEEeeCCCCCCHHHHHHHHHHHHHhcCCceeeecCCCceeeeccccccc
Confidence            3456778899999999999999999887643 2456777776666555555543

>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=96.19  E-value=0.0013  Score=56.01  Aligned_cols=25  Identities=32%  Similarity=0.498  Sum_probs=22.7

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHh
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRA  243 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l  243 (490)
                      ++.++|+||+|+||||+++.+.++.
T Consensus         2 G~iivl~GpsG~GK~tl~~~L~~~~   26 (182)
T d1znwa1           2 GRVVVLSGPSAVGKSTVVRCLRERI   26 (182)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHHHS
T ss_pred             CeEEEEECCCCCCHHHHHHHHHhhC
Confidence            5688999999999999999998876

>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=96.19  E-value=0.0015  Score=54.68  Aligned_cols=34  Identities=15%  Similarity=0.190  Sum_probs=26.3

Q ss_pred             CeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEE
Q psy200          220 GSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYI  254 (490)
Q Consensus       220 ~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v  254 (490)
                      +.+.|+|.+|+|||||+..++.++... ++.+..+
T Consensus         2 kii~I~G~~gSGKTTli~~l~~~L~~~-g~~v~vi   35 (165)
T d1xjca_           2 NVWQVVGYKHSGKTTLMEKWVAAAVRE-GWRVGTV   35 (165)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHHHHT-TCCEEEE
T ss_pred             cEEEEEeCCCCCHHHHHHHHHHHHHhC-CCeEEEE
Confidence            467799999999999999999998633 3444433

>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=96.10  E-value=0.0057  Score=57.07  Aligned_cols=46  Identities=24%  Similarity=0.322  Sum_probs=34.5

Q ss_pred             cCCCCeEEEECCCCCcHHHHHHHHHHHhhh-cCCceEEEEeccCCCC
Q psy200          216 NETSGSMYISGPPGTGKSASLNLLVSRAEI-KDAFKTIYINCNSVRN  261 (490)
Q Consensus       216 ~~~~~~ill~GppGtGKTtla~~l~~~l~~-~~~~~~~~v~~~~~~~  261 (490)
                      .+....|-|+|+||+|||||+..+...+.. ..++-++.++.++..+
T Consensus        48 ~~~~~~igitG~pGaGKSTli~~l~~~~~~~g~~vaViavDpss~~~   94 (323)
T d2qm8a1          48 TGRAIRVGITGVPGVGKSTTIDALGSLLTAAGHKVAVLAVDPSSTRT   94 (323)
T ss_dssp             CCCSEEEEEECCTTSCHHHHHHHHHHHHHHTTCCEEEEEECGGGGSS
T ss_pred             cCCceEEeeeCCCCCCHHHHHHHHHHHHhhcCCceeeeecccccHHH
Confidence            345667889999999999999999987642 3455677777665543

>d2bmfa2 c.37.1.14 (A:178-482) Dengue virus helicase {Dengue virus type 2 [TaxId: 11060]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: Dengue virus helicase
species: Dengue virus type 2 [TaxId: 11060]

Probab=96.09  E-value=0.0038  Score=57.41  Aligned_cols=51  Identities=20%  Similarity=0.279  Sum_probs=30.5

Q ss_pred             CCCeEEEECCCCCcHHH-HHHHHHHHhhhcCCceEEEEeccCCCCHHHHHHHHHHHhc
Q psy200          218 TSGSMYISGPPGTGKSA-SLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELK  274 (490)
Q Consensus       218 ~~~~ill~GppGtGKTt-la~~l~~~l~~~~~~~~~~v~~~~~~~~~~l~~~i~~~l~  274 (490)
                      .++.++|.+|+|+|||+ .+-.+...... .+..++++. +    ...+..++.+.+.
T Consensus         8 ~~~~~lv~~~TGsGKT~~~l~~~~~~~~~-~~~~~lvi~-P----tr~La~q~~~~l~   59 (305)
T d2bmfa2           8 KKRLTIMDLHPGAGKTKRYLPAIVREAIK-RGLRTLILA-P----TRVVAAEMEEALR   59 (305)
T ss_dssp             TTCEEEECCCTTSSTTTTHHHHHHHHHHH-HTCCEEEEE-S----SHHHHHHHHHHTT
T ss_pred             cCCcEEEEECCCCCHHHHHHHHHHHHHHh-cCCEEEEEc-c----HHHHHHHHHHHHh
Confidence            56789999999999995 33334333321 223455552 1    3456666666664

>d1pzna2 c.37.1.11 (A:96-349) DNA repair protein Rad51, catalytic domain {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=96.03  E-value=0.007  Score=53.81  Aligned_cols=46  Identities=17%  Similarity=0.187  Sum_probs=33.7

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhc-----CCceEEEEeccCCCCHH
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIK-----DAFKTIYINCNSVRNAA  263 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~-----~~~~~~~v~~~~~~~~~  263 (490)
                      .+..++|+|+||+|||+++-.++.+....     .+..++++.+.......
T Consensus        35 ~G~~~li~G~pGsGKT~~~lq~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   85 (254)
T d1pzna2          35 TQAITEVFGEFGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWIDTENTFRPE   85 (254)
T ss_dssp             SSEEEEEEESTTSSHHHHHHHHHHHTTSCGGGTSCSCEEEEEESSSCCCHH
T ss_pred             CCEEEEEEcCCCCCHHHHHHHHHHHhhchHHhcCCCceEEEEeccchhHHH
Confidence            56689999999999999999998776421     23467777776654443

>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=96.02  E-value=0.00057  Score=61.10  Aligned_cols=26  Identities=27%  Similarity=0.291  Sum_probs=22.6

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHh
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRA  243 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l  243 (490)
                      ..+.++|+||.+.|||++++.++-..
T Consensus        40 ~~~~~iiTGpN~~GKSt~lk~i~l~~   65 (234)
T d1wb9a2          40 QRRMLIITGPNMGGKSTYMRQTALIA   65 (234)
T ss_dssp             SSCEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CceEEEEeccCchhhHHHHHHHHHHH
Confidence            45789999999999999999997654

>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=96.02  E-value=0.0081  Score=51.90  Aligned_cols=23  Identities=17%  Similarity=0.239  Sum_probs=20.5

Q ss_pred             CeEEEECCCCCcHHHHHHHHHHH
Q psy200          220 GSMYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       220 ~~ill~GppGtGKTtla~~l~~~  242 (490)
                      +.|+|.|++|+|||+|++++...
T Consensus         1 k~V~ivG~~~~GKTsLl~~l~~~   23 (207)
T d2fh5b1           1 RAVLFVGLCDSGKTLLFVRLLTG   23 (207)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHS
T ss_pred             CEEEEECCCCCCHHHHHHHHHcC
Confidence            46899999999999999999764

>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=95.99  E-value=0.0032  Score=53.97  Aligned_cols=41  Identities=24%  Similarity=0.360  Sum_probs=30.4

Q ss_pred             HHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          201 VQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       201 ~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      .-+..|..+|..   ....++++|+|||+||||+++.++++-+.
T Consensus        38 ~Fl~~l~~~l~~---~PKkn~i~~~GP~~TGKS~f~~sl~~~l~   78 (205)
T d1tuea_          38 TFLGALKSFLKG---TPKKNCLVFCGPANTGKSYFGMSFIHFIQ   78 (205)
T ss_dssp             HHHHHHHHHHHT---CTTCSEEEEESCGGGCHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHcC---CCCceEEEEECCCCccHHHHHHHHHHHhC
Confidence            334445555532   23557899999999999999999999874

>d1gkub1 c.37.1.16 (B:1-250) Helicase-like "domain" of reverse gyrase {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Helicase-like "domain" of reverse gyrase
domain: Helicase-like "domain" of reverse gyrase
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=95.95  E-value=0.018  Score=50.86  Aligned_cols=36  Identities=17%  Similarity=0.136  Sum_probs=24.0

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEe
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYIN  255 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~  255 (490)
                      ++.++|.+|.|+|||.++-..+-.+.. .+..++++.
T Consensus        58 g~~~~i~apTGsGKT~~~~~~~~~~~~-~~~rvliv~   93 (237)
T d1gkub1          58 KESFAATAPTGVGKTSFGLAMSLFLAL-KGKRCYVIF   93 (237)
T ss_dssp             TCCEECCCCBTSCSHHHHHHHHHHHHT-TSCCEEEEE
T ss_pred             CCCEEEEecCCChHHHHHHHHHHHHHH-hcCeEEEEe
Confidence            568999999999999876555444322 234556553

>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=95.93  E-value=0.17  Score=41.91  Aligned_cols=23  Identities=43%  Similarity=0.576  Sum_probs=20.6

Q ss_pred             CeEEEECCCCCcHHHHHHHHHHH
Q psy200          220 GSMYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       220 ~~ill~GppGtGKTtla~~l~~~  242 (490)
                      +.|.|.|.+|+|||+|++++...
T Consensus         6 ~~I~lvG~~~~GKSSLin~l~~~   28 (178)
T d1wf3a1           6 GFVAIVGKPNVGKSTLLNNLLGV   28 (178)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHTS
T ss_pred             cEEEEECCCCCCHHHHHHHHhCC
Confidence            46899999999999999999754

>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=95.88  E-value=0.0068  Score=54.66  Aligned_cols=40  Identities=23%  Similarity=0.337  Sum_probs=28.2

Q ss_pred             HHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHH
Q psy200          201 VQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       201 ~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~  242 (490)
                      ..+.++...+..  .....-.|+|.|.+|+||||+++.++.+
T Consensus        16 ~~l~e~~~~l~~--~~~~~l~I~LvG~tg~GKSSliN~ilg~   55 (257)
T d1h65a_          16 TKLLELLGNLKQ--EDVNSLTILVMGKGGVGKSSTVNSIIGE   55 (257)
T ss_dssp             HHHHHHHHHHHH--TTCCEEEEEEEESTTSSHHHHHHHHHTS
T ss_pred             HHHHHHHHHHhh--cCCCCcEEEEECCCCCcHHHHHHHHhCC
Confidence            344445555543  2234457889999999999999999864

>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=95.77  E-value=0.0042  Score=53.72  Aligned_cols=27  Identities=22%  Similarity=0.181  Sum_probs=24.0

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      .+..++|+|+||+|||+++..++.+..
T Consensus        22 ~G~v~~i~G~~GsGKT~l~l~la~~~~   48 (242)
T d1n0wa_          22 TGSITEMFGEFRTGKTQICHTLAVTCQ   48 (242)
T ss_dssp             TTSEEEEECCTTSSHHHHHHHHHHHTT
T ss_pred             CCEEEEEEeCCCCCHHHHHHHHHHHHH
Confidence            567899999999999999999987764

>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=95.74  E-value=0.0043  Score=54.95  Aligned_cols=33  Identities=27%  Similarity=0.462  Sum_probs=25.7

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEe
Q psy200          221 SMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYIN  255 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~  255 (490)
                      .++|.|++|+|||||++++.+++.  ....+.-+|
T Consensus         2 vi~v~G~~GsGKTTLl~~ll~~~~--~~~~~~ivn   34 (244)
T d1yrba1           2 IVVFVGTAGSGKTTLTGEFGRYLE--DNYKVAYVN   34 (244)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHT--TTSCEEEEE
T ss_pred             EEEEEcCCCCcHHHHHHHHHHHHh--hCCeEEEEe
Confidence            478999999999999999998775  333444454

>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=95.66  E-value=0.035  Score=50.38  Aligned_cols=43  Identities=19%  Similarity=0.321  Sum_probs=29.3

Q ss_pred             HHHHHHHHHHhhhccCC--CCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          202 QLEGIRQFLLGHVNNET--SGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       202 ~~~~l~~~L~~~~~~~~--~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      .++.+..++..+...+.  +-.|.|.|++|+||||++..|...+.
T Consensus         8 ~~~~~~~~~~~~~~~~~~~P~iIGi~G~qGSGKSTl~~~l~~~L~   52 (286)
T d1odfa_           8 TIEFLDKYIPEWFETGNKCPLFIFFSGPQGSGKSFTSIQIYNHLM   52 (286)
T ss_dssp             HHHHHHHHHHHHHTTTCCSCEEEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhcCCCCCEEEEeECCCCCCHHHHHHHHHHHHH
Confidence            34445555555443333  33555899999999999999988774

>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=95.66  E-value=0.0035  Score=54.57  Aligned_cols=25  Identities=28%  Similarity=0.482  Sum_probs=22.6

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHh
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRA  243 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l  243 (490)
                      +..++|+||+|+|||||++.++...
T Consensus         2 G~livi~GPSG~GK~tl~~~L~~~~   26 (205)
T d1s96a_           2 GTLYIVSAPSGAGKSSLIQALLKTQ   26 (205)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHHS
T ss_pred             CeEEEEECCCCCCHHHHHHHHHhhC
Confidence            5678999999999999999998875

>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=95.66  E-value=0.01  Score=49.12  Aligned_cols=22  Identities=18%  Similarity=0.320  Sum_probs=19.2

Q ss_pred             eEEEECCCCCcHHHHHHHHHHH
Q psy200          221 SMYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~  242 (490)
                      .++|.|++|+|||+|++.+...
T Consensus         4 ki~ivG~~~~GKTsLi~~l~~~   25 (165)
T d1ksha_           4 RLLMLGLDNAGKTTILKKFNGE   25 (165)
T ss_dssp             EEEEECSTTSSHHHHHHHHTTC
T ss_pred             EEEEECCCCCCHHHHHHHHcCC
Confidence            4789999999999999998653

>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=95.66  E-value=0.006  Score=55.37  Aligned_cols=96  Identities=16%  Similarity=0.229  Sum_probs=55.4

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCCC-CHHHHHHHHHHH--hcC-----CCCCC------cH
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVR-NAASVYETIVNE--LKL-----KPGGK------SE  282 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~~-~~~~l~~~i~~~--l~~-----~~~~~------s~  282 (490)
                      ..++.++|.|++|+|||+++..+..... .....++++.+..-. ...+++.++...  +..     .....      -.
T Consensus        65 g~GQr~~Ifg~~g~GKt~l~~~~~~~~~-~~~~v~V~~~iGer~~Ev~e~~~~~~~~~~~~~tvvv~~tsd~p~~~r~~a  143 (276)
T d1fx0a3          65 GRGQRELIIGDRQTGKTAVATDTILNQQ-GQNVICVYVAIGQKASSVAQVVTNFQERGAMEYTIVVAETADSPATLQYLA  143 (276)
T ss_dssp             BTTCBCBEEESSSSSHHHHHHHHHHTCC-TTTCEEEEEEESCCHHHHHHHHHHTGGGTGGGSEEEEEECTTSCGGGTTHH
T ss_pred             cCCceEeeccCCCCChHHHHHHHHhhhc-ccCceeeeeeecchhHHHHHHHHhhccCCcceeeeecccccCccHHHHHHH
Confidence            4677889999999999999987655433 223345565544432 223344443322  000     00001      11


Q ss_pred             HHHHHHHHHHHhcCCCeEEEEEecCcccccc
Q psy200          283 RHQLGAILKYFDTKHKSILLILDEIDALESR  313 (490)
Q Consensus       283 ~~~~~~l~~~l~~~~~~~vI~IDEid~l~~~  313 (490)
                      ....-.+.+++...++.++|++|++-++...
T Consensus       144 ~~~a~tiAEyfrd~G~~Vlll~Dsltr~A~A  174 (276)
T d1fx0a3         144 PYTGAALAEYFMYRERHTLIIYDDLSKQAQA  174 (276)
T ss_dssp             HHHHHHHHHHHHHTTCEEEEEEECHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCceeEEeeccHHHHHH
Confidence            1233345666766788999999999887644

>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=95.63  E-value=0.00086  Score=59.44  Aligned_cols=24  Identities=33%  Similarity=0.332  Sum_probs=21.0

Q ss_pred             CeEEEECCCCCcHHHHHHHHHHHh
Q psy200          220 GSMYISGPPGTGKSASLNLLVSRA  243 (490)
Q Consensus       220 ~~ill~GppGtGKTtla~~l~~~l  243 (490)
                      +.++|+||...|||++++.++-..
T Consensus        36 ~~~iiTGpN~~GKSt~lk~i~l~~   59 (224)
T d1ewqa2          36 ELVLITGPNMAGKSTFLRQTALIA   59 (224)
T ss_dssp             CEEEEESCSSSSHHHHHHHHHHHH
T ss_pred             cEEEEECCCccccchhhhhhHHHH
Confidence            478999999999999999887654

>d1hv8a1 c.37.1.19 (A:3-210) Putative DEAD box RNA helicase {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative DEAD box RNA helicase
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=95.60  E-value=0.029  Score=48.49  Aligned_cols=41  Identities=17%  Similarity=0.208  Sum_probs=26.5

