Citrus Sinensis ID: 005987

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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-------500-------510-------520-------530-------540-------550-------560-------570-------580-------590-------600-------610-------620-------630-------640-------650-------660------
Protein Sequence
MQISLSFEKFDEVLNGSKVSNVIWNQENDSALGSSSTQQLWTDKYKLCSLEEPDVQKKNVEHFLTPSRFEGLVNPKRDLALGSSSRQQLWTNKNKPCSLEEHAIQKENVGRFLTPSRFEGLVNPDHDSASASSSTQQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASGGDIRQAITSLQFSSLKQDPMLNLSLSISKPNFPEEKADGHGGFSIQFGRDETLSLFHALGKFLHNKRETDNLVKMDQDAFVVKDKFSRLPLKMDAPEKVLSQAHGQARPVLDFLHENFLDFISEDAIDDAWAVASYLSDADLLLASFRGRLVRYNEADNVLQSAAASVAARGVLFGNSHPVPPRWHAIRKPKLWRVDQSSLQKKKELLKKKFMAWDGSISADVYNGSSSSDVSVLATEYAPALKWLGNRTSVGLEAHEAPIPDNETQDVDIFEGMSLDDHESEISNYESEDDWMSEM
Secondary Structure (PSIPRED)
ccccHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHccccccccccccccccccccccccccccccccEEEcccccccHHHccHHHHHHHHHHHHHHHccccccccccEEEEEcccccHHHHHHHHHHHHccccEEEEcccccHHHHHHHcccccccccccHHHHHHHHHHHHHHcccccccccccccccEEEEEEcccccccHHHHHHHHHHHHHHHHHccccEEEEEcccccccccccccccHHHHHHHHHHccEEEEEEcccccHHHHHHHHHHHHHHcccccHHHHHHHHHHccccHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccHHHHHHHHHcccccccHHHHHccccHHHHHHccccccccccHHHHHHHHcccHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHccccccccccccccccHHHHHHHHHHHHHHHHHHHccccccccccccccccccHHHHHcHHHHHHHHHHHHHHHHccccccccccccccccHHHHHHHHHHHHHHHccccccccccccccccccccccHHHHHcccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccEEEEEHHHcHHEccccccEEEEEEcccccccccccccccccHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccHcccccccccccccccccccccccccccccccHHHccccccHHHHHHcHHHHHHHHHHHHHHHcccccccccEEEEEEccccccHHHHHHHHHHHcccEEEEEcccccccHHHHHcccccccccccHHHHHHHHHHHHHHHccccccccccccccEEEEEEcccccccccccHHHHHHHHHHHHHccccEEEEEEcccccccccHHHHHccccHHHHHcccEEEEEcccccHHHHHHHHHHHHHHHcccccHHHHHHHHHHcccHHHHHHHHHHHHHcccccccccccccccccccccccccHHHHHHHccccccccHHHHHHHHHHcccccccccccccccccccHHHcccccccccHHHHHHHHcccHHHHHHHHHHcccccccHHHHHHHHHHHHHHHcccHHcHHHHccccccccHHHHHHHHHHHHHHHcHEcccccccccccEcccccccEEEccccccHHHHHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHcccccccHHHHccccccccHHHHHHHHHHcccccccHcccccccccccccc
Coil and Loop (DISEMBL)
MQISLSFEKfdevlngskvSNVIwnqendsalgssstqqlwtdkyklcsleepdvqkknvehfltpsrfeglvnpkrdlalgsssrqqlwtnknkpcsleeHAIQKenvgrfltpsrfeglvnpdhdsasassSTQQLWAEKYKPRSLEELAVQRKKVEEVRAWFEErlgdskdkfstNVLVItgqagvgktATVRQIASHLGArlyewdtptptIWQEYMHNCKTGLEYTSKLDEFENFVERIRRygstspsipgeskssailliddlpvtngrTAFERLRQCLLLLVRSTHIPTAVVLTecgkadsvdsTAQSFEELQSILVDAGArkvalnpitngsikrTLSKICRQEQYSLSTEQIDLVAQASGGDIRQAITSLQfsslkqdpmlnlslsiskpnfpeekadghggfsiqfgRDETLSLFHALGKFlhnkretdnlvkmdqdafvvkdkfsrlplkmdapekvlsqahgqarpvlDFLHENFLDFISEDAIDDAWAVASYLSDADLLLASFRGRLVRYNEADNVLQSAAASVAARGVlfgnshpvpprwhairkpklwrvDQSSLQKKKELLKKKFMAWDgsisadvyngssssdVSVLATEYApalkwlgnrtsvgleaheapipdnetqdvdifegmslddheseisnyeseddwmsem
Flexible Loop (DISEMBL)
MQISLSFEKFDEVLNGSKVSNVIWNQEndsalgssstqQLWTDKYKLCSLEEPDVQKKNVEHFltpsrfeglvnpKRDLALGSSSRQQLWTNKNKPCSLEEHAIQKENVGRFLTPSRFEGLVNPDHDSASASSSTQQLWAEKYKPRSLEELAVQRKKVEEVRAWFeerlgdskdkfstNVLVItgqagvgktatVRQIASHLGARLYEWDTPTPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRygstspsipgesksSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAgarkvalnpitngsikrtlSKICRQEQYSLSTEQIDLVAQASGGDIRQAITSLQFSSLKQDPMLNLSLSISKPNFPEEKADGHGGFSIQFGRDETLSLFHALGKFLHnkretdnlvkmdqdafVVKDKFSRLPLKMDAPEKVLSQAHGQARPVLDFLHENFLDFISEDAIDDAWAVASYLSDADLLLASFRGRLVRYNEADNVLQSAAASVAARGVLfgnshpvpprwhairkpklwrvdqSSLQKKKELLKKKFMAWDGSISADVYNGSSSSDVSVLATEYAPALKWLGNRTSVGLEAheapipdnetqdVDIFEGmslddheseisnyeseddwmSEM
Low Complexity Region (SEG)
MQISLSFEKFDEVLNGSKVSNVIWNQENDSALGSSSTQQLWTDKYKLCSLEEPDVQKKNVEHFLTPSRFEGLVNPKRDLALGSSSRQQLWTNKNKPCSLEEHAIQKENVGRFLTPSRFEGLVNPDHDSASASSSTQQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASGGDIRQAITSLQFSSLKQDPMLNLSLSISKPNFPEEKADGHGGFSIQFGRDETLSLFHALGKFLHNKRETDNLVKMDQDAFVVKDKFSRLPLKMDAPEKVLSQAHGQARPVLDFLHENFLDFISEDAIDDAWAVASYlsdadlllasFRGRLVRYNEADNVLQSAAASVAARGVLFGNSHPVPPRWHAIRKPKLWRVDQSSlqkkkellkkkFMAWDGSISADVYNGSSSSDVSVLATEYAPALKWLGNRTSVGLEAHEAPIPDNETQDVDIFEGMSLDDHESEISNYESEDDWMSEM
Disordered region (IsUnstruct)
************VLNGSKVSNVIWN*************QLWTDKYKLCSLE********VEHFLT*******************************************************************************************KVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRY**************AILLIDDLPVTNGRTAFERLRQCLLLLVRSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASGGDIRQAITSL*******************************GFSIQFGRDETLSLFHALGKFLHNKRETDNLVKMDQDAFVVKDKFSRLPL********L**AHGQARPVLDFLHENFLDFISEDAIDDAWAVASYLSDADLLLASFRGRLVRYNEADNVLQSAAASVAARGVLFGNSHPVPPRWHAIRKPKLWRVDQS*****KELLKKKFMAWDGSISADVYNGS**SDVSVLATEYAPALKWLGNRTSVGL*******************************************
Disordered Region (DISOPRED)
****L***KFDEVLNGSKV************************************************************************************************************************AEKYKPRSLEELAVQRKKVEEVRAWFEERL******FSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTIWQE*********EYTSKLDEFENFVERIR****************AILLIDDLPVTNGRTAFERLRQCLLLLVRSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASGGDIRQAITSLQFSSLKQDP************************SIQFGRDETLSLFHALGKFLHNKRETDNLVKMDQDAFVVKDKFSRLPLKMDAPEKVLSQAHGQARPVLDFLHENFLDFISEDAIDDAWAVASYLSDADLLLASFRGRLVRYNEADNVLQSAAASVAARGVLFG**************************************************SSSSDVSVLATEYAPALKWLG*****************ET************************DDWM***
Disordered Region (DISEMBL)
MQISLSFEKFDEVLNGSKVSNVIWNQEN***********LWTDKYKLCSLEEPDVQKKNVEHFLTPSRFEGLVNPKRDLALGSSSRQQLWTNKNKPCSLEEHAIQKENVGRFLTPSRFEGLVNP****************EKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYG*********SKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASGGDIRQAITSLQFSSLKQDPMLNLSLSISKPNFPEEKADGHGGFSIQFGRDETLSLFHALGKFLHNKRETDNLVKMDQDAFVVKDKFSRLPLKMDAPEKVLSQAHGQARPVLDFLHENFLDFISEDAIDDAWAVASYLSDADLLLASFRGRLVRYNEADNVLQSAAASVAARGVLFGNSHPVPPRWHAIRKPKLWRVDQSSLQKKKELLKKKFMAWDGSISADVYNGSSSSDVSVLATEYAPALKWLGNRTSVGLEAHEAPIPDNETQDVDIFEGMSLDDHE****************
Disordered Region (DISPRO)
*QISLSFEKFDEVLNGSKVSNVIWNQEN*************TDKYKLCSLEEP**********************************************************************************QQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTIWQE*****KTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASGGDIRQAITSLQFSSLKQ*****************************FGRDETLSLFHALGKFLHNKRETDNLVKMDQDAFVVKDKFSRLPLKMDAPEKVLSQAHGQARPVLDFLHENFLDFISEDAIDDAWAVASYLSDADLLLASFRGRLVRYNEADNVLQSAAASVAARGVLFGNSHPVPPRWHAIRKPKLWRVDQSSLQKKKELLKKKFMAWDGSISADVYNGSSSSDVSVLATEYAPALKWLGNRTSVGLEAHEAPIPDNETQDVDIFEGMSL***********S********
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
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TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MQISLSFEKFDEVLNGSKVSNVIWNQENDSALGSSSTQQLWTDKYKLCSLEEPDVQKKNVEHFLTPSRFEGLVNPKRDLALGSSSRQQLWTNKNKPCSLEEHAIQKENVGRFLTPSRFEGLVNPDHDSASASSSTQQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASGGDIRQAITSLQFSSLKQDPMLNLSLSISKPNFPEEKADGHGGFSIQFGRDETLSLFHALGKFLHNKRETDNLVKMDQDAFVVKDKFSRLPLKMDAPEKVLSQAHGQARPVLDFLHENFLDFISEDAIDDAWAVASYLSDADLLLASFRGRLVRYNEADNVLQSAAASVAARGVLFGNSHPVPPRWHAIRKPKLWRVDQSSLQKKKELLKKKFMAWDGSISADVYNGSSSSDVSVLATEYAPALKWLGNRTSVGLEAHEAPIPDNETQDVDIFEGMSLDDHESEISNYESEDDWMSEM
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	666	2.2.26 [Sep-21-2011]
Q9MBA3	599	Cell cycle checkpoint pro	yes	no	0.750	0.834	0.537	1e-154
Q5R652	681	Cell cycle checkpoint pro	yes	no	0.638	0.624	0.271	2e-34
O75943	681	Cell cycle checkpoint pro	yes	no	0.638	0.624	0.271	4e-34
Q9XT62	670	Cell cycle checkpoint pro	N/A	no	0.638	0.634	0.267	1e-32
Q6NXW6	688	Cell cycle checkpoint pro	yes	no	0.621	0.601	0.276	1e-32
P32641	659	Checkpoint protein RAD24	yes	no	0.402	0.406	0.251	1e-16
P50531	606	Checkpoint protein rad17	yes	no	0.584	0.641	0.248	2e-15
Q8TPU4	607	Replication factor C larg	yes	no	0.484	0.532	0.214	1e-10
Q46AT6	642	Replication factor C larg	yes	no	0.489	0.507	0.216	1e-10
Q12TX1	497	Replication factor C larg	yes	no	0.477	0.639	0.219	6e-10

>sp|Q9MBA3|RAD17_ARATH Cell cycle checkpoint protein RAD17 OS=Arabidopsis thaliana GN=RAD17 PE=2 SV=1

 Score =  545 bits (1403), Expect = e-154,   Method: Compositional matrix adjust.
 Identities = 292/543 (53%), Positives = 371/543 (68%), Gaps = 43/543 (7%)

Query: 133 SSTQQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKT 192
           S    LW +KY+PR+LEEL+V +KKV+EV+ WF+E L   K+    NVL++TGQAGVGK+
Sbjct: 87  SKNTDLWVDKYRPRTLEELSVHKKKVDEVKLWFQESLDFLKNGLRNNVLLVTGQAGVGKS 146

Query: 193 ATVRQIASHLGARLYEWDTPTPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSP 252
           AT+  I S LG  ++EW+ P PTIWQE++HN  +GL+YTSKLDEFENFVE  R+YG  + 
Sbjct: 147 ATIHLITSILGVTVHEWNAPIPTIWQEHVHNTSSGLKYTSKLDEFENFVESTRKYGVMAS 206

Query: 253 SIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHIPTAVVLTECGKADSVDST 312
           S     K+  +LLIDDLP+ NGR AFERL+ CLLLLV+ST IPT +++T+   ADS D T
Sbjct: 207 SSTDGIKAPVVLLIDDLPLANGRHAFERLQNCLLLLVKSTQIPTVILITDHNNADSSDQT 266

Query: 313 AQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASGGDI 372
           A+  E+ QS L  AGA KVA NPIT  SIK+ L +ICR+E   ++T +ID +A ASGGDI
Sbjct: 267 ARRMEDTQSSLERAGALKVAFNPITKNSIKKVLQRICREEHCKVTTMEIDQMATASGGDI 326

Query: 373 RQAITSLQFSSLKQDPMLNLSLSISKPNFPEEKADGHG-----------GFSIQFGRDET 421
           R AITSLQ  S+K  P LN +  I  P  P  + + HG           G S  FGRDET
Sbjct: 327 RHAITSLQLFSVK--PELNHT-KIKSPR-PGMEDNYHGNEQTMYSGLDSGISSCFGRDET 382

Query: 422 LSLFHALGKFLHNKRETDNLVKMDQDAFVVKDKFSRLPLKMDAPEKVLSQAHGQARPVLD 481
           LSLFHALGKFLHNKRETDN++  +  + +V D+F+RLPLKMDAPEKVLSQAHGQA  V+D
Sbjct: 383 LSLFHALGKFLHNKRETDNVIISECSSSLVHDEFARLPLKMDAPEKVLSQAHGQAGRVVD 442

Query: 482 FLHENFLDFISEDAIDDAWAVASYLSDADLLLASFRGRLVRYNEADNVLQSAAASVAARG 541
           FLHEN LDF+S+ AI+DAW V+SYL+DADLLLA  RG++  +N  ++V QSA ASVA RG
Sbjct: 443 FLHENVLDFVSDGAIEDAWCVSSYLADADLLLADIRGKMSGHNNTEDVPQSAGASVAVRG 502

Query: 542 VLFGNSHPVPPRWHAIRKPKLWRVDQSSLQKKKELLKKKFMAWDGSISADVYNGSSSSDV 601
           VL+GN  P   RWH IRKPKLW+V+QSS+Q KK L +++ ++         Y GS  +D+
Sbjct: 503 VLYGNKQPCSSRWHVIRKPKLWQVEQSSIQTKKNLREQRNIS---------YEGSRVADI 553

Query: 602 SVLATEYAPALKWLGNRTSVGLEAHEAPIPDNETQDVDIFEGMS--LDDHESEISNYESE 659
           SV+ATEY+P LKWL  R S                  D F GM    D+ +S+IS  +  
Sbjct: 554 SVMATEYSPVLKWLSYRAS-----------------PDAFPGMGEETDEEDSDISEDDEI 596

Query: 660 DDW 662
            DW
Sbjct: 597 QDW 599

Seems to be involved in regulation of DNA repair correlated to non-homologous double strand breaks (DSBs) repair. In vitro, involved in rapid but not in slow DSB repair mechanism.
Arabidopsis thaliana (taxid: 3702)

>sp|Q5R652|RAD17_PONAB Cell cycle checkpoint protein RAD17 OS=Pongo abelii GN=RAD17 PE=2 SV=1

 Score =  147 bits (372), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 132/486 (27%), Positives = 219/486 (45%), Gaps = 61/486 (12%)

Query: 93  KNKPCSLEEHAIQKENVGRFLTPSRFEGLVNPDHDSASASSSTQQLWAEKYKPRSLEELA 152
           KN P +LE         G   +  +  GL N     +    S  + W +KYKP +  ELA
Sbjct: 50  KNGPSTLESSRFPARKRGNLSSLEQIYGLEN-----SKEYLSENEPWVDKYKPETQHELA 104

Query: 153 VQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTP 212
           V +KK+EEV  W + ++ + + K   ++L+ITG  G GKT T++ ++   G ++ EW  P
Sbjct: 105 VHKKKIEEVETWLKAQVLERQPKQGGSILLITGPPGCGKTTTIKILSKEHGIQVQEWINP 164

Query: 213 TPTIWQ----EYMHNCKTGLE---YTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILL 265
               +Q    + M N ++      Y S++  F+ F+ R  +Y               I+L
Sbjct: 165 VLPDFQKDDFKGMFNTESSFHMFPYQSQIAVFKEFLLRATKYNKLQMLGDDLRTDKKIIL 224

Query: 266 IDDLPVTNGRTAFERLRQCLLLLVRSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVD 325
           ++DLP    R +   L + L   VR    P   ++++    D+     Q     + I  +
Sbjct: 225 VEDLPNQFYRDS-HTLHEVLRKYVRIGRCPLIFIISDSLSGDN----NQRLLFPKEIQEE 279

Query: 326 AGARKVALNPITNGSIKRTLSKICRQEQYSLSTE-------QIDLVAQASGGDIRQAITS 378
                ++ NP+    + + L++I   E      +        ++L+ Q   GDIR AI S
Sbjct: 280 CSISNISFNPVAPTIMMKFLNRIVTIEANKNGGKITVPDKTSLELLCQGCSGDIRSAINS 339

Query: 379 LQFS---------------SLKQDPMLNLSLSISKPN--FPEEKADGHGGFSIQFGRDET 421
           LQFS               SLK D +L+ S    KP+  F  ++    G      G+D +
Sbjct: 340 LQFSSSKGENNLWPRKKGMSLKSDAVLSKSKQRKKPDRVFENQEVQAIG------GKDVS 393

Query: 422 LSLFHALGKFLHNKRETDNLVKMDQDAFVVK-DKFSRLPLKMDAPEKVLSQAHGQARPVL 480
           L LF ALGK L+ KR +  L ++D         ++ R  L ++ PE+V+  +H       
Sbjct: 394 LFLFRALGKILYCKRAS--LTELDSPRLPSHLSEYERDTLLVE-PEEVVEMSHMPGDLFN 450

Query: 481 DFLHENFLDFISEDAIDDAWAVASYLSDADLLLASFRGRLVRYNEADNVLQSAAASVAAR 540
            +LH+N++DF  E  IDD    + +LS AD+L   +  R        ++L+  + S+A R
Sbjct: 451 LYLHQNYIDFFME--IDDIVRASEFLSFADILSGDWNTR--------SLLREYSTSIATR 500

Query: 541 GVLFGN 546
           GV+  N
Sbjct: 501 GVMHSN 506

Essential for sustained cell growth, maintenance of chromosomal stability, and ATR-dependent checkpoint activation upon DNA damage. Has a weak ATPase activity required for binding to chromatin. Participates in the recruitment of the RAD1-RAD9-HUS1 complex and RHINO onto chromatin, and in CHEK1 activation. May also serve as a sensor of DNA replication progression, and may be involved in homologous recombination.

Pongo abelii (taxid: 9601)

>sp|O75943|RAD17_HUMAN Cell cycle checkpoint protein RAD17 OS=Homo sapiens GN=RAD17 PE=1 SV=2

 Score =  147 bits (370), Expect = 4e-34,   Method: Compositional matrix adjust.
 Identities = 132/486 (27%), Positives = 219/486 (45%), Gaps = 61/486 (12%)

Query: 93  KNKPCSLEEHAIQKENVGRFLTPSRFEGLVNPDHDSASASSSTQQLWAEKYKPRSLEELA 152
           KN P +LE         G   +  +  GL N     +    S  + W +KYKP +  ELA
Sbjct: 50  KNGPSTLESSRFPARKRGNLSSLEQIYGLEN-----SKEYLSENEPWVDKYKPETQHELA 104

Query: 153 VQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTP 212
           V +KK+EEV  W + ++ + + K   ++L+ITG  G GKT T++ ++   G ++ EW  P
Sbjct: 105 VHKKKIEEVETWLKAQVLERQPKQGGSILLITGPPGCGKTTTLKILSKEHGIQVQEWINP 164

Query: 213 TPTIWQ----EYMHNCKTGLE---YTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILL 265
               +Q    + M N ++      Y S++  F+ F+ R  +Y               I+L
Sbjct: 165 VLPDFQKDDFKGMFNTESSFHMFPYQSQIAVFKEFLLRATKYNKLQMLGDDLRTDKKIIL 224

Query: 266 IDDLPVTNGRTAFERLRQCLLLLVRSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVD 325
           ++DLP    R +   L + L   VR    P   ++++    D+     Q     + I  +
Sbjct: 225 VEDLPNQFYRDS-HTLHEVLRKYVRIGRCPLIFIISDSLSGDN----NQRLLFPKEIQEE 279

Query: 326 AGARKVALNPITNGSIKRTLSKICRQEQYSLSTE-------QIDLVAQASGGDIRQAITS 378
                ++ NP+    + + L++I   E      +        ++L+ Q   GDIR AI S
Sbjct: 280 CSISNISFNPVAPTIMMKFLNRIVTIEANKNGGKITVPDKTSLELLCQGCSGDIRSAINS 339

Query: 379 LQFS---------------SLKQDPMLNLSLSISKPN--FPEEKADGHGGFSIQFGRDET 421
           LQFS               SLK D +L+ S    KP+  F  ++    G      G+D +
Sbjct: 340 LQFSSSKGENNLRPRKKGMSLKSDAVLSKSKRRKKPDRVFENQEVQAIG------GKDVS 393

Query: 422 LSLFHALGKFLHNKRETDNLVKMDQDAFVVK-DKFSRLPLKMDAPEKVLSQAHGQARPVL 480
           L LF ALGK L+ KR +  L ++D         ++ R  L ++ PE+V+  +H       
Sbjct: 394 LFLFRALGKILYCKRAS--LTELDSPRLPSHLSEYERDTLLVE-PEEVVEMSHMPGDLFN 450

Query: 481 DFLHENFLDFISEDAIDDAWAVASYLSDADLLLASFRGRLVRYNEADNVLQSAAASVAAR 540
            +LH+N++DF  E  IDD    + +LS AD+L   +  R        ++L+  + S+A R
Sbjct: 451 LYLHQNYIDFFME--IDDIVRASEFLSFADILSGDWNTR--------SLLREYSTSIATR 500

Query: 541 GVLFGN 546
           GV+  N
Sbjct: 501 GVMHSN 506

Essential for sustained cell growth, maintenance of chromosomal stability, and ATR-dependent checkpoint activation upon DNA damage. Has a weak ATPase activity required for binding to chromatin. Participates in the recruitment of the RAD1-RAD9-HUS1 complex and C12orf32/RHINO onto chromatin, and in CHEK1 activation. May also serve as a sensor of DNA replication progression, and may be involved in homologous recombination.

Homo sapiens (taxid: 9606)

>sp|Q9XT62|RAD17_CHLAE Cell cycle checkpoint protein RAD17 OS=Chlorocebus aethiops GN=RAD17 PE=1 SV=1

 Score =  142 bits (357), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 130/486 (26%), Positives = 218/486 (44%), Gaps = 61/486 (12%)

Query: 93  KNKPCSLEEHAIQKENVGRFLTPSRFEGLVNPDHDSASASSSTQQLWAEKYKPRSLEELA 152
           KN P +LE         G   +  +   L N     +  S S  + W +KYKP +  ELA
Sbjct: 39  KNGPSTLESSKFPVRKRGNLSSLEQIYSLEN-----SKESLSENEPWVDKYKPETQHELA 93

Query: 153 VQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTP 212
           V +KK+EEV  W + ++ + + K   ++L+ITG  G GKT T++ ++   G ++ EW  P
Sbjct: 94  VHKKKIEEVETWLKAQVLERQPKQGGSILLITGPPGCGKTTTIKVLSKEHGIQVQEWINP 153

Query: 213 TPTIWQE----YMHNCKTGLE---YTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILL 265
               +Q+     + N ++      Y S++  F+ F+ R  +Y               I+L
Sbjct: 154 VLPDFQKDDFREIFNTESSFHMFPYQSQIAVFKEFLLRATKYNKLQMLGDDLRTDKKIIL 213

Query: 266 IDDLPVTNGRTAFERLRQCLLLLVRSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVD 325
           ++DLP    R +   L + L   VR    P   V+++    D+     Q     + I  +
Sbjct: 214 VEDLPNQFYRDS-HTLHEVLRKYVRIGRCPLIFVISDSLSGDN----NQRLLFPKEIQEE 268

Query: 326 AGARKVALNPITNGSIKRTLSKICRQEQYSLSTE-------QIDLVAQASGGDIRQAITS 378
                ++ NP+    + + L++I   E      +        ++L+ Q   GDIR AI S
Sbjct: 269 CSISNISFNPVAPTIMMKFLNRIVTIEANKNGGKITVPDKTSLELLCQGCSGDIRSAINS 328

Query: 379 LQFS---------------SLKQDPMLNLSLSISKPN--FPEEKADGHGGFSIQFGRDET 421
           LQFS               SLK D +L+ S    KP+  F  ++    G      G+D +
Sbjct: 329 LQFSSSKGENNLWPRKKGMSLKSDAVLSKSKRRKKPDRVFENQEVQAIG------GKDVS 382

Query: 422 LSLFHALGKFLHNKRETDNLVKMDQDAFVVK-DKFSRLPLKMDAPEKVLSQAHGQARPVL 480
           L LF ALGK L+ KR +  L ++D         ++ R  L ++ PE+V+  +H       
Sbjct: 383 LFLFRALGKILYCKRAS--LTELDSPRLPSHLSEYERDTLLVE-PEEVVEMSHMPGDLFN 439

Query: 481 DFLHENFLDFISEDAIDDAWAVASYLSDADLLLASFRGRLVRYNEADNVLQSAAASVAAR 540
            +LH+N++DF  +  IDD    + +LS AD+L   +           ++L+  + S+A R
Sbjct: 440 LYLHQNYIDFFMD--IDDIVRASEFLSFADILSGDW--------NTCSLLREYSTSIATR 489

Query: 541 GVLFGN 546
           GV+  N
Sbjct: 490 GVIHSN 495

Essential for sustained cell growth, maintenance of chromosomal stability, and ATR-dependent checkpoint activation upon DNA damage. Has a weak ATPase activity required for binding to chromatin. Participates in the recruitment of the RAD1-RAD9-HUS1 complex and RHINO onto chromatin, and in CHEK1 activation. May also serve as a sensor of DNA replication progression, and may be involved in homologous recombination.