Q ss_pred             CCeEEEEEecCccccccC-HHHHHHhHhCCCCCCCcEEEEEec
Q psy200          297 HKSILLILDEIDALESRK-QTILYTIFEWPSIPGSKLVLVGVA  338 (490)
Q Consensus       297 ~~~~vI~IDEid~l~~~~-~~~L~~l~~~~~~~~~~vilI~~t  338 (490)
                      ..-..|+|||+|.+.... ...+..+++... ...+++++++|
T Consensus       144 ~~l~~lViDEad~l~~~~~~~~i~~I~~~~~-~~~Q~i~~SAT  185 (208)
T d1hv8a1         144 KNVKYFILDEADEMLNMGFIKDVEKILNACN-KDKRILLFSAT  185 (208)
T ss_dssp             TSCCEEEEETHHHHHTTTTHHHHHHHHHTSC-SSCEEEEECSS
T ss_pred             ccCcEEEEEChHHhhcCCChHHHHHHHHhCC-CCCeEEEEEcc
Confidence            345599999999986553 455666665432 34566666655

>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=95.56  E-value=0.0036  Score=54.58  Aligned_cols=26  Identities=23%  Similarity=0.186  Sum_probs=22.9

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      +-.|.|.|++|+||||+++.+++.++
T Consensus         2 P~iIgI~G~~gSGKSTla~~L~~~l~   27 (213)
T d1uj2a_           2 PFLIGVSGGTASGKSSVCAKIVQLLG   27 (213)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHTT
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHhc
Confidence            34577999999999999999999886

>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=95.55  E-value=0.043  Score=44.75  Aligned_cols=22  Identities=45%  Similarity=0.709  Sum_probs=19.3

Q ss_pred             eEEEECCCCCcHHHHHHHHHHH
Q psy200          221 SMYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~  242 (490)
                      .|+|.|.+|+|||||++++...
T Consensus         3 kI~lvG~~nvGKSsLin~l~~~   24 (161)
T d2gj8a1           3 KVVIAGRPNAGKSSLLNALAGR   24 (161)
T ss_dssp             EEEEEESTTSSHHHHHHHHHTS
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            4789999999999999999743

>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=95.46  E-value=0.0049  Score=52.26  Aligned_cols=25  Identities=20%  Similarity=0.433  Sum_probs=22.3

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHh
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRA  243 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l  243 (490)
                      .+.++|+||+|+||+||++.+++..
T Consensus         3 ~k~ivl~Gpsg~GK~tl~~~L~~~~   27 (178)
T d1kgda_           3 RKTLVLLGAHGVGRRHIKNTLITKH   27 (178)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHC
T ss_pred             CCcEEEECCCCCCHHHHHHHHHHhC
Confidence            4679999999999999999998775

>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=95.42  E-value=0.019  Score=52.23  Aligned_cols=98  Identities=15%  Similarity=0.183  Sum_probs=56.5

Q ss_pred             cCCCCeEEEECCCCCcHHHHHHHHHHHhhh-------cCCceEEEEeccCC-CCHHHHHHHHHHHhcC--------CCCC
Q psy200          216 NETSGSMYISGPPGTGKSASLNLLVSRAEI-------KDAFKTIYINCNSV-RNAASVYETIVNELKL--------KPGG  279 (490)
Q Consensus       216 ~~~~~~ill~GppGtGKTtla~~l~~~l~~-------~~~~~~~~v~~~~~-~~~~~l~~~i~~~l~~--------~~~~  279 (490)
                      -..++.++|.|++|+|||+++..++.....       ...+.+++.-+..- ....+|+..+...-..        ....
T Consensus        65 ig~GQr~~If~~~g~GKt~ll~~~~~~~~~~~~~~~~~~~~~~v~~~IGer~~E~~e~~~~~~~~~~~~~tvvv~~ts~~  144 (285)
T d2jdia3          65 IGRGQRELIIGDRQTGKTSIAIDTIINQKRFNDGTDEKKKLYCIYVAIGQKRSTVAQLVKRLTDADAMKYTIVVSATASD  144 (285)
T ss_dssp             CBTTCBCEEEESTTSSHHHHHHHHHHHTHHHHTSSCTTTCCEEEEEEESCCHHHHHHHHHHHHHTTCGGGEEEEEECTTS
T ss_pred             ccCCCEEEeecCCCCChHHHHHHHHHhHHhhccccccccceEEEEeeeCccHHHHHHHHHHhcccccccceEEEEECCCC
Confidence            356788999999999999999887765421       12233444433332 2334455554433111        1111


Q ss_pred             CcHHHH-----HHHHHHHHhcCCCeEEEEEecCcccccc
Q psy200          280 KSERHQ-----LGAILKYFDTKHKSILLILDEIDALESR  313 (490)
Q Consensus       280 ~s~~~~-----~~~l~~~l~~~~~~~vI~IDEid~l~~~  313 (490)
                      .....+     .-.+.+++...++.+++++|++-++...
T Consensus       145 ~~~~r~~~~~~a~tiAEyfrd~G~~VLll~Dsltr~A~A  183 (285)
T d2jdia3         145 AAPLQYLAPYSGCSMGEYFRDNGKHALIIYDDLSKQAVA  183 (285)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHTTCEEEEEEETHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHHHHHHcCCcEEEEEcChHHHHHH
Confidence            111111     1235566666788999999999887644

>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=95.39  E-value=0.011  Score=53.87  Aligned_cols=43  Identities=12%  Similarity=0.257  Sum_probs=34.0

Q ss_pred             cCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCC
Q psy200          216 NETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSV  259 (490)
Q Consensus       216 ~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~  259 (490)
                      .+.++.++++|..|+||||++-.++..+... +.+++.+++-..
T Consensus         5 ~~~p~~i~~sGKGGVGKTTvaa~lA~~lA~~-G~rVLlvD~Dp~   47 (296)
T d1ihua1           5 QNIPPYLFFTGKGGVGKTSISCATAIRLAEQ-GKRVLLVSTDPA   47 (296)
T ss_dssp             SSCCSEEEEECSTTSSHHHHHHHHHHHHHHT-TCCEEEEECCTT
T ss_pred             CCCCeEEEEECCCcChHHHHHHHHHHHHHHC-CCCEEEEeCCCC
Confidence            3568899999999999999999999988633 456777776543

>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=95.38  E-value=0.022  Score=49.52  Aligned_cols=28  Identities=25%  Similarity=0.375  Sum_probs=25.1

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      +++..|.|.|+-|+||||+++.+++.+.
T Consensus         1 ~kGk~I~iEG~DGsGKST~~~~L~~~L~   28 (214)
T d1tmka_           1 GRGKLILIEGLDRTGKTTQCNILYKKLQ   28 (214)
T ss_dssp             CCCCEEEEEESTTSSHHHHHHHHHHHTT
T ss_pred             CCeEEEEEECCCCCcHHHHHHHHHHHHH
Confidence            3577899999999999999999999885

>d1q0ua_ c.37.1.19 (A:) Probable DEAD box RNA helicase YqfR {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable DEAD box RNA helicase YqfR
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=95.35  E-value=0.029  Score=48.34  Aligned_cols=40  Identities=15%  Similarity=0.142  Sum_probs=26.8

Q ss_pred             CeEEEEEecCccccccC-HHHHHHhHhCCCCCCCcEEEEEec
Q psy200          298 KSILLILDEIDALESRK-QTILYTIFEWPSIPGSKLVLVGVA  338 (490)
Q Consensus       298 ~~~vI~IDEid~l~~~~-~~~L~~l~~~~~~~~~~vilI~~t  338 (490)
                      .-..++|||+|.+.... .+.+..++... ..+.++++.++|
T Consensus       147 ~l~~lViDEad~ll~~~f~~~v~~I~~~~-~~~~Q~il~SAT  187 (209)
T d1q0ua_         147 TAHILVVDEADLMLDMGFITDVDQIAARM-PKDLQMLVFSAT  187 (209)
T ss_dssp             GCCEEEECSHHHHHHTTCHHHHHHHHHTS-CTTCEEEEEESC
T ss_pred             cceEEEEeecccccccccHHHHHHHHHHC-CCCCEEEEEEcc
Confidence            35589999999998764 44555555433 245677777766

>d1s2ma1 c.37.1.19 (A:46-251) Putative ATP-dependent RNA helicase DHH1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative ATP-dependent RNA helicase DHH1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=95.35  E-value=0.042  Score=47.28  Aligned_cols=40  Identities=30%  Similarity=0.497  Sum_probs=25.1

Q ss_pred             CeEEEEEecCccccccC-HHHHHHhHhCCCCCCCcEEEEEec
Q psy200          298 KSILLILDEIDALESRK-QTILYTIFEWPSIPGSKLVLVGVA  338 (490)
Q Consensus       298 ~~~vI~IDEid~l~~~~-~~~L~~l~~~~~~~~~~vilI~~t  338 (490)
                      +-..|+|||+|.|...+ ...+..+++... ...+++++++|
T Consensus       143 ~l~~lV~DEaD~l~~~~f~~~v~~I~~~l~-~~~Q~il~SAT  183 (206)
T d1s2ma1         143 DCSLFIMDEADKMLSRDFKTIIEQILSFLP-PTHQSLLFSAT  183 (206)
T ss_dssp             TCCEEEEESHHHHSSHHHHHHHHHHHTTSC-SSCEEEEEESC
T ss_pred             cceEEEeechhhhhhhhhHHHHHHHHHhCC-CCCEEEEEEEe
Confidence            34489999999998653 344555554332 34566666665

>d1t6na_ c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Spliceosome RNA helicase BAT1 (UAP56)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.31  E-value=0.035  Score=47.91  Aligned_cols=41  Identities=17%  Similarity=0.268  Sum_probs=25.5

Q ss_pred             CCeEEEEEecCcccccc--CHHHHHHhHhCCCCCCCcEEEEEec
Q psy200          297 HKSILLILDEIDALESR--KQTILYTIFEWPSIPGSKLVLVGVA  338 (490)
Q Consensus       297 ~~~~vI~IDEid~l~~~--~~~~L~~l~~~~~~~~~~vilI~~t  338 (490)
                      .+-..++|||+|.|...  ..+.+..++.... ...+++++.+|
T Consensus       144 ~~l~~lVlDEaD~ll~~~~~~~~i~~I~~~~~-~~~Q~il~SAT  186 (207)
T d1t6na_         144 KHIKHFILDECDKMLEQLDMRRDVQEIFRMTP-HEKQVMMFSAT  186 (207)
T ss_dssp             TTCCEEEEESHHHHHSSHHHHHHHHHHHHTSC-SSSEEEEEESC
T ss_pred             cccceeehhhhhhhhhcCCcHHHHHHHHHhCC-CCCEEEEEeee
Confidence            34559999999998764  2344445554332 34567776666

>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=95.28  E-value=0.043  Score=45.56  Aligned_cols=22  Identities=27%  Similarity=0.359  Sum_probs=19.2

Q ss_pred             CeEEEECCCCCcHHHHHHHHHH
Q psy200          220 GSMYISGPPGTGKSASLNLLVS  241 (490)
Q Consensus       220 ~~ill~GppGtGKTtla~~l~~  241 (490)
                      --|+|.|++|+|||+|++.+..
T Consensus        17 ~kI~vvG~~~vGKSsLi~~l~~   38 (176)
T d1fzqa_          17 VRILLLGLDNAGKTTLLKQLAS   38 (176)
T ss_dssp             EEEEEEESTTSSHHHHHHHHCC
T ss_pred             EEEEEECCCCCCHHHHHHHHhc
Confidence            4688999999999999998854

>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=95.27  E-value=0.039  Score=45.83  Aligned_cols=26  Identities=19%  Similarity=0.193  Sum_probs=21.1

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHH
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~  242 (490)
                      ...-.|+|.|++|+|||+|++.+...
T Consensus        10 ~k~~kIvlvG~~~vGKTSli~rl~~~   35 (173)
T d1e0sa_          10 NKEMRILMLGLDAAGKTTILYKLKLG   35 (173)
T ss_dssp             TCCEEEEEEEETTSSHHHHHHHTTCC
T ss_pred             CCeEEEEEECCCCCCHHHHHHHHhcC
Confidence            34456889999999999999988643

>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=95.26  E-value=0.0049  Score=50.50  Aligned_cols=22  Identities=23%  Similarity=0.279  Sum_probs=19.4

Q ss_pred             eEEEECCCCCcHHHHHHHHHHH
Q psy200          221 SMYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~  242 (490)
                      -|+|.|++|+|||||++.+...
T Consensus         2 kivlvG~~~vGKSsLi~~l~~~   23 (160)
T d1r8sa_           2 RILMVGLDAAGKTTILYKLKLG   23 (160)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            3789999999999999998765

>d1qdea_ c.37.1.19 (A:) Initiation factor 4a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=95.25  E-value=0.052  Score=46.95  Aligned_cols=40  Identities=33%  Similarity=0.526  Sum_probs=26.6

Q ss_pred             CeEEEEEecCcccccc-CHHHHHHhHhCCCCCCCcEEEEEec
Q psy200          298 KSILLILDEIDALESR-KQTILYTIFEWPSIPGSKLVLVGVA  338 (490)
Q Consensus       298 ~~~vI~IDEid~l~~~-~~~~L~~l~~~~~~~~~~vilI~~t  338 (490)
                      +...++|||+|.+... -.+.+..+++... ...++++.++|
T Consensus       151 ~l~~lVlDEad~lld~~f~~~v~~I~~~~~-~~~Q~vl~SAT  191 (212)
T d1qdea_         151 KIKMFILDEADEMLSSGFKEQIYQIFTLLP-PTTQVVLLSAT  191 (212)
T ss_dssp             TCCEEEEETHHHHHHTTCHHHHHHHHHHSC-TTCEEEEEESS
T ss_pred             cceEEeehhhhhhcccchHHHHHHHHHhCC-CCCeEEEEEee
Confidence            4669999999999765 3455666655432 34566666665

>d2g9na1 c.37.1.19 (A:21-238) Initiation factor 4a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.22  E-value=0.06  Score=46.78  Aligned_cols=41  Identities=27%  Similarity=0.476  Sum_probs=27.0

Q ss_pred             CCeEEEEEecCccccccC-HHHHHHhHhCCCCCCCcEEEEEec
Q psy200          297 HKSILLILDEIDALESRK-QTILYTIFEWPSIPGSKLVLVGVA  338 (490)
Q Consensus       297 ~~~~vI~IDEid~l~~~~-~~~L~~l~~~~~~~~~~vilI~~t  338 (490)
                      ..-..+||||+|.|.... .+.+..+++... ...++++.++|
T Consensus       154 ~~l~~lVlDEaD~ll~~~f~~~~~~Il~~~~-~~~Q~il~SAT  195 (218)
T d2g9na1         154 KYIKMFVLDEADEMLSRGFKDQIYDIFQKLN-SNTQVVLLSAT  195 (218)
T ss_dssp             TTCCEEEEESHHHHHHTTCHHHHHHHHHHSC-TTCEEEEEESC
T ss_pred             ccceEEEeeecchhhcCchHHHHHHHHHhCC-CCCeEEEEEec
Confidence            345599999999998763 555555555332 34567776666

>d1veca_ c.37.1.19 (A:) DEAD box RNA helicase rck/p54 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEAD box RNA helicase rck/p54
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.98  E-value=0.035  Score=47.90  Aligned_cols=40  Identities=23%  Similarity=0.307  Sum_probs=25.6

Q ss_pred             CeEEEEEecCccccccC-HHHHHHhHhCCCCCCCcEEEEEec
Q psy200          298 KSILLILDEIDALESRK-QTILYTIFEWPSIPGSKLVLVGVA  338 (490)
Q Consensus       298 ~~~vI~IDEid~l~~~~-~~~L~~l~~~~~~~~~~vilI~~t  338 (490)
                      .-..|||||+|.|...+ ...+..+++... ...++++.++|
T Consensus       146 ~l~~lVlDEaD~ll~~~f~~~i~~I~~~~~-~~~Q~~l~SAT  186 (206)
T d1veca_         146 HVQMIVLDEADKLLSQDFVQIMEDIILTLP-KNRQILLYSAT  186 (206)
T ss_dssp             TCCEEEEETHHHHTSTTTHHHHHHHHHHSC-TTCEEEEEESC
T ss_pred             ccceEEEeccccccccchHHHHHHHHHhCC-CCCEEEEEEec
Confidence            35589999999998664 444555554332 34566666665

>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=94.96  E-value=0.02  Score=51.67  Aligned_cols=43  Identities=16%  Similarity=0.285  Sum_probs=34.6

Q ss_pred             cCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCC
Q psy200          216 NETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSV  259 (490)
Q Consensus       216 ~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~  259 (490)
                      ....+.++++|..|+||||++-.++..+... +.+++.+++-..
T Consensus        17 ~~~~~iii~sGKGGVGKTT~a~nLA~~lA~~-G~rVllvD~Dp~   59 (279)
T d1ihua2          17 RNEHGLIMLMGKGGVGKTTMAAAIAVRLADM-GFDVHLTTSDPA   59 (279)
T ss_dssp             TTSCEEEEEECSTTSSHHHHHHHHHHHHHHT-TCCEEEEESCCC
T ss_pred             cCCCEEEEEECCCCCCHHHHHHHHHHHHHHC-CCcEEEEeCCCC
Confidence            4667888899999999999999998888643 457888877654

>d1rifa_ c.37.1.23 (A:) DNA helicase UvsW {Bacteriophage T4 [TaxId: 10665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: DNA helicase UvsW
domain: DNA helicase UvsW
species: Bacteriophage T4 [TaxId: 10665]

Probab=94.96  E-value=0.037  Score=50.31  Aligned_cols=53  Identities=17%  Similarity=0.088  Sum_probs=39.6

Q ss_pred             CCCChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEE
Q psy200          195 ELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYI  254 (490)
Q Consensus       195 ~lvgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v  254 (490)
                      .+.-|+-+.+.+..++..       +..+|.-|.|+|||.++-.++..+....+.+++.+
T Consensus       111 ~~~~rdyQ~~av~~~l~~-------~~~il~~pTGsGKT~i~~~i~~~~~~~~~~k~Lii  163 (282)
T d1rifa_         111 RIEPHWYQKDAVFEGLVN-------RRRILNLPTSAGRSLIQALLARYYLENYEGKILII  163 (282)
T ss_dssp             ECCCCHHHHHHHHHHHHH-------SEEEECCCTTSCHHHHHHHHHHHHHHHCSSEEEEE
T ss_pred             ccccchHHHHHHHHHHhc-------CCceeEEEcccCccHHHHHHHHHhhhcccceEEEE
Confidence            477788888888888864       34567779999999998888876654444566665

>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=94.87  E-value=0.083  Score=43.24  Aligned_cols=22  Identities=23%  Similarity=0.382  Sum_probs=19.0

Q ss_pred             eEEEECCCCCcHHHHHHHHHHH
Q psy200          221 SMYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~  242 (490)
                      .|+|.|++|+|||+|++.+...
T Consensus         4 ki~i~G~~~~GKTsLl~~l~~~   25 (164)
T d1zd9a1           4 ELTLVGLQYSGKTTFVNVIASG   25 (164)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            4778899999999999988654

>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=94.78  E-value=0.0078  Score=51.99  Aligned_cols=27  Identities=22%  Similarity=0.433  Sum_probs=23.7

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      .+..+.|.||.|+|||||++.++..+.
T Consensus        26 ~Gei~~l~G~NGsGKSTLl~~i~gl~~   52 (200)
T d1sgwa_          26 KGNVVNFHGPNGIGKTTLLKTISTYLK   52 (200)
T ss_dssp             TTCCEEEECCTTSSHHHHHHHHTTSSC
T ss_pred             CCCEEEEECCCCChHHHHHHHHhcccc
Confidence            567888999999999999999987663

>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=94.71  E-value=0.0088  Score=48.89  Aligned_cols=22  Identities=23%  Similarity=0.412  Sum_probs=19.6

Q ss_pred             eEEEECCCCCcHHHHHHHHHHH
Q psy200          221 SMYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~  242 (490)
                      -|+|.|++|+|||+|++.+...
T Consensus         2 KI~liG~~nvGKSSLln~l~~~   23 (166)
T d2qtvb1           2 KLLFLGLDNAGKTTLLHMLKND   23 (166)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            4789999999999999998764

>d2j0sa1 c.37.1.19 (A:22-243) Probable ATP-dependent RNA helicase DDX48 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable ATP-dependent RNA helicase DDX48
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.66  E-value=0.078  Score=46.16  Aligned_cols=40  Identities=23%  Similarity=0.581  Sum_probs=26.9

Q ss_pred             CeEEEEEecCccccccC-HHHHHHhHhCCCCCCCcEEEEEec
Q psy200          298 KSILLILDEIDALESRK-QTILYTIFEWPSIPGSKLVLVGVA  338 (490)
Q Consensus       298 ~~~vI~IDEid~l~~~~-~~~L~~l~~~~~~~~~~vilI~~t  338 (490)
                      .--.+||||+|.|.... ...+..+++... ...+++++.+|
T Consensus       159 ~l~~lVlDEaD~ll~~~f~~~i~~I~~~l~-~~~Q~ilfSAT  199 (222)
T d2j0sa1         159 AIKMLVLDEADEMLNKGFKEQIYDVYRYLP-PATQVVLISAT  199 (222)
T ss_dssp             TCCEEEEETHHHHTSTTTHHHHHHHHTTSC-TTCEEEEEESC
T ss_pred             cceeeeecchhHhhhcCcHHHHHHHHHhCC-CCCEEEEEEEe
Confidence            34589999999998763 455666655432 34567777766

>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=94.64  E-value=0.015  Score=51.27  Aligned_cols=27  Identities=26%  Similarity=0.458  Sum_probs=23.4

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHh
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRA  243 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l  243 (490)
                      ..+..+.|.||.|+|||||++.++.-+
T Consensus        24 ~~Gei~~liGpsGsGKSTLl~~i~Gl~   50 (232)
T d2awna2          24 HEGEFVVFVGPSGCGKSTLLRMIAGLE   50 (232)
T ss_dssp             CTTCEEEEECCTTSSHHHHHHHHHTSS
T ss_pred             cCCCEEEEECCCCChHHHHHHHHhcCC
Confidence            456789999999999999999997655

>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=94.64  E-value=0.012  Score=51.49  Aligned_cols=33  Identities=27%  Similarity=0.471  Sum_probs=25.4

Q ss_pred             HHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHHH
Q psy200          203 LEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       203 ~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~~  242 (490)
                      ++.|..+|.       ++..+|.|++|+|||||++++...
T Consensus        86 ~~~L~~~l~-------~kt~~~~G~SGVGKSTLiN~L~~~  118 (225)
T d1u0la2          86 IEELKEYLK-------GKISTMAGLSGVGKSSLLNAINPG  118 (225)
T ss_dssp             HHHHHHHHS-------SSEEEEECSTTSSHHHHHHHHSTT
T ss_pred             HhhHHHHhc-------CCeEEEECCCCCCHHHHHHhhcch
Confidence            445566553       467889999999999999998644

>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=94.62  E-value=0.0086  Score=49.28  Aligned_cols=22  Identities=32%  Similarity=0.395  Sum_probs=19.7

Q ss_pred             eEEEECCCCCcHHHHHHHHHHH
Q psy200          221 SMYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~  242 (490)
                      .|+|+|.+|+|||||++++...
T Consensus         7 kI~ivG~~~vGKSSLi~~~~~~   28 (169)
T d1upta_           7 RILILGLDGAGKTTILYRLQVG   28 (169)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            4789999999999999998764

>d1oywa2 c.37.1.19 (A:1-206) RecQ helicase domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: RecQ helicase domain
species: Escherichia coli [TaxId: 562]

Probab=94.61  E-value=0.034  Score=47.72  Aligned_cols=22  Identities=23%  Similarity=0.350  Sum_probs=17.4

Q ss_pred             CCeEEEECCCCCcHHHHHHHHH
Q psy200          219 SGSMYISGPPGTGKSASLNLLV  240 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~  240 (490)
                      ++.+++.-|.|+|||.+.....
T Consensus        40 g~~vlv~apTGsGKT~~~~~~~   61 (206)
T d1oywa2          40 GRDCLVVMPTGGGKSLCYQIPA   61 (206)
T ss_dssp             TCCEEEECSCHHHHHHHHHHHH
T ss_pred             CCCEEEEcCCCCCCcchhhhhh
Confidence            3578999999999998765443

>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=94.55  E-value=0.012  Score=51.97  Aligned_cols=28  Identities=25%  Similarity=0.552  Sum_probs=23.9

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      ..+..+.|.||.|+|||||++.+...+.
T Consensus        30 ~~Ge~~~liGpsGaGKSTLl~~i~Gl~~   57 (239)
T d1v43a3          30 KDGEFLVLLGPSGCGKTTTLRMIAGLEE   57 (239)
T ss_dssp             CTTCEEEEECCTTSSHHHHHHHHHTSSC
T ss_pred             CCCCEEEEECCCCChHHHHHHHHHcCCC
Confidence            4567889999999999999999977653

>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=94.55  E-value=0.029  Score=51.58  Aligned_cols=42  Identities=17%  Similarity=0.163  Sum_probs=29.3

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhc-CCceEEEEeccCC
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIK-DAFKTIYINCNSV  259 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~-~~~~~~~v~~~~~  259 (490)
                      .+-.|.|.|++|+||||+++.+...+... ....+..++.-.+
T Consensus        79 ~P~iIGIaG~sgSGKSTla~~L~~lL~~~~~~~~v~~Is~D~F  121 (308)
T d1sq5a_          79 IPYIISIAGSVAVGKSTTARVLQALLSRWPEHRRVELITTDGF  121 (308)
T ss_dssp             CCEEEEEEECTTSSHHHHHHHHHHHHTTSTTCCCEEEEEGGGG
T ss_pred             CCEEEEEeCCCCCCCcHHHHHHHHHHhhhcCCCceEEEeeeee
Confidence            44577799999999999999999888532 2234444443333

>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=94.36  E-value=0.011  Score=49.53  Aligned_cols=21  Identities=33%  Similarity=0.460  Sum_probs=18.9

Q ss_pred             EEEECCCCCcHHHHHHHHHHH
Q psy200          222 MYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       222 ill~GppGtGKTtla~~l~~~  242 (490)
                      ++|.|++|+|||+|++.+.+.
T Consensus         6 ivvvG~~~vGKTsli~r~~~~   26 (173)
T d2a5ja1           6 YIIIGDTGVGKSCLLLQFTDK   26 (173)
T ss_dssp             EEEESSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHhcC
Confidence            778999999999999998764

>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=94.33  E-value=0.0068  Score=51.87  Aligned_cols=29  Identities=24%  Similarity=0.332  Sum_probs=24.4

Q ss_pred             cCCCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          216 NETSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       216 ~~~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      ...+-.|.|.|+-|+||||+++.+++.+.
T Consensus         6 ~~kp~~I~ieG~~GsGKTTl~~~L~~~l~   34 (197)
T d2vp4a1           6 GTQPFTVLIEGNIGSGKTTYLNHFEKYKN   34 (197)
T ss_dssp             TCCCEEEEEECSTTSCHHHHHHTTGGGTT
T ss_pred             CCCceEEEEECCCCCCHHHHHHHHHHHhC
Confidence            34556788999999999999999988764

>d1uaaa1 c.37.1.19 (A:2-307) DEXX box DNA helicase {Escherichia coli, RepD [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEXX box DNA helicase
species: Escherichia coli, RepD [TaxId: 562]

Probab=94.30  E-value=0.012  Score=53.96  Aligned_cols=24  Identities=21%  Similarity=0.457  Sum_probs=17.9

Q ss_pred             CCCeEEEECCCCCcHHHHH-HHHHH
Q psy200          218 TSGSMYISGPPGTGKSASL-NLLVS  241 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla-~~l~~  241 (490)
                      ..++++|.|+||||||+++ ..++.
T Consensus        13 ~~~~~lI~g~aGTGKTt~l~~rv~~   37 (306)
T d1uaaa1          13 VTGPCLVLAGAGSGKTRVITNKIAH   37 (306)
T ss_dssp             CSSEEEECCCTTSCHHHHHHHHHHH
T ss_pred             CCCCEEEEeeCCccHHHHHHHHHHH
Confidence            3567899999999999765 33433

>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=94.29  E-value=0.012  Score=49.18  Aligned_cols=25  Identities=24%  Similarity=0.472  Sum_probs=21.2

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHH
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVS  241 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~  241 (490)
                      ....-|+|.|.+|+|||||++++..
T Consensus        11 ~k~~kI~lvG~~~vGKTsLl~~l~~   35 (186)
T d1f6ba_          11 KKTGKLVFLGLDNAGKTTLLHMLKD   35 (186)
T ss_dssp             TCCEEEEEEEETTSSHHHHHHHHSC
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHhC
Confidence            4556788999999999999998854

>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=94.25  E-value=0.015  Score=51.53  Aligned_cols=26  Identities=27%  Similarity=0.557  Sum_probs=22.9

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHh
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRA  243 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l  243 (490)
                      .+..+.|.||.|+|||||++.++..+
T Consensus        28 ~Ge~~~liG~sGaGKSTll~~i~gl~   53 (240)
T d1g2912          28 DGEFMILLGPSGCGKTTTLRMIAGLE   53 (240)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHHTSS
T ss_pred             CCCEEEEECCCCChHHHHHHHHhcCC
Confidence            56788899999999999999998655

>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=94.15  E-value=0.014  Score=51.53  Aligned_cols=25  Identities=32%  Similarity=0.518  Sum_probs=21.6

Q ss_pred             CeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          220 GSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       220 ~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      ..+.|.||.|+|||||++.++..+.
T Consensus        25 e~~~liGpnGaGKSTll~~i~Gl~~   49 (240)
T d2onka1          25 DYCVLLGPTGAGKSVFLELIAGIVK   49 (240)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHTSSC
T ss_pred             EEEEEECCCCChHHHHHHHHHcCCC
Confidence            4677899999999999999987663

>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=94.14  E-value=0.014  Score=52.28  Aligned_cols=28  Identities=21%  Similarity=0.367  Sum_probs=24.1

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      ..+..+.|+||.|+|||||++.++..+.
T Consensus        39 ~~Ge~iaivG~sGsGKSTLl~ll~gl~~   66 (253)
T d3b60a1          39 PAGKTVALVGRSGSGKSTIASLITRFYD   66 (253)
T ss_dssp             CTTCEEEEEECTTSSHHHHHHHHTTTTC
T ss_pred             cCCCEEEEECCCCChHHHHHHHHhcccC
Confidence            4677899999999999999999977653

>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=94.13  E-value=0.019  Score=47.83  Aligned_cols=26  Identities=19%  Similarity=0.243  Sum_probs=21.6

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHH
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~  242 (490)
                      +....|+|+|.+|+|||+|++++...
T Consensus        13 ~k~~kI~vvG~~~~GKSsLi~rl~~~   38 (177)
T d1zj6a1          13 HQEHKVIIVGLDNAGKTTILYQFSMN   38 (177)
T ss_dssp             TSCEEEEEEESTTSSHHHHHHHHHTT
T ss_pred             CCeEEEEEECCCCCCHHHHHHHHhcC
Confidence            44567889999999999999988653

>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=94.11  E-value=0.013  Score=48.45  Aligned_cols=22  Identities=23%  Similarity=0.336  Sum_probs=19.2

Q ss_pred             eEEEECCCCCcHHHHHHHHHHH
Q psy200          221 SMYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~  242 (490)
                      -++|.|.+|+|||+|++.+.+.
T Consensus         4 Kv~liG~~~vGKSsLi~rl~~~   25 (164)
T d1z2aa1           4 KMVVVGNGAVGKSSMIQRYCKG   25 (164)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHC
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3789999999999999988763

>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=94.10  E-value=0.014  Score=51.90  Aligned_cols=28  Identities=25%  Similarity=0.270  Sum_probs=24.2

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      ..+..+.|+|+.|+|||||++.++..+.
T Consensus        27 ~~Ge~vaIvG~sGsGKSTLl~ll~gl~~   54 (241)
T d2pmka1          27 KQGEVIGIVGRSGSGKSTLTKLIQRFYI   54 (241)
T ss_dssp             ETTCEEEEECSTTSSHHHHHHHHTTSSC
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHHhcCC
Confidence            3567899999999999999999987654

>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=94.05  E-value=0.014  Score=48.44  Aligned_cols=21  Identities=33%  Similarity=0.482  Sum_probs=18.9

Q ss_pred             EEEECCCCCcHHHHHHHHHHH
Q psy200          222 MYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       222 ill~GppGtGKTtla~~l~~~  242 (490)
                      ++|.|.+|+|||+|++.+.+.
T Consensus         7 ivlvG~~~vGKTsli~~~~~~   27 (166)
T d1z0fa1           7 YIIIGDMGVGKSCLLHQFTEK   27 (166)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            778899999999999998764

>d1xbta1 c.37.1.24 (A:18-150) Thymidine kinase, TK1, 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: Type II thymidine kinase
domain: Thymidine kinase, TK1, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.01  E-value=0.035  Score=44.27  Aligned_cols=38  Identities=32%  Similarity=0.361  Sum_probs=25.4

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEecc
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCN  257 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~  257 (490)
                      +..-+|+||-.+|||+-+-..++...... ..++.++..
T Consensus         2 G~L~li~GpMfsGKTt~Li~~~~~~~~~g-~~v~~ikp~   39 (133)
T d1xbta1           2 GQIQVILGPMFSGKSTELMRRVRRFQIAQ-YKCLVIKYA   39 (133)
T ss_dssp             CEEEEEECCTTSCHHHHHHHHHHHHHTTT-CCEEEEEET
T ss_pred             cEEEEEEecccCHHHHHHHHHHHHHHHcC-CcEEEEecc
Confidence            34567899999999998777776664332 344555433

>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=93.98  E-value=0.015  Score=48.27  Aligned_cols=22  Identities=32%  Similarity=0.406  Sum_probs=19.6

Q ss_pred             eEEEECCCCCcHHHHHHHHHHH
Q psy200          221 SMYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~  242 (490)
                      -|+|.|.+|+|||+|++.+...
T Consensus         5 Ki~lvG~~~vGKTsLi~r~~~~   26 (167)
T d1kaoa_           5 KVVVLGSGGVGKSALTVQFVTG   26 (167)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            4788999999999999999764

>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=93.97  E-value=0.016  Score=51.86  Aligned_cols=28  Identities=29%  Similarity=0.410  Sum_probs=24.2