Chlorocebus aethiops (taxid: 9534)

>sp|Q6NXW6|RAD17_MOUSE Cell cycle checkpoint protein RAD17 OS=Mus musculus GN=Rad17 PE=1 SV=2

 Score =  141 bits (356), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 137/496 (27%), Positives = 226/496 (45%), Gaps = 82/496 (16%)

Query: 93  KNKPCSLEEHAIQKENVGRFLTPSRFEGLVNPDHDSASASSSTQQLWAEKYKPRSLEELA 152
           K  P +LE + +     GR L+  +  GL     +++    S  + W +KYKP +  ELA
Sbjct: 50  KYLPSTLESNRLSARKRGR-LSLEQTHGL-----ETSRERLSDNEPWVDKYKPETQHELA 103

Query: 153 VQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTP 212
           V +KK+EEV  W + ++ + K K   +VL+ITG  G GKT T++ ++  LG ++ EW  P
Sbjct: 104 VHKKKIEEVETWLKAQVLEVKPKQGGSVLLITGPPGCGKTTTIKILSKELGIQVQEWVNP 163

Query: 213 TPTIWQEYMHNCKTGLE-------YTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILL 265
               +Q+  +     LE       Y S++  F +F+ R  +Y          +    I+L
Sbjct: 164 ILPDFQKDDYKELLSLESNFSVVPYQSQIAVFNDFLLRATKYSKLQMLGDDLTTDKKIIL 223

Query: 266 IDDLPVTNGRTAFERLRQCLLLLVRSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVD 325
           +++LP    R     L + L   V+    P   ++++    D+     Q     ++I  +
Sbjct: 224 VEELPNQFYRDP-NALHEILRKHVQIGRCPLVFIVSDSVSGDN----NQRLLFPRNIQEE 278

Query: 326 AGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQI--------DLVAQASGGDIRQAIT 377
                ++ NP+    + + L++I   E  S + E+I        +L+ Q   GDIR AI 
Sbjct: 279 CSVSNISFNPVAPTIMMKFLNRIVTIEA-SKNGEKIIVPNKTSLELLCQGCSGDIRSAIN 337

Query: 378 SLQFS---------------SLKQDPMLNLSLSISKPNFPEEKADGHGGFSIQF--GRDE 420
           SLQFS               SLK D  ++ S    K N   E  +      IQ   G+D 
Sbjct: 338 SLQFSSSKGENSSWSKKKRMSLKSDAAISKSKQKKKHNSTLENQE------IQAIGGKDV 391

Query: 421 TLSLFHALGKFLHNKR----ETD------NLVKMDQDAFVVKDKFSRLPLKMDAPEKVLS 470
           +L LF ALGK L+ KR    E D      +L + D+D  +V+            PE+++ 
Sbjct: 392 SLFLFRALGKILYCKRAPLTELDSPRLPAHLSEHDRDTLLVQ------------PEEIVE 439

Query: 471 QAHGQARPVLDFLHENFLDFISEDAIDDAWAVASYLSDADLLLASFRGRLVRYNEADNVL 530
            +H        +LH+N++DF +E  +DD    + +LS AD+L   +  R        ++L
Sbjct: 440 MSHMPGDFFNLYLHQNYIDFFAE--VDDLVPASEFLSFADILGGDWNTR--------SLL 489

Query: 531 QSAAASVAARGVLFGN 546
           +  + SVA RGV+  N
Sbjct: 490 REYSTSVATRGVMHSN 505

Essential for sustained cell growth, maintenance of chromosomal stability, and ATR-dependent checkpoint activation upon DNA damage. Has a weak ATPase activity required for binding to chromatin. Participates in the recruitment of the RAD1-RAD9-HUS1 complex and RHINO onto chromatin, and in CHEK1 activation. May also serve as a sensor of DNA replication progression, and may be involved in homologous recombination (By similarity). Essential for embryonic development. May be involved in homologous recombination.

Mus musculus (taxid: 10090)

>sp|P32641|RAD24_YEAST Checkpoint protein RAD24 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=RAD24 PE=1 SV=1

 Score = 89.0 bits (219), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 86/342 (25%), Positives = 154/342 (45%), Gaps = 74/342 (21%)

Query: 139 WAEKYKPRSLEELAVQRKKVEEVRAWFEER-LGDSKDKFSTNVLVITGQAGVGKTATVRQ 197
           W EK+KP  LE++A+ ++K+++V+   +   L ++K +    +L+++G +G  K+  +++
Sbjct: 66  WYEKFKPNCLEQVAIHKRKLKDVQEALDAMFLPNAKHR----ILLLSGPSGCSKSTVIKE 121

Query: 198 IASHLGARLYE-------WDTPTPTIWQEYMHNCKTGLEYTSKLDEFENFVERIR--RYG 248
           ++  L  +  +         TP      E+  +C       + L + E+F E ++  RY 
Sbjct: 122 LSKILVPKYRQNSNGTSFRSTPNEHKVTEFRGDC-----IVNDLPQMESFSEFLKGARYL 176

Query: 249 STSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHI---PTAVVLTECGK 305
             S        + +++LI+DLP         R +Q +L  + S+     P  + +TEC  
Sbjct: 177 VMS--------NLSLILIEDLPNVFHIDTRRRFQQLILQWLYSSEPLLPPLVICITECEI 228

Query: 306 ADSVDSTAQSF--------EEL--QSILVDAGARKVALNPITNGSIKRTLSKICRQEQYS 355
            ++ D+  + F        E +  + IL+    +++  NPI +  +K+ L  IC Q    
Sbjct: 229 PEN-DNNYRKFGIDYTFSAETIMNKEILMHPRLKRIKFNPINSTLLKKHLKFICVQNMKM 287

Query: 356 LS--------TEQIDLVAQASGGDIRQAITSLQFSSLKQDPMLNLSLSISKPNFPEEKAD 407
           L          E ID +AQ +G DIR AIT+LQF                        A 
Sbjct: 288 LKEKNKWNKRQEVIDYIAQETG-DIRSAITTLQFW-----------------------AT 323

Query: 408 GHGGFSIQFGRDETLSLFHALGKFLHNKRETDNLVKMDQDAF 449
             G   I   R+ T+S FHA+GK +H    T+N  +M  + F
Sbjct: 324 SSGSLPIS-TRESTISYFHAIGKVIHGSHSTNNDNEMINNLF 364

Participates in checkpoint pathways arrest of the cell cycle, a mechanism that allows the DNA repair pathways to act to restore the integrity of the DNA prior to DNA synthesis or separation of the replicated chromosomes. Regulates the DNA damage checkpoint pathway throughout the cell cycle, when associated with RCF5. Component of the RFC-like RAD24-RFC complex which loads the checkpoint clamp DDC1:MEC3:RAD17 complex and is involved in DNA repair pathways. During a clamp loading circle, the RFC:clamp complex binds to DNA and the recognition of the double-stranded/single-stranded junction stimulates ATP hydrolysis by RFC. The complex presumably provides bipartite ATP sites in which one subunit supplies a catalytic site for hydrolysis of ATP bound to the neighboring subunit. Dissociation of RFC from the clamp leaves the clamp encircling DNA.

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (taxid: 559292)

>sp|P50531|RAD17_SCHPO Checkpoint protein rad17 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rad17 PE=1 SV=1

 Score = 84.7 bits (208), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 129/520 (24%), Positives = 204/520 (39%), Gaps = 131/520 (25%)

Query: 137 QLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVR 196
           QLW EKY P+   +LAV + K+  ++ W    L DS     + +L+I G +G GK+  V+
Sbjct: 70  QLWFEKYIPQKAADLAVHKSKISAIKQWM---LTDS---LESRLLLICGPSGCGKSTAVQ 123

Query: 197 QIASHLGARLYEWDTPTPTIWQEYMHNCKTGLEYTSKLDEFENFVE-----------RIR 245
            +A  LG  L EW  P     +E  +     L  T K   F +  E            I+
Sbjct: 124 VLAKELGYSLIEWLNPMN--LKEPSNQESDTLSLTEKFSRFMSLCETYPELELMDSNNIQ 181

Query: 246 RYGSTSPSIPGESKSSAILLIDDLP-VTNGRTAFERLRQCL-LLLVRSTHIPTAVVLTEC 303
           + G  +    G+ K    + +D++P ++    + +  R  +   L         +VLTE 
Sbjct: 182 KRGKNA---QGKKK---FIFLDEIPHLSKFNGSLDAFRNVIRTALTSRGAFSIIMVLTEI 235

Query: 304 --GKADSVDSTAQ-SFEELQ----SILVDAGARKVALNPITNGSIKRTLSKICRQEQYSL 356
                + ++S  + SF  +Q     +L D     +  NPI    +K+ L  I R+E    
Sbjct: 236 QLNNLEGINSQDRNSFNSVQIMGNDLLQDPRVTVLQFNPIAPTYMKKCLGSILRKEGVPK 295

Query: 357 STEQIDLV---AQASGGDIRQAITSLQFSSLKQDPMLNLSLSISK---PNFPEEK-ADGH 409
           S + + LV     AS GD+R AI SLQ         L++S S  K    N  E K   G 
Sbjct: 296 SPKLLSLVENICSASEGDLRSAINSLQ---------LSISQSFEKKGTKNIREVKEGKGK 346

Query: 410 GG-FSIQ-------------------------------------FGRDETLSLFHALGKF 431
           G  FS++                                     F +D  L + HA+GK 
Sbjct: 347 GNDFSLEAAQVLERLSKSDSEAYARFKNYKSAYIPKSDKNENSFFKKDVGLGMMHAIGKV 406

Query: 432 LHNKRETDNLV------KMDQDAFVVKDKFSR-------LPLKMDAPEKVLSQAH---GQ 475
           + NKRE D+ V      +      +   K S+       + LK D  E++L+       +
Sbjct: 407 VWNKREGDDEVLKASSQQTGNSERIKGVKVSKSQENKNCISLKSDQRERMLNVDQCFTSK 466

Query: 476 ARPVLDF-----------------LHENFLDFISEDAIDDAWAVASYLSDADLLLASFRG 518
            R ++D                  L EN++D  S    D+A+ V   LS +D L   F  
Sbjct: 467 RRSLVDIESTINQSGLSGSVFRYGLFENYVD--SCVTTDEAFNVCDLLSISDCLSHDF-- 522

Query: 519 RLVRYNEADNVLQSAAASVAARGVLFGNSHPVPPRWHAIR 558
               Y+   + +   +   + +G LF    PVP +W  +R
Sbjct: 523 ---PYSYTGDEI---STWFSVQGTLFYLPSPVPRKWRQLR 556

Participates in checkpoint pathways arrest of the cell cycle. A mechanism that allows the DNA repair pathways to act to restore the integrity of the DNA prior to DNA synthesis or separation of the replicated chromosomes.

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

>sp|Q8TPU4|RFCL_METAC Replication factor C large subunit OS=Methanosarcina acetivorans (strain ATCC 35395 / DSM 2834 / JCM 12185 / C2A) GN=rfcL PE=3 SV=1

 Score = 68.9 bits (167), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 94/438 (21%), Positives = 171/438 (39%), Gaps = 115/438 (26%)

Query: 139 WAEKYKPRSLEELAVQRKKVEEVRAWFEE---RLGDSKDKFSTNVLVITGQAGVGKTATV 195
           WAEKY+PR+LE++   +K V + RAW EE   R+ +      T  +++ G AG+GKT++ 
Sbjct: 12  WAEKYRPRTLEDVVGNKKAVRDFRAWAEEWQSRIPE------TRAVILYGPAGIGKTSS- 64

Query: 196 RQIASHLGARLYEWDTPTPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIP 255
               +H  AR  +WD                 +E  +        +E+I    ++  ++ 
Sbjct: 65  ----AHALARDMDWDV----------------IELNASDQRTAGVIEKIAGSAASMNTLF 104

Query: 256 GESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHIPTAVVLTECGKADSVDSTAQS 315
           G   S  ++++D+    +G TA     + +  +++ T  P  ++      A+ +     +
Sbjct: 105 G---SKRLIILDEADNIHG-TADRGGMRAISGIIKGTLQPIVLI------ANDIYGLTPT 154

Query: 316 FEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASGGDIRQA 375
              L          ++    + + S+   L K+C  E    S E +  +A+ +GGD R A
Sbjct: 155 IRNL--------CLEIKFGSVQSRSMVPALKKVCGAEGVYCSQEALLQIAENAGGDFRSA 206

Query: 376 ITSLQFSSLKQDPMLNLSLSISKPNFPEEKADGHGGFSIQFGRDETLSLFHALGKFLHNK 435
           I  LQ ++  ++ +    +  +                   GRD   ++F A+ K     
Sbjct: 207 INDLQAAASGKEKLEVEDIGTA-------------------GRDVKENIFKAMQKIF--- 244

Query: 436 RETDNLVKMDQDAFVVKDKFSRLPLKMDAPEKVLSQAHGQARPVLDFLH---ENF-LDFI 491
           + TD                          +K L  A+G      D +H   EN  + + 
Sbjct: 245 KSTDC-------------------------KKALESAYGLDESPEDLVHWIDENLPIQYA 279

Query: 492 SEDA-IDDAWAVASYLSDADLLLASFRG----RLVRYNEADNVLQSAAASVAARGVLFGN 546
            +D  ++D      YLS ADL L   +     R+ RY          A+ +   G     
Sbjct: 280 RKDGNLEDIKTGFGYLSKADLYLGRVKKRQNYRMWRY----------ASMLMVCGAALSK 329

Query: 547 SHPVPPRWHAIRKPKLWR 564
           + P P  +   ++P LWR
Sbjct: 330 TKPYPG-FIKYQQPSLWR 346

Part of the RFC clamp loader complex which loads the PCNA sliding clamp onto DNA.

Methanosarcina acetivorans (strain ATCC 35395 / DSM 2834 / JCM 12185 / C2A) (taxid: 188937)

>sp|Q46AT6|RFCL_METBF Replication factor C large subunit OS=Methanosarcina barkeri (strain Fusaro / DSM 804) GN=rfcL PE=3 SV=1

 Score = 68.9 bits (167), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 94/435 (21%), Positives = 169/435 (38%), Gaps = 109/435 (25%)

Query: 139 WAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQI 198
           WAEKY+P++L+E+   +K V+ +R W E+ L    D+     +V+ G AGVGKT+T    
Sbjct: 7   WAEKYRPQTLKEIVGNKKAVQYLRTWAEKWLSGIPDR---RAVVLHGPAGVGKTST---- 59

Query: 199 ASHLGARLYEWDTPTPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGES 258
            +H  AR  +W+                 +E  +        +ER+    ++  +  G  
Sbjct: 60  -AHALARDLDWEV----------------IELNASDQRTAGVIERVAGSAASMNTFFGGK 102

Query: 259 KSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHIPTAVVLTECGKADSVDSTAQSFEE 318
           +   ++++D+    +G TA     + +  ++++T  P  ++      A+ +     +   
Sbjct: 103 R---LIILDEADNIHG-TADRGGMRAIAGIIKNTLQPIVLI------ANDIYGLTPTIRN 152

Query: 319 LQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASGGDIRQAITS 378
           L          ++    + + S+   L K+C  E    S + I  +A+ +GGD+R AI  
Sbjct: 153 L--------CLEIKFGSVQSRSMVPALKKVCESEDILCSPDAIQQIAEGAGGDLRSAIND 204

Query: 379 LQFSSLKQDPMLNLSLSISKPNFPEEKADGHGGFSIQFGRDETLSLFHALGKFLHNKRET 438
           LQ ++  +  +    LS S                   GRD   ++F A+ +     + T
Sbjct: 205 LQAAATGRKTLEVEDLSTS-------------------GRDVKENIFKAMQRIF---KST 242

Query: 439 DNLVKMDQDAFVVKDKFSRLPLKMDAPEKVLSQAHGQARPVLDFLH---ENF-LDFISED 494
           D                          +K L  A G      D +H   EN    + S+D
Sbjct: 243 DC-------------------------KKALEAARGLDESPEDLVHWIDENLPFQYASKD 277

Query: 495 A-IDDAWAVASYLSDADLLLASFRG----RLVRYNEADNVLQSAAASVAARGVLFGNSHP 549
             ++D      YLS ADL L   +     R+ RY          A+ +   G     + P
Sbjct: 278 GNLEDIKTGFGYLSKADLYLGRVKKRQNYRMWRY----------ASMLMVCGTSVSKTRP 327

Query: 550 VPPRWHAIRKPKLWR 564
             P +   + P LW+
Sbjct: 328 Y-PGFIKYQPPSLWK 341

Part of the RFC clamp loader complex which loads the PCNA sliding clamp onto DNA.

Methanosarcina barkeri (strain Fusaro / DSM 804) (taxid: 269797)

>sp|Q12TX1|RFCL_METBU Replication factor C large subunit OS=Methanococcoides burtonii (strain DSM 6242) GN=rfcL PE=3 SV=1

 Score = 66.6 bits (161), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 94/429 (21%), Positives = 168/429 (39%), Gaps = 111/429 (25%)

Query: 139 WAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQI 198
           W EKY+P+SL ++   +K V ++R W +  L  + +K     +++ G AGVGKT+     
Sbjct: 7   WVEKYRPQSLTDIVGNKKSVVDMREWAQSWLSGTPEK---RAIILHGPAGVGKTS----- 58

Query: 199 ASHLGARLYEWDTPTPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGES 258
           A+H  AR  +W+T                +E  +        +ER+    S   S+ G +
Sbjct: 59  AAHALARDLDWET----------------IELNASDQRTAGVIERVAGSASKMSSLTG-T 101

Query: 259 KSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHIPTAVVLTEC-GKADSVDSTAQSFE 317
            +  ++++D+    +G       R  +  ++++T  P  ++  +  G   SV        
Sbjct: 102 TAKRLIILDEADNIHGNADRGGAR-AIGGIIKNTDQPIVLIANDLYGLTPSV-------- 152

Query: 318 ELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASGGDIRQAIT 377
             +S+ ++     +  N +   S+   + +IC +E+       ++ +A+++GGD+R AI 
Sbjct: 153 --RSLCIE-----LKFNSVQGRSMIPAMKRICVEEKIMCGVGVLEKLAESAGGDLRSAIK 205

Query: 378 SLQFSSLKQDPMLNLSLSISKPNFPEEKADGHGGFSIQFGRDETLSLFHALGKFLHNKRE 437
            LQ  +  +D +    ++ S+                   RD   S+F  LGK     + 
Sbjct: 206 DLQAVATGRDEIHIEDIATSE-------------------RDTKESIFKVLGKIF---KS 243

Query: 438 TDNLVKMDQDAFVVKDKFSRLPLKMDAPEKVLSQAHGQARPVLDFLHENFLDFISED--- 494
           TD                         P+K L   +G     LD   EN + +I E+   
Sbjct: 244 TD-------------------------PKKALEATYG-----LDETPENLIHWIDENLPL 273

Query: 495 -------AIDDAWAVASYLSDADLLLASFRG----RLVRYNEADNVLQSAAASVAARGVL 543
                    +D      YL+ AD  L   R     RL RY  A   L +    V+   V 
Sbjct: 274 QYGTEEGTQEDLITGYEYLAKADRYLGRVRKRQSYRLWRYAGA---LMTCGTVVSKTHVG 330

Query: 544 FGNSHPVPP 552
            G +   PP
Sbjct: 331 RGFTKYQPP 339

Part of the RFC clamp loader complex which loads the PCNA sliding clamp onto DNA.

Methanococcoides burtonii (strain DSM 6242) (taxid: 259564)

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	666
297734977	605	unnamed protein product [Vitis vinifera]	0.792	0.872	0.611	0.0
359476809	1013	PREDICTED: cell cycle checkpoint protein	0.797	0.524	0.610	0.0
224133656	613	predicted protein [Populus trichocarpa]	0.794	0.862	0.610	0.0
449434132	605	PREDICTED: cell cycle checkpoint protein	0.773	0.851	0.554	1e-163
147780512	1125	hypothetical protein VITISV_009206 [Viti	0.900	0.533	0.498	1e-161
357517967	604	Cell cycle checkpoint protein RAD17 [Med	0.774	0.854	0.524	1e-156
356561124	651	PREDICTED: cell cycle checkpoint protein	0.758	0.775	0.546	1e-155
297797775	588	predicted protein [Arabidopsis lyrata su	0.710	0.804	0.582	1e-155
15239269	599	cell cycle checkpoint protein RAD17 [Ara	0.750	0.834	0.537	1e-152
255577520	439	cell cycle checkpoint protein rad17, put	0.618	0.938	0.620	1e-141

>gi|297734977|emb|CBI17339.3| unnamed protein product [Vitis vinifera]

 Score =  660 bits (1704), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 335/548 (61%), Positives = 416/548 (75%), Gaps = 20/548 (3%)

Query: 119 EGLVNPDHDSASASSSTQQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFST 178
           EGL      + S+    ++LW +KYKPRSLEELAV +KKVEEV  WFE+RL  S+++   
Sbjct: 71  EGLTGFKVSAGSSRCGGKELWVDKYKPRSLEELAVHKKKVEEVTVWFEKRLRTSREEM-C 129

Query: 179 NVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTIWQEYMHNCKTGLEYTSKLDEFE 238
           N+LVITGQAGVGK+AT+  IASHLGARL EW+TP PTIWQE++HN  +G+ YTSKLDEFE
Sbjct: 130 NLLVITGQAGVGKSATIHAIASHLGARLCEWNTPIPTIWQEHLHNTNSGIRYTSKLDEFE 189

Query: 239 NFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHIPTAV 298
           +FVER+R+YG   PS  GESKSS ILLIDDLPVTNG  ++ RLR CL LL +ST IPTA+
Sbjct: 190 SFVERMRKYGLIPPSFAGESKSSVILLIDDLPVTNGNASYRRLRNCLQLLAQSTQIPTAI 249

Query: 299 VLTECGKADSVD--STAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSL 356
           ++T+ GKADS D  +TA+  EELQ  L +AGA K+A NPIT+ SIK+TLSKICRQEQ  +
Sbjct: 250 LITDYGKADSADNIATARCLEELQLSLENAGACKIAFNPITSNSIKKTLSKICRQEQCGV 309

Query: 357 STEQIDLVAQASGGDIRQAITSLQFSSLKQDPMLNLSLSISKPNFPEEKADG----HGGF 412
           + +QIDL+A++SGGD+R AITSLQ+  LK DPML+LS S     + +EK+D       GF
Sbjct: 310 TADQIDLIARSSGGDVRHAITSLQYFCLKPDPMLSLSFSEPARTYSKEKSDELNPLDDGF 369

Query: 413 SIQFGRDETLSLFHALGKFLHNKRETDNLVKMDQDAFVVKDKFSRLPLKMDAPEKVLSQA 472
           S+ FGRDETLSLFHALGKFLHNKRE++N +   Q+AF+V+++ +RLPLKMDAPE+VL QA
Sbjct: 370 SLPFGRDETLSLFHALGKFLHNKRESENAIAPGQEAFLVRERLTRLPLKMDAPERVLCQA 429

Query: 473 HGQARPVLDFLHENFLDFISEDAIDDAWAVASYLSDADLLLASFRGRLVRYNEADNVLQS 532
           H QARPV+DFLHEN LDF+SE+AIDDA AVASYLSD+D LLA+ RG L    EA NVLQS
Sbjct: 430 HVQARPVVDFLHENVLDFLSEEAIDDASAVASYLSDSDFLLAAHRGMLATSYEAGNVLQS 489

Query: 533 AAASVAARGVLFGNSHPVPPRWHAIRKPKLWRVDQSSLQKKKELLKKKFMAWDGSISADV 592
           AAASVAARGVLFGNSHP+  RWHAIR+PKLW+V+QSSL  K E+L ++ +A         
Sbjct: 490 AAASVAARGVLFGNSHPLASRWHAIRRPKLWQVEQSSLHNKCEILGQRLVAL-------- 541

Query: 593 YNGSSSSDVSVLATEYAPALKWLGNRTSVGLEAHEAPIPDNETQDVDIFEGMSLDDHESE 652
               S+S+VSV+ATEY P  KWL    S G E ++A I  NET+ +D  + M LD+ E+E
Sbjct: 542 ----STSNVSVIATEYIPIFKWLRYGASGGFEDYQALIQGNETE-LDDNDSMILDEKENE 596