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      ..+..+.|+|+.|+|||||++.+...+.
T Consensus        38 ~~Ge~vaivG~sGsGKSTLl~li~gl~~   65 (251)
T d1jj7a_          38 RPGEVTALVGPNGSGKSTVAALLQNLYQ   65 (251)
T ss_dssp             CTTCEEEEECSTTSSHHHHHHHHTTSSC
T ss_pred             cCCCEEEEECCCCCcHHHHHHHHhcccC
Confidence            4677899999999999999999977653

>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=93.95  E-value=0.036  Score=49.87  Aligned_cols=28  Identities=18%  Similarity=0.398  Sum_probs=24.5

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      ..-..++|+||+++|||+++..+.+.++
T Consensus       102 ~k~n~~~l~G~~~tGKS~f~~~i~~~lg  129 (267)
T d1u0ja_         102 GKRNTIWLFGPATTGKTNIAEAIAHTVP  129 (267)
T ss_dssp             TTCCEEEEECSTTSSHHHHHHHHHHHSS
T ss_pred             CccEEEEEEcCCCCCHHHHHHHHHHHhc
Confidence            3557889999999999999999998874

>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=93.94  E-value=0.015  Score=49.86  Aligned_cols=23  Identities=39%  Similarity=0.687  Sum_probs=20.5

Q ss_pred             CeEEEECCCCCcHHHHHHHHHHH
Q psy200          220 GSMYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       220 ~~ill~GppGtGKTtla~~l~~~  242 (490)
                      ..|+|.|+||+|||||++++...
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            46889999999999999999865

>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=93.94  E-value=0.013  Score=51.54  Aligned_cols=27  Identities=33%  Similarity=0.522  Sum_probs=23.7

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHh
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRA  243 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l  243 (490)
                      ..+..+.|.||.|+|||||++.++.-+
T Consensus        24 ~~Ge~~~liGpsGaGKSTll~~l~Gl~   50 (229)
T d3d31a2          24 ESGEYFVILGPTGAGKTLFLELIAGFH   50 (229)
T ss_dssp             CTTCEEEEECCCTHHHHHHHHHHHTSS
T ss_pred             CCCCEEEEECCCCCcHHHHHHHHhcCc
Confidence            456789999999999999999998765

>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=93.88  E-value=0.033  Score=47.75  Aligned_cols=36  Identities=17%  Similarity=0.166  Sum_probs=27.3

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEecc
Q psy200          221 SMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCN  257 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~  257 (490)
                      .|.|.|.-|+||||+++.+.+.+.. .++.++.+..+
T Consensus         2 lI~ieG~dGsGKST~~~~L~~~l~~-~g~~v~~~~~P   37 (208)
T d1gsia_           2 LIAIEGVDGAGKRTLVEKLSGAFRA-AGRSVATLAFP   37 (208)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHHH-TTCCEEEEESS
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHH-CCCCEEEEecC
Confidence            4778999999999999999998853 23455555444

>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=93.88  E-value=0.013  Score=51.92  Aligned_cols=27  Identities=19%  Similarity=0.208  Sum_probs=23.2

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHh
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRA  243 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l  243 (490)
                      ..+..+.|.||.|+|||||++.++--+
T Consensus        29 ~~Ge~~~iiG~sGsGKSTLl~~i~Gl~   55 (240)
T d3dhwc1          29 PAGQIYGVIGASGAGKSTLIRCVNLLE   55 (240)
T ss_dssp             CSSCEEEEEESTTSSHHHHHHHHTTSS
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHcCCc
Confidence            356788999999999999999997654

>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=93.82  E-value=0.016  Score=48.20  Aligned_cols=21  Identities=24%  Similarity=0.316  Sum_probs=19.0

Q ss_pred             EEEECCCCCcHHHHHHHHHHH
Q psy200          222 MYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       222 ill~GppGtGKTtla~~l~~~  242 (490)
                      ++|.|.+|+|||+|++.+...
T Consensus         8 i~vvG~~~vGKTsLi~~l~~~   28 (169)
T d3raba_           8 ILIIGNSSVGKTSFLFRYADD   28 (169)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHcC
Confidence            789999999999999998764

>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=93.78  E-value=0.017  Score=48.05  Aligned_cols=22  Identities=32%  Similarity=0.489  Sum_probs=19.5

Q ss_pred             eEEEECCCCCcHHHHHHHHHHH
Q psy200          221 SMYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~  242 (490)
                      -++|.|++|+|||+|++.+...
T Consensus         4 Ki~lvG~~~vGKTsli~r~~~~   25 (168)
T d2atva1           4 KLAIFGRAGVGKSALVVRFLTK   25 (168)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            3788999999999999999874

>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=93.76  E-value=0.017  Score=47.89  Aligned_cols=22  Identities=14%  Similarity=0.172  Sum_probs=19.2

Q ss_pred             eEEEECCCCCcHHHHHHHHHHH
Q psy200          221 SMYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~  242 (490)
                      -|+|.|.+|+|||+|++.+...
T Consensus         5 KivlvG~~~vGKTsLi~r~~~~   26 (167)
T d1z08a1           5 KVVLLGEGCVGKTSLVLRYCEN   26 (167)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHC
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3789999999999999998763

>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=93.73  E-value=0.017  Score=48.65  Aligned_cols=33  Identities=21%  Similarity=0.187  Sum_probs=24.1

Q ss_pred             HHHhhhccCCCCeEEEECCCCCcHHHHHHHHHH
Q psy200          209 FLLGHVNNETSGSMYISGPPGTGKSASLNLLVS  241 (490)
Q Consensus       209 ~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~  241 (490)
                      ++.........-.|+|.|.+|+|||+|++.+..
T Consensus         7 ~~~~l~~~~k~~KI~lvG~~~vGKTsLi~~l~~   39 (182)
T d1moza_           7 MFDKLWGSNKELRILILGLDGAGKTTILYRLQI   39 (182)
T ss_dssp             HHGGGTTCSSCEEEEEEEETTSSHHHHHHHTCC
T ss_pred             HHHHHhCCCceEEEEEECCCCCCHHHHHHHHhc
Confidence            333333444556788999999999999988743

>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=93.71  E-value=0.017  Score=52.56  Aligned_cols=28  Identities=32%  Similarity=0.561  Sum_probs=24.4

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      ..+..+.|+||.|+|||||++.++..+.
T Consensus        60 ~~Ge~vaivG~nGsGKSTLl~~i~Gl~~   87 (281)
T d1r0wa_          60 EKGEMLAITGSTGSGKTSLLMLILGELE   87 (281)
T ss_dssp             CTTCEEEEEESTTSSHHHHHHHHHTSSC
T ss_pred             cCCCEEEEECCCCChHHHHHHHHhCCCc
Confidence            3677899999999999999999987664

>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=93.62  E-value=0.019  Score=48.12  Aligned_cols=25  Identities=36%  Similarity=0.445  Sum_probs=21.9

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHH
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~  242 (490)
                      .+..++|.|++|+|||+++-.+...
T Consensus        13 ~g~gvl~~G~sG~GKStlal~l~~~   37 (176)
T d1kkma_          13 YGLGVLITGDSGVGKSETALELVQR   37 (176)
T ss_dssp             TTEEEEEECCTTSCHHHHHHHHHHT
T ss_pred             CCEEEEEEeCCCCCHHHHHHHHHHc
Confidence            4678999999999999999887764

>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=93.61  E-value=0.017  Score=48.12  Aligned_cols=22  Identities=27%  Similarity=0.385  Sum_probs=19.4

Q ss_pred             eEEEECCCCCcHHHHHHHHHHH
Q psy200          221 SMYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~  242 (490)
                      -|+|.|.+|+|||+|++.+...
T Consensus         7 Ki~lvG~~~vGKTsLi~r~~~~   28 (171)
T d2erya1           7 RLVVVGGGGVGKSALTIQFIQS   28 (171)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            4888999999999999998764

>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=93.60  E-value=0.017  Score=48.15  Aligned_cols=22  Identities=18%  Similarity=0.394  Sum_probs=19.5

Q ss_pred             eEEEECCCCCcHHHHHHHHHHH
Q psy200          221 SMYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~  242 (490)
                      -++|.|.+|+|||+|++.+.+.
T Consensus         7 Ki~lvG~~~vGKTsLi~~l~~~   28 (171)
T d2ew1a1           7 KIVLIGNAGVGKTCLVRRFTQG   28 (171)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3789999999999999999864

>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=93.58  E-value=0.019  Score=47.78  Aligned_cols=22  Identities=23%  Similarity=0.329  Sum_probs=19.3

Q ss_pred             eEEEECCCCCcHHHHHHHHHHH
Q psy200          221 SMYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~  242 (490)
                      -|+|.|.+|+|||+|++.+.+.
T Consensus         8 Ki~vvG~~~vGKTsLi~~l~~~   29 (170)
T d1r2qa_           8 KLVLLGESAVGKSSLVLRFVKG   29 (170)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3678999999999999998864

>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=93.58  E-value=0.019  Score=48.06  Aligned_cols=22  Identities=27%  Similarity=0.439  Sum_probs=19.2

Q ss_pred             eEEEECCCCCcHHHHHHHHHHH
Q psy200          221 SMYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~  242 (490)
                      .++|.|.+|+|||+|++.+...
T Consensus         6 Ki~vvG~~~vGKTsLi~~~~~~   27 (175)
T d2f9la1           6 KVVLIGDSGVGKSNLLSRFTRN   27 (175)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3789999999999999998764

>d1pjra1 c.37.1.19 (A:1-318) DEXX box DNA helicase {Bacillus stearothermophilus, PcrA [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEXX box DNA helicase
species: Bacillus stearothermophilus, PcrA [TaxId: 1422]

Probab=93.56  E-value=0.019  Score=52.89  Aligned_cols=20  Identities=30%  Similarity=0.537  Sum_probs=16.4

Q ss_pred             CCeEEEECCCCCcHHHHHHH
Q psy200          219 SGSMYISGPPGTGKSASLNL  238 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~  238 (490)
                      .++++|.|+|||||||++-.
T Consensus        24 ~g~~lV~g~aGSGKTt~l~~   43 (318)
T d1pjra1          24 EGPLLIMAGAGSGKTRVLTH   43 (318)
T ss_dssp             SSCEEEEECTTSCHHHHHHH
T ss_pred             CCCEEEEecCCccHHHHHHH
Confidence            46799999999999976643

>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=93.53  E-value=0.02  Score=48.58  Aligned_cols=24  Identities=33%  Similarity=0.326  Sum_probs=19.5

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHh
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRA  243 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l  243 (490)
                      +-.|.|+|++|+||||+|+.+ .+.
T Consensus         3 p~IIgitG~~gSGKstva~~l-~~~   26 (191)
T d1uf9a_           3 PIIIGITGNIGSGKSTVAALL-RSW   26 (191)
T ss_dssp             CEEEEEEECTTSCHHHHHHHH-HHT
T ss_pred             CEEEEEECCCCCCHHHHHHHH-HHC
Confidence            345669999999999999988 444

>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=93.50  E-value=0.02  Score=47.19  Aligned_cols=21  Identities=14%  Similarity=0.267  Sum_probs=19.0

Q ss_pred             EEEECCCCCcHHHHHHHHHHH
Q psy200          222 MYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       222 ill~GppGtGKTtla~~l~~~  242 (490)
                      |+|.|.+|+|||+|++.+...
T Consensus         5 v~liG~~~vGKTsLl~~~~~~   25 (165)
T d1z06a1           5 IIVIGDSNVGKTCLTYRFCAG   25 (165)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            789999999999999998764

>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=93.49  E-value=0.019  Score=48.52  Aligned_cols=21  Identities=24%  Similarity=0.365  Sum_probs=18.5

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q psy200          221 SMYISGPPGTGKSASLNLLVS  241 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~  241 (490)
                      -|+|.|.+|+|||+|++.+.+
T Consensus         7 Ki~ivG~~~vGKTsLi~~l~~   27 (186)
T d2f7sa1           7 KLLALGDSGVGKTTFLYRYTD   27 (186)
T ss_dssp             EEEEESCTTSSHHHHHHHHHC
T ss_pred             EEEEECCCCcCHHHHHHHHhc
Confidence            378899999999999998865

>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=93.48  E-value=0.017  Score=51.29  Aligned_cols=27  Identities=30%  Similarity=0.470  Sum_probs=23.5

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHh
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRA  243 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l  243 (490)
                      .++..+.|+||.|+|||||++.++..+
T Consensus        26 ~~Ge~vaivG~sGsGKSTLl~ll~gl~   52 (242)
T d1mv5a_          26 QPNSIIAFAGPSGGGKSTIFSLLERFY   52 (242)
T ss_dssp             CTTEEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHHHhh
Confidence            456788999999999999999997765

>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=93.47  E-value=0.018  Score=48.05  Aligned_cols=22  Identities=27%  Similarity=0.389  Sum_probs=19.6

Q ss_pred             eEEEECCCCCcHHHHHHHHHHH
Q psy200          221 SMYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~  242 (490)
                      -|+|.|.+|+|||+|++.+.+.
T Consensus         8 Kv~lvG~~~vGKTsLi~r~~~~   29 (173)
T d2fn4a1           8 KLVVVGGGGVGKSALTIQFIQS   29 (173)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            5889999999999999988764

>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=93.46  E-value=0.02  Score=47.36  Aligned_cols=22  Identities=27%  Similarity=0.427  Sum_probs=19.3

Q ss_pred             eEEEECCCCCcHHHHHHHHHHH
Q psy200          221 SMYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~  242 (490)
                      -|+|.|.+|+|||+|++.+.+.
T Consensus         6 Ki~lvG~~~vGKTsli~rl~~~   27 (167)
T d1z0ja1           6 KVCLLGDTGVGKSSIMWRFVED   27 (167)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3778899999999999998764

>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=93.42  E-value=0.021  Score=47.61  Aligned_cols=21  Identities=29%  Similarity=0.506  Sum_probs=18.7

Q ss_pred             EEEECCCCCcHHHHHHHHHHH
Q psy200          222 MYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       222 ill~GppGtGKTtla~~l~~~  242 (490)
                      ++|.|++|+|||+|++.+...
T Consensus         5 i~~vG~~~vGKSsLi~~~~~~   25 (175)
T d1ky3a_           5 VIILGDSGVGKTSLMHRYVND   25 (175)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHcC
Confidence            789999999999999998753

>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=93.41  E-value=0.02  Score=47.59  Aligned_cols=22  Identities=27%  Similarity=0.357  Sum_probs=18.9

Q ss_pred             eEEEECCCCCcHHHHHHHHHHH
Q psy200          221 SMYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~  242 (490)
                      -|+|.|.+|+|||+|++.+...
T Consensus         4 Ki~viG~~~vGKTsLi~r~~~~   25 (171)
T d2erxa1           4 RVAVFGAGGVGKSSLVLRFVKG   25 (171)
T ss_dssp             EEEEECCTTSSHHHHHHHHHTC
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            3678899999999999988753

>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=93.39  E-value=0.02  Score=50.44  Aligned_cols=26  Identities=27%  Similarity=0.328  Sum_probs=23.7

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      ++.|+|-|.-|+||||+++.+++.+.
T Consensus         2 pk~IviEG~~GsGKST~~~~L~~~l~   27 (241)
T d2ocpa1           2 PRRLSIEGNIAVGKSTFVKLLTKTYP   27 (241)
T ss_dssp             CEEEEEEECTTSSHHHHHHHHHHHCT
T ss_pred             CeEEEEECCCCCcHHHHHHHHHHHHh
Confidence            56789999999999999999999874

>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=93.39  E-value=0.014  Score=51.72  Aligned_cols=27  Identities=26%  Similarity=0.502  Sum_probs=23.5

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHh
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRA  243 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l  243 (490)
                      ..+..+.|.||.|+||||+++.++.-.
T Consensus        29 ~~Ge~~~iiG~sGsGKSTll~~i~gl~   55 (242)
T d1oxxk2          29 ENGERFGILGPSGAGKTTFMRIIAGLD   55 (242)
T ss_dssp             CTTCEEEEECSCHHHHHHHHHHHHTSS
T ss_pred             CCCCEEEEECCCCCcHHHHHHHHHcCc
Confidence            356789999999999999999998754

>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=93.39  E-value=0.019  Score=47.52  Aligned_cols=22  Identities=32%  Similarity=0.456  Sum_probs=19.4

Q ss_pred             eEEEECCCCCcHHHHHHHHHHH
Q psy200          221 SMYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~  242 (490)
                      -|+|.|.+|+|||+|++.+...
T Consensus         5 Ki~viG~~~vGKTsli~~l~~~   26 (166)
T d1ctqa_           5 KLVVVGAGGVGKSALTIQLIQN   26 (166)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            3788999999999999998764

>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=93.37  E-value=0.019  Score=47.44  Aligned_cols=21  Identities=33%  Similarity=0.504  Sum_probs=19.0

Q ss_pred             EEEECCCCCcHHHHHHHHHHH
Q psy200          222 MYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       222 ill~GppGtGKTtla~~l~~~  242 (490)
                      +++.|.+|+|||+|++.+...
T Consensus         5 i~vvG~~~vGKTSli~~l~~~   25 (166)
T d1g16a_           5 ILLIGDSGVGKSCLLVRFVED   25 (166)
T ss_dssp             EEEEESTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            789999999999999998764