Query: 653 ISNYESED 660
           IS+ E ED
Sbjct: 597 ISDDEIED 604

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359476809|ref|XP_002264968.2| PREDICTED: cell cycle checkpoint protein RAD17-like [Vitis vinifera]

 Score =  659 bits (1699), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 337/552 (61%), Positives = 418/552 (75%), Gaps = 21/552 (3%)

Query: 119 EGLVNPDHDSASASSSTQQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFST 178
           EGL      + S+    ++LW +KYKPRSLEELAV +KKVEEV  WFE+RL  S+++   
Sbjct: 71  EGLTGFKVSAGSSRCGGKELWVDKYKPRSLEELAVHKKKVEEVTVWFEKRLRTSREEM-C 129

Query: 179 NVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTIWQEYMHNCKTGLEYTSKLDEFE 238
           N+LVITGQAGVGK+AT+  IASHLGARL EW+TP PTIWQE++HN  +G+ YTSKLDEFE
Sbjct: 130 NLLVITGQAGVGKSATIHAIASHLGARLCEWNTPIPTIWQEHLHNTNSGIRYTSKLDEFE 189

Query: 239 NFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHIPTAV 298
           +FVER+R+YG   PS  GESKSS ILLIDDLPVTNG  ++ RLR CL LL +ST IPTA+
Sbjct: 190 SFVERMRKYGLIPPSFAGESKSSVILLIDDLPVTNGNASYRRLRNCLQLLAQSTQIPTAI 249

Query: 299 VLTECGKADSVD--STAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSL 356
           ++T+ GKADS D  +TA+  EELQ  L +AGA K+A NPIT+ SIK+TLSKICRQEQ  +
Sbjct: 250 LITDYGKADSADNIATARCLEELQLSLENAGACKIAFNPITSNSIKKTLSKICRQEQCGV 309

Query: 357 STEQIDLVAQASGGDIRQAITSLQFSSLKQDPMLNLSLSISKPNFPEEKADG----HGGF 412
           + +QIDL+A++SGGD+R AITSLQ+  LK DPML+LS S     + +EK+D       GF
Sbjct: 310 TADQIDLIARSSGGDVRHAITSLQYFCLKPDPMLSLSFSEPARTYSKEKSDELNPLDDGF 369

Query: 413 SIQFGRDETLSLFHALGKFLHNKRETDNLVKMDQDAFVVKDKFSRLPLKMDAPEKVLSQA 472
           S+ FGRDETLSLFHALGKFLHNKRE++N +   Q+AF+V+++ +RLPLKMDAPE+VL QA
Sbjct: 370 SLPFGRDETLSLFHALGKFLHNKRESENAIAPGQEAFLVRERLTRLPLKMDAPERVLCQA 429

Query: 473 HGQARPVLDFLHENFLDFISEDAIDDAWAVASYLSDADLLLASFRGRLVRYNEADNVLQS 532
           H QARPV+DFLHEN LDF+SE+AIDDA AVASYLSD+D LLA+ RG L    EA NVLQS
Sbjct: 430 HVQARPVVDFLHENVLDFLSEEAIDDASAVASYLSDSDFLLAAHRGMLATSYEAGNVLQS 489

Query: 533 AAASVAARGVLFGNSHPVPPRWHAIRKPKLWRVDQSSLQKKKELLKKKFMAWDGSISADV 592
           AAASVAARGVLFGNSHP+  RWHAIR+PKLW+V+QSSL  K E+L ++ +A         
Sbjct: 490 AAASVAARGVLFGNSHPLASRWHAIRRPKLWQVEQSSLHNKCEILGQRLVAL-------- 541

Query: 593 YNGSSSSDVSVLATEYAPALKWLGNRTSVGLEAHEAPIPDNETQDVDIFEGMSLDDHESE 652
               S+S+VSV+ATEY P  KWL    S G E ++A I  NET+ +D  + M LD+ E+E
Sbjct: 542 ----STSNVSVIATEYIPIFKWLRYGASGGFEDYQALIQGNETE-LDDNDSMILDEKENE 596

Query: 653 ISNYESEDDWMS 664
           IS+ E E DW S
Sbjct: 597 ISDDEIE-DWES 607

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224133656|ref|XP_002327648.1| predicted protein [Populus trichocarpa] gi|222836733|gb|EEE75126.1| predicted protein [Populus trichocarpa]

 Score =  649 bits (1674), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 336/550 (61%), Positives = 420/550 (76%), Gaps = 21/550 (3%)

Query: 118 FEGLVNPDHDSA-SASSSTQQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKF 176
           FE L +    SA S  S+ ++LW +K+KP+SLEELAV +KKVEEV++WFEERL  +K   
Sbjct: 77  FEELFSGSKVSAGSGRSNVKELWVDKHKPQSLEELAVHKKKVEEVKSWFEERLKTTKGNL 136

Query: 177 STNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTIWQEYMHNCKTGLEYTSKLDE 236
             NV+VI G+AGVGK+ T++ IASH GARL EW+TPTPTIWQE++HN  TG++YTSKLDE
Sbjct: 137 INNVVVINGKAGVGKSTTIQVIASHFGARLCEWNTPTPTIWQEHVHNTNTGIQYTSKLDE 196

Query: 237 FENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHIPT 296
           F NF+E+IR+YG    S   + K S ILLIDDLP+TNGR AFERL+ CLL LVRST +PT
Sbjct: 197 FVNFIEKIRKYGLIPSSSSEDVKPSIILLIDDLPMTNGRVAFERLQSCLLHLVRSTQLPT 256

Query: 297 AVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSL 356
           A+++++  +ADS D TA+  E+LQ  L +AGA KV+ NPITN SIK+TLS+ICRQEQ S+
Sbjct: 257 AILVSDYDEADSADHTARRLEQLQLSLENAGACKVSFNPITNNSIKKTLSRICRQEQCSV 316

Query: 357 STEQIDLVAQASGGDIRQAITSLQFSSLKQDPMLNLSLSISKPNFPEEKADG----HGGF 412
           + EQ+DL+A+ SGGDIR AITSLQ   +K D +LN S S   P++   K D       G 
Sbjct: 317 TDEQLDLIAKGSGGDIRHAITSLQLFCVKPDLVLNGSYST--PSYLYGKEDDIDALVSGI 374

Query: 413 SIQFGRDETLSLFHALGKFLHNKRETD--NLVKMDQDAFVVKDKFSRLPLKMDAPEKVLS 470
           S+ FGRDETLSLFHALGKFLHNKRET+  N +    DAF+V++ FSRLPLKMDAPEKVL 
Sbjct: 375 SLLFGRDETLSLFHALGKFLHNKRETEVANAI-TPGDAFLVQENFSRLPLKMDAPEKVLC 433

Query: 471 QAHGQARPVLDFLHENFLDFISEDAIDDAWAVASYLSDADLLLASFRGRLVRYNEADNVL 530
           QAHGQARPV DFLHEN LDFIS++A+DDAW V+SY SD+DLLL+SFRG L RYNEA+NVL
Sbjct: 434 QAHGQARPVTDFLHENVLDFISDEAMDDAWHVSSYFSDSDLLLSSFRGMLARYNEAENVL 493

Query: 531 QSAAASVAARGVLFGNSHPVPPRWHAIRKPKLWRVDQSSLQKKKELLKKKFMAWDGSISA 590
           QSAAASVA RGVLFGNSHP PPRWHAIRKPKLW+V++S L  +KE+++++F+A       
Sbjct: 494 QSAAASVAVRGVLFGNSHPSPPRWHAIRKPKLWQVEKSMLHNQKEIVRQRFIA------- 546

Query: 591 DVYNGSSSSDVSVLATEYAPALKWLGNRTSVGLEAHEAPIPDNETQDVDIFEGMSLDDHE 650
             YNGSSS +VS +ATEY P LKWL +R S G E ++A +   +T D +  + MSLDD E
Sbjct: 547 --YNGSSSCNVSDVATEYMPLLKWLEHRAS-GFEDNQALVYCKKT-DGESCDRMSLDDKE 602

Query: 651 SEISNYESED 660
           S+IS+ E E+
Sbjct: 603 SDISDDEIEE 612

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449434132|ref|XP_004134850.1| PREDICTED: cell cycle checkpoint protein RAD17-like [Cucumis sativus] gi|449491306|ref|XP_004158856.1| PREDICTED: cell cycle checkpoint protein RAD17-like [Cucumis sativus]

 Score =  581 bits (1498), Expect = e-163,   Method: Compositional matrix adjust.
 Identities = 298/537 (55%), Positives = 374/537 (69%), Gaps = 22/537 (4%)

Query: 128 SASASSSTQQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQA 187
           + S S    +LW +KY+P SLEELAVQ+KKV+EV+ WFE+RL    D   +NV++ITG A
Sbjct: 86  AGSGSVCRNELWIDKYRPHSLEELAVQKKKVDEVKVWFEDRLRTPMDANGSNVILITGPA 145

Query: 188 GVGKTATVRQIASHLGARLYEWDTPTPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRY 247
           GVGK+ATV  IASHLGARL EWDTPTP IW+E++HN   G++YTSKLDEFE+F+ R+R+Y
Sbjct: 146 GVGKSATVHVIASHLGARLCEWDTPTPVIWREHLHNLTAGIQYTSKLDEFESFIGRMRKY 205

Query: 248 GSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHIPTAVVLTECGKAD 307
           G        +SK   ILLIDDLP+TNG+ A  RL+ CL L V+ST +PTA+V+T+C KA+
Sbjct: 206 GVIPSCFSIDSKQPVILLIDDLPLTNGKAALRRLQSCLHLYVQSTQVPTAIVITDCAKAE 265

Query: 308 SVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQA 367
           + D T Q  EE+Q  L +AGA KVA NPITN SIK+T+S+IC  EQY L+ EQID +A++
Sbjct: 266 TTDFTVQYLEEIQLCLENAGACKVAFNPITNNSIKKTISRICSCEQYDLAVEQIDAIAKS 325

Query: 368 SGGDIRQAITSLQFSSLKQDPMLNLSL----SISKPNFPEEKADGHGGFSIQFGRDETLS 423
           SGGD+R AI SLQ   LK   + + S     S+     P    D    FS QFGRDETLS
Sbjct: 326 SGGDVRHAIMSLQLFCLKPSQICSSSSSAQESLKDEEMPHTLVDDR--FSFQFGRDETLS 383

Query: 424 LFHALGKFLHNKRETDNLVKMDQDAFVVKDKFSRLPLKMDAPEKVLSQAHGQARPVLDFL 483
           LFHALGKFLHNKR + N + +D + F V++   R PL MD PEKVL QAHGQARP+ DFL
Sbjct: 384 LFHALGKFLHNKRHSVNELVLDSE-FSVQESLLRRPLNMDPPEKVLCQAHGQARPIADFL 442

Query: 484 HENFLDFISEDAIDDAWAVASYLSDADLLLASFRGRLVRYNEADNVLQSAAASVAARGVL 543
           HEN LDF++E+AIDDAW VASYL DAD LL+S+ G L R+N+A+N+L  AAASVA RGVL
Sbjct: 443 HENVLDFMNEEAIDDAWVVASYLGDADTLLSSYDGMLARHNDAENILHLAAASVAVRGVL 502

Query: 544 FGNSHPVPPRWHAIRKPKLWRVDQSSLQKKKELLKKKFMAWDGSISADVYNGSSSSDVSV 603
           FGNSHP+  RWHAIR+PKLW+++ SSL  KK ++K++F+          Y G S +  SV
Sbjct: 503 FGNSHPLSSRWHAIRRPKLWQIEGSSLSNKK-MVKQRFVP---------YGGISLAHFSV 552

Query: 604 LATEYAPALKWLGNRTSVGLEAHEAPIPDNETQDVDIFEGMSLDDHESEISNYESED 660
           +ATEY PALKWLGN  S   E   A   +N   D+ +  G    D ES  S  E ED
Sbjct: 553 VATEYVPALKWLGNSVSEDHEKLWALTEENTGFDM-VISG----DQESHTSEEEIED 604

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147780512|emb|CAN62558.1| hypothetical protein VITISV_009206 [Vitis vinifera]

 Score =  576 bits (1484), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 337/676 (49%), Positives = 426/676 (63%), Gaps = 76/676 (11%)

Query: 2   QISLSFEKFDEVLNGSKVSNVIWNQENDSALGSSST--QQLWTDKYKLCSLEEPDVQKKN 59
           Q+ L  E+F E L G KVS            GSS    ++LW DKYK  SLEE  V KK 
Sbjct: 73  QMRLFCEEFGEGLTGFKVS-----------AGSSRCGGKELWVDKYKPRSLEELAVHKKK 121

Query: 60  VEHFLTPSRFEGLVNPKRDLALGSSSRQQLWTNKNKPCSLEEHAIQKENVGRFLTPSRFE 119
           VE       FE  +   R +  G      L  +      +    I  +  G F    ++ 
Sbjct: 122 VEEVTV--WFEKRLRTSR-VCFG------LLISTKIGNVVRIVKIFADTAGVFQGGLKWY 172

Query: 120 GLVNPDHDS-----ASASSSTQQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKD 174
           G+V+  H +     A  +      + E   P++ EE+                       
Sbjct: 173 GIVSRIHPADPDIWAQLNDDYDDAYYEPIIPKNAEEMC---------------------- 210

Query: 175 KFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTIWQEYMHNCKTGLEYTSKL 234
               N+LVITGQAGVGK+AT+  I SHLGARL EW+TP PTIWQE++HN  +G+ YTSKL
Sbjct: 211 ----NLLVITGQAGVGKSATIHAIVSHLGARLCEWNTPIPTIWQEHLHNTNSGIRYTSKL 266

Query: 235 DEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHI 294
           DEFE+FVER+R+YG   PS  GESKSS ILLIDDLPVTNG  ++ RLR CL LL +ST I
Sbjct: 267 DEFESFVERMRKYGLIPPSFAGESKSSVILLIDDLPVTNGNASYRRLRNCLQLLAQSTQI 326

Query: 295 PTAVVLTECGKADSVD--STAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQE 352
           PTA+++T+ GKADS D  +TA+  EELQ  L +AGA K+A NPIT+ SIK+TLSKICRQE
Sbjct: 327 PTAILITDYGKADSADNIATARCLEELQLSLENAGACKIAFNPITSNSIKKTLSKICRQE 386

Query: 353 QYSLSTEQIDLVAQASGGDIRQAITSLQFSSLKQDPMLNLSLSISKPNFPEEKADG---- 408
           Q  ++ +QIDL+A++SGGDIR AITSLQ+  LK DPML+LS S     + +EK D     
Sbjct: 387 QCGVTADQIDLIARSSGGDIRHAITSLQYFCLKPDPMLSLSFSEPARTYSKEKXDELNPL 446

Query: 409 HGGFSIQFGRDETLSLFHALGKFLHNKRETDNLVKMDQDAFVVKDKFSR-LPLKMDA--- 464
             GFS+ FGRDETLSLFHALGKFLHNKRE++N +   Q+AF+V+++  + +PLKM     
Sbjct: 447 DDGFSLPFGRDETLSLFHALGKFLHNKRESENAIAPGQEAFLVRERLDKIIPLKMTVLML 506

Query: 465 PEKVLSQAHGQARPVLDFLHENFLDFISEDAIDDAWAVASYLSDADLLLASFRGRLVRYN 524
            +    + H QARPV+DFLHEN LDF+SE+AIDDA AVASYLSD+D LLA+ RG L    
Sbjct: 507 QKGFFVKQHVQARPVVDFLHENVLDFLSEEAIDDASAVASYLSDSDFLLAAHRGMLATSY 566

Query: 525 EADNVLQSAAASVAARGVLFGNSHPVPPRWHAIRKPKLWRVDQSSLQKKKELLKKKFMAW 584
           EA NVLQSAAASVAARGVLF NSHP+  RWHAIR+PKLW+V+QSSL  K E+L ++ +A 
Sbjct: 567 EAGNVLQSAAASVAARGVLFANSHPLASRWHAIRRPKLWQVEQSSLHNKCEILGQRLVAL 626

Query: 585 DGSISADVYNGSSSSDVSVLATEYAPALKWLGNRTSVGLEAHEAPIPDNETQDVDIFEGM 644
                       S+S+VSV+ATEY P  KWL    S G E ++A I  NET+  D  + M
Sbjct: 627 ------------STSNVSVIATEYIPMFKWLRYGASGGFEDYQALIQGNETELXD-NDSM 673

Query: 645 SLDDHESEISNYESED 660
            L + E+EIS+ E ED
Sbjct: 674 ILXEKENEISDDEIED 689

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357517967|ref|XP_003629272.1| Cell cycle checkpoint protein RAD17 [Medicago truncatula] gi|355523294|gb|AET03748.1| Cell cycle checkpoint protein RAD17 [Medicago truncatula]

 Score =  557 bits (1435), Expect = e-156,   Method: Compositional matrix adjust.
 Identities = 282/538 (52%), Positives = 377/538 (70%), Gaps = 22/538 (4%)

Query: 128 SASASSSTQQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQA 187
           + +  S+ ++LW +KYKP SLEELAV +KKVEEV+ WFEERL  SK  +  NVLV++GQA
Sbjct: 83  AGTQRSTAEELWVDKYKPHSLEELAVHKKKVEEVKTWFEERLKPSKGVYRNNVLVVSGQA 142

Query: 188 GVGKTATVRQIASHLGARLYEWDTPTPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRY 247
           G+GK+A +  IASHLGA +  W+TPTP IWQE+++N  T  +YTSKLDEF +FVERIR +
Sbjct: 143 GIGKSAAIHVIASHLGAMVCGWNTPTPVIWQEHLYNSGTETKYTSKLDEFVSFVERIRTF 202

Query: 248 GSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHIPTAVVLTECGKAD 307
           G    S  GESK S I LIDDLP+ + + A  RL+ CL LLV +T IPTA+++T+ G  D
Sbjct: 203 GLIPTSFTGESKPSIIYLIDDLPMMHSKAALGRLKDCLNLLVHTTRIPTAILVTDYGNTD 262

Query: 308 SVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQA 367
           S D  A+S EEL++ L  +GA K+A NPIT  SIK+ L +IC+ EQ  ++ + +DL+A+A
Sbjct: 263 SADYNARSVEELKTSLESSGACKIAFNPITVNSIKKILFRICQMEQCDVTADNVDLIAKA 322

Query: 368 SGGDIRQAITSLQFSSLKQDPMLNLSLSISKPNFPEEKADG----HGGFSIQFGRDETLS 423
           SGGDIR AITSLQF  L  + + +LS S   P+  +E+++       G S+ FGRDETLS
Sbjct: 323 SGGDIRHAITSLQFFCLNPNQVHSLSQSTRSPHALKEESNKPVELDDGSSLYFGRDETLS 382

Query: 424 LFHALGKFLHNKRETDNLVKMDQDAFVVKDKFSRLPLKMDAPEKVLSQAHGQARPVLDFL 483
           LFHALGKFLHNKRET   V+ DQ+ F++ ++FSRLPLKMD PEK+L Q+H Q  PV DFL
Sbjct: 383 LFHALGKFLHNKRETGVAVEYDQNGFLIHERFSRLPLKMDVPEKILCQSHVQPGPVADFL 442

Query: 484 HENFLDFISEDAIDDAWAVASYLSDADLLLASFRGRLVRYNEADNVLQSAAASVAARGVL 543
           HEN LDF++++A++DAW ++SYL DAD+LL   RG +  YNEA+++LQSAAAS+A RGVL
Sbjct: 443 HENVLDFLNDEAVEDAWILSSYLGDADILLTKLRGMVSSYNEAESILQSAAASIAVRGVL 502

Query: 544 FGNSHPVPPRWHAIRKPKLWRVDQSSLQKKKELLKKKFMAWDGSISADVYNGSSSSDVSV 603
           FGNS P+  RWHAIR+PKLW+V++    +K ++L+++  A          N  SS  +SV
Sbjct: 503 FGNSCPLSSRWHAIRRPKLWQVEKELSYQKNKMLRQRIPAC---------NQLSSYHMSV 553

Query: 604 LATEYAPALKWLGNRTSVGL-EAHEAPIPDNETQDVDIFEGMSLDDHESEISNYESED 660
           +ATEY P  K LGNR   G  E H+         ++DI + MSLD    EIS+ + ED
Sbjct: 554 MATEYMPMFKLLGNRVGSGYDELHQE-------SNIDI-DKMSLDGEAMEISDDDIED 603

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356561124|ref|XP_003548835.1| PREDICTED: cell cycle checkpoint protein RAD17-like [Glycine max]

 Score =  555 bits (1431), Expect = e-155,   Method: Compositional matrix adjust.
 Identities = 289/529 (54%), Positives = 370/529 (69%), Gaps = 24/529 (4%)

Query: 136 QQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATV 195
           + LW +KYKP SLEELAV +KKVEEV+ WFEERL  SK  +  NVLVI+GQAGVGK+A +
Sbjct: 142 EDLWIDKYKPCSLEELAVHKKKVEEVKTWFEERLKPSKGAYCNNVLVISGQAGVGKSAAI 201

Query: 196 RQIASHLGARLYEWDTPTPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIP 255
             IASHLGA +  W+TPTP IWQE+++N  TG +YTSKLDEFE+FV+R+R+YG    S  
Sbjct: 202 HVIASHLGAVVCGWNTPTPVIWQEHLYNSGTGTKYTSKLDEFESFVDRVRKYGLLLTSHT 261

Query: 256 GESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHIPTAVVLTECGKADSVDSTAQS 315
           GESK S ILLIDDLP+TNG++AF RL+ CL +LV ST IPTA++ T+ G ADS D  A+ 
Sbjct: 262 GESKPSVILLIDDLPLTNGKSAFRRLKDCLHVLVNSTQIPTAILFTDYGNADSADYNARC 321

Query: 316 FEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASGGDIRQA 375
            EEL+  L  +GA KVA NPIT  ++K+ L +IC+ E   ++ E +DL+A+ SGGDIR A
Sbjct: 322 LEELKLSLESSGACKVAFNPITLNTMKKILFRICQMEHCDVTAEYVDLIAKTSGGDIRHA 381

Query: 376 ITSLQFSSLKQDPMLNLSLSISKPNFPEEKADGHGGFSIQFGRDETLSLFHALGKFLHNK 435
           ITSLQF  LK       +L   + + P    D   G+S+ FGRDETLSLFHALGKFLHNK
Sbjct: 382 ITSLQFFCLKPSTCYRGALK-EESDKPVRSDD---GYSLHFGRDETLSLFHALGKFLHNK 437

Query: 436 RETDNLVKMDQDAFVVKDKFSRLPLKMDAPEKVLSQAHGQARPVLDFLHENFLDFISEDA 495
           RE+   V  + D F+++++ SRLPLKMD PEK+L QAH Q  PV DFLHEN LDF++++A
Sbjct: 438 RESG--VSTEYDGFLMQERLSRLPLKMDVPEKILYQAHVQPGPVADFLHENVLDFLNDEA 495

Query: 496 IDDAWAVASYLSDADLLLASFRGRLVRYNEADNVLQSAAASVAARGVLFGNSHPVPPRWH 555
           IDDAW ++SYL DAD+LL   RG L  YNEA++VL+SAAAS+A RGVLFGNSHP+  RWH
Sbjct: 496 IDDAWTLSSYLGDADILLTKLRGMLSTYNEAESVLRSAAASIAVRGVLFGNSHPLSSRWH 555

Query: 556 AIRKPKLWRVDQSSLQKKKELLKKKFMAWDGSISADVYNGSSSSDVSVLATEYAPALKWL 615
           AIR+PKLW+V+++SL  K E+ + +  A             SS  +S++ TEY P LK L
Sbjct: 556 AIRRPKLWQVEKASLY-KNEVDRLRIPAC---------RRFSSYHMSIMTTEYMPMLKLL 605

Query: 616 GNRTSVGLEAHEAPIPDN----ETQDVDIFEGMSLDDHESEISNYESED 660
           GN    G   H  P P++    E +D D F+ M LD    EIS+ + ED
Sbjct: 606 GNGAWGG---HHEPSPESLLNLEMEDFD-FDKMDLDGQSREISDDDIED 650

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297797775|ref|XP_002866772.1| predicted protein [Arabidopsis lyrata subsp. lyrata] gi|297312607|gb|EFH43031.1| predicted protein [Arabidopsis lyrata subsp. lyrata]

 Score =  555 bits (1431), Expect = e-155,   Method: Compositional matrix adjust.
 Identities = 292/501 (58%), Positives = 358/501 (71%), Gaps = 28/501 (5%)

Query: 133 SSTQQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKT 192
           S    LW +KY+PR+LEELAV +KKVE+V+ WFEE L  SKD    NVL++TGQAGVGK+
Sbjct: 76  SKNTDLWVDKYRPRTLEELAVHKKKVEQVKLWFEESLDFSKDGLRNNVLLVTGQAGVGKS 135

Query: 193 ATVRQIASHLGARLYEWDTPTPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSP 252
           AT+  IAS LG  +YEW+ P PTIWQE++HN  +GL+YTSKLDEFENFVE  R+YG  + 
Sbjct: 136 ATIHLIASILGVTVYEWNAPIPTIWQEHVHNSSSGLKYTSKLDEFENFVESTRKYGVMAS 195

Query: 253 SIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHIPTAVVLTECGKADSVDST 312
           S     K+  ILLIDDLP+ NGR A ERL+ CLLLLVRST IPT +++T+  KADS D T
Sbjct: 196 SSTEGIKAPVILLIDDLPLANGRHACERLQNCLLLLVRSTQIPTVILITDYDKADSSDQT 255

Query: 313 AQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASGGDI 372
           A+S E+ QS L  AGA KVA NPIT  SIK+ L +ICR+E   ++T +ID +A ASGGDI
Sbjct: 256 ARSMEDAQSSLERAGALKVAFNPITKNSIKKALQRICREEHCKVTTMEIDQMASASGGDI 315

Query: 373 RQAITSLQFSSLKQDPMLNLSLSISKPNFPEEKADG--HG-----------GFSIQFGRD 419
           R AITSLQ  S+K D      L+ +K   P    D   HG           G S  FGRD
Sbjct: 316 RHAITSLQLFSVKPD------LNHTKIKSPRPGMDDSYHGNEQTMYSGLDSGISSCFGRD 369

Query: 420 ETLSLFHALGKFLHNKRETDNLVKMDQDAFVVKDKFSRLPLKMDAPEKVLSQAHGQARPV 479
           ETLSLFHALGKFLHNKRETDN++  D    +V D+F+RLPLKMDAPEKVLSQAHGQA  V
Sbjct: 370 ETLSLFHALGKFLHNKRETDNVIVSDCSNSLVHDEFARLPLKMDAPEKVLSQAHGQAGRV 429

Query: 480 LDFLHENFLDFISEDAIDDAWAVASYLSDADLLLASFRGRLVRYNEADNVLQSAAASVAA 539
           +DFLHEN LDF+SE AI+DAW V+SYL+DADLLLA  RG++  +N+ ++V QSA ASVA 
Sbjct: 430 VDFLHENVLDFVSEGAIEDAWCVSSYLADADLLLADLRGKMSGHNKTEDVPQSAGASVAV 489

Query: 540 RGVLFGNSHPVPPRWHAIRKPKLWRVDQSSLQKKKELLKKKFMAWDGSISADVYNGSSSS 599
           RGVL+GN  P   RWH IRKPKLW+V+QSS+Q KK L +++ ++         Y GS  +
Sbjct: 490 RGVLYGNKQPCSSRWHVIRKPKLWQVEQSSMQTKKNLREQRNIS---------YEGSRVA 540

Query: 600 DVSVLATEYAPALKWLGNRTS 620
           D+SV+ATEY+P LKWL  R S
Sbjct: 541 DISVMATEYSPVLKWLSYRAS 561

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15239269|ref|NP_201414.1| cell cycle checkpoint protein RAD17 [Arabidopsis thaliana] gi|55976607|sp|Q9MBA3.1|RAD17_ARATH RecName: Full=Cell cycle checkpoint protein RAD17; Short=AtRAD17; AltName: Full=Radiation-sensitive protein 17 gi|6855472|dbj|BAA90479.1| AtRAD17 [Arabidopsis thaliana] gi|10177128|dbj|BAB10418.1| AtRAD17 [Arabidopsis thaliana] gi|332010780|gb|AED98163.1| cell cycle checkpoint protein RAD17 [Arabidopsis thaliana]

 Score =  545 bits (1403), Expect = e-152,   Method: Compositional matrix adjust.
 Identities = 292/543 (53%), Positives = 371/543 (68%), Gaps = 43/543 (7%)

Query: 133 SSTQQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKT 192
           S    LW +KY+PR+LEEL+V +KKV+EV+ WF+E L   K+    NVL++TGQAGVGK+
Sbjct: 87  SKNTDLWVDKYRPRTLEELSVHKKKVDEVKLWFQESLDFLKNGLRNNVLLVTGQAGVGKS 146

Query: 193 ATVRQIASHLGARLYEWDTPTPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSP 252
           AT+  I S LG  ++EW+ P PTIWQE++HN  +GL+YTSKLDEFENFVE  R+YG  + 
Sbjct: 147 ATIHLITSILGVTVHEWNAPIPTIWQEHVHNTSSGLKYTSKLDEFENFVESTRKYGVMAS 206

Query: 253 SIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHIPTAVVLTECGKADSVDST 312
           S     K+  +LLIDDLP+ NGR AFERL+ CLLLLV+ST IPT +++T+   ADS D T
Sbjct: 207 SSTDGIKAPVVLLIDDLPLANGRHAFERLQNCLLLLVKSTQIPTVILITDHNNADSSDQT 266

Query: 313 AQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASGGDI 372
           A+  E+ QS L  AGA KVA NPIT  SIK+ L +ICR+E   ++T +ID +A ASGGDI
Sbjct: 267 ARRMEDTQSSLERAGALKVAFNPITKNSIKKVLQRICREEHCKVTTMEIDQMATASGGDI 326

Query: 373 RQAITSLQFSSLKQDPMLNLSLSISKPNFPEEKADGHG-----------GFSIQFGRDET 421
           R AITSLQ  S+K  P LN +  I  P  P  + + HG           G S  FGRDET
Sbjct: 327 RHAITSLQLFSVK--PELNHT-KIKSPR-PGMEDNYHGNEQTMYSGLDSGISSCFGRDET 382

Query: 422 LSLFHALGKFLHNKRETDNLVKMDQDAFVVKDKFSRLPLKMDAPEKVLSQAHGQARPVLD 481
           LSLFHALGKFLHNKRETDN++  +  + +V D+F+RLPLKMDAPEKVLSQAHGQA  V+D
Sbjct: 383 LSLFHALGKFLHNKRETDNVIISECSSSLVHDEFARLPLKMDAPEKVLSQAHGQAGRVVD 442

Query: 482 FLHENFLDFISEDAIDDAWAVASYLSDADLLLASFRGRLVRYNEADNVLQSAAASVAARG 541
           FLHEN LDF+S+ AI+DAW V+SYL+DADLLLA  RG++  +N  ++V QSA ASVA RG
Sbjct: 443 FLHENVLDFVSDGAIEDAWCVSSYLADADLLLADIRGKMSGHNNTEDVPQSAGASVAVRG 502

Query: 542 VLFGNSHPVPPRWHAIRKPKLWRVDQSSLQKKKELLKKKFMAWDGSISADVYNGSSSSDV 601
           VL+GN  P   RWH IRKPKLW+V+QSS+Q KK L +++ ++         Y GS  +D+
Sbjct: 503 VLYGNKQPCSSRWHVIRKPKLWQVEQSSIQTKKNLREQRNIS---------YEGSRVADI 553

Query: 602 SVLATEYAPALKWLGNRTSVGLEAHEAPIPDNETQDVDIFEGMS--LDDHESEISNYESE 659
           SV+ATEY+P LKWL  R S                  D F GM    D+ +S+IS  +  
Sbjct: 554 SVMATEYSPVLKWLSYRAS-----------------PDAFPGMGEETDEEDSDISEDDEI 596

Query: 660 DDW 662
            DW
Sbjct: 597 QDW 599

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255577520|ref|XP_002529638.1| cell cycle checkpoint protein rad17, putative [Ricinus communis] gi|223530864|gb|EEF32725.1| cell cycle checkpoint protein rad17, putative [Ricinus communis]

 Score =  507 bits (1305), Expect = e-141,   Method: Compositional matrix adjust.
 Identities = 266/429 (62%), Positives = 324/429 (75%), Gaps = 17/429 (3%)

Query: 227 GLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLL 286
           G+ YTSKLDEF NF+E+IR+YG   PS   ESKS  +LLIDDLPV NGR AFERL+ CLL
Sbjct: 13  GVNYTSKLDEFMNFIEKIRKYGLI-PSFSAESKSPVMLLIDDLPVANGRAAFERLQNCLL 71

Query: 287 LLVRSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLS 346
           LLVRST +PTA++LT+ GK DS D +A+  EEL   L  AGA KVA NPIT+ SIK+ L+
Sbjct: 72  LLVRSTQVPTAILLTDYGKEDSADYSARYMEELLQSLERAGACKVAFNPITSSSIKKVLT 131

Query: 347 KICRQEQYSLSTEQIDLVAQASGGDIRQAITSLQFSSLKQDPMLNLSLSISK-PNFPEEK 405
           +IC+Q+Q++++ EQI+L+A+ASGGDIR AITSLQ  S+K D ML+LS   +  P++ + +
Sbjct: 132 RICKQKQHNVTAEQIELIAKASGGDIRHAITSLQLFSVKPDIMLSLSSLSTLTPSYSDGR 191

Query: 406 ADG----HGGFSIQFGRDETLSLFHALGKFLHNKRETDNLVKMDQDAFVVKDKFSRLPLK 461
           AD       GFS+ FGRDETLSLFHALGKFLHNKRET+     DQDAF+V+DKFSRLPLK
Sbjct: 192 ADEINALTSGFSLLFGRDETLSLFHALGKFLHNKRETEAPSVFDQDAFLVRDKFSRLPLK 251

Query: 462 MDAPEKVLSQAHGQARPVLDFLHENFLDFISEDAIDDAWAVASYLSDADLLLASFRGRLV 521
           MDAPEK+L QAHGQARP+ DFLHEN LDFIS+DA+D    VASYLSDADLLL+SFRG LV
Sbjct: 252 MDAPEKILCQAHGQARPIADFLHENVLDFISDDAMDATGNVASYLSDADLLLSSFRGMLV 311

Query: 522 RYNEADNVLQSAAASVAARGVLFGNSHPVPPRWHAIRKPKLWRVDQSSLQKKKELLKKKF 581
           R NEA++VLQSAAASVA RGVLFGNSHP P RWHAIR+PKLW+  QS L+ +K +L ++ 
Sbjct: 312 RCNEAESVLQSAAASVAVRGVLFGNSHPSPSRWHAIRRPKLWQAGQSMLRNQKAMLSQRL 371

Query: 582 MAWDGSISADVYNGSSSSDVSVLATEYAPALKWLGNRTSVGLEAHEAPIPDNETQDVDIF 641
           +A           GSS S+V+ + TEY P LKWLG+R   G+EAH+     NE  D D  
Sbjct: 372 IA---------NGGSSFSNVAEIVTEYVPVLKWLGHRAP-GVEAHQVFEHHNEAYD-DSS 420

Query: 642 EGMSLDDHE 650
           E MSL+D E
Sbjct: 421 ERMSLEDGE 429

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	666
TAIR|locus:2156952	599	ATRAD17 "RADIATION SENSITIVE 1	0.878	0.976	0.478	3.8e-144
UNIPROTKB|F1NTX9	693	RAD17 "Uncharacterized protein	0.360	0.346	0.285	7.9e-32
UNIPROTKB|F1NC53	694	RAD17 "Uncharacterized protein	0.360	0.345	0.285	8e-32
DICTYBASE|DDB_G0292504	1191	rad17 "Checkpoint protein RAD2	0.396	0.221	0.263	7.8e-26
FB|FBgn0025808	535	Rad17 "Rad17" [Drosophila mela	0.448	0.558	0.271	5.2e-25
RGD|1309515	686	Rad17 "RAD17 homolog (S. pombe	0.436	0.424	0.285	5e-22
UNIPROTKB|E9PTL1	686	Rad17 "Protein Rad17" [Rattus	0.436	0.424	0.285	5e-22
ZFIN|ZDB-GENE-040718-409	666	rad17 "RAD17 homolog (S. pombe	0.465	0.465	0.285	3.5e-20
UNIPROTKB|I3L290	681	RAD17 "Cell cycle checkpoint p	0.439	0.430	0.264	1e-19
UNIPROTKB|O75943	681	RAD17 "Cell cycle checkpoint p	0.439	0.430	0.264	1e-19

TAIR|locus:2156952 ATRAD17 "RADIATION SENSITIVE 17" [Arabidopsis thaliana (taxid:3702)]

 Score = 1331 (473.6 bits), Expect = 3.8e-144, Sum P(2) = 3.8e-144
 Identities = 295/616 (47%), Positives = 382/616 (62%)

Query:    44 KYKLCSLEEPDVQKKNVEHFLTPSRFEGLVNPKRDLALGSSSRQQLWTNKNKPCSLEEHA 103
             K KL SLE+ D  +    + L  SR      P+      ++ R       +   + +E +
Sbjct:     3 KKKL-SLEDEDDDRS---YNLRSSRSNAKSKPRSSAGTATNPRASKRARLSGASATQEDS 58

Query:   104 IQKENVGRFLTPSRFEGLVNPDHDSASASSSTQQLWAEKYKPRSLEELAVQRKKVEEVRA 163
                + + R       E L      S    S    LW +KY+PR+LEEL+V +KKV+EV+ 
Sbjct:    59 SLVDKI-RLSFEDFDEALSGFKVSSGYERSKNTDLWVDKYRPRTLEELSVHKKKVDEVKL 117

Query:   164 WFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTIWQEYMHN 223
             WF+E L   K+    NVL++TGQAGVGK+AT+  I S LG  ++EW+ P PTIWQE++HN
Sbjct:   118 WFQESLDFLKNGLRNNVLLVTGQAGVGKSATIHLITSILGVTVHEWNAPIPTIWQEHVHN 177

Query:   224 CKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQ 283
               +GL+YTSKLDEFENFVE  R+YG  + S     K+  +LLIDDLP+ NGR AFERL+ 
Sbjct:   178 TSSGLKYTSKLDEFENFVESTRKYGVMASSSTDGIKAPVVLLIDDLPLANGRHAFERLQN 237

Query:   284 CLLLLVRSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKR 343
             CLLLLV+ST IPT +++T+   ADS D TA+  E+ QS L  AGA KVA NPIT  SIK+
Sbjct:   238 CLLLLVKSTQIPTVILITDHNNADSSDQTARRMEDTQSSLERAGALKVAFNPITKNSIKK 297

Query:   344 TLSKICRQEQYSLSTEQIDLVAQASGGDIRQAITSLQFSSLKQDPMLNLSLSISKPNFPE 403
              L +ICR+E   ++T +ID +A ASGGDIR AITSLQ  S+K  P LN +  I  P  P 
Sbjct:   298 VLQRICREEHCKVTTMEIDQMATASGGDIRHAITSLQLFSVK--PELNHT-KIKSPR-PG 353

Query:   404 EKADGHG-----------GFSIQFGRDETLSLFHALGKFLHNKRETDNLVKMDQDAFVVK 452
              + + HG           G S  FGRDETLSLFHALGKFLHNKRETDN++  +  + +V 
Sbjct:   354 MEDNYHGNEQTMYSGLDSGISSCFGRDETLSLFHALGKFLHNKRETDNVIISECSSSLVH 413

Query:   453 DKFSRLPLKMDAPEKVLSQAHGQARPVLDFLHENFLDFISEDAIDDAWAVASYXXXXXXX 512
             D+F+RLPLKMDAPEKVLSQAHGQA  V+DFLHEN LDF+S+ AI+DAW V+SY       
Sbjct:   414 DEFARLPLKMDAPEKVLSQAHGQAGRVVDFLHENVLDFVSDGAIEDAWCVSSYLADADLL 473

Query:   513 XXXFRGRLVRYNEADNVLQSAAASVAARGVLFGNSHPVPPRWHAIRKPKLWRVDQSSXXX 572
                 RG++  +N  ++V QSA ASVA RGVL+GN  P   RWH IRKPKLW+V+QSS   
Sbjct:   474 LADIRGKMSGHNNTEDVPQSAGASVAVRGVLYGNKQPCSSRWHVIRKPKLWQVEQSSIQT 533

Query:   573 XXXXXXXXFMAWDGSISADVYNGSSSSDVSVLATEYAPALKWLGNRTSVGLEAHEAPIPD 632
                      +    +IS   Y GS  +D+SV+ATEY+P LKWL  R S   +A      +
Sbjct:   534 KKN------LREQRNIS---YEGSRVADISVMATEYSPVLKWLSYRASP--DAFPGMGEE 582

Query:   633 NETQDVDIFEGMSLDD 648
              + +D DI E   + D
Sbjct:   583 TDEEDSDISEDDEIQD 598

GO:0005634 "nucleus" evidence=ISM;IEA

GO:0006281 "DNA repair" evidence=IEA

GO:0006282 "regulation of DNA repair" evidence=IMP

GO:0006259 "DNA metabolic process" evidence=RCA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=RCA

GO:0007126 "meiosis" evidence=RCA

GO:0033044 "regulation of chromosome organization" evidence=RCA

GO:0043687 "post-translational protein modification" evidence=RCA

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=RCA

UNIPROTKB|F1NTX9 RAD17 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 274 (101.5 bits), Expect = 7.9e-32, Sum P(3) = 7.9e-32
 Identities = 75/263 (28%), Positives = 131/263 (49%)

Query:   139 WAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQI 198
             W +KYKP +  +LAVQ+KK+EEV  W +  +   + K    VL++TG AG GKTATV+ +
Sbjct:    97 WVDKYKPETQNDLAVQKKKIEEVETWLKMHIFQRQPKQDGCVLLLTGPAGCGKTATVQIL 156

Query:   199 ASHLGARLYEWDTPTPTIW-QEYMHNCK----TGLEYTSKLDE--FENFVERIRRYGSTS 251
             A  LG ++ +W  P    + +E + N          + S+     F++F+ R  +Y    
Sbjct:   157 AKDLGVQVQDWTNPISLDFTKEDLRNISGHNSNSHTFPSQAQAALFQDFLLRANKYNKLQ 216

Query:   252 PSIPGESKSS--AILLIDDLPVTNGRTAFERLRQCLLLLVRSTHIPTAVVLTECGKADSV 309
               + GES  +   ++LI+D+P    R     L + L   VR++  P   ++++    DS 
Sbjct:   217 --MLGESSENDKKLILIEDMPNQFYRDP-SSLHEILRRFVRTSRCPLIFIISDNFSGDSN 273

Query:   310 DSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKIC-------RQEQYSLSTEQID 362
                    E L+ + +      ++  P+   ++ + L++I        R++ Y+     ++
Sbjct:   274 QRLLFPKEILEELCISI----ISFKPVAPTNMMKVLNRIATAEANMNREKNYAPDRASLE 329

Query:   363 LVAQASGGDIRQAITSLQFSSLK 385
             L+ +   GDIR AI SLQF S+K
Sbjct:   330 LLCKGCSGDIRSAINSLQFFSMK 352

GO:0005634 "nucleus" evidence=IEA

GO:0006281 "DNA repair" evidence=IEA

GO:0007049 "cell cycle" evidence=IEA

UNIPROTKB|F1NC53 RAD17 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 274 (101.5 bits), Expect = 8.0e-32, Sum P(3) = 8.0e-32
 Identities = 75/263 (28%), Positives = 131/263 (49%)

Query:   139 WAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQI 198
             W +KYKP +  +LAVQ+KK+EEV  W +  +   + K    VL++TG AG GKTATV+ +
Sbjct:    98 WVDKYKPETQNDLAVQKKKIEEVETWLKMHIFQRQPKQDGCVLLLTGPAGCGKTATVQIL 157

Query:   199 ASHLGARLYEWDTPTPTIW-QEYMHNCK----TGLEYTSKLDE--FENFVERIRRYGSTS 251
             A  LG ++ +W  P    + +E + N          + S+     F++F+ R  +Y    
Sbjct:   158 AKDLGVQVQDWTNPISLDFTKEDLRNISGHNSNSHTFPSQAQAALFQDFLLRANKYNKLQ 217

Query:   252 PSIPGESKSS--AILLIDDLPVTNGRTAFERLRQCLLLLVRSTHIPTAVVLTECGKADSV 309
               + GES  +   ++LI+D+P    R     L + L   VR++  P   ++++    DS 
Sbjct:   218 --MLGESSENDKKLILIEDMPNQFYRDP-SSLHEILRRFVRTSRCPLIFIISDNFSGDSN 274

Query:   310 DSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKIC-------RQEQYSLSTEQID 362
                    E L+ + +      ++  P+   ++ + L++I        R++ Y+     ++
Sbjct:   275 QRLLFPKEILEELCISI----ISFKPVAPTNMMKVLNRIATAEANMNREKNYAPDRASLE 330

Query:   363 LVAQASGGDIRQAITSLQFSSLK 385
             L+ +   GDIR AI SLQF S+K
Sbjct:   331 LLCKGCSGDIRSAINSLQFFSMK 353

GO:0006281 "DNA repair" evidence=IEA

GO:0000077 "DNA damage checkpoint" evidence=IEA

GO:0000781 "chromosome, telomeric region" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0007093 "mitotic cell cycle checkpoint" evidence=IEA

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

GO:0042325 "regulation of phosphorylation" evidence=IEA

DICTYBASE|DDB_G0292504 rad17 "Checkpoint protein RAD24" [Dictyostelium discoideum (taxid:44689)]

 Score = 243 (90.6 bits), Expect = 7.8e-26, Sum P(2) = 7.8e-26
 Identities = 75/285 (26%), Positives = 141/285 (49%)

Query:   123 NPDHDSASASSSTQQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGD--SKDKFSTNV 180
             N  +D++    ++ +++ +K+ PRS  +L V +K+++ V+ W + R  +  +       +
Sbjct:   525 NNKNDNSENIDNSDKMFVDKHFPRSESDLVVHKKRIDMVKIWLQSRFKELSTNQPIEQKL 584

Query:   181 LVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTIWQEYMHNCKTGLEYTSKLDEFENF 240
             L +TG  GVGK++ +R ++  +   + EW  P+  + ++   +  T   Y+S L+EF+ +
Sbjct:   585 LFLTGPTGVGKSSLIRVLSKSMEFDIEEWINPSIVLTRDMNDSLST--PYSSTLEEFKKW 642

Query:   241 VERIRRYGSTSPSI--PGESKSSAILLIDDLP-VT-NGRTAFERLRQCLLLLVRSTHIPT 296
             +    ++     SI   G + +  IL +++ P VT + R  F    +  L    S+  P 
Sbjct:   643 L----KFNGQGFSIFGNGNNNNKKILFVEEFPNVTLDNRIDFVETFENFL---HSSRYPL 695

Query:   297 AVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYS- 355
               +L++    +S  S  Q F     +  +     +  NPI    + +TL KI   E YS 
Sbjct:   696 IFILSDTFSGNS--SLYQLFPS-SFLNNNPQILHINFNPIAPTQLLKTLEKITYLEGYSH 752

Query:   356 -LSTEQIDLVAQASGGDIRQAITSLQFSSL-KQDPMLNLSLSISK 398
              +S+ Q+  +A  S GDIR AI SL+F  + K   ++N S +I K
Sbjct:   753 SISSVQLKSIADESAGDIRAAIHSLEFYCVGKNHKLINKSTTIPK 797

GO:0007049 "cell cycle" evidence=IEA

GO:0006281 "DNA repair" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0031389 "Rad17 RFC-like complex" evidence=ISS

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

GO:0000077 "DNA damage checkpoint" evidence=ISS

GO:0000076 "DNA replication checkpoint" evidence=ISS

FB|FBgn0025808 Rad17 "Rad17" [Drosophila melanogaster (taxid:7227)]

 Score = 277 (102.6 bits), Expect = 5.2e-25, Sum P(2) = 5.2e-25
 Identities = 89/328 (27%), Positives = 152/328 (46%)

Query:   125 DHDSASASSSTQQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVIT 184
             D D        ++ W E ++P + ++LAV  KKV E+R W        K KF   + ++T
Sbjct:    75 DADITVPPPEVKENWMESFEPATSDDLAVHPKKVGELRDWLRHCEAVRK-KFPAQMCLLT 133

Query:   185 GQAGVGKTATVRQIASHLGARLYEWDTPTPTIWQEYMHNCKTGLEYT-SKLDEFENFVER 243
             G  G GKT T+R +A   G +L EW  P        + +  TG  Y  S L+ F++F+ R
Sbjct:   134 GPTGAGKTTTLRVLAKEFGYQLQEWINPIDCEVVNTLGDQTTGASYVGSHLEAFKSFLLR 193

Query:   244 IRRYGSTSPSIPGESKSSAILLIDDLP---VTNGRTAFERLRQCLLLLVRSTHIPTAVVL 300
               RY S       +S++  +LL++D P   +++    FE L +      +S   P   ++
Sbjct:   194 ASRYKSLL-----DSQNKRLLLVEDFPNVLLSDKEVNFEELLEEYTAYGKS---PLVFIV 245

Query:   301 TECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQ-----YS 355
              +  K+  ++ + + F +   +        ++ N I +  +++++   C   Q     Y 
Sbjct:   246 ADA-KSRGLNISYRLFPD--QLKAKHRIEHISFNAIASTIMQKSMKTFCSVMQQNKATYK 302

Query:   356 L-STEQIDLVAQASGGDIRQAITSLQFSSLK---QDPMLNLSLSISKPNFPEEKADGHGG 411
             + ST  +D +   + GDIR A+ +L  SSLK     P   L++S+S       K      
Sbjct:   303 VPSTAVVDSIVVGAQGDIRNALINLHLSSLKGVSSMPTKQLNVSVSAKG---RKKKMQST 359

Query:   412 FSIQFGRDETLSLFHALGKFLHNKRETD 439
                  GRDE+++L HALG+ L+ K   D
Sbjct:   360 LK-SIGRDESITLMHALGRVLNPKFNED 386

GO:0006281 "DNA repair" evidence=ISS;NAS

GO:0005634 "nucleus" evidence=IEA

GO:0007049 "cell cycle" evidence=IEA

RGD|1309515 Rad17 "RAD17 homolog (S. pombe)" [Rattus norvegicus (taxid:10116)]

 Score = 288 (106.4 bits), Expect = 5.0e-22, P = 5.0e-22
 Identities = 92/322 (28%), Positives = 156/322 (48%)

Query:    79 LALGSSSRQQLWTNKNKPCSLEEHAIQKENVGRFLTPSRFEGLVNPDHDSASASSSTQQL 138
             L+L +SS ++    K  P +LE + +     GR L   +  GL     +++    S  + 
Sbjct:    40 LSLNNSSHRR----KYLPSTLESNRLSARKRGR-LPLEQTNGL-----ETSKEYLSDDEP 89

Query:   139 WAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQI 198
             W +KYKP +  ELAV +KK+EEV  W + ++ + K K   ++L+ITG  G GKT T++ +
Sbjct:    90 WVDKYKPETQHELAVHKKKIEEVETWLKTQVLEVKPKHGGSILLITGPPGCGKTTTIKIL 149