>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=93.36  E-value=0.02  Score=47.53  Aligned_cols=21  Identities=43%  Similarity=0.659  Sum_probs=19.0

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q psy200          221 SMYISGPPGTGKSASLNLLVS  241 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~  241 (490)
                      .|.|.|++|+|||||++++..
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            478999999999999999974

>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=93.35  E-value=0.033  Score=50.02  Aligned_cols=39  Identities=23%  Similarity=0.311  Sum_probs=32.0

Q ss_pred             CeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCC
Q psy200          220 GSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSV  259 (490)
Q Consensus       220 ~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~  259 (490)
                      +.|.|+|-.|+||||++-.++..+.. .+.+++.|++-..
T Consensus         2 r~Iai~gKGGvGKTT~a~nLA~~LA~-~G~rVllID~D~q   40 (269)
T d1cp2a_           2 RQVAIYGKGGIGKSTTTQNLTSGLHA-MGKTIMVVGCDPK   40 (269)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHHHHT-TTCCEEEEEECTT
T ss_pred             CEEEEECCCcCCHHHHHHHHHHHHHh-CCCcEEEEecCCC
Confidence            45778999999999999999999974 3568888887643

>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=93.26  E-value=0.021  Score=51.14  Aligned_cols=27  Identities=26%  Similarity=0.335  Sum_probs=23.3

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHh
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRA  243 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l  243 (490)
                      ..+..+.|.||.|+|||||++.++.-+
T Consensus        26 ~~GEi~~iiG~sGsGKSTLl~~i~Gl~   52 (258)
T d1b0ua_          26 RAGDVISIIGSSGSGKSTFLRCINFLE   52 (258)
T ss_dssp             CTTCEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             cCCCEEEEECCCCCcHHHHHHHHHcCc
Confidence            467789999999999999999997644

>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=93.24  E-value=0.021  Score=47.09  Aligned_cols=21  Identities=14%  Similarity=0.314  Sum_probs=18.8

Q ss_pred             EEEECCCCCcHHHHHHHHHHH
Q psy200          222 MYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       222 ill~GppGtGKTtla~~l~~~  242 (490)
                      |+|.|.+|+|||+|++.+...
T Consensus         3 v~vvG~~~vGKTsLi~r~~~~   23 (164)
T d1yzqa1           3 LVFLGEQSVGKTSLITRFMYD   23 (164)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            678899999999999998753

>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=93.23  E-value=0.023  Score=47.87  Aligned_cols=21  Identities=33%  Similarity=0.604  Sum_probs=18.9

Q ss_pred             EEEECCCCCcHHHHHHHHHHH
Q psy200          222 MYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       222 ill~GppGtGKTtla~~l~~~  242 (490)
                      |+|.|.+|+|||+|++.+.+.
T Consensus         5 v~vvG~~~vGKSSLi~~l~~~   25 (184)
T d1vg8a_           5 VIILGDSGVGKTSLMNQYVNK   25 (184)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            789999999999999988763

>d2b8ta1 c.37.1.24 (A:11-149) Thymidine kinase, TK1, N-terminal domain {Ureaplasma urealyticum [TaxId: 2130]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Type II thymidine kinase
domain: Thymidine kinase, TK1, N-terminal domain
species: Ureaplasma urealyticum [TaxId: 2130]

Probab=93.22  E-value=0.011  Score=47.67  Aligned_cols=34  Identities=29%  Similarity=0.373  Sum_probs=21.2

Q ss_pred             eEEEECCCCCcHHH-HHHHHHHHhhhcCCceEEEEec
Q psy200          221 SMYISGPPGTGKSA-SLNLLVSRAEIKDAFKTIYINC  256 (490)
Q Consensus       221 ~ill~GppGtGKTt-la~~l~~~l~~~~~~~~~~v~~  256 (490)
                      .-+|+||-.+|||+ |++.+ +.+.. .+.+++.++.
T Consensus         4 L~~i~GpMfsGKTteLi~~~-~~~~~-~~~kv~~ikp   38 (139)
T d2b8ta1           4 IEFITGPMFAGKTAELIRRL-HRLEY-ADVKYLVFKP   38 (139)
T ss_dssp             EEEEECSTTSCHHHHHHHHH-HHHHH-TTCCEEEEEE
T ss_pred             EEEEEccccCHHHHHHHHHH-HHHHH-CCCcEEEEEE
Confidence            45789999999999 55554 44432 2234444443

>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=93.21  E-value=0.021  Score=47.25  Aligned_cols=23  Identities=26%  Similarity=0.208  Sum_probs=19.8

Q ss_pred             CeEEEECCCCCcHHHHHHHHHHH
Q psy200          220 GSMYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       220 ~~ill~GppGtGKTtla~~l~~~  242 (490)
                      .-|+|.|.+|+|||+|++.+...
T Consensus         5 ~Kv~liG~~~vGKTsLl~~~~~~   27 (167)
T d1xtqa1           5 RKIAILGYRSVGKSSLTIQFVEG   27 (167)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHS
T ss_pred             eEEEEECCCCcCHHHHHHHHHhC
Confidence            35788999999999999998764

>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=93.13  E-value=0.024  Score=46.87  Aligned_cols=22  Identities=32%  Similarity=0.404  Sum_probs=19.4

Q ss_pred             eEEEECCCCCcHHHHHHHHHHH
Q psy200          221 SMYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~  242 (490)
                      -|+|.|.+|+|||+|++.+...
T Consensus         5 KivvvG~~~vGKTsli~r~~~~   26 (167)
T d1c1ya_           5 KLVVLGSGGVGKSALTVQFVQG   26 (167)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            3789999999999999998764

>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=93.02  E-value=0.02  Score=48.02  Aligned_cols=22  Identities=23%  Similarity=0.436  Sum_probs=19.5

Q ss_pred             eEEEECCCCCcHHHHHHHHHHH
Q psy200          221 SMYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~  242 (490)
                      .|+|+|.||+|||||++++..+
T Consensus         2 ~I~lvG~~nvGKSsLin~l~~~   23 (184)
T d2cxxa1           2 TIIFAGRSNVGKSTLIYRLTGK   23 (184)
T ss_dssp             EEEEEEBTTSSHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            4789999999999999999753

>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=92.99  E-value=0.025  Score=47.15  Aligned_cols=25  Identities=32%  Similarity=0.446  Sum_probs=21.9

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHH
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~  242 (490)
                      .+..++|.|++|+|||+++-.+.+.
T Consensus        14 ~g~gvli~G~sg~GKS~la~~l~~~   38 (169)
T d1ko7a2          14 YGVGVLITGDSGIGKSETALELIKR   38 (169)
T ss_dssp             TTEEEEEEESTTSSHHHHHHHHHHT
T ss_pred             CCEEEEEEeCCCCCHHHHHHHHHHc
Confidence            4678999999999999999887765

>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=92.98  E-value=0.02  Score=48.05  Aligned_cols=25  Identities=24%  Similarity=0.373  Sum_probs=21.7

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHH
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~  242 (490)
                      .+..++|.|++|+|||+++-.+...
T Consensus        14 ~g~gvli~G~sG~GKS~lal~l~~~   38 (177)
T d1knxa2          14 FGVGVLLTGRSGIGKSECALDLINK   38 (177)
T ss_dssp             TTEEEEEEESSSSSHHHHHHHHHTT
T ss_pred             CCEEEEEEcCCCCCHHHHHHHHHHc
Confidence            4678999999999999999888653

>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=92.98  E-value=0.026  Score=46.80  Aligned_cols=22  Identities=23%  Similarity=0.385  Sum_probs=19.3

Q ss_pred             eEEEECCCCCcHHHHHHHHHHH
Q psy200          221 SMYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~  242 (490)
                      -++|.|++|+|||++++.+...
T Consensus         8 Ki~vvG~~~vGKTsli~~~~~~   29 (170)
T d2g6ba1           8 KVMLVGDSGVGKTCLLVRFKDG   29 (170)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3789999999999999988764

>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=92.95  E-value=0.027  Score=46.72  Aligned_cols=22  Identities=27%  Similarity=0.383  Sum_probs=19.2

Q ss_pred             eEEEECCCCCcHHHHHHHHHHH
Q psy200          221 SMYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~  242 (490)
                      -++|.|.+|+|||+|++.+...
T Consensus         5 Ki~vvG~~~vGKTsLi~~~~~~   26 (170)
T d1ek0a_           5 KLVLLGEAAVGKSSIVLRFVSN   26 (170)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            4778999999999999988764

>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=92.93  E-value=0.027  Score=46.88  Aligned_cols=21  Identities=33%  Similarity=0.526  Sum_probs=18.9

Q ss_pred             EEEECCCCCcHHHHHHHHHHH
Q psy200          222 MYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       222 ill~GppGtGKTtla~~l~~~  242 (490)
                      |+|.|.+|+|||+|++.+.+.
T Consensus         9 I~vvG~~~vGKSSli~~~~~~   29 (174)
T d1wmsa_           9 VILLGDGGVGKSSLMNRYVTN   29 (174)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            789999999999999888764

>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=92.90  E-value=0.029  Score=49.72  Aligned_cols=28  Identities=18%  Similarity=0.353  Sum_probs=24.0

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      ..+..+.|.||.|+|||||++.++..+.
T Consensus        30 ~~Gei~~liGpnGaGKSTl~~~i~Gl~~   57 (240)
T d1ji0a_          30 PRGQIVTLIGANGAGKTTTLSAIAGLVR   57 (240)
T ss_dssp             ETTCEEEEECSTTSSHHHHHHHHTTSSC
T ss_pred             CCCCEEEEECCCCCcHHHHHHHHhCCCC
Confidence            3567889999999999999999987653

>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=92.89  E-value=0.027  Score=47.08  Aligned_cols=22  Identities=32%  Similarity=0.454  Sum_probs=19.4

Q ss_pred             eEEEECCCCCcHHHHHHHHHHH
Q psy200          221 SMYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~  242 (490)
                      -++|.|.+|+|||+|++.+...
T Consensus         9 Ki~vvG~~~vGKTsli~~l~~~   30 (177)
T d1x3sa1           9 KILIIGESGVGKSSLLLRFTDD   30 (177)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3789999999999999998763

>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=92.87  E-value=0.027  Score=47.34  Aligned_cols=22  Identities=18%  Similarity=0.238  Sum_probs=19.6

Q ss_pred             eEEEECCCCCcHHHHHHHHHHH
Q psy200          221 SMYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~  242 (490)
                      -++|.|.+|+|||+|++.+...
T Consensus         7 KivviG~~~vGKTsli~~~~~~   28 (183)
T d1mh1a_           7 KCVVVGDGAVGKTCLLISYTTN   28 (183)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            4789999999999999998764

>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=92.85  E-value=0.025  Score=47.26  Aligned_cols=22  Identities=23%  Similarity=0.268  Sum_probs=19.2

Q ss_pred             eEEEECCCCCcHHHHHHHHHHH
Q psy200          221 SMYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~  242 (490)
                      -|+|.|.+|+|||+|+..+...
T Consensus         4 KivvvG~~~vGKTsLi~~~~~~   25 (177)
T d1kmqa_           4 KLVIVGDGACGKTCLLIVNSKD   25 (177)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            4778899999999999988765

>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=92.83  E-value=0.025  Score=47.05  Aligned_cols=21  Identities=33%  Similarity=0.635  Sum_probs=18.8

Q ss_pred             EEEECCCCCcHHHHHHHHHHH
Q psy200          222 MYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       222 ill~GppGtGKTtla~~l~~~  242 (490)
                      |+|.|.+|+|||+|++.+...
T Consensus         8 I~lvG~~~vGKTsll~~~~~~   28 (174)
T d2bmea1           8 FLVIGNAGTGKSCLLHQFIEK   28 (174)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            789999999999999988753

>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=92.83  E-value=0.027  Score=46.65  Aligned_cols=21  Identities=33%  Similarity=0.551  Sum_probs=18.4

Q ss_pred             EEEECCCCCcHHHHHHHHHHH
Q psy200          222 MYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       222 ill~GppGtGKTtla~~l~~~  242 (490)
                      ++|.|.+|+|||+|++.+...
T Consensus         4 i~lvG~~~vGKTsLi~~~~~~   24 (168)
T d2gjsa1           4 VLLLGAPGVGKSALARIFGGV   24 (168)
T ss_dssp             EEEECCTTSSHHHHHHHHHTC
T ss_pred             EEEECCCCcCHHHHHHHHhCC
Confidence            678999999999999988653

>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=92.81  E-value=0.029  Score=46.53  Aligned_cols=22  Identities=27%  Similarity=0.339  Sum_probs=19.3

Q ss_pred             eEEEECCCCCcHHHHHHHHHHH
Q psy200          221 SMYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~  242 (490)
                      -|+|.|.+|+|||+|++.+...
T Consensus         6 KivlvG~~~vGKTsli~~~~~~   27 (168)
T d1u8za_           6 KVIMVGSGGVGKSALTLQFMYD   27 (168)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            4789999999999999998753

>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=92.75  E-value=0.013  Score=51.59  Aligned_cols=26  Identities=31%  Similarity=0.371  Sum_probs=23.2

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      .+.|.|.|+-|+||||+++.+++.+.
T Consensus         2 ~k~I~ieG~dGsGKST~~~~L~~~l~   27 (241)
T d1p5zb_           2 IKKISIEGNIAAGKSTFVNILKQLCE   27 (241)
T ss_dssp             CEEEEEECSTTSSHHHHHTTTGGGCT
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHHh
Confidence            46789999999999999999998874

>d1wrba1 c.37.1.19 (A:164-401) putative ATP-dependent RNA helicase VlgB {Flatworm (Dugesia japonica) [TaxId: 6161]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase VlgB
species: Flatworm (Dugesia japonica) [TaxId: 6161]

Probab=92.67  E-value=0.32  Score=42.48  Aligned_cols=42  Identities=14%  Similarity=0.161  Sum_probs=25.5

Q ss_pred             CCeEEEEEecCccccccC-HHHHHHhHhCCC---CCCCcEEEEEec
Q psy200          297 HKSILLILDEIDALESRK-QTILYTIFEWPS---IPGSKLVLVGVA  338 (490)
Q Consensus       297 ~~~~vI~IDEid~l~~~~-~~~L~~l~~~~~---~~~~~vilI~~t  338 (490)
                      ..-..++|||+|.+.... .+.+..+++...   ....+++++++|
T Consensus       171 ~~v~~lViDEaD~ll~~~f~~~i~~Il~~~~~~~~~~~Q~il~SAT  216 (238)
T d1wrba1         171 EFCKYIVLDEADRMLDMGFEPQIRKIIEESNMPSGINRQTLMFSAT  216 (238)
T ss_dssp             TTCCEEEEETHHHHHHTTCHHHHHHHHHSSCCCCGGGCEEEEEESS
T ss_pred             cccceeeeehhhhhhhhccHHHHHHHHHHhcCCCCCCCEEEEEeee
Confidence            345689999999997653 344555554322   123456666665

>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=92.62  E-value=0.047  Score=49.56  Aligned_cols=39  Identities=26%  Similarity=0.328  Sum_probs=31.1

Q ss_pred             CeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCC
Q psy200          220 GSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSV  259 (490)
Q Consensus       220 ~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~  259 (490)
                      +.|.|+|-.|+||||++-.++..+.. .+.+++-++|-..
T Consensus         3 r~IaisgKGGVGKTT~a~NLA~~LA~-~G~rVLlID~DpQ   41 (289)
T d2afhe1           3 RQCAIYGKGGIGKSTTTQNLVAALAE-MGKKVMIVGCDPK   41 (289)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHHHHH-TTCCEEEEEECSS
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHHHH-CCCCEEEEecCCC
Confidence            45678999999999999999988863 3567888887543

>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=92.57  E-value=0.028  Score=47.79  Aligned_cols=21  Identities=29%  Similarity=0.428  Sum_probs=18.9

Q ss_pred             EEEECCCCCcHHHHHHHHHHH
Q psy200          222 MYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       222 ill~GppGtGKTtla~~l~~~  242 (490)
                      |+|.|++|+|||+|++.+...
T Consensus         9 ivvvG~~~vGKTsli~~l~~~   29 (194)
T d2bcgy1           9 LLLIGNSGVGKSCLLLRFSDD   29 (194)
T ss_dssp             EEEEESTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCcCHHHHHHHHhhC
Confidence            778999999999999998764

>d1xx6a1 c.37.1.24 (A:2-142) Thymidine kinase, TK1, N-terminal domain {Clostridium acetobutylicum [TaxId: 1488]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Type II thymidine kinase
domain: Thymidine kinase, TK1, N-terminal domain
species: Clostridium acetobutylicum [TaxId: 1488]

Probab=92.56  E-value=0.025  Score=45.66  Aligned_cols=37  Identities=30%  Similarity=0.240  Sum_probs=25.6

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEe
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYIN  255 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~  255 (490)
                      .+..=+|+||-.+||||-+-..++.+... +..++.++
T Consensus         6 ~G~l~lI~GpMfSGKTteLi~~~~~~~~~-g~~vl~i~   42 (141)
T d1xx6a1           6 HGWVEVIVGPMYSGKSEELIRRIRRAKIA-KQKIQVFK   42 (141)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHHHHHHT-TCCEEEEE
T ss_pred             ceeEEEEEeccccHHHHHHHHHHHHhhhc-CCcEEEEE
Confidence            45566789999999999887777766432 23444444