Query:   199 ASHLGARLYEWDTPTPTIWQ--EY--MHNCKTG---LEYTSKLDEFENFVERIRRYGSTS 251
             +  LG ++ EW  P    +Q  +Y  + N ++    + Y S++  F +F+ R  +Y    
Sbjct:   150 SKELGIQVQEWVNPILQDFQKDDYKELFNSESNFSVIPYQSQIAVFNDFLLRATKYNKLQ 209

Query:   252 PSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHIPTAVVLTECGKADSVDS 311
                   +    I+L++DLP    R A   L + L   V     P   ++++    DS  +
Sbjct:   210 MLGDALTTDKKIILVEDLPNQFYRDA-NALHEILRKYVHIGRCPLVFIVSDSVSGDS--N 266

Query:   312 TAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQI--------DL 363
                 F +  +I  +     ++ NP+    + + L++I   E  S + E+I        +L
Sbjct:   267 HRLLFPK--NIQEECSVSNISFNPVAPTIMMKFLNRIVTIEA-SKNGEKITVPNKASLEL 323

Query:   364 VAQASGGDIRQAITSLQFSSLK 385
             + Q   GDIR AI SLQFSS K
Sbjct:   324 LCQGCSGDIRSAINSLQFSSSK 345

GO:0000077 "DNA damage checkpoint" evidence=ISO

GO:0005634 "nucleus" evidence=ISO

GO:0006974 "response to DNA damage stimulus" evidence=ISO

GO:0007093 "mitotic cell cycle checkpoint" evidence=ISO

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

GO:0042325 "regulation of phosphorylation" evidence=ISO

GO:0005730 "nucleolus" evidence=ISO

GO:0000781 "chromosome, telomeric region" evidence=ISO

UNIPROTKB|E9PTL1 Rad17 "Protein Rad17" [Rattus norvegicus (taxid:10116)]

 Score = 288 (106.4 bits), Expect = 5.0e-22, P = 5.0e-22
 Identities = 92/322 (28%), Positives = 156/322 (48%)

Query:    79 LALGSSSRQQLWTNKNKPCSLEEHAIQKENVGRFLTPSRFEGLVNPDHDSASASSSTQQL 138
             L+L +SS ++    K  P +LE + +     GR L   +  GL     +++    S  + 
Sbjct:    40 LSLNNSSHRR----KYLPSTLESNRLSARKRGR-LPLEQTNGL-----ETSKEYLSDDEP 89

Query:   139 WAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQI 198
             W +KYKP +  ELAV +KK+EEV  W + ++ + K K   ++L+ITG  G GKT T++ +
Sbjct:    90 WVDKYKPETQHELAVHKKKIEEVETWLKTQVLEVKPKHGGSILLITGPPGCGKTTTIKIL 149

Query:   199 ASHLGARLYEWDTPTPTIWQ--EY--MHNCKTG---LEYTSKLDEFENFVERIRRYGSTS 251
             +  LG ++ EW  P    +Q  +Y  + N ++    + Y S++  F +F+ R  +Y    
Sbjct:   150 SKELGIQVQEWVNPILQDFQKDDYKELFNSESNFSVIPYQSQIAVFNDFLLRATKYNKLQ 209

Query:   252 PSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHIPTAVVLTECGKADSVDS 311
                   +    I+L++DLP    R A   L + L   V     P   ++++    DS  +
Sbjct:   210 MLGDALTTDKKIILVEDLPNQFYRDA-NALHEILRKYVHIGRCPLVFIVSDSVSGDS--N 266

Query:   312 TAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQI--------DL 363
                 F +  +I  +     ++ NP+    + + L++I   E  S + E+I        +L
Sbjct:   267 HRLLFPK--NIQEECSVSNISFNPVAPTIMMKFLNRIVTIEA-SKNGEKITVPNKASLEL 323

Query:   364 VAQASGGDIRQAITSLQFSSLK 385
             + Q   GDIR AI SLQFSS K
Sbjct:   324 LCQGCSGDIRSAINSLQFSSSK 345

GO:0000077 "DNA damage checkpoint" evidence=IEA

GO:0000781 "chromosome, telomeric region" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0006281 "DNA repair" evidence=IEA

GO:0007093 "mitotic cell cycle checkpoint" evidence=IEA

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

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

GO:0042325 "regulation of phosphorylation" evidence=IEA

ZFIN|ZDB-GENE-040718-409 rad17 "RAD17 homolog (S. pombe)" [Danio rerio (taxid:7955)]

 Score = 271 (100.5 bits), Expect = 3.5e-20, P = 3.5e-20
 Identities = 98/343 (28%), Positives = 154/343 (44%)

Query:    73 VNPKRDLALGSSSRQQLWTNKNKPCSLEEHAIQKENVGRFLTPSRFEGLVNPDHDSASAS 132
             V P     LG  SR      K  P S E    +K++  R + P   +  +     S+ A+
Sbjct:    20 VEPSFGELLGGVSRSL----KKGPLSGESKTAEKKSRKRKVDPYVSDNQITV---SSEAN 72

Query:   133 SSTQ-QLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGK 191
             +  Q + W + + P+S  ELAV +KKVEEV +W    L   K K    +L++TG +G GK
Sbjct:    73 NPDQDEPWVDIHAPQSQAELAVHKKKVEEVESWLRVHL--DKSKKGGAILLLTGPSGCGK 130

Query:   192 TATVRQIASHLGARLYEWDTPTPT--------IWQEYMHNCKTGLEY-TSKLDEFENFVE 242
             TATV+ +A  LG ++ EW  P+ T          Q +  + +    + +S+   F+ F+ 
Sbjct:   131 TATVQVLAKELGFQVQEWSNPSTTSQYKTEDLFTQSFDPDSRFNRFHGSSQTGLFQEFLL 190

Query:   243 RIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHIPTAVVLTE 302
             R  +Y     S    ++   I+LI++ P    R     L   L   ++    P  ++++ 
Sbjct:   191 RANKYSRLRMSGETWTEDRKIILIEEFPNQFYRQP-GCLHDILRQFIKCGRCPLVLIVS- 248

Query:   303 CGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTE--- 359
                 DS+     S    + +L + G   ++ NP+   S+ + LS+I   E    S     
Sbjct:   249 ----DSLSGDKNSRLLFKDVLQELGIHNISFNPVAPTSMMKVLSRIVTIEAVKSSGRISV 304

Query:   360 ----QIDLVAQASGGDIRQAITSLQFSSLKQDPMLNLSLSISK 398
                  +DL+   S GDIR AI SLQFSS   D  L   L  SK
Sbjct:   305 PDKAALDLLCSGSSGDIRSAINSLQFSSFT-DNSLERRLWASK 346

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

GO:0005634 "nucleus" evidence=IEA

GO:0007049 "cell cycle" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0006281 "DNA repair" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

UNIPROTKB|I3L290 RAD17 "Cell cycle checkpoint protein RAD17" [Homo sapiens (taxid:9606)]

 Score = 267 (99.0 bits), Expect = 1.0e-19, P = 1.0e-19
 Identities = 85/321 (26%), Positives = 149/321 (46%)

Query:    79 LALGSSSRQQLWTNKNKPCSLEEHAIQKENVGRFLTPSRFEGLVNPDHDSASASSSTQQL 138
             L + +SS ++    KN P +LE         G   +  +  GL N     +    S  + 
Sbjct:    40 LGVNNSSHRR----KNGPSTLESSRFPARKRGNLSSLEQIYGLEN-----SKEYLSENEP 90

Query:   139 WAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQI 198
             W +KYKP +  ELAV +KK+EEV  W + ++ + + K   ++L+ITG  G GKT T++ +
Sbjct:    91 WVDKYKPETQHELAVHKKKIEEVETWLKAQVLERQPKQGGSILLITGPPGCGKTTTLKIL 150

Query:   199 ASHLGARLYEWDTPTPTIWQEY----MHNCKTGLE---YTSKLDEFENFVERIRRYGSTS 251
             +   G ++ EW  P    +Q+     M N ++      Y S++  F+ F+ R  +Y    
Sbjct:   151 SKEHGIQVQEWINPVLPDFQKDDFKGMFNTESSFHMFPYQSQIAVFKEFLLRATKYNKLQ 210

Query:   252 PSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHIPTAVVLTECGKADSVDS 311
                        I+L++DLP    R +   L + L   VR    P   ++++    D+ + 
Sbjct:   211 MLGDDLRTDKKIILVEDLPNQFYRDS-HTLHEVLRKYVRIGRCPLIFIISDSLSGDN-NQ 268

Query:   312 TAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQE------QYSLSTE-QIDLV 364
                  +E+Q    +     ++ NP+    + + L++I   E      + ++  +  ++L+
Sbjct:   269 RLLFPKEIQE---ECSISNISFNPVAPTIMMKFLNRIVTIEANKNGGKITVPDKTSLELL 325

Query:   365 AQASGGDIRQAITSLQFSSLK 385
              Q   GDIR AI SLQFSS K
Sbjct:   326 CQGCSGDIRSAINSLQFSSSK 346

GO:0005634 "nucleus" evidence=IEA

GO:0006281 "DNA repair" evidence=IEA

GO:0007049 "cell cycle" evidence=IEA

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

GO:0005524 "ATP binding" evidence=IEA

UNIPROTKB|O75943 RAD17 "Cell cycle checkpoint protein RAD17" [Homo sapiens (taxid:9606)]

 Score = 267 (99.0 bits), Expect = 1.0e-19, P = 1.0e-19
 Identities = 85/321 (26%), Positives = 149/321 (46%)

Query:    79 LALGSSSRQQLWTNKNKPCSLEEHAIQKENVGRFLTPSRFEGLVNPDHDSASASSSTQQL 138
             L + +SS ++    KN P +LE         G   +  +  GL N     +    S  + 
Sbjct:    40 LGVNNSSHRR----KNGPSTLESSRFPARKRGNLSSLEQIYGLEN-----SKEYLSENEP 90

Query:   139 WAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQI 198
             W +KYKP +  ELAV +KK+EEV  W + ++ + + K   ++L+ITG  G GKT T++ +
Sbjct:    91 WVDKYKPETQHELAVHKKKIEEVETWLKAQVLERQPKQGGSILLITGPPGCGKTTTLKIL 150

Query:   199 ASHLGARLYEWDTPTPTIWQEY----MHNCKTGLE---YTSKLDEFENFVERIRRYGSTS 251
             +   G ++ EW  P    +Q+     M N ++      Y S++  F+ F+ R  +Y    
Sbjct:   151 SKEHGIQVQEWINPVLPDFQKDDFKGMFNTESSFHMFPYQSQIAVFKEFLLRATKYNKLQ 210

Query:   252 PSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHIPTAVVLTECGKADSVDS 311
                        I+L++DLP    R +   L + L   VR    P   ++++    D+ + 
Sbjct:   211 MLGDDLRTDKKIILVEDLPNQFYRDS-HTLHEVLRKYVRIGRCPLIFIISDSLSGDN-NQ 268

Query:   312 TAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQE------QYSLSTE-QIDLV 364
                  +E+Q    +     ++ NP+    + + L++I   E      + ++  +  ++L+
Sbjct:   269 RLLFPKEIQE---ECSISNISFNPVAPTIMMKFLNRIVTIEANKNGGKITVPDKTSLELL 325

Query:   365 AQASGGDIRQAITSLQFSSLK 385
              Q   GDIR AI SLQFSS K
Sbjct:   326 CQGCSGDIRSAINSLQFSSSK 346

GO:0006281 "DNA repair" evidence=IEA

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

GO:0005524 "ATP binding" evidence=IEA

GO:0000077 "DNA damage checkpoint" evidence=IMP

GO:0007093 "mitotic cell cycle checkpoint" evidence=IMP

GO:0042325 "regulation of phosphorylation" evidence=IMP

GO:0005515 "protein binding" evidence=IPI

GO:0006974 "response to DNA damage stimulus" evidence=IMP

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

GO:0000076 "DNA replication checkpoint" evidence=TAS

GO:0000075 "cell cycle checkpoint" evidence=TAS

GO:0005654 "nucleoplasm" evidence=TAS

GO:0006260 "DNA replication" evidence=TAS

GO:0000781 "chromosome, telomeric region" evidence=IDA

GO:0005634 "nucleus" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q9MBA3	RAD17_ARATH	No assigned EC number	0.5377	0.7507	0.8347	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	666
pfam03215	490	pfam03215, Rad17, Rad17 cell cycle checkpoint prot	3e-50
TIGR00602	637	TIGR00602, rad24, checkpoint protein rad24	3e-32
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	5e-17
PRK12402	337	PRK12402, PRK12402, replication factor C small sub	3e-09
PRK00440	319	PRK00440, rfc, replication factor C small subunit;	4e-04
TIGR02397	355	TIGR02397, dnaX_nterm, DNA polymerase III, subunit	0.001
pfam13401	124	pfam13401, AAA_22, AAA domain	0.003

>gnl|CDD|217429 pfam03215, Rad17, Rad17 cell cycle checkpoint protein

 Score =  182 bits (462), Expect = 3e-50
 Identities = 128/450 (28%), Positives = 207/450 (46%), Gaps = 58/450 (12%)

Query: 137 QLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVR 196
           +LW EKYKPR  +ELA+ +KK+ EV  W +    +S  +    +L++TG +G GK+ TV+
Sbjct: 7   ELWTEKYKPRRRDELAIHKKKIAEVDHWLKAVFLESNKQ---LILLLTGPSGCGKSTTVK 63

Query: 197 QIASHLGARLYEWDTPT-----PTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTS 251
            ++  LG  + EW  P          Q+        +   S++++F  F+ R  RYGS  
Sbjct: 64  VLSKELGIEIIEWSNPEYLHNPDNECQKPDFRGDCIVNSLSQMEQFREFLLRGARYGS-- 121

Query: 252 PSIPGESKSSAILLIDDLP-VTNGRTAFERLRQCLLLLVRST-HIPTAVVLTECGKA--- 306
             + G      ++L+++LP         E+ R+ +  +++S  H+P    LTEC      
Sbjct: 122 --LQGGGLKKKLILVEELPNQFYSDA--EKFREVIREVLQSIWHLPLIFCLTECNSLEGD 177

Query: 307 DSVDSTAQSFEEL--QSILVDAGARKVALNPITNGSIKRTLSKICRQE---QYSLSTEQI 361
           ++ D      E +  + IL+      +  NPI    +K+ L +I  QE   +   S  ++
Sbjct: 178 NNQDRFGIDAETIMTKDILIMPRIDTITFNPIAPTFMKKALVRISVQEGKLKSPKSDSKL 237

Query: 362 DLVAQASGGDIRQAITSLQFSSLKQDPMLNLSLSISKPNFPEEKADGHGGFSIQFGRDET 421
           +++ Q +GGD+R AI SLQFSS             S PN   +        + +  R+ET
Sbjct: 238 EVICQEAGGDLRSAINSLQFSS-------------SGPNNDRKSGSNSVLCASKSNREET 284

Query: 422 LSLFHALGKFLHNKRETDN----------LVKMDQDAFVVKDKFSRLPLKMDAPEKVLSQ 471
           LS FHA+GK L+ KR T+N            K  + +  + +   R  L +D PE +++ 
Sbjct: 285 LSAFHAIGKVLYAKRSTNNDNERIPKPSRFSKRRRKSAPILEPLVRTELLVD-PEDIITM 343

Query: 472 AHGQARPVLDFLHENFLDFISEDAIDDAWAVASYLSDADLLLASFRGRLVRYNEADNVLQ 531
           +       L  L EN+ DF S   I DA  VA  LS  D L   +  R         +L+
Sbjct: 344 SSLSGEKFLLGLFENYPDFCSN--ISDARYVADTLSMCDFLSGDWTTR-------KYLLR 394

Query: 532 SAAASVAARGVLFGN-SHPVPPRWHAIRKP 560
             +   A R V++ N   P P    A+ +P
Sbjct: 395 EYSTQFATRSVMWNNYKEPYPGTLFAVGRP 424

Length = 490

>gnl|CDD|129690 TIGR00602, rad24, checkpoint protein rad24

 Score =  132 bits (332), Expect = 3e-32
 Identities = 123/442 (27%), Positives = 197/442 (44%), Gaps = 50/442 (11%)

Query: 137 QLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVR 196
           + W EKYKP +  ELAV +KK+EEV  W + ++ ++  K    +L+ITG +G GK+ T++
Sbjct: 72  EPWVEKYKPETQHELAVHKKKIEEVETWLKAQVLENAPK---RILLITGPSGCGKSTTIK 128

Query: 197 QIASHLGARLYEWDTPTPTIWQ--EYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSI 254
            ++  LG ++ EW  PT   +Q  ++         +++   + E F E + R  +    +
Sbjct: 129 ILSKELGIQVQEWSNPTLPDFQKNDHKVTLSLESCFSNFQSQIEVFSEFLLRATNKLQML 188

Query: 255 PGESKSS-AILLIDDLP-VTNGRTAFER--LRQCLLLLVRSTHIPTAVVLTECGKADSVD 310
             +  +   I+L++DLP      T      LR      V     P   ++TE  + D+ +
Sbjct: 189 GDDLMTDKKIILVEDLPNQFYRDTRALHEILRW---KYVSIGRCPLVFIITESLEGDN-N 244

Query: 311 STAQSFEELQ----SILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLS-------TE 359
                F         IL +     ++ NPI    +K+ L++I   E              
Sbjct: 245 QRRLLFPAETIMNKEILEEPRVSNISFNPIAPTIMKKFLNRIVTIEAKKNGEKIKVPKKT 304

Query: 360 QIDLVAQASGGDIRQAITSLQFSSLKQDPMLNLSLSISKPNFPEEKADGHGGFS------ 413
            ++L+ Q   GDIR AI SLQFSS K   +       +K +    K+   G  S      
Sbjct: 305 SVELLCQGCSGDIRSAINSLQFSSSKSGSLPIKKRMSTKSDAHASKSKIKGKHSSNNENQ 364

Query: 414 -IQ--FGRDETLSLFHALGKFLHNKRETDN-LVKMDQDAFVVKDKFSRLPLKMDAPEKVL 469
            IQ   G+D +L LF ALGK L+ KR T N L      + +   + SR  L M  PE+V+
Sbjct: 365 EIQALGGKDVSLFLFRALGKILYCKRATLNELDSPRLPSHL--SELSRDTL-MVGPEEVV 421

Query: 470 SQAHGQARPVLD-FLHENFLDFISEDAIDDAWAVASYLSDADLLLASFRGR-LVRYNEAD 527
             +H       + + H+N+ DF  E   DD    + +L+ AD+L   +  R L+R     
Sbjct: 422 EMSHMPGDKTFNLYSHQNYNDFFVE--FDDEVKASEFLNFADILSGDWNTRSLLREY--- 476

Query: 528 NVLQSAAASVAARGVLFGNSHP 549
                 + S A RGV+  N   
Sbjct: 477 ------STSSARRGVMHSNKAR 492

All proteins in this family for which functions are known are involved in DNA damage tolerance (likely cell cycle checkpoints).This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University) [DNA metabolism, DNA replication, recombination, and repair]. Length = 637

>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional

 Score = 83.8 bits (208), Expect = 5e-17
 Identities = 95/442 (21%), Positives = 154/442 (34%), Gaps = 125/442 (28%)

Query: 139 WAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQI 198
           W EKY+P++L ++    K  E++R W E  L     K     L++ G  GVGKT+     
Sbjct: 4   WVEKYRPKTLSDVVGNEKAKEQLREWIESWLKGKPKK----ALLLYGPPGVGKTSLA--- 56

Query: 199 ASHLGARLYEWDTPTPTIWQEYMHNCKTGLE-----YTSKLDEFENFVERIRRY---GST 250
             H  A  Y W+                 +E       +         + I R     +T
Sbjct: 57  --HALANDYGWEV----------------IELNASDQRTA--------DVIERVAGEAAT 90

Query: 251 SPSIPGESKSSAILL--IDDLPVTNGRTAFERLRQCLLLLVRSTHIPTAVVLTECGKADS 308
           S S+ G ++   ILL  +D +     R       + +L L++    P  ++LT    A+ 
Sbjct: 91  SGSLFG-ARRKLILLDEVDGIHGNEDRGGA----RAILELIKKAKQP--IILT----AN- 138

Query: 309 VDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQAS 368
            D    S  EL++         +    ++  SI   L +ICR+E      E +  +A+ S
Sbjct: 139 -DPYDPSLRELRNA-----CLMIEFKRLSTRSIVPVLKRICRKEGIECDDEALKEIAERS 192

Query: 369 GGDIRQAITSLQFSSLKQDPMLNLSLSISKPNFPEEKADGHGGFSIQFGRDETLSLFHAL 428
           GGD+R AI  LQ            +++        E     G       RD   S+F AL
Sbjct: 193 GGDLRSAINDLQ------------AIAEGYGKLTLEDVKTLG------RRDREESIFDAL 234

Query: 429 GKFLHNKRETDNLVKMDQDAFVVKDKFSRLPLKMDAPEKVLSQAHGQARPVLDFLHENFL 488
                                           K    ++ L  ++      +D   ++ +
Sbjct: 235 DAV----------------------------FKARNADQALEASYD-----VDEDPDDLI 261

Query: 489 DFISE------DAIDDAWAVASYLSDADLLLASFRGRLVRYNEADNVLQSAAASVAARGV 542
           ++I E      D  +D       LS AD+    F GR+ R    D  L   A+ +   GV
Sbjct: 262 EWIDENIPKEYDDPEDIARAYDALSRADI----FLGRVKRTQNYD--LWRYASDLMTAGV 315

Query: 543 LFGNSHPVPPRWHAIRKPKLWR 564
                      +   + P  WR
Sbjct: 316 ALAKEKK-KRGFTRYQPPSYWR 336

Length = 482

>gnl|CDD|237090 PRK12402, PRK12402, replication factor C small subunit 2; Reviewed

 Score = 58.8 bits (143), Expect = 3e-09
 Identities = 65/276 (23%), Positives = 108/276 (39%), Gaps = 66/276 (23%)

Query: 136 QQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATV 195
             LW EKY+P  LE++  Q    +EV     ERL  + D  +   L++ G  G GKTA V
Sbjct: 2   APLWTEKYRPALLEDILGQ----DEVV----ERLSRAVDSPNLPHLLVQGPPGSGKTAAV 53

Query: 196 RQIASHLGARLYEWDTPTPTIWQ--EYMHNCKTGLE---------------YTSKLDEFE 238
           R +A  L    +E +    T +   ++    K  L                 +SK+D   
Sbjct: 54  RALARELYGDPWENNF---TEFNVADFFDQGKKYLVEDPRFAHFLGTDKRIRSSKID--- 107

Query: 239 NFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLR----QCLLLLVRSTHI 294
           NF   ++ Y S  P +  + K    +L+D+          E LR    Q L  ++     
Sbjct: 108 NFKHVLKEYASYRP-LSADYK---TILLDNA---------EALREDAQQALRRIMEQYSR 154

Query: 295 PTAVVLTECGKADSVDSTAQSFEELQSILVDAGARK---VALNPITNGSIKRTLSKICRQ 351
               ++          +T Q      S L+     +   +     T+  +   L  I   
Sbjct: 155 TCRFII----------ATRQ-----PSKLIPPIRSRCLPLFFRAPTDDELVDVLESIAEA 199

Query: 352 EQYSLSTEQIDLVAQASGGDIRQAITSLQFSSLKQD 387
           E      + ++L+A  +GGD+R+AI +LQ ++L   
Sbjct: 200 EGVDYDDDGLELIAYYAGGDLRKAILTLQTAALAAG 235

Length = 337

>gnl|CDD|234763 PRK00440, rfc, replication factor C small subunit; Reviewed

 Score = 42.6 bits (101), Expect = 4e-04
 Identities = 20/66 (30%), Positives = 37/66 (56%), Gaps = 12/66 (18%)

Query: 136 QQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNV--LVITGQAGVGKTA 193
           +++W EKY+PR+L+E+  Q + VE ++++ +E+          N+  L+  G  G GKT 
Sbjct: 4   EEIWVEKYRPRTLDEIVGQEEIVERLKSYVKEK----------NMPHLLFAGPPGTGKTT 53

Query: 194 TVRQIA 199
               +A
Sbjct: 54  AALALA 59

Length = 319

>gnl|CDD|233847 TIGR02397, dnaX_nterm, DNA polymerase III, subunit gamma and tau

 Score = 41.4 bits (98), Expect = 0.001
 Identities = 16/56 (28%), Positives = 26/56 (46%), Gaps = 1/56 (1%)

Query: 333 LNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASGGDIRQAITSL-QFSSLKQD 387
              I    I   L KI  +E   +  E ++L+A+A+ G +R A++ L Q  S    
Sbjct: 173 FKRIPLEDIVERLKKILDKEGIKIEDEALELIARAADGSLRDALSLLDQLISFGNG 228

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 [DNA metabolism, DNA replication, recombination, and repair]. Length = 355

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

 Score = 38.0 bits (89), Expect = 0.003
 Identities = 26/131 (19%), Positives = 50/131 (38%), Gaps = 28/131 (21%)

Query: 179 NVLVITGQAGVGKTATVRQIA-SHLGARLYEWDTPTPTIWQEYMHN----CKTGLEYTSK 233
            + V+TG++G GKT  +R++A      R+   + P+    ++ +          L   + 
Sbjct: 5   GIGVLTGESGSGKTTLLRRLARQLPNRRVVYVEAPSLGTPKDLLRKILRALGLPLSGGTT 64

Query: 234 LDEFENFVERIRRYGSTSPSIPGESKSSAILLIDD---LPVTNGRTAFERLRQCLLLLVR 290
            +  E  ++ ++R G              +L+ID+   L       A E LR     L  
Sbjct: 65  AELLEAILDALKRRG------------RPLLIIDEAQHLS----LEALEELR----DLYD 104

Query: 291 STHIPTAVVLT 301
            +     V+L 
Sbjct: 105 LSEKGIQVILV 115

Length = 124

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	666
PF03215	519	Rad17: Rad17 cell cycle checkpoint protein	100.0
KOG1970	634	consensus Checkpoint RAD17-RFC complex, RAD17/RAD2	100.0
TIGR00602	637	rad24 checkpoint protein rad24. This family is bas	100.0
PRK04195	482	replication factor C large subunit; Provisional	100.0
KOG1969	877	consensus DNA replication checkpoint protein CHL12	100.0
KOG0989	346	consensus Replication factor C, subunit RFC4 [Repl	99.97
KOG0991	333	consensus Replication factor C, subunit RFC2 [Repl	99.96
PLN03025	319	replication factor C subunit; Provisional	99.95
PRK14956	484	DNA polymerase III subunits gamma and tau; Provisi	99.94
PRK07003	830	DNA polymerase III subunits gamma and tau; Validat	99.94
PRK14960	702	DNA polymerase III subunits gamma and tau; Provisi	99.93
PRK14958	509	DNA polymerase III subunits gamma and tau; Provisi	99.92
KOG1968	871	consensus Replication factor C, subunit RFC1 (larg	99.92
COG2256	436	MGS1 ATPase related to the helicase subunit of the	99.92
PRK14949	944	DNA polymerase III subunits gamma and tau; Provisi	99.92
PRK12323	700	DNA polymerase III subunits gamma and tau; Provisi	99.92
PRK14964	491	DNA polymerase III subunits gamma and tau; Provisi	99.91
PRK14962	472	DNA polymerase III subunits gamma and tau; Provisi	99.91
PRK14952	584	DNA polymerase III subunits gamma and tau; Provisi	99.91
PRK00440	319	rfc replication factor C small subunit; Reviewed	99.91
PRK12402	337	replication factor C small subunit 2; Reviewed	99.91
PRK06645	507	DNA polymerase III subunits gamma and tau; Validat	99.91
PRK08691	709	DNA polymerase III subunits gamma and tau; Validat	99.91
PRK14957	546	DNA polymerase III subunits gamma and tau; Provisi	99.9
PRK07994	647	DNA polymerase III subunits gamma and tau; Validat	99.9
PRK14961	363	DNA polymerase III subunits gamma and tau; Provisi	99.9
PRK14951	618	DNA polymerase III subunits gamma and tau; Provisi	99.9
PRK14963	504	DNA polymerase III subunits gamma and tau; Provisi	99.9
PRK05896	605	DNA polymerase III subunits gamma and tau; Validat	99.9
PHA02544	316	44 clamp loader, small subunit; Provisional	99.9
PRK07764	824	DNA polymerase III subunits gamma and tau; Validat	99.9
PRK08451	535	DNA polymerase III subunits gamma and tau; Validat	99.9
PRK14959	624	DNA polymerase III subunits gamma and tau; Provisi	99.89
PRK14969	527	DNA polymerase III subunits gamma and tau; Provisi	99.89
PRK07133	725	DNA polymerase III subunits gamma and tau; Validat	99.89
PRK05563	559	DNA polymerase III subunits gamma and tau; Validat	99.89
PRK09111	598	DNA polymerase III subunits gamma and tau; Validat	99.88
KOG2035	351	consensus Replication factor C, subunit RFC3 [Cell	99.88
PRK14953	486	DNA polymerase III subunits gamma and tau; Provisi	99.88
PRK14965	576	DNA polymerase III subunits gamma and tau; Provisi	99.88
TIGR02397	355	dnaX_nterm DNA polymerase III, subunit gamma and t	99.88
PRK14970	367	DNA polymerase III subunits gamma and tau; Provisi	99.87
PRK14948	620	DNA polymerase III subunits gamma and tau; Provisi	99.87
PRK06305	451	DNA polymerase III subunits gamma and tau; Validat	99.87
PF05496	233	RuvB_N: Holliday junction DNA helicase ruvB N-term	99.87
PRK14971	614	DNA polymerase III subunits gamma and tau; Provisi	99.87
PRK14955	397	DNA polymerase III subunits gamma and tau; Provisi	99.86
PRK14950	585	DNA polymerase III subunits gamma and tau; Provisi	99.86
PRK14954	620	DNA polymerase III subunits gamma and tau; Provisi	99.86
PRK13342	413	recombination factor protein RarA; Reviewed	99.86
PRK06647	563	DNA polymerase III subunits gamma and tau; Validat	99.86
KOG2028	554	consensus ATPase related to the helicase subunit o	99.86
COG2812	515	DnaX DNA polymerase III, gamma/tau subunits [DNA r	99.85
PRK13341	725	recombination factor protein RarA/unknown domain f	99.84
KOG0990	360	consensus Replication factor C, subunit RFC5 [Repl	99.84
PRK00080	328	ruvB Holliday junction DNA helicase RuvB; Reviewed	99.8
PRK04132	846	replication factor C small subunit; Provisional	99.77
TIGR00635	305	ruvB Holliday junction DNA helicase, RuvB subunit.	99.72
PTZ00112	1164	origin recognition complex 1 protein; Provisional	99.71
COG2255	332	RuvB Holliday junction resolvasome, helicase subun	99.71
COG0470	325	HolB ATPase involved in DNA replication [DNA repli	99.69
PRK06893	229	DNA replication initiation factor; Validated	99.67
PRK09112	351	DNA polymerase III subunit delta'; Validated	99.67
PRK08084	235	DNA replication initiation factor; Provisional	99.66
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	99.66
TIGR02902	531	spore_lonB ATP-dependent protease LonB. Members of	99.65
PRK08727	233	hypothetical protein; Validated	99.65
PRK07940	394	DNA polymerase III subunit delta'; Validated	99.63
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	99.62
PRK06620	214	hypothetical protein; Validated	99.62
TIGR02928	365	orc1/cdc6 family replication initiation protein. M	99.61
COG1223	368	Predicted ATPase (AAA+ superfamily) [General funct	99.61
COG1222	406	RPT1 ATP-dependent 26S proteasome regulatory subun	99.59
PRK07471	365	DNA polymerase III subunit delta'; Validated	99.59
PRK00411	394	cdc6 cell division control protein 6; Reviewed	99.59
PRK05642	234	DNA replication initiation factor; Validated	99.58
PRK08903	227	DnaA regulatory inactivator Hda; Validated	99.58
PRK07399	314	DNA polymerase III subunit delta'; Validated	99.57
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	99.57
PRK05564	313	DNA polymerase III subunit delta'; Validated	99.53
CHL00181	287	cbbX CbbX; Provisional	99.52
CHL00195	489	ycf46 Ycf46; Provisional	99.51
TIGR02880	284	cbbX_cfxQ probable Rubsico expression protein CbbX	99.51
COG1474	366	CDC6 Cdc6-related protein, AAA superfamily ATPase	99.51
PRK09087	226	hypothetical protein; Validated	99.51
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	99.51
PRK00149	450	dnaA chromosomal replication initiation protein; R	99.5
PF00308	219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	99.5
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	99.5
PTZ00361	438	26 proteosome regulatory subunit 4-like protein; P	99.5
CHL00176	638	ftsH cell division protein; Validated	99.49
TIGR01241	495	FtsH_fam ATP-dependent metalloprotease FtsH. HflB(	99.49
TIGR02903	615	spore_lon_C ATP-dependent protease, Lon family. Me	99.49
TIGR00678	188	holB DNA polymerase III, delta' subunit. At positi	99.48
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	99.48
PRK14087	450	dnaA chromosomal replication initiation protein; P	99.47
KOG0730	693	consensus AAA+-type ATPase [Posttranslational modi	99.47
PTZ00454	398	26S protease regulatory subunit 6B-like protein; P	99.47
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	99.47
PRK12422	445	chromosomal replication initiation protein; Provis	99.44
PRK14088	440	dnaA chromosomal replication initiation protein; P	99.43
PRK03992	389	proteasome-activating nucleotidase; Provisional	99.43
PLN00020	413	ribulose bisphosphate carboxylase/oxygenase activa	99.41
KOG0738	491	consensus AAA+-type ATPase [Posttranslational modi	99.4
TIGR03689	512	pup_AAA proteasome ATPase. In the Actinobacteria,	99.39
PRK14086	617	dnaA chromosomal replication initiation protein; P	99.38
TIGR01242	364	26Sp45 26S proteasome subunit P45 family. Many pro	99.37
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	99.36
CHL00095	821	clpC Clp protease ATP binding subunit	99.36
KOG0734	752	consensus AAA+-type ATPase containing the peptidas	99.36
PRK08058	329	DNA polymerase III subunit delta'; Validated	99.35
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	99.33
PF06068	398	TIP49: TIP49 C-terminus; InterPro: IPR010339 This	99.31
PF05673	249	DUF815: Protein of unknown function (DUF815); Inte	99.31
PRK10865	857	protein disaggregation chaperone; Provisional	99.31
KOG0731	774	consensus AAA+-type ATPase containing the peptidas	99.3
PRK05707	328	DNA polymerase III subunit delta'; Validated	99.3
TIGR00763	775	lon ATP-dependent protease La. This protein is ind	99.29
COG0593	408	DnaA ATPase involved in DNA replication initiation	99.29
KOG0743	457	consensus AAA+-type ATPase [Posttranslational modi	99.28
KOG0737	386	consensus AAA+-type ATPase [Posttranslational modi	99.27
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	99.26
PF00004	132	AAA: ATPase family associated with various cellula	99.25
COG0464	494	SpoVK ATPases of the AAA+ class [Posttranslational	99.24
KOG0736	953	consensus Peroxisome assembly factor 2 containing	99.23
PRK10733	644	hflB ATP-dependent metalloprotease; Reviewed	99.23
PRK07993	334	DNA polymerase III subunit delta'; Validated	99.23
KOG0727	408	consensus 26S proteasome regulatory complex, ATPas	99.22
PRK06871	325	DNA polymerase III subunit delta'; Validated	99.22
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	99.21
PRK08769	319	DNA polymerase III subunit delta'; Validated	99.21
KOG2227	529	consensus Pre-initiation complex, subunit CDC6, AA	99.19
COG1224	450	TIP49 DNA helicase TIP49, TBP-interacting protein	99.19
KOG0728	404	consensus 26S proteasome regulatory complex, ATPas	99.19
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	99.16
KOG0739	439	consensus AAA+-type ATPase [Posttranslational modi	99.16
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	99.15
TIGR03015	269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	99.14
CHL00206	2281	ycf2 Ycf2; Provisional	99.13
KOG0735	952	consensus AAA+-type ATPase [Posttranslational modi	99.13
PRK10787	784	DNA-binding ATP-dependent protease La; Provisional	99.13
KOG1514	767	consensus Origin recognition complex, subunit 1, a	99.12
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	99.11
PF13177	162	DNA_pol3_delta2: DNA polymerase III, delta subunit	99.1
PRK05342	412	clpX ATP-dependent protease ATP-binding subunit Cl	99.06
COG0465	596	HflB ATP-dependent Zn proteases [Posttranslational	99.05
KOG0652	424	consensus 26S proteasome regulatory complex, ATPas	99.05
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	99.04
KOG0729	435	consensus 26S proteasome regulatory complex, ATPas	99.04
KOG0730	693	consensus AAA+-type ATPase [Posttranslational modi	99.03
KOG0726	440	consensus 26S proteasome regulatory complex, ATPas	99.03
TIGR01650	327	PD_CobS cobaltochelatase, CobS subunit. This model	99.03
PRK06090	319	DNA polymerase III subunit delta'; Validated	99.03
KOG2004	906	consensus Mitochondrial ATP-dependent protease PIM	99.03
TIGR02640	262	gas_vesic_GvpN gas vesicle protein GvpN. Members o	99.02
PF01637	234	Arch_ATPase: Archaeal ATPase; InterPro: IPR011579	99.02
KOG0742	630	consensus AAA+-type ATPase [Posttranslational modi	99.01
KOG0740	428	consensus AAA+-type ATPase [Posttranslational modi	98.97
CHL00095	821	clpC Clp protease ATP binding subunit	98.97
KOG0744	423	consensus AAA+-type ATPase [Posttranslational modi	98.96
COG0466	782	Lon ATP-dependent Lon protease, bacterial type [Po	98.95
COG2607	287	Predicted ATPase (AAA+ superfamily) [General funct	98.95
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	98.94
PRK06964	342	DNA polymerase III subunit delta'; Validated	98.92
PRK10865	857	protein disaggregation chaperone; Provisional	98.91
KOG0651	388	consensus 26S proteasome regulatory complex, ATPas	98.9
KOG1942	456	consensus DNA helicase, TBP-interacting protein [R	98.9
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	98.89
PRK11331	459	5-methylcytosine-specific restriction enzyme subun	98.83
TIGR00382	413	clpX endopeptidase Clp ATP-binding regulatory subu	98.83
TIGR00390	441	hslU ATP-dependent protease HslVU, ATPase subunit.	98.82
PRK05201	443	hslU ATP-dependent protease ATP-binding subunit Hs	98.81
PRK05917	290	DNA polymerase III subunit delta'; Validated	98.8
PRK08699	325	DNA polymerase III subunit delta'; Validated	98.77
KOG0732	1080	consensus AAA+-type ATPase containing the bromodom	98.76
PRK07132	299	DNA polymerase III subunit delta'; Validated	98.71
KOG0735	952	consensus AAA+-type ATPase [Posttranslational modi	98.7
PRK07952	244	DNA replication protein DnaC; Validated	98.69
TIGR01817	534	nifA Nif-specific regulatory protein. This model r	98.69
KOG2680	454	consensus DNA helicase TIP49, TBP-interacting prot	98.68
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	98.67
PRK07276	290	DNA polymerase III subunit delta'; Validated	98.64
PRK12377	248	putative replication protein; Provisional	98.62
PRK05818	261	DNA polymerase III subunit delta'; Validated	98.6
KOG0736	953	consensus Peroxisome assembly factor 2 containing	98.58
smart00382	148	AAA ATPases associated with a variety of cellular	98.57
PRK08116	268	hypothetical protein; Validated	98.51
PRK08939	306	primosomal protein DnaI; Reviewed	98.49
PF05621	302	TniB: Bacterial TniB protein; InterPro: IPR008868	98.49
PRK13407	334	bchI magnesium chelatase subunit I; Provisional	98.47
TIGR02974	329	phageshock_pspF psp operon transcriptional activat	98.46
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	98.44
COG0714	329	MoxR-like ATPases [General function prediction onl	98.44
PRK06835	329	DNA replication protein DnaC; Validated	98.43
PHA02244	383	ATPase-like protein	98.43
PF13173	128	AAA_14: AAA domain	98.42
PRK13531	498	regulatory ATPase RavA; Provisional	98.41
PRK11388	638	DNA-binding transcriptional regulator DhaR; Provis	98.39
PF00931	287	NB-ARC: NB-ARC domain; InterPro: IPR002182 This is	98.37
PF07728	139	AAA_5: AAA domain (dynein-related subfamily); Inte	98.35
TIGR02329	526	propionate_PrpR propionate catabolism operon regul	98.32
PF07724	171	AAA_2: AAA domain (Cdc48 subfamily); InterPro: IPR	98.32
PRK10820	520	DNA-binding transcriptional regulator TyrR; Provis	98.29
PRK08181	269	transposase; Validated	98.29
PRK15424	538	propionate catabolism operon regulatory protein Pr	98.26
COG1219	408	ClpX ATP-dependent protease Clp, ATPase subunit [P	98.25
PRK14700	300	recombination factor protein RarA; Provisional	98.23
PF07726	131	AAA_3: ATPase family associated with various cellu	98.2
PRK15429	686	formate hydrogenlyase transcriptional activator Fh	98.19
PRK11608	326	pspF phage shock protein operon transcriptional ac	98.18
smart00763	361	AAA_PrkA PrkA AAA domain. This is a family of PrkA	98.17
COG1618	179	Predicted nucleotide kinase [Nucleotide transport	98.14
PF05729	166	NACHT: NACHT domain	98.14
PRK06921	266	hypothetical protein; Provisional	98.13
PRK05022	509	anaerobic nitric oxide reductase transcription reg	98.13
PRK06526	254	transposase; Provisional	98.12
KOG0741	744	consensus AAA+-type ATPase [Posttranslational modi	98.11
COG3267	269	ExeA Type II secretory pathway, component ExeA (pr	98.1
PF01695	178	IstB_IS21: IstB-like ATP binding protein; InterPro	98.09
PF03266	168	NTPase_1: NTPase; InterPro: IPR004948 This entry r	98.07
PF12775	272	AAA_7: P-loop containing dynein motor region D3; P	98.04
CHL00081	350	chlI Mg-protoporyphyrin IX chelatase	98.04
PRK13695	174	putative NTPase; Provisional	98.03
TIGR02030	337	BchI-ChlI magnesium chelatase ATPase subunit I. Th	98.03
PRK04132	846	replication factor C small subunit; Provisional	97.99
PHA02774	613	E1; Provisional	97.98
TIGR02442	633	Cob-chelat-sub cobaltochelatase subunit. A number	97.95
COG1484	254	DnaC DNA replication protein [DNA replication, rec	97.95
KOG1051	898	consensus Chaperone HSP104 and related ATP-depende	97.94
PRK09183	259	transposase/IS protein; Provisional	97.94
COG2204	464	AtoC Response regulator containing CheY-like recei	97.93
COG1221	403	PspF Transcriptional regulators containing an AAA-	97.92
PLN03210	1153	Resistant to P. syringae 6; Provisional	97.9
PF00910	107	RNA_helicase: RNA helicase; InterPro: IPR000605 He	97.9
PRK04841	903	transcriptional regulator MalT; Provisional	97.88
PHA00729	226	NTP-binding motif containing protein	97.84
KOG0741	744	consensus AAA+-type ATPase [Posttranslational modi	97.84
PF10443	431	RNA12: RNA12 protein; InterPro: IPR018850 Mitochon	97.82
PF13207	121	AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6	97.8
TIGR02915	445	PEP_resp_reg putative PEP-CTERM system response re	97.79
cd01120	165	RecA-like_NTPases RecA-like NTPases. This family i	97.79
PRK12723	388	flagellar biosynthesis regulator FlhF; Provisional	97.77
PRK05574	340	holA DNA polymerase III subunit delta; Reviewed	97.75
PRK10923	469	glnG nitrogen regulation protein NR(I); Provisiona	97.75
PRK15115	444	response regulator GlrR; Provisional	97.74
COG5271	4600	MDN1 AAA ATPase containing von Willebrand factor t	97.73
PRK00771	437	signal recognition particle protein Srp54; Provisi	97.71
) 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	97.69
KOG2170	344	consensus ATPase of the AAA+ superfamily [General	97.66
PRK06585	343	holA DNA polymerase III subunit delta; Reviewed	97.65
PRK11361	457	acetoacetate metabolism regulatory protein AtoC; P	97.64
PF14532	138	Sigma54_activ_2: Sigma-54 interaction domain; PDB:	97.64
PF12774	231	AAA_6: Hydrolytic ATP binding site of dynein motor	97.63
PRK05703	424	flhF flagellar biosynthesis regulator FlhF; Valida	97.62
PF12780	268	AAA_8: P-loop containing dynein motor region D4; I	97.62
PRK11889	436	flhF flagellar biosynthesis regulator FlhF; Provis	97.61
PF00158	168	Sigma54_activat: Sigma-54 interaction domain; Inte	97.61
COG5271	4600	MDN1 AAA ATPase containing von Willebrand factor t	97.61
PRK07452	326	DNA polymerase III subunit delta; Validated	97.6
KOG2543	438	consensus Origin recognition complex, subunit 5 [R	97.58
KOG2228	408	consensus Origin recognition complex, subunit 4 [R	97.58
cd03281	213	ABC_MSH5_euk MutS5 homolog in eukaryotes. The MutS	97.57
TIGR01818	463	ntrC nitrogen regulation protein NR(I). This model	97.56
PRK15455	644	PrkA family serine protein kinase; Provisional	97.56
PF14516	331	AAA_35: AAA-like domain	97.55
PTZ00202	550	tuzin; Provisional	97.55
PRK10536	262	hypothetical protein; Provisional	97.54
TIGR01128	302	holA DNA polymerase III, delta subunit. subunit ar	97.54
PRK14974	336	cell division protein FtsY; Provisional	97.54
PF13604	196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	97.51
PF13191	185	AAA_16: AAA ATPase domain; PDB: 2V1U_A.	97.51
PF00448	196	SRP54: SRP54-type protein, GTPase domain; InterPro	97.5
PLN02840	421	tRNA dimethylallyltransferase	97.48
PRK06581	263	DNA polymerase III subunit delta'; Validated	97.47
PF01078	206	Mg_chelatase: Magnesium chelatase, subunit ChlI; I	97.46
COG0324	308	MiaA tRNA delta(2)-isopentenylpyrophosphate transf	97.45
TIGR00174	287	miaA tRNA isopentenyltransferase (miaA). Catalyzes	97.44
TIGR02031	589	BchD-ChlD magnesium chelatase ATPase subunit D. Th	97.41
TIGR00368	499	Mg chelatase-related protein. The N-terminal end m	97.4
PRK00091	307	miaA tRNA delta(2)-isopentenylpyrophosphate transf	97.39
PF09848	352	DUF2075: Uncharacterized conserved protein (DUF207	97.39
COG4088	261	Predicted nucleotide kinase [Nucleotide transport	97.38
PRK04296	190	thymidine kinase; Provisional	97.38
PRK12727	559	flagellar biosynthesis regulator FlhF; Provisional	97.37
PRK00131	175	aroK shikimate kinase; Reviewed	97.37
PRK08485	206	DNA polymerase III subunit delta'; Validated	97.37
PRK08118	167	topology modulation protein; Reviewed	97.35
COG3829	560	RocR Transcriptional regulator containing PAS, AAA	97.33
PF13671	143	AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1	97.32
COG1239	423	ChlI Mg-chelatase subunit ChlI [Coenzyme metabolis	97.31
PF10923	416	DUF2791: P-loop Domain of unknown function (DUF279	97.31
COG1102	179	Cmk Cytidylate kinase [Nucleotide transport and me	97.3
COG1936	180	Predicted nucleotide kinase (related to CMP and AM	97.3
COG1373	398	Predicted ATPase (AAA+ superfamily) [General funct	97.29
PF00519	432	PPV_E1_C: Papillomavirus helicase; InterPro: IPR00	97.29
PRK10365	441	transcriptional regulatory protein ZraR; Provision	97.27
PRK14722	374	flhF flagellar biosynthesis regulator FlhF; Provis	97.27
PRK14729	300	miaA tRNA delta(2)-isopentenylpyrophosphate transf	97.27
cd01129	264	PulE-GspE PulE/GspE The type II secretory pathway	97.27
cd01121	372	Sms Sms (bacterial radA) DNA repair protein. This	97.27
cd01124	187	KaiC KaiC is a circadian clock protein primarily f	97.26
KOG3347	176	consensus Predicted nucleotide kinase/nuclear prot	97.26
PHA02624	647	large T antigen; Provisional	97.24
PRK13765	637	ATP-dependent protease Lon; Provisional	97.23
cd03283	199	ABC_MutS-like MutS-like homolog in eukaryotes. The	97.23
PRK12726	407	flagellar biosynthesis regulator FlhF; Provisional	97.22
PRK03839	180	putative kinase; Provisional	97.2
PRK11823	446	DNA repair protein RadA; Provisional	97.2
smart00350	509	MCM minichromosome maintenance proteins.	97.19
KOG0745	564	consensus Putative ATP-dependent Clp-type protease	97.18
PF08519	155	RFC1: Replication factor RFC1 C terminal domain; I	97.17
COG4619	223	ABC-type uncharacterized transport system, ATPase	97.16
TIGR03499	282	FlhF flagellar biosynthetic protein FlhF.	97.16
PF03969	362	AFG1_ATPase: AFG1-like ATPase; InterPro: IPR005654	97.13
PF00437	270	T2SE: Type II/IV secretion system protein; InterPr	97.12
PRK14737	186	gmk guanylate kinase; Provisional	97.12
PRK13947	171	shikimate kinase; Provisional	97.12
PRK12724	432	flagellar biosynthesis regulator FlhF; Provisional	97.11
COG2804	500	PulE Type II secretory pathway, ATPase PulE/Tfp pi	97.11
cd01131	198	PilT Pilus retraction ATPase PilT. PilT is a nucle	97.1
PRK06762	166	hypothetical protein; Provisional	97.1
cd03115	173	SRP The signal recognition particle (SRP) mediates	97.1
cd01128	249	rho_factor Transcription termination factor rho is	97.09
COG2909	894	MalT ATP-dependent transcriptional regulator [Tran	97.08
PRK00625	173	shikimate kinase; Provisional	97.07
TIGR02688	449	conserved hypothetical protein TIGR02688. Members	97.07
COG1116	248	TauB ABC-type nitrate/sulfonate/bicarbonate transp	97.05
PF07693	325	KAP_NTPase: KAP family P-loop domain; InterPro: IP	97.05
TIGR01359	183	UMP_CMP_kin_fam UMP-CMP kinase family. This subfam	97.04
TIGR02237	209	recomb_radB DNA repair and recombination protein R	97.03
TIGR01618	220	phage_P_loop phage nucleotide-binding protein. Thi	97.03
cd00464	154	SK Shikimate kinase (SK) is the fifth enzyme in th	97.03
cd03282	204	ABC_MSH4_euk MutS4 homolog in eukaryotes. The MutS	97.03
cd02021	150	GntK Gluconate kinase (GntK) catalyzes the phospho	97.03
PRK09361	225	radB DNA repair and recombination protein RadB; Pr	97.02
TIGR02533	486	type_II_gspE general secretory pathway protein E.	97.02
PRK05629	318	hypothetical protein; Validated	97.02
TIGR00764	608	lon_rel lon-related putative ATP-dependent proteas	97.01
TIGR01360	188	aden_kin_iso1 adenylate kinase, isozyme 1 subfamil	97.0
PRK14531	183	adenylate kinase; Provisional	97.0
PRK08154	309	anaerobic benzoate catabolism transcriptional regu	97.0
PRK14532	188	adenylate kinase; Provisional	96.99
PRK07261	171	topology modulation protein; Provisional	96.98
PRK13949	169	shikimate kinase; Provisional	96.97
cd02020	147	CMPK Cytidine monophosphate kinase (CMPK) catalyze	96.97
cd00227	175	CPT Chloramphenicol (Cm) phosphotransferase (CPT).	96.97
PRK08533	230	flagellar accessory protein FlaH; Reviewed	96.95
TIGR02782	299	TrbB_P P-type conjugative transfer ATPase TrbB. Th	96.94
cd01394	218	radB RadB. The archaeal protein radB shares simila	96.94
PRK10416	318	signal recognition particle-docking protein FtsY;	96.94
PRK10436	462	hypothetical protein; Provisional	96.93
PF02562	205	PhoH: PhoH-like protein; InterPro: IPR003714 PhoH	96.93
cd03243	202	ABC_MutS_homologs The MutS protein initiates DNA m	96.93
PRK06696	223	uridine kinase; Validated	96.93
TIGR00150	133	HI0065_YjeE ATPase, YjeE family. Members of this f	96.92
smart00534	185	MUTSac ATPase domain of DNA mismatch repair MUTS f	96.92
PRK14530	215	adenylate kinase; Provisional	96.91
cd03280	200	ABC_MutS2 MutS2 homologs in bacteria and eukaryote	96.9
PF10236	309	DAP3: Mitochondrial ribosomal death-associated pro	96.89
TIGR01420	343	pilT_fam pilus retraction protein PilT. This model	96.89
COG1220	444	HslU ATP-dependent protease HslVU (ClpYQ), ATPase	96.89
PRK06217	183	hypothetical protein; Validated	96.88
TIGR01313	163	therm_gnt_kin carbohydrate kinase, thermoresistant	96.87
cd01428	194	ADK Adenylate kinase (ADK) catalyzes the reversibl	96.85
cd03287	222	ABC_MSH3_euk MutS3 homolog in eukaryotes. The MutS	96.85
cd00267	157	ABC_ATPase ABC (ATP-binding cassette) transporter	96.85
TIGR00064	272	ftsY signal recognition particle-docking protein F	96.84
PF13245	76	AAA_19: Part of AAA domain	96.83
PRK04040	188	adenylate kinase; Provisional	96.83
cd00046	144	DEXDc DEAD-like helicases superfamily. A diverse f	96.82
cd01393	226	recA_like RecA is a bacterial enzyme which has rol	96.81
PRK06547	172	hypothetical protein; Provisional	96.81
COG1419	407	FlhF Flagellar GTP-binding protein [Cell motility	96.81
PF08298	358	AAA_PrkA: PrkA AAA domain; InterPro: IPR013153 Thi	96.8
TIGR03574	249	selen_PSTK L-seryl-tRNA(Sec) kinase, archaeal. Mem	96.8
PF01443	234	Viral_helicase1: Viral (Superfamily 1) RNA helicas	96.8
TIGR02012	321	tigrfam_recA protein RecA. This model describes or	96.8
PRK14528	186	adenylate kinase; Provisional	96.77
PRK01184	184	hypothetical protein; Provisional	96.76
PRK02496	184	adk adenylate kinase; Provisional	96.76
PRK14527	191	adenylate kinase; Provisional	96.76
PRK13946	184	shikimate kinase; Provisional	96.74
PF08433	270	KTI12: Chromatin associated protein KTI12 ; InterP	96.73
PF13086	236	AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV	96.73
TIGR02538	564	type_IV_pilB type IV-A pilus assembly ATPase PilB.	96.72
cd00984	242	DnaB_C DnaB helicase C terminal domain. The hexame	96.71
PTZ00088	229	adenylate kinase 1; Provisional	96.71
COG1126	240	GlnQ ABC-type polar amino acid transport system, A	96.7
PRK03731	171	aroL shikimate kinase II; Reviewed	96.7
PLN02200	234	adenylate kinase family protein	96.69
PRK05800	170	cobU adenosylcobinamide kinase/adenosylcobinamide-	96.69
TIGR01448	720	recD_rel helicase, putative, RecD/TraA family. Thi	96.69
PRK13948	182	shikimate kinase; Provisional	96.68
cd03222	177	ABC_RNaseL_inhibitor The ABC ATPase RNase L inhibi	96.68
TIGR00959	428	ffh signal recognition particle protein. This mode	96.67
cd00544	169	CobU Adenosylcobinamide kinase / adenosylcobinamid	96.67
PRK09862	506	putative ATP-dependent protease; Provisional	96.67
COG1117	253	PstB ABC-type phosphate transport system, ATPase c	96.66
cd02019	69	NK Nucleoside/nucleotide kinase (NK) is a protein	96.65
cd04138	162	H_N_K_Ras_like H-Ras/N-Ras/K-Ras subfamily. H-Ras,	96.65
COG0703	172	AroK Shikimate kinase [Amino acid transport and me	96.65
TIGR01447	586	recD exodeoxyribonuclease V, alpha subunit. This f	96.64
PF13238	129	AAA_18: AAA domain; PDB: 3IIK_A 3IIJ_A 3IIL_A 1RKB	96.64
cd03238	176	ABC_UvrA The excision repair protein UvrA; Nucleot	96.64
PRK04182	180	cytidylate kinase; Provisional	96.63
COG0606	490	Predicted ATPase with chaperone activity [Posttran	96.63
COG3604	550	FhlA Transcriptional regulator containing GAF, AAA	96.62
PRK05057	172	aroK shikimate kinase I; Reviewed	96.61
TIGR01351	210	adk adenylate kinases. Adenylate kinase (EC 2.7.4.	96.61
smart00173	164	RAS Ras subfamily of RAS small GTPases. Similar in	96.6
KOG1970	634	consensus Checkpoint RAD17-RFC complex, RAD17/RAD2	96.6
PRK00279	215	adk adenylate kinase; Reviewed	96.59
PRK13900	332	type IV secretion system ATPase VirB11; Provisiona	96.59
TIGR00416	454	sms DNA repair protein RadA. The gene protuct code	96.59
TIGR00767	415	rho transcription termination factor Rho. Members	96.57
cd04139	164	RalA_RalB RalA/RalB subfamily. The Ral (Ras-like)	96.57
cd03216	163	ABC_Carb_Monos_I This family represents the domain	96.57
cd00983	325	recA RecA is a bacterial enzyme which has roles in	96.56
PLN02748	468	tRNA dimethylallyltransferase	96.54
TIGR02173	171	cyt_kin_arch cytidylate kinase, putative. Proteins	96.53
PRK14723	767	flhF flagellar biosynthesis regulator FlhF; Provis	96.52
cd03221	144	ABCF_EF-3 ABCF_EF-3 Elongation factor 3 (EF-3) is	96.52
PHA02530	300	pseT polynucleotide kinase; Provisional	96.51
PRK10078	186	ribose 1,5-bisphosphokinase; Provisional	96.5
TIGR02525	372	plasmid_TraJ plasmid transfer ATPase TraJ. Members	96.5
PRK12339	197	2-phosphoglycerate kinase; Provisional	96.5
smart00072	184	GuKc Guanylate kinase homologues. Active enzymes c	96.49
cd03284	216	ABC_MutS1 MutS1 homolog in eukaryotes. The MutS pr	96.48
COG3265	161	GntK Gluconate kinase [Carbohydrate transport and	96.48
PF04665	241	Pox_A32: Poxvirus A32 protein; InterPro: IPR006758	96.47
PF13521	163	AAA_28: AAA domain; PDB: 1LW7_A.	96.47
PRK10867	433	signal recognition particle protein; Provisional	96.46
PF00488	235	MutS_V: MutS domain V C-terminus.; InterPro: IPR00	96.45
TIGR01425	429	SRP54_euk signal recognition particle protein SRP5	96.45
PRK10875	615	recD exonuclease V subunit alpha; Provisional	96.45
PRK09376	416	rho transcription termination factor Rho; Provisio	96.44
TIGR02322	179	phosphon_PhnN phosphonate metabolism protein/1,5-b	96.43
PRK05973	237	replicative DNA helicase; Provisional	96.43
PF06144	172	DNA_pol3_delta: DNA polymerase III, delta subunit;	96.42
cd01867	167	Rab8_Rab10_Rab13_like Rab8/Sec4/Ypt2. Rab8/Sec4/Yp	96.41
cd03286	218	ABC_MSH6_euk MutS6 homolog in eukaryotes. The MutS	96.41
cd00876	160	Ras Ras family. The Ras family of the Ras superfam	96.4
PRK08233	182	hypothetical protein; Provisional	96.4
PRK14721	420	flhF flagellar biosynthesis regulator FlhF; Provis	96.4
PRK06995	484	flhF flagellar biosynthesis regulator FlhF; Valida	96.39
PRK14526	211	adenylate kinase; Provisional	96.39
PRK08487	328	DNA polymerase III subunit delta; Validated	96.39
TIGR03877	237	thermo_KaiC_1 KaiC domain protein, Ph0284 family.	96.38
cd04160	167	Arfrp1 Arfrp1 subfamily. Arfrp1 (Arf-related prote	96.36
PRK06731	270	flhF flagellar biosynthesis regulator FlhF; Valida	96.36
cd01123	235	Rad51_DMC1_radA Rad51_DMC1_radA,B. This group of r	96.36
cd04145	164	M_R_Ras_like M-Ras/R-Ras-like subfamily. This subf	96.36
COG2884	223	FtsE Predicted ATPase involved in cell division [C	96.35
TIGR03878	259	thermo_KaiC_2 KaiC domain protein, AF_0795 family.	96.35
cd04137	180	RheB Rheb (Ras Homolog Enriched in Brain) subfamil	96.34
PF05970	364	PIF1: PIF1-like helicase; InterPro: IPR010285 This	96.34
cd01122	271	GP4d_helicase GP4d_helicase is a homohexameric 5'-	96.34
PLN02674	244	adenylate kinase	96.33
KOG1808	1856	consensus AAA ATPase containing von Willebrand fac	96.33
PLN02199	303	shikimate kinase	96.33
cd03223	166	ABCD_peroxisomal_ALDP Peroxisomal ATP-binding cass	96.33
cd02027	149	APSK Adenosine 5'-phosphosulfate kinase (APSK) cat	96.32
PRK00889	175	adenylylsulfate kinase; Provisional	96.32
PRK07914	320	hypothetical protein; Reviewed	96.32
cd03237	246	ABC_RNaseL_inhibitor_domain2 The ATPase domain 2 o	96.3
PRK06067	234	flagellar accessory protein FlaH; Validated	96.28
cd01866	168	Rab2 Rab2 subfamily. Rab2 is localized on cis-Golg	96.28
cd04119	168	RJL RJL (RabJ-Like) subfamily. RJLs are found in m	96.27
cd01869	166	Rab1_Ypt1 Rab1/Ypt1 subfamily. Rab1 is found in ev	96.27
COG1122	235	CbiO ABC-type cobalt transport system, ATPase comp	96.27
COG0563	178	Adk Adenylate kinase and related kinases [Nucleoti	96.26
KOG1051	898	consensus Chaperone HSP104 and related ATP-depende	96.26
PF00406	151	ADK: Adenylate kinase; InterPro: IPR000850 Adenyla	96.25
PF06745	226	KaiC: KaiC; InterPro: IPR014774 This entry represe	96.25
COG1125	309	OpuBA ABC-type proline/glycine betaine transport s	96.24
TIGR02524	358	dot_icm_DotB Dot/Icm secretion system ATPase DotB.	96.23
PLN02165	334	adenylate isopentenyltransferase	96.23
cd01130	186	VirB11-like_ATPase Type IV secretory pathway compo	96.22
PTZ00293	211	thymidine kinase; Provisional	96.22
PF01745	233	IPT: Isopentenyl transferase; InterPro: IPR002648	96.21
cd03233	202	ABC_PDR_domain1 The pleiotropic drug resistance (P	96.2
PRK14712	1623	conjugal transfer nickase/helicase TraI; Provision	96.19
smart00175	164	RAB Rab subfamily of small GTPases. Rab GTPases ar	96.18
PRK12338	319	hypothetical protein; Provisional	96.18
COG2805	353	PilT Tfp pilus assembly protein, pilus retraction	96.18
COG1134	249	TagH ABC-type polysaccharide/polyol phosphate tran	96.17
cd03230	173	ABC_DR_subfamily_A This family of ATP-binding prot	96.16
PRK12608	380	transcription termination factor Rho; Provisional	96.15
cd03246	173	ABCC_Protease_Secretion This family represents the	96.14
cd00154	159	Rab Rab family. Rab GTPases form the largest famil	96.14
PRK09354	349	recA recombinase A; Provisional	96.14
PRK05541	176	adenylylsulfate kinase; Provisional	96.13
cd04177	168	RSR1 RSR1 subgroup. RSR1/Bud1p is a member of the	96.12
COG0529	197	CysC Adenylylsulfate kinase and related kinases [I	96.11
TIGR02768	744	TraA_Ti Ti-type conjugative transfer relaxase TraA	96.11
cd04136	163	Rap_like Rap-like subfamily. The Rap subfamily con	96.1
PRK09825	176	idnK D-gluconate kinase; Provisional	96.06
PRK05907	311	hypothetical protein; Provisional	96.05
cd01672	200	TMPK Thymidine monophosphate kinase (TMPK), also k	96.05
PF03193	161	DUF258: Protein of unknown function, DUF258; Inter	96.05