>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=92.52  E-value=0.034  Score=46.13  Aligned_cols=22  Identities=27%  Similarity=0.401  Sum_probs=19.3

Q ss_pred             eEEEECCCCCcHHHHHHHHHHH
Q psy200          221 SMYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~  242 (490)
                      -++|.|.+|+|||+|++.+.+.
T Consensus         6 Ki~lvG~~~vGKTsll~~~~~~   27 (169)
T d1x1ra1           6 KLVVVGDGGVGKSALTIQFFQK   27 (169)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            4678899999999999998864

>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=92.51  E-value=0.028  Score=47.75  Aligned_cols=22  Identities=27%  Similarity=0.487  Sum_probs=19.8

Q ss_pred             CeEEEECCCCCcHHHHHHHHHH
Q psy200          220 GSMYISGPPGTGKSASLNLLVS  241 (490)
Q Consensus       220 ~~ill~GppGtGKTtla~~l~~  241 (490)
                      ..|.|.|.+|+|||||++++..
T Consensus        24 ~~I~lvG~~n~GKSTLin~L~g   45 (195)
T d1svia_          24 PEIALAGRSNVGKSSFINSLIN   45 (195)
T ss_dssp             CEEEEEEBTTSSHHHHHHHHHT
T ss_pred             CEEEEECCCCCCHHHHHHHhcC
Confidence            4689999999999999999974

>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=92.49  E-value=0.025  Score=51.32  Aligned_cols=41  Identities=15%  Similarity=0.232  Sum_probs=26.4

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccCC
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSV  259 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~~  259 (490)
                      +...|.|.|++|+||||+++++.+.+... ++..+.+..-.+
T Consensus         3 k~pIIgIaG~SGSGKTTva~~l~~i~~~~-~v~~~iI~~Dsf   43 (288)
T d1a7ja_           3 KHPIISVTGSSGAGTSTVKHTFDQIFRRE-GVKAVSIEGDAF   43 (288)
T ss_dssp             TSCEEEEESCC---CCTHHHHHHHHHHHH-TCCEEEEEGGGG
T ss_pred             CCCEEEEECCCCCcHHHHHHHHHHHHhhc-CCCeEEEeCCCC
Confidence            34578899999999999999998887532 344444544433

>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=92.49  E-value=0.03  Score=47.19  Aligned_cols=22  Identities=18%  Similarity=0.231  Sum_probs=19.2

Q ss_pred             eEEEECCCCCcHHHHHHHHHHH
Q psy200          221 SMYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~  242 (490)
                      -++|.|.+|+|||+|++.+.+.
T Consensus        11 Ki~lvG~~~vGKTsLi~r~~~~   32 (185)
T d2atxa1          11 KCVVVGDGAVGKTCLLMSYAND   32 (185)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhhC
Confidence            3779999999999999998764

>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=92.47  E-value=0.032  Score=46.41  Aligned_cols=21  Identities=29%  Similarity=0.512  Sum_probs=18.5

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q psy200          221 SMYISGPPGTGKSASLNLLVS  241 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~  241 (490)
                      -|+|.|.+|+|||+|++.+..
T Consensus         5 Kv~lvG~~~vGKTsLi~~~~~   25 (172)
T d2g3ya1           5 RVVLIGEQGVGKSTLANIFAG   25 (172)
T ss_dssp             EEEEECCTTSSHHHHHHHHHC
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            378999999999999998864

>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=92.45  E-value=0.033  Score=49.23  Aligned_cols=28  Identities=25%  Similarity=0.506  Sum_probs=23.9

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      ..+..+.|.||.|+|||||++.++..+.
T Consensus        26 ~~Gei~glvG~nGaGKSTLl~~l~G~~~   53 (238)
T d1vpla_          26 EEGEIFGLIGPNGAGKTTTLRIISTLIK   53 (238)
T ss_dssp             CTTCEEEEECCTTSSHHHHHHHHTTSSC
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHhcCCC
Confidence            3566888999999999999999987764

>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=92.43  E-value=0.022  Score=50.88  Aligned_cols=28  Identities=29%  Similarity=0.400  Sum_probs=23.8

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      ..+..+.|+|+.|+|||||++.++..+.
T Consensus        42 ~~Ge~vaivG~sGsGKSTLl~ll~gl~~   69 (255)
T d2hyda1          42 EKGETVAFVGMSGGGKSTLINLIPRFYD   69 (255)
T ss_dssp             CTTCEEEEECSTTSSHHHHHTTTTTSSC
T ss_pred             cCCCEEEEECCCCCcHHHHHHHHHhcCC
Confidence            4677899999999999999998876553

>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=92.39  E-value=0.028  Score=46.80  Aligned_cols=24  Identities=42%  Similarity=0.623  Sum_probs=20.7

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHH
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~  242 (490)
                      .+.|.|.|.+|+|||||++++.+.
T Consensus         5 ~~~I~iiG~~nvGKSSLin~L~~~   28 (179)
T d1egaa1           5 CGFIAIVGRPNVGKSTLLNKLLGQ   28 (179)
T ss_dssp             EEEEEEECSSSSSHHHHHHHHHTC
T ss_pred             ccEEEEECCCCCCHHHHHHHHhCC
Confidence            356889999999999999999753

>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=92.18  E-value=0.034  Score=46.61  Aligned_cols=21  Identities=24%  Similarity=0.458  Sum_probs=18.9

Q ss_pred             EEEECCCCCcHHHHHHHHHHH
Q psy200          222 MYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       222 ill~GppGtGKTtla~~l~~~  242 (490)
                      ++|.|.+|+|||+|++.+.+.
T Consensus         5 ivliG~~~vGKTsli~r~~~~   25 (179)
T d1m7ba_           5 IVVVGDSQCGKTALLHVFAKD   25 (179)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            678999999999999988774

>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=92.17  E-value=0.022  Score=47.45  Aligned_cols=21  Identities=24%  Similarity=0.431  Sum_probs=8.2

Q ss_pred             EEEECCCCCcHHHHHHHHHHH
Q psy200          222 MYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       222 ill~GppGtGKTtla~~l~~~  242 (490)
                      |+|.|.+|+|||+|++.+...
T Consensus         9 i~vvG~~~vGKTsLi~~l~~~   29 (173)
T d2fu5c1           9 LLLIGDSGVGKTCVLFRFSED   29 (173)
T ss_dssp             EEEECCCCC------------
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            778899999999999988753

>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=92.14  E-value=0.039  Score=48.53  Aligned_cols=25  Identities=20%  Similarity=0.460  Sum_probs=21.6

Q ss_pred             CeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          220 GSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       220 ~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      ..|.|+|..|+||||+|+.+.+.++
T Consensus         2 ~iIgiTG~igSGKsTva~~l~e~~g   26 (241)
T d1deka_           2 KLIFLSGVKRSGKDTTADFIMSNYS   26 (241)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHSC
T ss_pred             EEEEEECCCCCCHHHHHHHHHHhCC
Confidence            4688999999999999999987653

>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=91.95  E-value=0.038  Score=46.82  Aligned_cols=22  Identities=18%  Similarity=0.238  Sum_probs=19.1

Q ss_pred             eEEEECCCCCcHHHHHHHHHHH
Q psy200          221 SMYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~  242 (490)
                      -|+|.|.+|+|||+|++.+...
T Consensus         5 KvvllG~~~vGKTSli~r~~~~   26 (191)
T d2ngra_           5 KCVVVGDGAVGKTCLLISYTTN   26 (191)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3778899999999999988764

>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=91.85  E-value=0.036  Score=48.80  Aligned_cols=25  Identities=28%  Similarity=0.466  Sum_probs=22.1

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHH
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~  242 (490)
                      .+..+.|.||.|+|||||++.++..
T Consensus        24 ~Gei~~iiG~nGaGKSTLl~~l~Gl   48 (231)
T d1l7vc_          24 AGEILHLVGPNGAGKSTLLARMAGM   48 (231)
T ss_dssp             TTCEEECBCCTTSSHHHHHHHHHTS
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhCC
Confidence            5678889999999999999999763

>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=91.83  E-value=0.046  Score=47.08  Aligned_cols=23  Identities=26%  Similarity=0.367  Sum_probs=19.1

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHhh
Q psy200          221 SMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      .|.|+|..|+||||+++.+. +++
T Consensus         5 iIgitG~igSGKStv~~~l~-~~G   27 (208)
T d1vhta_           5 IVALTGGIGSGKSTVANAFA-DLG   27 (208)
T ss_dssp             EEEEECCTTSCHHHHHHHHH-HTT
T ss_pred             EEEEECCCcCCHHHHHHHHH-HCC
Confidence            57799999999999999774 543

>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=91.77  E-value=0.047  Score=48.69  Aligned_cols=27  Identities=30%  Similarity=0.513  Sum_probs=23.5

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      .+..+.|.||.|+|||||++.++..+.
T Consensus        29 ~Gei~~liG~nGaGKSTLl~~i~Gl~~   55 (254)
T d1g6ha_          29 KGDVTLIIGPNGSGKSTLINVITGFLK   55 (254)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTTSSC
T ss_pred             CCCEEEEECCCCCcHHHHHHHHHCCCc
Confidence            567888999999999999999987653

>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=91.59  E-value=0.023  Score=47.32  Aligned_cols=22  Identities=23%  Similarity=0.409  Sum_probs=17.7

Q ss_pred             eEEEECCCCCcHHHHHHHHHHH
Q psy200          221 SMYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~  242 (490)
                      -++|.|.+|+|||+|++.+.+.
T Consensus         5 Ki~vvG~~~vGKTsli~~~~~~   26 (170)
T d1i2ma_           5 KLVLVGDGGTGKTTFVKRHLTG   26 (170)
T ss_dssp             EEEEEECTTSSHHHHHHTTC--
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3778899999999999987654

>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=91.44  E-value=0.036  Score=46.55  Aligned_cols=21  Identities=33%  Similarity=0.491  Sum_probs=18.3

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q psy200          221 SMYISGPPGTGKSASLNLLVS  241 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~  241 (490)
                      -|.|.|+||+|||||++++..
T Consensus         3 ~VaiiG~~nvGKSSLin~L~~   23 (185)
T d1lnza2           3 DVGLVGFPSVGKSTLLSVVSS   23 (185)
T ss_dssp             CEEEESSTTSSHHHHHHHSEE
T ss_pred             eEEEECCCCCCHHHHHHHHhC
Confidence            478999999999999998854

>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=91.31  E-value=0.05  Score=46.74  Aligned_cols=20  Identities=30%  Similarity=0.489  Sum_probs=17.4

Q ss_pred             eEEEECCCCCcHHHHHHHHH
Q psy200          221 SMYISGPPGTGKSASLNLLV  240 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~  240 (490)
                      .|.|+|..|+||||+++.+.
T Consensus         4 iIgITG~igSGKStv~~~l~   23 (205)
T d1jjva_           4 IVGLTGGIGSGKTTIANLFT   23 (205)
T ss_dssp             EEEEECSTTSCHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHH
Confidence            46699999999999998774

>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=91.28  E-value=0.079  Score=45.36  Aligned_cols=35  Identities=17%  Similarity=0.332  Sum_probs=28.4

Q ss_pred             CeEEEECCC-CCcHHHHHHHHHHHhhhcCCceEEEEe
Q psy200          220 GSMYISGPP-GTGKSASLNLLVSRAEIKDAFKTIYIN  255 (490)
Q Consensus       220 ~~ill~Gpp-GtGKTtla~~l~~~l~~~~~~~~~~v~  255 (490)
                      +.++|+|-. |+||||++-.++..+... +++++.++
T Consensus         2 ~~~~i~gt~~GVGKTtvs~~La~aLa~~-G~rVl~id   37 (224)
T d1byia_           2 KRYFVTGTDTEVGKTVASCALLQAAKAA-GYRTAGYK   37 (224)
T ss_dssp             EEEEEEESSTTSCHHHHHHHHHHHHHHT-TCCEEEEC
T ss_pred             ceEEEEECCCCccHHHHHHHHHHHHHHC-CCeEEEEC
Confidence            468999996 999999999999998633 45677765

>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=91.26  E-value=0.04  Score=48.10  Aligned_cols=24  Identities=21%  Similarity=0.379  Sum_probs=21.2

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHH
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~  242 (490)
                      -...+|+|.-|+||||+++.+++.
T Consensus         3 iPv~iitGFLGaGKTTll~~lL~~   26 (222)
T d1nija1           3 IAVTLLTGFLGAGKTTLLRHILNE   26 (222)
T ss_dssp             EEEEEEEESSSSSCHHHHHHHHHS
T ss_pred             CCEEEEeeCCCCCHHHHHHHHHhc
Confidence            356889999999999999999885

>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=91.18  E-value=0.05  Score=46.06  Aligned_cols=19  Identities=26%  Similarity=0.441  Sum_probs=17.5

Q ss_pred             eEEEECCCCCcHHHHHHHH
Q psy200          221 SMYISGPPGTGKSASLNLL  239 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l  239 (490)
                      -|+|.|.+|+|||+|++.+
T Consensus         4 KivllG~~~vGKTsll~r~   22 (200)
T d1zcba2           4 KILLLGAGESGKSTFLKQM   22 (200)
T ss_dssp             EEEEECSTTSSHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHH
Confidence            4789999999999999998

>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=91.07  E-value=0.055  Score=45.27  Aligned_cols=23  Identities=30%  Similarity=0.508  Sum_probs=19.8

Q ss_pred             CeEEEECCCCCcHHHHHHHHHHH
Q psy200          220 GSMYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       220 ~~ill~GppGtGKTtla~~l~~~  242 (490)
                      -.|.|.|.+|+|||||++++...
T Consensus         9 ~kV~iiG~~~~GKSTLin~l~~~   31 (186)
T d1mkya2           9 IKVAIVGRPNVGKSTLFNAILNK   31 (186)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHTS
T ss_pred             CEEEEECCCCCCHHHHHHHHHCC
Confidence            35788999999999999999753

>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=90.97  E-value=0.065  Score=49.71  Aligned_cols=26  Identities=31%  Similarity=0.442  Sum_probs=22.7

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHhhhc
Q psy200          221 SMYISGPPGTGKSASLNLLVSRAEIK  246 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~l~~~  246 (490)
                      .|+|-|+-|+||||+++.+++.+...
T Consensus         8 rI~iEG~iGsGKSTl~~~L~~~l~~~   33 (333)
T d1p6xa_           8 RIYLDGVYGIGKSTTGRVMASAASGG   33 (333)
T ss_dssp             EEEEECSTTSSHHHHHHHHHSGGGCS
T ss_pred             EEEEECCccCCHHHHHHHHHHHhccC
Confidence            57799999999999999999988633

>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=90.83  E-value=0.042  Score=45.89  Aligned_cols=21  Identities=29%  Similarity=0.447  Sum_probs=18.6

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q psy200          221 SMYISGPPGTGKSASLNLLVS  241 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~  241 (490)
                      .|.|.|.+|+|||||++++..
T Consensus         3 ~VaivG~~nvGKSTLin~L~~   23 (180)
T d1udxa2           3 DVGLVGYPNAGKSSLLAAMTR   23 (180)
T ss_dssp             SEEEECCGGGCHHHHHHHHCS
T ss_pred             EEEEECCCCCCHHHHHHHHhC
Confidence            378899999999999999864

>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=90.82  E-value=0.57  Score=41.60  Aligned_cols=24  Identities=21%  Similarity=0.432  Sum_probs=21.0

Q ss_pred             CeEEEECCCCCcHHHHHHHHHHHh
Q psy200          220 GSMYISGPPGTGKSASLNLLVSRA  243 (490)
Q Consensus       220 ~~ill~GppGtGKTtla~~l~~~l  243 (490)
                      +++.|.|..|+|||||+.+++...
T Consensus         3 RNv~iiGh~~~GKTtL~e~ll~~~   26 (267)
T d2dy1a2           3 RTVALVGHAGSGKTTLTEALLYKT   26 (267)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHHT
T ss_pred             eEEEEEcCCCCcHHHHHHHHHHHc
Confidence            578899999999999999997654

>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=90.79  E-value=0.024  Score=46.27  Aligned_cols=22  Identities=45%  Similarity=0.655  Sum_probs=19.6

Q ss_pred             eEEEECCCCCcHHHHHHHHHHH
Q psy200          221 SMYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~  242 (490)
                      .|.|.|.+|+|||||++++..+
T Consensus         2 kI~liG~~n~GKSSLin~l~g~   23 (160)
T d1xzpa2           2 RMVIVGKPNVGKSTLLNRLLNE   23 (160)
T ss_dssp             EEEEECCHHHHTCHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            3789999999999999999765

>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=90.58  E-value=0.072  Score=44.41  Aligned_cols=22  Identities=18%  Similarity=0.356  Sum_probs=19.5

Q ss_pred             eEEEECCCCCcHHHHHHHHHHH
Q psy200          221 SMYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~  242 (490)
                      .|+|.|.+|+|||+|++.+...
T Consensus         7 ki~vlG~~~vGKTsLi~~~~~~   28 (175)
T d2bmja1           7 RLGVLGDARSGKSSLIHRFLTG   28 (175)
T ss_dssp             EEEEECCTTTTHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            5789999999999999988764

>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=90.46  E-value=0.043  Score=45.70  Aligned_cols=24  Identities=33%  Similarity=0.457  Sum_probs=20.4

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHH
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVS  241 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~  241 (490)
                      ....|.|.|.+++|||||++++..
T Consensus        15 ~~~~I~lvG~~NvGKSSL~n~L~~   38 (188)
T d1puia_          15 TGIEVAFAGRSNAGKSSALNTLTN   38 (188)
T ss_dssp             CSEEEEEEECTTSSHHHHHTTTCC
T ss_pred             cCCEEEEECCCCCCHHHHHHHHhC
Confidence            455789999999999999998854

>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=90.18  E-value=0.034  Score=48.67  Aligned_cols=25  Identities=28%  Similarity=0.466  Sum_probs=20.5

Q ss_pred             CCCeEEEECCCCCcHHHHHHHHHHH
Q psy200          218 TSGSMYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       218 ~~~~ill~GppGtGKTtla~~l~~~  242 (490)
                      .++..+|.|++|+|||||++++...
T Consensus        96 ~~~~~vl~G~SGVGKSSLiN~L~~~  120 (231)
T d1t9ha2          96 QDKTTVFAGQSGVGKSSLLNAISPE  120 (231)
T ss_dssp             TTSEEEEEESHHHHHHHHHHHHCC-
T ss_pred             ccceEEEECCCCccHHHHHHhhccH
Confidence            3567788999999999999998644

>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=90.12  E-value=0.55  Score=41.91  Aligned_cols=26  Identities=12%  Similarity=0.135  Sum_probs=23.0

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      -+++.|.|..|+|||||+.+++...+
T Consensus         6 iRni~i~gh~~~GKTtL~e~ll~~~g   31 (276)
T d2bv3a2           6 LRNIGIAAHIDAGKTTTTERILYYTG   31 (276)
T ss_dssp             EEEEEEEECTTSCHHHHHHHHHHHHT
T ss_pred             ceEEEEEeCCCCCHHHHHHHHHHhcC
Confidence            46899999999999999999987654

>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=89.97  E-value=0.16  Score=42.24  Aligned_cols=22  Identities=18%  Similarity=0.279  Sum_probs=19.0

Q ss_pred             eEEEECCCCCcHHHHHHHHHHH
Q psy200          221 SMYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~  242 (490)
                      -++|.|..|+|||++++.+...
T Consensus         4 KivllG~~~vGKTsl~~r~~~~   25 (195)
T d1svsa1           4 KLLLLGAGESGKSTIVKQMKII   25 (195)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhhC
Confidence            4788999999999999988654

>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=89.89  E-value=0.077  Score=44.64  Aligned_cols=22  Identities=18%  Similarity=0.271  Sum_probs=19.2

Q ss_pred             eEEEECCCCCcHHHHHHHHHHH
Q psy200          221 SMYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~  242 (490)
                      -|+|.|..|+|||++++.+...
T Consensus         4 Kiv~lG~~~vGKTsll~r~~~~   25 (200)
T d2bcjq2           4 KLLLLGTGESGKSTFIKQMRII   25 (200)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            4788999999999999998654

>d1e9ra_ c.37.1.11 (A:) Bacterial conjugative coupling protein TrwB {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Bacterial conjugative coupling protein TrwB
species: Escherichia coli [TaxId: 562]

Probab=89.28  E-value=0.13  Score=49.25  Aligned_cols=25  Identities=32%  Similarity=0.482  Sum_probs=21.8

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHh
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRA  243 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l  243 (490)
                      .++++|.|++|+|||+++..++.++
T Consensus        50 ~~H~~I~G~tGsGKT~~l~~li~~~   74 (433)
T d1e9ra_          50 PRHLLVNGATGTGKSVLLRELAYTG   74 (433)
T ss_dssp             GGCEEEEECTTSSHHHHHHHHHHHH
T ss_pred             cceEEEEeCCCCcHHHHHHHHHHHH
Confidence            4689999999999999998777665

>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=89.23  E-value=0.089  Score=45.64  Aligned_cols=23  Identities=17%  Similarity=0.241  Sum_probs=19.4

Q ss_pred             CeEEEECCCCCcHHHHHHHHHHH
Q psy200          220 GSMYISGPPGTGKSASLNLLVSR  242 (490)
Q Consensus       220 ~~ill~GppGtGKTtla~~l~~~  242 (490)
                      .-|+|.|..|+|||++++.+...
T Consensus         7 ~KilllG~~~vGKTsll~~~~~~   29 (221)
T d1azta2           7 HRLLLLGAGESGKSTIVKQMRIL   29 (221)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHhcC
Confidence            35889999999999999988543

>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=89.20  E-value=0.13  Score=48.94  Aligned_cols=38  Identities=24%  Similarity=0.306  Sum_probs=26.7

Q ss_pred             HHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHHHHHH
Q psy200          202 QLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVS  241 (490)
Q Consensus       202 ~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~~l~~  241 (490)
                      ....+.+.+...  ...+-.|.|.|.+|+|||||++++..
T Consensus        41 ~~~~i~~~l~~~--~~~~l~Iai~G~~n~GKSSLiNaL~G   78 (400)
T d1tq4a_          41 TNSAISDALKEI--DSSVLNVAVTGETGSGKSSFINTLRG   78 (400)
T ss_dssp             HHHHHHHHHHHH--HHCCEEEEEEECTTSSHHHHHHHHHT
T ss_pred             HHHHHHHHHHhc--ccCCcEEEEECCCCCCHHHHHHHHhC
Confidence            344444444431  12456799999999999999999974

>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=88.92  E-value=0.033  Score=47.02  Aligned_cols=25  Identities=28%  Similarity=0.351  Sum_probs=21.0

Q ss_pred             CeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          220 GSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       220 ~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      +..+|+|+.|+|||+++.+|.-.+.
T Consensus        25 ~~tvi~G~NGsGKStil~Ai~~~L~   49 (222)
T d1qhla_          25 LVTTLSGGNGAGKSTTMAAFVTALI   49 (222)
T ss_dssp             HHHHHHSCCSHHHHHHHHHHHHHHS
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHhc
Confidence            3566889999999999999987664

>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=88.06  E-value=0.25  Score=42.60  Aligned_cols=37  Identities=22%  Similarity=0.205  Sum_probs=29.2

Q ss_pred             CeEEEE-CCCCCcHHHHHHHHHHHhhhcCCceEEEEecc
Q psy200          220 GSMYIS-GPPGTGKSASLNLLVSRAEIKDAFKTIYINCN  257 (490)
Q Consensus       220 ~~ill~-GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~  257 (490)
                      +.|.|+ +-.|+||||++-.++..+.. .+.+++.+++-
T Consensus         3 ~vIav~~~kGGvGKTtia~nLA~~la~-~g~~VlliD~D   40 (237)
T d1g3qa_           3 RIISIVSGKGGTGKTTVTANLSVALGD-RGRKVLAVDGD   40 (237)
T ss_dssp             EEEEEECSSTTSSHHHHHHHHHHHHHH-TTCCEEEEECC
T ss_pred             eEEEEECCCCCCcHHHHHHHHHHHHHh-CCCCEEEEeCC
Confidence            455566 77899999999999999874 45678888764

>d1z63a1 c.37.1.19 (A:432-661) Helicase of the SNF2/Rad54 hamily {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Helicase of the SNF2/Rad54 hamily
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=87.95  E-value=2.1  Score=36.49  Aligned_cols=30  Identities=17%  Similarity=0.196  Sum_probs=22.7

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHhhhcCC
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRAEIKDA  248 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l~~~~~  248 (490)
                      ..+.+|-=+.|+|||..+-+++..+.....
T Consensus        31 ~~g~iLaDe~GlGKT~~~i~~~~~~~~~~~   60 (230)
T d1z63a1          31 GFGICLADDMGLGKTLQTIAVFSDAKKENE   60 (230)
T ss_dssp             TCCEEECCCTTSCHHHHHHHHHHHHHHTTC
T ss_pred             CCCEEEEeCCCCChHHHHHHhhhhhhhccc
Confidence            456777779999999999888777654433

>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=87.86  E-value=0.25  Score=42.51  Aligned_cols=36  Identities=19%  Similarity=0.155  Sum_probs=28.4

Q ss_pred             EEEECCCCCcHHHHHHHHHHHhhhcCCceEEEEeccC
Q psy200          222 MYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNS  258 (490)
Q Consensus       222 ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v~~~~  258 (490)
                      .+..|-+|+||||++..++..+.. .+.+++.+++-.
T Consensus         5 av~s~KGGvGKTtia~nlA~~la~-~g~~VlliD~D~   40 (232)
T d1hyqa_           5 TVASGKGGTGKTTITANLGVALAQ-LGHDVTIVDADI   40 (232)
T ss_dssp             EEEESSSCSCHHHHHHHHHHHHHH-TTCCEEEEECCC
T ss_pred             EEECCCCCChHHHHHHHHHHHHHh-CCCCEEEEeCCC
Confidence            345599999999999999999874 356788887653

>d1z3ix2 c.37.1.19 (X:92-389) Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxId: 7955]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Rad54-like, Rad54L
species: Zebra fish (Danio rerio) [TaxId: 7955]

Probab=87.62  E-value=3.7  Score=36.39  Aligned_cols=44  Identities=30%  Similarity=0.329  Sum_probs=26.6

Q ss_pred             hHHHHHHHHHHHHhhhc---cCCCCeEEEECCCCCcHHHHHHHHHHHh
Q psy200          199 REVQLEGIRQFLLGHVN---NETSGSMYISGPPGTGKSASLNLLVSRA  243 (490)
Q Consensus       199 re~~~~~l~~~L~~~~~---~~~~~~ill~GppGtGKTtla~~l~~~l  243 (490)
                      |..+++.|. ||...+.   .....+.+|.=..|+|||..+-+++..+
T Consensus        57 r~hQ~~gv~-~l~~~~~~~~~~~~~g~iLaDemGlGKT~qaia~l~~l  103 (298)
T d1z3ix2          57 RPHQREGVK-FLWDCVTGRRIENSYGCIMADEMGLGKTLQCITLIWTL  103 (298)
T ss_dssp             CHHHHHHHH-HHHHHHTTSSSTTCCEEEECCCTTSCHHHHHHHHHHHH
T ss_pred             cHHHHHHHH-HHHHHHHhhhhccCCceEEEeCCCCCHHHHHHHHHHHH
Confidence            345555543 4433322   2345678888899999998765555444

>d1e69a_ c.37.1.12 (A:) Smc head domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Smc head domain
species: Thermotoga maritima [TaxId: 2336]

Probab=87.29  E-value=0.14  Score=46.46  Aligned_cols=25  Identities=28%  Similarity=0.365  Sum_probs=20.6

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHh
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRA  243 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l  243 (490)
                      .+..+|+|+.|+|||+++.++.-.+
T Consensus        24 ~~lnvlvG~NgsGKS~iL~Ai~~~l   48 (308)
T d1e69a_          24 DRVTAIVGPNGSGKSNIIDAIKWVF   48 (308)
T ss_dssp             SSEEEEECCTTTCSTHHHHHHHHTS
T ss_pred             CCeEEEECCCCCcHHHHHHHHHHHh
Confidence            3467899999999999999995433

>d1bg2a_ c.37.1.9 (A:) Kinesin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=87.25  E-value=0.25  Score=45.37  Aligned_cols=41  Identities=15%  Similarity=0.332  Sum_probs=28.6

Q ss_pred             CChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHHH
Q psy200          197 PGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLN  237 (490)
Q Consensus       197 vgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla~  237 (490)
                      ...++..+.+..-+-..+..+....++-||+.|+|||.++-
T Consensus        54 ~~q~~vf~~~~~~lv~~~l~G~n~~i~aYGqtgSGKTyT~~   94 (323)
T d1bg2a_          54 TSQEQVYNDCAKKIVKDVLEGYNGTIFAYGQTSSGKTHTME   94 (323)
T ss_dssp             CCHHHHHHHHTHHHHHHHHTTCCEEEEEECSTTSSHHHHHT
T ss_pred             CCHHHHHHHHHHHHHHHHHcCCCcceeeecccCCCCceecc
Confidence            44566666654333333345778899999999999999873

>d1lkxa_ c.37.1.9 (A:) Myosin S1, motor domain {Dictyostelium discoideum, class-I myosin MyoE [TaxId: 44689]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Myosin S1, motor domain
species: Dictyostelium discoideum, class-I myosin MyoE [TaxId: 44689]

Probab=87.19  E-value=0.27  Score=50.05  Aligned_cols=30  Identities=20%  Similarity=0.369  Sum_probs=26.8

Q ss_pred             ccCCCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          215 NNETSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       215 ~~~~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      ..+...+|+|.|+.|+|||..++.+.+.+.
T Consensus        82 ~~~~~QsIiisGeSGsGKTe~~k~il~yL~  111 (684)
T d1lkxa_          82 QSQENQCVIISGESGAGKTEASKKIMQFLT  111 (684)
T ss_dssp             HHCCCEEEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             HcCCCeEEEEEcCCCCCHHHHHHHHHHHHH
Confidence            456788999999999999999999999874

>d1d0xa2 c.37.1.9 (A:2-33,A:80-759) Myosin S1, motor domain {Dictyostelium discoideum [TaxId: 44689]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Myosin S1, motor domain
species: Dictyostelium discoideum [TaxId: 44689]

Probab=87.15  E-value=0.27  Score=50.22  Aligned_cols=30  Identities=20%  Similarity=0.452  Sum_probs=26.8

Q ss_pred             ccCCCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          215 NNETSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       215 ~~~~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      ..+...+|+|+|+.|+|||..++.+.+.+.
T Consensus       121 ~~~~nQsIiisGeSGaGKTe~~k~il~yL~  150 (712)
T d1d0xa2         121 DDRQNQSLLITGESGAGKTENTKKVIQYLA  150 (712)
T ss_dssp             HHTCCEEEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             HhCCCceEEEeCCCCCCHHHHHHHHHHHHH
Confidence            457789999999999999999999998874

>d1br2a2 c.37.1.9 (A:80-789) Myosin S1, motor domain {Chicken (Gallus gallus), pectoral muscle [TaxId: 9031]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Myosin S1, motor domain
species: Chicken (Gallus gallus), pectoral muscle [TaxId: 9031]

Probab=86.60  E-value=0.24  Score=50.81  Aligned_cols=30  Identities=17%  Similarity=0.370  Sum_probs=27.0

Q ss_pred             ccCCCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          215 NNETSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       215 ~~~~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      ..+...+|+|.|+.|+|||..++.+.+.+.
T Consensus        87 ~~~~~Q~IiisGeSGaGKTe~~k~il~yL~  116 (710)
T d1br2a2          87 QDREDQSILCTGESGAGKTENTKKVIQYLA  116 (710)
T ss_dssp             HHTCCEEEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             HhCCCcEEEEEeCCCCCHHHHHHHHHHHHH
Confidence            346789999999999999999999999885

>d2mysa2 c.37.1.9 (A:4-33,A:80-843) Myosin S1, motor domain {Chicken (Gallus gallus), pectoral muscle [TaxId: 9031]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Myosin S1, motor domain
species: Chicken (Gallus gallus), pectoral muscle [TaxId: 9031]

Probab=85.87  E-value=0.25  Score=51.26  Aligned_cols=30  Identities=20%  Similarity=0.417  Sum_probs=26.8

Q ss_pred             ccCCCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          215 NNETSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       215 ~~~~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      ..+...+|+|+|+.|+|||..++.+.+.+.
T Consensus       119 ~~~~~QsIiisGeSGaGKTe~~K~il~yL~  148 (794)
T d2mysa2         119 TDRENQSILITGESGAGKTVNTKRVIQYFA  148 (794)
T ss_dssp             HHTCCEEEEEEECTTSCHHHHHHHHHHHHH
T ss_pred             HcCCCcEEEEEcCCCCCHHHHHHHHHHHHH
Confidence            456789999999999999999999998874

>d1w1wa_ c.37.1.12 (A:) Smc head domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Smc head domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=85.54  E-value=0.23  Score=46.99  Aligned_cols=25  Identities=32%  Similarity=0.412  Sum_probs=20.9

Q ss_pred             CCeEEEECCCCCcHHHHHHHHHHHh
Q psy200          219 SGSMYISGPPGTGKSASLNLLVSRA  243 (490)
Q Consensus       219 ~~~ill~GppGtGKTtla~~l~~~l  243 (490)
                      ++.-+|+|+.|+|||+++.++.=.+
T Consensus        25 ~~l~~i~G~NGsGKS~ileAi~~~l   49 (427)
T d1w1wa_          25 SNFTSIIGPNGSGKSNMMDAISFVL   49 (427)
T ss_dssp             CSEEEEECSTTSSHHHHHHHHHHHT
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHh
Confidence            4567899999999999999996443

>d1goja_ c.37.1.9 (A:) Kinesin {Neurospora crassa [TaxId: 5141]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin
species: Neurospora crassa [TaxId: 5141]

Probab=85.53  E-value=0.36  Score=44.93  Aligned_cols=38  Identities=18%  Similarity=0.253  Sum_probs=26.3