>PF03215 Rad17: Rad17 cell cycle checkpoint protein

Probab=100.00  E-value=6.4e-68  Score=588.40  Aligned_cols=451  Identities=34%  Similarity=0.523  Sum_probs=334.8

Q ss_pred             CCCccccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCc
Q 005987          135 TQQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTP  214 (666)
Q Consensus       135 ~~~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~  214 (666)
                      .+++|+|||+|++++||++|++|+++|+.||+..+.   +..+.++|||+|||||||||++++||+++|++++||.++..
T Consensus         5 ~~~~W~~ky~P~~~~eLavhkkKv~eV~~wl~~~~~---~~~~~~iLlLtGP~G~GKtttv~~La~elg~~v~Ew~np~~   81 (519)
T PF03215_consen    5 ESEPWVEKYAPKTLDELAVHKKKVEEVRSWLEEMFS---GSSPKRILLLTGPSGCGKTTTVKVLAKELGFEVQEWINPVS   81 (519)
T ss_pred             ccCccchhcCCCCHHHhhccHHHHHHHHHHHHHHhc---cCCCcceEEEECCCCCCHHHHHHHHHHHhCCeeEEecCCCC
Confidence            478999999999999999999999999999998775   33344799999999999999999999999999999987764


Q ss_pred             h---hhh--hhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHH
Q 005987          215 T---IWQ--EYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLV  289 (666)
Q Consensus       215 ~---~~~--e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~  289 (666)
                      .   .+.  ++.........+.++.+.|.+|+.+..+|..+.....+....++||||||+|++...+. ..++++|+.++
T Consensus        82 ~~~~~~~~~d~~s~~~~~~~f~sq~~~F~~f~l~~s~y~~l~~~g~~~~~~~kvILVEDlPN~~~~~~-~~f~~~L~~~l  160 (519)
T PF03215_consen   82 FRESDNQEDDFESDFNKFDEFLSQSDKFSEFLLRASKYSSLSMSGSNSSSNKKVILVEDLPNVFHRDT-SRFREALRQYL  160 (519)
T ss_pred             ccccccccccccccccccccccchhhhhccccccccccccccccCCCcCCCceEEEeeccccccchhH-HHHHHHHHHHH
Confidence            1   111  11111112223467788899997777788766432222334578999999999888766 88999999999


Q ss_pred             hcCCC-ceEEEEecCCCCCCccc------hhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHh-----C-CCC
Q 005987          290 RSTHI-PTAVVLTECGKADSVDS------TAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQE-----Q-YSL  356 (666)
Q Consensus       290 ~~~~~-PiViIit~~~~~~s~d~------~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e-----~-i~v  356 (666)
                      ..++. |+|||++++......+.      ..+.+. -++++.++++..|.|||++++.|+|+|++||..|     + ..+
T Consensus       161 ~~~~~~PlV~iiSe~~~~~~~~~~~~~~~t~~~L~-~~~il~~~~i~~I~FNpIa~T~mkKaL~rI~~~E~~~~~~~~~~  239 (519)
T PF03215_consen  161 RSSRCLPLVFIISETESLSGDNSYRSNSFTAERLF-PKEILNHPGITRIKFNPIAPTFMKKALKRILKKEARSSSGKNKV  239 (519)
T ss_pred             HcCCCCCEEEEEecccccCCCCcccccchhhhhcc-CHHHHhCCCceEEEecCCCHHHHHHHHHHHHHHHhhhhcCCccC
Confidence            99888 99999997632111111      111222 1677888899999999999999999999999998     2 233


Q ss_pred             C--HHHHHHHHHHcCCcHHHHHHHHHHHhcCCCCccccccc-----C-C--CCCCCcc-----ccCCCCCcccccCCccc
Q 005987          357 S--TEQIDLVAQASGGDIRQAITSLQFSSLKQDPMLNLSLS-----I-S--KPNFPEE-----KADGHGGFSIQFGRDET  421 (666)
Q Consensus       357 ~--~~~l~~Ia~~s~GDIR~AIn~LQf~~~~~~~~~~~~~~-----~-~--~~~~~k~-----~~~~~~~~~~~~~RD~~  421 (666)
                      +  .++|+.|++.|+||||+|||+|||+|..+.......+.     . .  ...+.+.     +..+...+..+++||.+
T Consensus       240 p~~~~~l~~I~~~s~GDIRsAIn~LQf~~~~g~~~~~~~k~g~~~~~~~v~~~~ks~~~~~~~~~~~~~~~~~i~~Rd~s  319 (519)
T PF03215_consen  240 PDKQSVLDSIAESSNGDIRSAINNLQFWCLKGDNNLRPKKKGFSLKADAVLSLSKSKRKSKPDTVKEESSLQSIGGRDES  319 (519)
T ss_pred             CChHHHHHHHHHhcCchHHHHHHHHHHHhcCCCCCCCccccCCcccccceeccccCCCcccccccccccccccccccccc
Confidence            3  45699999999999999999999999954332211100     0 0  0001111     11113345678899999


Q ss_pred             cchHHHHhHHhhCCCCCCccccc-cccchhhhhccccCCCCCCChHHHHHhcCCChhHHHHHHHhhcCCCCCcchHHHHH
Q 005987          422 LSLFHALGKFLHNKRETDNLVKM-DQDAFVVKDKFSRLPLKMDAPEKVLSQAHGQARPVLDFLHENFLDFISEDAIDDAW  500 (666)
Q Consensus       422 l~lFhalGkil~~Kr~~~~~~~~-~~~~~~~~~~~~r~pl~~~~pE~vl~~~~~~~~~~~~~LhENy~~f~~d~~i~~~~  500 (666)
                      |++||||||||||||......+. ..+.++.  .+.|.++. ..||+++++++++.++|.+||||||++||.+  |++++
T Consensus       320 L~lFHAlGKILynKR~~~~~~~~~~l~~~l~--~~~R~~l~-~~~e~vi~~s~~~~~~f~~~LhENY~~f~~~--i~~~~  394 (519)
T PF03215_consen  320 LSLFHALGKILYNKREPDDEVDSERLPSHLS--HHERDPLL-VDPEEVIEESHMDSSTFVLFLHENYLDFCSD--IEDAS  394 (519)
T ss_pred             hHHHHHhhhheeccccCCCccccccCcchhh--hcccCccc-cCHHHHHHHhcCChHHHHHHHHHhccchhhh--HHHHH
Confidence            99999999999999988753221 1122222  34566664 4699999999999999999999999999976  99999


Q ss_pred             HHHHHhhHhhhccccccCccccccchhHHHHHHHHHHHHHHHhhhCCC-------CCCCCcccccCCcchhhhhhhHHHH
Q 005987          501 AVASYLSDADLLLASFRGRLVRYNEADNVLQSAAASVAARGVLFGNSH-------PVPPRWHAIRKPKLWRVDQSSLQKK  573 (666)
Q Consensus       501 ~~~d~LS~aD~l~~~~~~~~~~~~~~~~~l~~~a~sva~RGv~~~n~~-------p~~~~~~~~~~P~~~~~~~~~~~~~  573 (666)
                      .|+||||+||+|.+.|+.        .+.++.|+.++|+||+|++|..       +..++|++++||+||.+.++...+ 
T Consensus       395 ~~~d~LS~aD~l~~~~~~--------~~~~~~~~~s~a~rg~~~~n~~~~~~~~~~~~~~~~~~~Kpq~~~~~~~~~~~-  465 (519)
T PF03215_consen  395 DASDYLSDADLLSSDWES--------RSSLREYRASVAVRGLMHSNRGKAFFPRQWKMRRFRPLHKPQWFGYYKPYIEN-  465 (519)
T ss_pred             HHHHHhhHHHhccCcccc--------chhHHHHHHHHHhhhcchhccCcccCCCcccccccccccchHHHHHHHHHHHH-
Confidence            999999999999876543        2567889999999999987654       334689999999999999887654 


Q ss_pred             HHHHHhhhccccCCcccccccCCCCCchhhhhhhhhhhhHHhhc
Q 005987          574 KELLKKKFMAWDGSISADVYNGSSSSDVSVLATEYAPALKWLGN  617 (666)
Q Consensus       574 ~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~e~lP~l~~i~~  617 (666)
                       ++..+.+..       ++|     ++.-.+.+|++|||..+..
T Consensus       466 -~~~~~~~~~-------~~~-----l~~l~~~~~~~~~l~~~~~  496 (519)
T PF03215_consen  466 -CLAAKSLFL-------DYC-----LPPLCLQTELLPYLAKLTD  496 (519)
T ss_pred             -HHHHHHHHH-------HHh-----hhhhccchhhHHHHHHccc
Confidence             333333322       123     2223689999999999864

>KOG1970 consensus Checkpoint RAD17-RFC complex, RAD17/RAD24 component [Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]

Probab=100.00  E-value=4e-66  Score=550.67  Aligned_cols=520  Identities=32%  Similarity=0.460  Sum_probs=388.0

Q ss_pred             ccccccccccccccccCCCCCc-hhhhchhhhhhccccCCccccccCCCCCCCCccCCCCCCccccccCCCCccccccCH
Q 005987           77 RDLALGSSSRQQLWTNKNKPCS-LEEHAIQKENVGRFLTPSRFEGLVNPDHDSASASSSTQQLWAEKYKPRSLEELAVQR  155 (666)
Q Consensus        77 r~~~~~~~~~~~~w~~~~~~~s-~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~W~eKY~P~sl~eLvg~~  155 (666)
                      ++..+..+++...|.+.+++.+ ++-+....+||..+-+...+        ..+.......++|+|||+|++++||++|+
T Consensus        17 ~~~~~~~~s~~~r~~s~s~~~~~~~~~d~~~~d~~a~~d~~~~--------~l~~~~~d~~elW~eKy~P~t~eeLAVHk   88 (634)
T KOG1970|consen   17 KKASNIRKSEKPRLSSKSSTTKPSSIPDIHEEDFEAFDDEESV--------HLNNEKEDEFELWVEKYKPRTLEELAVHK   88 (634)
T ss_pred             cccccccccccccccCCCCCCCCccccccchhhhhhhchhhhc--------ccCCCCccccchhHHhcCcccHHHHhhhH
Confidence            3334455567777855565555 55556666667665553332        11222334589999999999999999999


Q ss_pred             HHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCchhhhhhhhcccCCcc--ccch
Q 005987          156 KKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTIWQEYMHNCKTGLE--YTSK  233 (666)
Q Consensus       156 k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~~~~e~l~~~~~g~~--~~s~  233 (666)
                      +|+.+|+.||+ .+.....+.+.++|||+||+||||||++++||+++|+.++||++|....+.+++++...+..  |.++
T Consensus        89 kKI~eVk~WL~-~~~~~~~~l~~~iLLltGPsGcGKSTtvkvLskelg~~~~Ew~Npi~~~~~~~~h~~t~~~~~~~~s~  167 (634)
T KOG1970|consen   89 KKISEVKQWLK-QVAEFTPKLGSRILLLTGPSGCGKSTTVKVLSKELGYQLIEWSNPINLKEPENLHNETSFLMFPYQSQ  167 (634)
T ss_pred             HhHHHHHHHHH-HHHHhccCCCceEEEEeCCCCCCchhHHHHHHHhhCceeeeecCCccccccccccccchhcccchhhH
Confidence            99999999999 22222255556899999999999999999999999999999999998888888888666655  8899


Q ss_pred             hHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcCCCceEEEEecCCCCCCccchh
Q 005987          234 LDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHIPTAVVLTECGKADSVDSTA  313 (666)
Q Consensus       234 ~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~~~PiViIit~~~~~~s~d~~~  313 (666)
                      +..|+.|++++.+|+.+..+.....+.+++|||||+|+.+..+.++.++++|+.+...+.+|+|||+|++...+..+++.
T Consensus       168 L~~fesFler~~kyg~l~~~g~~~~~~~~liLveDLPn~~~~d~~~~f~evL~~y~s~g~~PlIf~iTd~~~~g~nnq~r  247 (634)
T KOG1970|consen  168 LAVFESFLLRATKYGSLQMSGDDLRTDKKLILVEDLPNQFYRDDSETFREVLRLYVSIGRCPLIFIITDSLSNGNNNQDR  247 (634)
T ss_pred             HHHHHHHHHHHHhhchhhhcccccccCceEEEeeccchhhhhhhHHHHHHHHHHHHhcCCCcEEEEEeccccCCCcchhh
Confidence            99999999999889988776666666788999999999988877888999999999999999999999988765555544