Q ss_pred             ChHHHHHHHH-HHHHhhhccCCCCeEEEECCCCCcHHHHH
Q psy200          198 GREVQLEGIR-QFLLGHVNNETSGSMYISGPPGTGKSASL  236 (490)
Q Consensus       198 gre~~~~~l~-~~L~~~~~~~~~~~ill~GppGtGKTtla  236 (490)
                      ..++..+.+. ..+.. +..+....++-||..|+|||.++
T Consensus        59 ~q~~vy~~~~~plv~~-~l~G~n~ti~aYG~tgSGKT~Tm   97 (354)
T d1goja_          59 KQSDIFDFSIKPTVDD-ILNGYNGTVFAYGQTGAGKSYTM   97 (354)
T ss_dssp             CHHHHHHHHTHHHHHH-HTTTCCEEEEEECSTTSSHHHHH
T ss_pred             CHHHHHHHHHHHHHHH-hhccCceeEEecccCCCCcceee
Confidence            4555555543 34433 34567778999999999999875

>d1kk8a2 c.37.1.9 (A:1-28,A:77-837) Myosin S1, motor domain {Bay scallop (Aequipecten irradians) [TaxId: 31199]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Myosin S1, motor domain
species: Bay scallop (Aequipecten irradians) [TaxId: 31199]

Probab=85.20  E-value=0.33  Score=50.28  Aligned_cols=30  Identities=20%  Similarity=0.373  Sum_probs=26.8

Q ss_pred             ccCCCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          215 NNETSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       215 ~~~~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      ..+...+|+|+|+.|+|||..++.+.+.+.
T Consensus       117 ~~~~nQ~IiisGESGaGKTe~~K~il~yL~  146 (789)
T d1kk8a2         117 TDRENQSCLITGESGAGKTENTKKVIMYLA  146 (789)
T ss_dssp             HHTSEEEEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             HhCCCcEEEEEeCCCCCHHHHHHHHHHHHH
Confidence            456789999999999999999999999875

>d1osna_ c.37.1.1 (A:) Thymidine kinase {Varicella-zoster virus [TaxId: 10335]}

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: Varicella-zoster virus [TaxId: 10335]

Probab=84.96  E-value=0.17  Score=46.74  Aligned_cols=33  Identities=21%  Similarity=0.457  Sum_probs=25.1

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHhhhcCCceEEEE
Q psy200          221 SMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYI  254 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~l~~~~~~~~~~v  254 (490)
                      .|.|-|+-|+||||+++.+.+.+... +..++++
T Consensus         7 rI~IEG~iGsGKSTl~~~L~~~l~~~-g~~v~~~   39 (331)
T d1osna_           7 RIYLDGAYGIGKTTAAEEFLHHFAIT-PNRILLI   39 (331)
T ss_dssp             EEEEEESSSSCTTHHHHHHHHTTTTS-GGGEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHhhc-CCceEEE
Confidence            37799999999999999999987522 2344444

>d1f6va_ a.49.1.1 (A:) C-terminal domain of B transposition protein {Bacteriophage mu [TaxId: 10677]}

class: All alpha proteins
fold: C-terminal domain of B transposition protein
superfamily: C-terminal domain of B transposition protein
family: C-terminal domain of B transposition protein
domain: C-terminal domain of B transposition protein
species: Bacteriophage mu [TaxId: 10677]

Probab=84.83  E-value=0.027  Score=40.78  Aligned_cols=75  Identities=11%  Similarity=0.038  Sum_probs=55.7

Q ss_pred             eEEeCCCCHHHHHHHHHHHHhccCCCCCCC-HHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHhccccCCcccccCHHH
Q psy200          361 LMNFAPYSREQILEIISQKLKQTDKFNMFN-ASALQLLAGKVAAVSGDIRKAIDITNHLIDLTYDNVKENGEVTGIGLKE  439 (490)
Q Consensus       361 ~i~~~pls~~e~~~il~~~l~~~~~~~~~~-~~~i~~i~~~i~~~~Gd~r~ai~ll~~a~~~a~~~~~~~~~~~~It~~~  439 (490)
                      ...+.....+++..++...        .++ ++.++.+.. |....|.+|.+-..|+.|.+.|..++      ..|+.++
T Consensus         7 r~~i~k~kk~Di~Aia~AW--------~v~d~~~~k~l~~-I~~KpGaLR~l~kTLrLA~M~A~g~g------~~v~~~~   71 (91)
T d1f6va_           7 RTAINKTKKADVKAIADAW--------QINGEKELELLQQ-IAQKPGALRILNHSLRLAAMTAHGKG------ERVNEDY   71 (91)
T ss_dssp             TTCCSSCSGGGTTHHHHSS--------TTSSSHHHHHHHT-TSSSCSCHHHHHHHHGGGTCTTCTTS------CCSSHHH
T ss_pred             hhhhcCCCHHHHHHHHHHh--------CCCCHHHHHHHHH-HccCccHHHHHHHHHHHHHHHhCCCC------CcCCHHH
Confidence            4556677788888887642        233 344444443 66789999999999999998888887      4799999


Q ss_pred             HHHHHHHhccC
Q psy200          440 VLGVISSVYCT  450 (490)
Q Consensus       440 v~~a~~~~~~~  450 (490)
                      |..|+.+...+
T Consensus        72 Ir~A~~~ld~d   82 (91)
T d1f6va_          72 LRQAFRELDLD   82 (91)
T ss_dssp             HHHHHTSSCSS
T ss_pred             HHHHHHHhhhh
Confidence            99999987543

>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=84.70  E-value=0.24  Score=41.03  Aligned_cols=21  Identities=24%  Similarity=0.289  Sum_probs=19.1

Q ss_pred             eEEEECCCCCcHHHHHHHHHH
Q psy200          221 SMYISGPPGTGKSASLNLLVS  241 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~  241 (490)
                      .|.|.|.+++|||||++++..
T Consensus         7 nIaiiG~~naGKSTL~n~L~~   27 (179)
T d1wb1a4           7 NLGIFGHIDHGKTTLSKVLTE   27 (179)
T ss_dssp             EEEEEECTTSSHHHHHHHHHT
T ss_pred             EEEEEeCCCCcHHHHHHHHHH
Confidence            588999999999999999974

>d1w7ja2 c.37.1.9 (A:63-792) Myosin S1, motor domain {Chicken (Gallus gallus), Va isoform [TaxId: 9031]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Myosin S1, motor domain
species: Chicken (Gallus gallus), Va isoform [TaxId: 9031]

Probab=84.69  E-value=0.33  Score=49.88  Aligned_cols=30  Identities=27%  Similarity=0.424  Sum_probs=26.6

Q ss_pred             ccCCCCeEEEECCCCCcHHHHHHHHHHHhh
Q psy200          215 NNETSGSMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       215 ~~~~~~~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      ..+.+.+|+|.|+.|+|||...+.+.+.+.
T Consensus        90 ~~~~~Q~IiisGeSGsGKTe~~k~il~~l~  119 (730)
T d1w7ja2          90 RDERNQSIIVSGESGAGKTVSAKYAMRYFA  119 (730)
T ss_dssp             HHTCCEEEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             HhCCCeEEEEEeCCCCCHHHHHHHHHHHHH
Confidence            346789999999999999999999998874

>d1f9va_ c.37.1.9 (A:) Kinesin motor Ncd (non-claret disjunctional) {Baker's yeast (Saccharomyces cerevisiae), Kar [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin motor Ncd (non-claret disjunctional)
species: Baker's yeast (Saccharomyces cerevisiae), Kar [TaxId: 4932]

Probab=83.93  E-value=0.58  Score=43.18  Aligned_cols=39  Identities=13%  Similarity=0.289  Sum_probs=29.2

Q ss_pred             CChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHH
Q psy200          197 PGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASL  236 (490)
Q Consensus       197 vgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla  236 (490)
                      ...++..+.+...+...+ .+....++-||..|+|||.++
T Consensus        62 ~~q~~vy~~v~~~v~~~l-~G~n~~i~aYGqtgSGKT~T~  100 (342)
T d1f9va_          62 DTNVDVFKEVGQLVQSSL-DGYNVCIFAYGQTGSGKTFTM  100 (342)
T ss_dssp             CCHHHHHHHHHHHHGGGG-GTCCEEEEEECCTTSSHHHHH
T ss_pred             CCHHHHHHHhhhhhcchh-cccccceeeeeccCCcccccc
Confidence            345666667666665554 456788999999999999887

>d1x88a1 c.37.1.9 (A:18-362) Kinesin {Human (Homo sapiens), mitotic kinesin eg5 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin
species: Human (Homo sapiens), mitotic kinesin eg5 [TaxId: 9606]

Probab=83.37  E-value=0.46  Score=43.97  Aligned_cols=40  Identities=18%  Similarity=0.221  Sum_probs=26.6

Q ss_pred             CChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHH
Q psy200          197 PGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASL  236 (490)
Q Consensus       197 vgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla  236 (490)
                      ...++..+.+..-+-..+..+....++.||..|+|||.++
T Consensus        59 ~~q~~vy~~~~~~lv~~~l~G~n~~i~aYGqtgSGKTyTm   98 (345)
T d1x88a1          59 TKQIDVYRSVVCPILDEVIMGYNCTIFAYGQTGTGKTFTM   98 (345)
T ss_dssp             CCHHHHHHHHHHHHHHHHHTTCEEEEEEEECTTSSHHHHH
T ss_pred             CCHHHHHHHHHHHhHHHHhccCCceEEeeeeccccceEEe
Confidence            3445555554333323334567779999999999999876

>d1ry6a_ c.37.1.9 (A:) Kinesin {Malaria parasite (Plasmodium falciparum) [TaxId: 5833]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin
species: Malaria parasite (Plasmodium falciparum) [TaxId: 5833]

Probab=83.14  E-value=0.4  Score=44.06  Aligned_cols=41  Identities=17%  Similarity=0.269  Sum_probs=27.6

Q ss_pred             CChHHHHHHH-HHHHHhhhccCCCCeEEEECCCCCcHHHHHH
Q psy200          197 PGREVQLEGI-RQFLLGHVNNETSGSMYISGPPGTGKSASLN  237 (490)
Q Consensus       197 vgre~~~~~l-~~~L~~~~~~~~~~~ill~GppGtGKTtla~  237 (490)
                      ...++..+.+ ...+...+..+....|+.||..|+|||.++-
T Consensus        62 ~~q~~vy~~~~~plv~~~~~~G~n~~i~aYGqTGSGKTyTm~  103 (330)
T d1ry6a_          62 VDNFTVYENTIKPLIIDLYENGCVCSCFAYGQTGSGKTYTML  103 (330)
T ss_dssp             CCHHHHHHHHTHHHHHHHHHHCCEEEEEEECCTTSSHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHHHHhcCCCeEEEeeeccccccceeee
Confidence            3445555443 3344444445677889999999999999873

>d2zfia1 c.37.1.9 (A:4-352) Kinesin {Mouse (Mus musculus), kif1a [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin
species: Mouse (Mus musculus), kif1a [TaxId: 10090]

Probab=83.07  E-value=0.47  Score=43.99  Aligned_cols=39  Identities=21%  Similarity=0.333  Sum_probs=27.6

Q ss_pred             ChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHH
Q psy200          198 GREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASL  236 (490)
Q Consensus       198 gre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla  236 (490)
                      ..++..+.+..-+-..+..+....|+-||..|+|||.++
T Consensus        66 sQ~~vy~~~~~plv~~~l~G~n~ti~aYGqTgSGKT~Tm  104 (349)
T d2zfia1          66 SQKQVYRDIGEEMLQHAFEGYNVCIFAYGQTGAGKSYTM  104 (349)
T ss_dssp             CHHHHHHHTHHHHHHHHHTTCCEEEEEECSTTSSHHHHH
T ss_pred             cHHHHHHHhhHHHHHHHHhccCceeeeeccCCCCCceee
Confidence            355566654443333344577789999999999999987

>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=82.53  E-value=0.2  Score=46.11  Aligned_cols=24  Identities=42%  Similarity=0.786  Sum_probs=19.2

Q ss_pred             eEEEECCCCCcHHHHHHHHHHHhh
Q psy200          221 SMYISGPPGTGKSASLNLLVSRAE  244 (490)
Q Consensus       221 ~ill~GppGtGKTtla~~l~~~l~  244 (490)
                      .|.|-|+-|+||||+++.+++.+.
T Consensus         6 rI~IEG~iGsGKTTl~~~La~~l~   29 (329)
T d1e2ka_           6 RVYIDGPHGMGKTTTTQLLVALGS   29 (329)
T ss_dssp             EEEECSCTTSSHHHHHHHHTC---
T ss_pred             EEEEECCcCCCHHHHHHHHHHHhC
Confidence            377899999999999999987764

>d1v8ka_ c.37.1.9 (A:) Kinesin {Mouse (Mus musculus), kif2c [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin
species: Mouse (Mus musculus), kif2c [TaxId: 10090]

Probab=82.01  E-value=0.39  Score=44.81  Aligned_cols=40  Identities=15%  Similarity=0.253  Sum_probs=27.3

Q ss_pred             CChHHHHHHHHH-HHHhhhccCCCCeEEEECCCCCcHHHHHH
Q psy200          197 PGREVQLEGIRQ-FLLGHVNNETSGSMYISGPPGTGKSASLN  237 (490)
Q Consensus       197 vgre~~~~~l~~-~L~~~~~~~~~~~ill~GppGtGKTtla~  237 (490)
                      ...++..+.+.. .+... ..+....|+-||..|+|||.++.
T Consensus        92 ~~Q~~Vy~~~~~plv~~~-l~G~n~tifaYGqTGSGKTyTm~  132 (362)
T d1v8ka_          92 ASNEVVYRFTARPLVQTI-FEGGKATCFAYGQTGSGKTHTMG  132 (362)
T ss_dssp             CCHHHHHHHTTHHHHHHH-HTTCEEEEEEEESTTSSHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHHH-HhccCceEEeeccCCCCCceeee
Confidence            445555655433 44433 34677789999999999998873

>d1sdma_ c.37.1.9 (A:) Kinesin heavy chain-like protein {Potato (Solanum tuberosum) [TaxId: 4113]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin heavy chain-like protein
species: Potato (Solanum tuberosum) [TaxId: 4113]

Probab=81.54  E-value=0.39  Score=44.86  Aligned_cols=39  Identities=15%  Similarity=0.346  Sum_probs=27.2

Q ss_pred             CChHHHHHHHHHHHHhhhccCCCCeEEEECCCCCcHHHHH
Q psy200          197 PGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASL  236 (490)
Q Consensus       197 vgre~~~~~l~~~L~~~~~~~~~~~ill~GppGtGKTtla  236 (490)
                      ...++..+.+...+...+ .+....++-||..|+|||.++
T Consensus        54 ~~q~~vy~~v~~lv~~~l-~G~n~~i~aYGqTGSGKTyTm   92 (364)
T d1sdma_          54 ATQDDVFEDTKYLVQSAV-DGYNVCIFAYGQTGSGKTFTI   92 (364)
T ss_dssp             CCHHHHHHTTTHHHHHHH-TTCEEEEEEECSTTSSHHHHH
T ss_pred             CCHHHHHHHHHHHHHHHh-cCCceeeeccccCCCCccccc
Confidence            344555555555554443 456778999999999999995

>d1g8fa3 c.37.1.15 (A:390-511) ATP sulfurylase C-terminal 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: ATP sulfurylase C-terminal domain
domain: ATP sulfurylase C-terminal domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=81.43  E-value=0.7  Score=35.46  Aligned_cols=29  Identities=10%  Similarity=-0.040  Sum_probs=25.0

Q ss_pred             CCCCeEEEECCCCCcHHHHHHHHHHHhhh
Q psy200          217 ETSGSMYISGPPGTGKSASLNLLVSRAEI  245 (490)
Q Consensus       217 ~~~~~ill~GppGtGKTtla~~l~~~l~~  245 (490)
                      ..+-.|+++|-.|+||+++++++...+..
T Consensus         4 kqgf~i~~tg~~~~gk~~ia~al~~~l~q   32 (122)
T d1g8fa3           4 KQGFSIVLGNSLTVSREQLSIALLSTFLQ   32 (122)
T ss_dssp             GCCEEEEECTTCCSCHHHHHHHHHHHHTT
T ss_pred             ccceEEEEeCCCCCCHHHHHHHHHHHHHH
Confidence            34668999999999999999999888853

>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=81.41  E-value=0.52  Score=40.60  Aligned_cols=24  Identities=21%  Similarity=0.256  Sum_probs=20.8

Q ss_pred             CeEEEECCCCCcHHHHHHHHHHHh
Q psy200          220 GSMYISGPPGTGKSASLNLLVSRA  243 (490)
Q Consensus       220 ~~ill~GppGtGKTtla~~l~~~l  243 (490)
                      ..|.|.|.+++|||||++++....
T Consensus         6 p~IaIiGh~d~GKSTL~~~L~~~~   29 (227)
T d1g7sa4           6 PIVSVLGHVDHGKTTLLDHIRGSA   29 (227)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CEEEEEeCCCccHHHHHHHHHhhc
Confidence            348899999999999999998754