Q ss_pred             hhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCC------HHHHHHHHHHcCCcHHHHHHHHHHHhcCCC
Q 005987          314 QSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLS------TEQIDLVAQASGGDIRQAITSLQFSSLKQD  387 (666)
Q Consensus       314 r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~------~~~l~~Ia~~s~GDIR~AIn~LQf~~~~~~  387 (666)
                      .....++   .++|+..|.|||++++.|+|.|.+||..++....      ...++.|+..++||||+|||+|||++..+.
T Consensus       248 lf~~d~q---~~~ri~~IsFNPIa~T~MKK~L~ric~~e~~~~s~~k~~~~~~v~~i~~~s~GDIRsAInsLQlssskg~  324 (634)
T KOG1970|consen  248 LFPKDIQ---EEPRISNISFNPIAPTIMKKFLKRICRIEANKKSGIKVPDTAEVELICQGSGGDIRSAINSLQLSSSKGE  324 (634)
T ss_pred             hchhhhh---hccCcceEeecCCcHHHHHHHHHHHHHHhcccccCCcCchhHHHHHHHHhcCccHHHHHhHhhhhcccCc
Confidence            4444444   5678999999999999999999999999987666      688999999999999999999999986665


Q ss_pred             CcccccccCCCC----CCCccc---cCCCCCcccccCCccccchHHHHhHHhhCCCCCCccccccccchhhhhccccCCC
Q 005987          388 PMLNLSLSISKP----NFPEEK---ADGHGGFSIQFGRDETLSLFHALGKFLHNKRETDNLVKMDQDAFVVKDKFSRLPL  460 (666)
Q Consensus       388 ~~~~~~~~~~~~----~~~k~~---~~~~~~~~~~~~RD~~l~lFhalGkil~~Kr~~~~~~~~~~~~~~~~~~~~r~pl  460 (666)
                      ......++++..    +..+.+   ...++.+..+++||++|.+||++|+++|+||......+...-+..+ +.+.|.++
T Consensus       325 ~~~~~~ks~rs~~s~~~kg~~~~~~s~~nq~i~~ig~~de~L~~f~al~~~l~pkr~s~~~~~s~~~~~~~-a~~~r~~L  403 (634)
T KOG1970|consen  325 NNLRPRKSGRSGKSDIGKGKSKRMESPENQELQSIGGRDESLFLFRALGKVLYPKRNSDNELKSPRSPSHL-AEYERDTL  403 (634)
T ss_pred             cCCCcccccccccchhhccccccccCchHHHHHHhhcchHHHHHHHhhcccccccccccccccccCCcchh-hhhhhhhh
Confidence            444433332111    111111   1112356678999999999999999999999887654333222222 55778888


Q ss_pred             CCCChHHHHHhcCCChhHHHHHHHhhcCCCCCcchHHHHHHHHHHhhHhhhccccccCc----------------cc-c-
Q 005987          461 KMDAPEKVLSQAHGQARPVLDFLHENFLDFISEDAIDDAWAVASYLSDADLLLASFRGR----------------LV-R-  522 (666)
Q Consensus       461 ~~~~pE~vl~~~~~~~~~~~~~LhENy~~f~~d~~i~~~~~~~d~LS~aD~l~~~~~~~----------------~~-~-  522 (666)
                      +++ ||+|+.++++.+..++.|+|+||++|+..  |++++.+.+++|+||.+...|...                ++ . 
T Consensus       404 ~~~-peevl~~S~~~~~~~v~fl~~N~~~f~~n--id~i~~~se~~~~~d~~s~~w~~~~~L~~~y~~~~a~rsvm~~n~  480 (634)
T KOG1970|consen  404 KHE-PEEVLEMSHMQGGNFVRFLHQNYSDFFSN--IDDIVRASEFLSFADQLSGDWNTRQSLLREYRTLIATRSVMNSNK  480 (634)
T ss_pred             hcC-chhhhhhcccccchhhhhhhhccchhhhc--ccceeeehhhhhHHHHhcccchhHHHHHHHHHHHHHHHHhhcccc
Confidence            877 99999999999999999999999999987  899999999999999987755211                00 0 


Q ss_pred             cc----------------------------chhHHHHHHHHHHHHH---HHhhhCC---CCCCCCcccccCCcchhhhhh
Q 005987          523 YN----------------------------EADNVLQSAAASVAAR---GVLFGNS---HPVPPRWHAIRKPKLWRVDQS  568 (666)
Q Consensus       523 ~~----------------------------~~~~~l~~~a~sva~R---Gv~~~n~---~p~~~~~~~~~~P~~~~~~~~  568 (666)
                      |.                            ....+.+..++.+|+|   |+++.+-   .|.-++|.++++|..|+.+.-
T Consensus       481 y~~p~~~~~~l~n~p~~s~~~~~~~~~~~~~~~~vp~ig~~~~avr~~~gi~~~~di~d~~~~s~~~~~k~p~~~~~~~~  560 (634)
T KOG1970|consen  481 YAHPQGGQWFLINKPYRSLAAKALFPDFCLQTQLVPRIGLLTVAVRNCAGISFINDIGDLPLISHFGRLKKPKLINREHG  560 (634)
T ss_pred             cccccccceeecccccccchhhhcccchhccccccccccchhhhhhccccchhhhhcccccchhhhhhccchhhhhhhhc
Confidence            00                            0011112223346666   6666652   344578999999999886655


Q ss_pred             hHHHHHHHHHhhhccccCCcccccccCCCCCchhhhhhhhh----hhhHHhhcCCCC
Q 005987          569 SLQKKKELLKKKFMAWDGSISADVYNGSSSSDVSVLATEYA----PALKWLGNRTSV  621 (666)
Q Consensus       569 ~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~e~l----P~l~~i~~~~~~  621 (666)
                      ..+-...+..|+...         +.+..+......+|++-    |..+++...+++
T Consensus       561 ~~q~e~~l~~q~~~~---------~~g~~~~~~p~~at~~~~~~~p~~~~~~~~~~~  608 (634)
T KOG1970|consen  561 SIQPESNLEEQYNGG---------YVGRKSLDLPLQATEPETWSLPLSKNSASIAGK  608 (634)
T ss_pred             ccchhhhhHHHhcCC---------cccccccCCcceecCcccccCCcccceeeecCc
Confidence            555555666666654         22344445556776766    888888876663

>TIGR00602 rad24 checkpoint protein rad24

Probab=100.00  E-value=5.4e-57  Score=508.90  Aligned_cols=509  Identities=26%  Similarity=0.366  Sum_probs=346.1

Q ss_pred             CCccccccccccccccccccCCCCCc-hhhhchhhhhhccccCCccccccCCC-CCCCC--ccCCCCCCccccccCCCCc
Q 005987           73 VNPKRDLALGSSSRQQLWTNKNKPCS-LEEHAIQKENVGRFLTPSRFEGLVNP-DHDSA--SASSSTQQLWAEKYKPRSL  148 (666)
Q Consensus        73 ~~~~r~~~~~~~~~~~~w~~~~~~~s-~~~~~~~~~~~~~~~~~~~i~~~~~~-~~~~~--~~~~~~~~~W~eKY~P~sl  148 (666)
                      .+.+|+..+.+++++++| +..+++| .+..+.+..++-    ..+....+.. +.+..  ........+|++||+|+++
T Consensus         9 ~~~~~~~~~~~~~~~~~~-s~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~pW~eKyrP~~l   83 (637)
T TIGR00602         9 PSFDDFLLSSLISTITKW-SLSRPTSSHRRKNSPSTDIH----ARKRGFLSLEQDTGLELSSENLDGNEPWVEKYKPETQ   83 (637)
T ss_pred             cchhhhhhhccccccccc-ccccCcccccccccccccch----hhhccccccchhhhhcCCcccccccCchHHHhCCCCH
Confidence            455666677788888888 5444555 444333332211    1111111100 00000  0011346799999999999


Q ss_pred             cccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCchhhhhhhhc----c
Q 005987          149 EELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTIWQEYMHN----C  224 (666)
Q Consensus       149 ~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~~~~e~l~~----~  224 (666)
                      +||++|++++++|+.|+.....   +..+.++++|+|||||||||+++++|+++++.++||.++..+.+....+.    .
T Consensus        84 del~~~~~ki~~l~~~l~~~~~---~~~~~~illL~GP~GsGKTTl~~~la~~l~~~~~Ew~npv~~~~~~~~~~~~~s~  160 (637)
T TIGR00602        84 HELAVHKKKIEEVETWLKAQVL---ENAPKRILLITGPSGCGKSTTIKILSKELGIQVQEWSNPTLPDFQKNDHKVTLSL  160 (637)
T ss_pred             HHhcCcHHHHHHHHHHHHhccc---ccCCCcEEEEECCCCCCHHHHHHHHHHHhhhHHHHHhhhhhhcccccccccchhh
Confidence            9999999999999999997654   22233689999999999999999999999999999854432222111110    0


Q ss_pred             cC-CccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHH-HHHhcCCCceEEEEec
Q 005987          225 KT-GLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLL-LLVRSTHIPTAVVLTE  302 (666)
Q Consensus       225 ~~-g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~-~l~~~~~~PiViIit~  302 (666)
                      .. ...+.+..+.|..|+.++........  .+..+.++||||||+|++..+.. ..++++|+ .+.+.++.|+|+|+++
T Consensus       161 ~~~~~~~~s~~~~F~~fl~~a~~~~~~~g--~~~~~~~~IILIDEiPn~~~r~~-~~lq~lLr~~~~e~~~~pLI~I~TE  237 (637)
T TIGR00602       161 ESCFSNFQSQIEVFSEFLLRATNKLQMLG--DDLMTDKKIILVEDLPNQFYRDT-RALHEILRWKYVSIGRCPLVFIITE  237 (637)
T ss_pred             hhccccccchHHHHHHHHHHHHhhhcccc--cccCCceeEEEeecchhhchhhH-HHHHHHHHHHhhcCCCceEEEEecC
Confidence            01 11235678889999998863221110  11123567999999999875432 34666666 5667788899999887


Q ss_pred             CCCCCCcc----chhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCC------C-CHHHHHHHHHHcCCc
Q 005987          303 CGKADSVD----STAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYS------L-STEQIDLVAQASGGD  371 (666)
Q Consensus       303 ~~~~~s~d----~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~------v-~~~~l~~Ia~~s~GD  371 (666)
                      +.......    ..++.+- .+++++++++.+|.|+|+++++|+++|.+||..|+..      + ++++++.|+..++||
T Consensus       238 ~~~~~~~~~~~~f~~~~lL-~~eLls~~rv~~I~FnPia~t~l~K~L~rIl~~E~~~~~~~~~~p~~~~l~~I~~~s~GD  316 (637)
T TIGR00602       238 SLEGDNNQRRLLFPAETIM-NKEILEEPRVSNISFNPIAPTIMKKFLNRIVTIEAKKNGEKIKVPKKTSVELLCQGCSGD  316 (637)
T ss_pred             Cccccccccccccchhccc-CHhHhcccceeEEEeCCCCHHHHHHHHHHHHHhhhhccccccccCCHHHHHHHHHhCCCh
Confidence            53211110    0111110 1567777889999999999999999999999987532      2 468999999999999


Q ss_pred             HHHHHHHHHHHhcCCCCcccc----ccc----CCCCCC-CccccCCCCCcccccCCccccchHHHHhHHhhCCCCCCccc
Q 005987          372 IRQAITSLQFSSLKQDPMLNL----SLS----ISKPNF-PEEKADGHGGFSIQFGRDETLSLFHALGKFLHNKRETDNLV  442 (666)
Q Consensus       372 IR~AIn~LQf~~~~~~~~~~~----~~~----~~~~~~-~k~~~~~~~~~~~~~~RD~~l~lFhalGkil~~Kr~~~~~~  442 (666)
                      ||+|||+|||+|.++......    .++    .++..+ ...+..+.+.+..+++||.+|++|||||||||+||......
T Consensus       317 iRsAIn~LQf~~~~~g~~a~~~~~~~vs~~hv~~a~~k~~~~t~~e~~~l~~~~~rd~sl~lfhalgkily~Kr~~~~~~  396 (637)
T TIGR00602       317 IRSAINSLQFSSSKSGSLPIKKRMSTKSDAHASKSKIKGKHSSNNENQEIQALGGKDVSLFLFRALGKILYCKRATLNEL  396 (637)
T ss_pred             HHHHHHHHHHHHhcCCccccccccccccHHHhhhccccCCCCCchhHHHHHhhccccchhHHHHHhChhhcccccCcccc
Confidence            999999999998865211100    000    000000 01111123345567999999999999999999999876543


Q ss_pred             cccccchhhhhccccCCCCCCChHHHHHhcCCChh-HHHHHHHhhcCCCCCcchHHHHHHHHHHhhHhhhccccccCccc
Q 005987          443 KMDQDAFVVKDKFSRLPLKMDAPEKVLSQAHGQAR-PVLDFLHENFLDFISEDAIDDAWAVASYLSDADLLLASFRGRLV  521 (666)
Q Consensus       443 ~~~~~~~~~~~~~~r~pl~~~~pE~vl~~~~~~~~-~~~~~LhENy~~f~~d~~i~~~~~~~d~LS~aD~l~~~~~~~~~  521 (666)
                      +....+. .-+.+.|.++ ++.||++++.++++.. +|..||||||++|+.+  +++++.+++|||+||++...|+.   
T Consensus       397 ~~~~~p~-~l~~~~r~~l-~~~~~~v~e~~~~~~~~~f~~~lheny~~f~~~--~~~~~~~~~~ls~~D~l~~d~~~---  469 (637)
T TIGR00602       397 DSPRLPS-HLSELSRDTL-MVGPEEVVEMSHMPGDKTFNLYSHQNYNDFFVE--FDDEVKASEFLNFADILSGDWNT---  469 (637)
T ss_pred             ccCccch-hhhhhcccch-hcChHhhhhhccccHHHHHHHHHhcccchhhhh--hhHHHHHHHHhhHHHhcccchhh---
Confidence            2222111 2255677776 6889999999999997 9999999999999987  99999999999999999887643   


Q ss_pred             cccchhHHHHHHHHHHHHHHHhhhCCCCC-------CCCcccccCCcchhhhhhhHHHHHHHHHhhhccccCCccccccc
Q 005987          522 RYNEADNVLQSAAASVAARGVLFGNSHPV-------PPRWHAIRKPKLWRVDQSSLQKKKELLKKKFMAWDGSISADVYN  594 (666)
Q Consensus       522 ~~~~~~~~l~~~a~sva~RGv~~~n~~p~-------~~~~~~~~~P~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~  594 (666)
                           .+++..|++++|+||+|++|..|.       .++|+|+++|+|+..++++.+  .+.....+..     ..+.| 
T Consensus       470 -----~~l~~~~~~~~~~r~~m~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~-----v~~~~-  536 (637)
T TIGR00602       470 -----RSLLREYSTSSARRGVMHSNKARGIAHCQGGKSSFRPLHKPQWFLISKKYRE--NCLAAKALFK-----VEDFC-  536 (637)
T ss_pred             -----hhhhcccceeeeeeeEEEecCCccchhcccCccccccccchhhhhhhHHHHH--HHHHHHHHhc-----ccccc-
Confidence                 456777899999999999997763       247999999999998876654  3333333321     11222 


Q ss_pred             CCCCCchhhhhhhhhhhhHHhhc
Q 005987          595 GSSSSDVSVLATEYAPALKWLGN  617 (666)
Q Consensus       595 ~~~~~~~~~~~~e~lP~l~~i~~  617 (666)
                          ..+..+.++++||+.....
T Consensus       537 ----~~~~~l~~~~~~~~~~~~~  555 (637)
T TIGR00602       537 ----LPADCLQTQLLPYLALDTI  555 (637)
T ss_pred             ----chHHHhcccccceeecccc
Confidence                2345799999999988763

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

>PRK04195 replication factor C large subunit; Provisional

Probab=100.00  E-value=3.5e-46  Score=417.73  Aligned_cols=380  Identities=22%  Similarity=0.342  Sum_probs=284.5

Q ss_pred             CccccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCchh
Q 005987          137 QLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTI  216 (666)
Q Consensus       137 ~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~~  216 (666)
                      .+|++||+|++++||+||++.++.|+.|++.|..   |.++ +++||+|||||||||+|+++|+++++.++++|+++.+ 
T Consensus         2 ~~W~eKyrP~~l~dlvg~~~~~~~l~~~l~~~~~---g~~~-~~lLL~GppG~GKTtla~ala~el~~~~ielnasd~r-   76 (482)
T PRK04195          2 MPWVEKYRPKTLSDVVGNEKAKEQLREWIESWLK---GKPK-KALLLYGPPGVGKTSLAHALANDYGWEVIELNASDQR-   76 (482)
T ss_pred             CCchhhcCCCCHHHhcCCHHHHHHHHHHHHHHhc---CCCC-CeEEEECCCCCCHHHHHHHHHHHcCCCEEEEcccccc-
Confidence            5899999999999999999999999999999874   4443 7999999999999999999999999999999998732 


Q ss_pred             hhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcCCCce
Q 005987          217 WQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHIPT  296 (666)
Q Consensus       217 ~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~~~Pi  296 (666)
                                      ..+.+..++..+.....+    .+  ..++||||||+|++....... ....|..+++....|+
T Consensus        77 ----------------~~~~i~~~i~~~~~~~sl----~~--~~~kvIiIDEaD~L~~~~d~~-~~~aL~~~l~~~~~~i  133 (482)
T PRK04195         77 ----------------TADVIERVAGEAATSGSL----FG--ARRKLILLDEVDGIHGNEDRG-GARAILELIKKAKQPI  133 (482)
T ss_pred             ----------------cHHHHHHHHHHhhccCcc----cC--CCCeEEEEecCcccccccchh-HHHHHHHHHHcCCCCE
Confidence                            122344455444333222    11  245799999999986533222 2345677777888898


Q ss_pred             EEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCcHHHHH
Q 005987          297 AVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASGGDIRQAI  376 (666)
Q Consensus       297 ViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~s~GDIR~AI  376 (666)
                      |+++++....        ....|++     +|..|.|++++..++.++|..+|..+++.+++++++.|++.++||+|.||
T Consensus       134 Ili~n~~~~~--------~~k~Lrs-----r~~~I~f~~~~~~~i~~~L~~i~~~egi~i~~eaL~~Ia~~s~GDlR~ai  200 (482)
T PRK04195        134 ILTANDPYDP--------SLRELRN-----ACLMIEFKRLSTRSIVPVLKRICRKEGIECDDEALKEIAERSGGDLRSAI  200 (482)
T ss_pred             EEeccCcccc--------chhhHhc-----cceEEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHH
Confidence            8877653211        1112222     69999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHhcCCCCcccccccCCCCCCCccccCCCCCcccccCCccccchHHHHhHHhhCCCCCCccccccccchhhhhccc
Q 005987          377 TSLQFSSLKQDPMLNLSLSISKPNFPEEKADGHGGFSIQFGRDETLSLFHALGKFLHNKRETDNLVKMDQDAFVVKDKFS  456 (666)
Q Consensus       377 n~LQf~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~~~~~RD~~l~lFhalGkil~~Kr~~~~~~~~~~~~~~~~~~~~  456 (666)
                      |.||+++.+.....                  .+.+..+..||...++|+++++||+++.....                
T Consensus       201 n~Lq~~a~~~~~it------------------~~~v~~~~~~d~~~~if~~l~~i~~~k~~~~a----------------  246 (482)
T PRK04195        201 NDLQAIAEGYGKLT------------------LEDVKTLGRRDREESIFDALDAVFKARNADQA----------------  246 (482)
T ss_pred             HHHHHHhcCCCCCc------------------HHHHHHhhcCCCCCCHHHHHHHHHCCCCHHHH----------------
Confidence            99999775432110                  01122345699999999999999997743210                


Q ss_pred             cCCCCCCChHHHHHhcCCChhHHHHHHHhhcCCCCCcchHHHHHHHHHHhhHhhhccccccCccccccchhHHHHHHHHH
Q 005987          457 RLPLKMDAPEKVLSQAHGQARPVLDFLHENFLDFISEDAIDDAWAVASYLSDADLLLASFRGRLVRYNEADNVLQSAAAS  536 (666)
Q Consensus       457 r~pl~~~~pE~vl~~~~~~~~~~~~~LhENy~~f~~d~~i~~~~~~~d~LS~aD~l~~~~~~~~~~~~~~~~~l~~~a~s  536 (666)
                               -..+....++++.++.|||||||..|.+  +++++.++++||.||+++++++.++ .|.     |..|++.
T Consensus       247 ---------~~~~~~~~~~~~~i~~~l~en~~~~~~~--~~~~~~a~~~ls~ad~~~~~~~~~~-~~~-----l~~~~~~  309 (482)
T PRK04195        247 ---------LEASYDVDEDPDDLIEWIDENIPKEYDD--PEDIARAYDALSRADIFLGRVKRTQ-NYD-----LWRYASD  309 (482)
T ss_pred             ---------HHHHHcccCCHHHHHHHHHhccccccCC--HHHHHHHHHHHhHHHHHHHHHHhcC-Ccc-----hHHHHHH
Confidence                     0122334568999999999999998876  8999999999999999999987642 343     3456777


Q ss_pred             HHHHHHhhhCCCCCCCCcccccCCcchhhhhhhHHHHHHHHHhhhccccCCcccccccCCCCCchhhhhhhhhhhhHHhh
Q 005987          537 VAARGVLFGNSHPVPPRWHAIRKPKLWRVDQSSLQKKKELLKKKFMAWDGSISADVYNGSSSSDVSVLATEYAPALKWLG  616 (666)
Q Consensus       537 va~RGv~~~n~~p~~~~~~~~~~P~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~e~lP~l~~i~  616 (666)
                      +++.||++++..| ..+|.++++|+||+...+....+ .+++.....         .....++..+.++++|+|||..|.
T Consensus       310 ~m~~gv~~~~~~~-~~~~~~~~~p~~~~~~~~~~~~~-~~~~~~~~~---------~~~~~~~s~~~~~~~~~~~~~~~~  378 (482)
T PRK04195        310 LMTAGVALAKEKK-KRGFTRYQPPSYWRLLSKTKEKR-ETRDSIAKK---------IAEKLHTSKRKVRREVLPFLSIIF  378 (482)
T ss_pred             HhhhHHHHhcccc-CCCCCCcCCcHHHHHHhhhhHHH-HHHHHHHHH---------HHHHhCCCHHHHHHHHHHHHHHHH
Confidence            7888999988776 46899999999999987654322 222221211         111233445589999999999998


Q ss_pred             cCC
Q 005987          617 NRT  619 (666)
Q Consensus       617 ~~~  619 (666)
                      ...
T Consensus       379 ~~~  381 (482)
T PRK04195        379 KHN  381 (482)
T ss_pred             hcC
Confidence            764

>KOG1969 consensus DNA replication checkpoint protein CHL12/CTF18 [Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]

Probab=100.00  E-value=1.2e-40  Score=364.68  Aligned_cols=399  Identities=18%  Similarity=0.252  Sum_probs=292.0

Q ss_pred             CCccccccCCCCccccccCHHHHHHHHHHHHHhhcC--------------------------CCCCCCccEEEEECCCCc
Q 005987          136 QQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGD--------------------------SKDKFSTNVLVITGQAGV  189 (666)
Q Consensus       136 ~~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~--------------------------~~g~~~~k~LLL~GPpG~  189 (666)
                      ..+||+||+|+.|.||++.++..+.+..||+.|...                          ..++++++++||+||||.
T Consensus       258 ~kLWVdky~Pk~FtdLLsDe~tNR~~L~WLK~WD~~VFg~~vsrl~~s~~~~~ke~~~~~~~~s~RP~kKilLL~GppGl  337 (877)
T KOG1969|consen  258 DKLWVDKYRPKKFTDLLSDEKTNRRMLGWLKQWDPCVFGQKVSRLLASKGPTEKEVLDMELDPSKRPPKKILLLCGPPGL  337 (877)
T ss_pred             cceeecccChhHHHHHhcchhHHHHHHHHHHhhcHHhhcchHhhhccccccchhhhhhcccCccCCCccceEEeecCCCC
Confidence            459999999999999999999999999999988642                          115677899999999999


Q ss_pred             hHHHHHHHHHHHcCCcEEEEcCCCchhhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCC
Q 005987          190 GKTATVRQIASHLGARLYEWDTPTPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDL  269 (666)
Q Consensus       190 GKTtla~~LAkelg~~viE~nasd~~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEi  269 (666)
                      ||||+||++|++.||.|+|+||||.+.                 ...+.+-++.+-...+    ..+...+|.|++||||
T Consensus       338 GKTTLAHViAkqaGYsVvEINASDeRt-----------------~~~v~~kI~~avq~~s----~l~adsrP~CLViDEI  396 (877)
T KOG1969|consen  338 GKTTLAHVIAKQAGYSVVEINASDERT-----------------APMVKEKIENAVQNHS----VLDADSRPVCLVIDEI  396 (877)
T ss_pred             ChhHHHHHHHHhcCceEEEeccccccc-----------------HHHHHHHHHHHHhhcc----ccccCCCcceEEEecc
Confidence            999999999999999999999999542                 2345555555543332    2222346889999999


Q ss_pred             CCCcchhHHHHHHHHHHHHHhc-----------------------CCCceEEEEecCCCCCCccchhhhhhHHHHHHhhc
Q 005987          270 PVTNGRTAFERLRQCLLLLVRS-----------------------THIPTAVVLTECGKADSVDSTAQSFEELQSILVDA  326 (666)
Q Consensus       270 d~l~~~~~~~~l~~~L~~l~~~-----------------------~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~  326 (666)
                      |+..     ..+.++|+.+++.                       -.+||||||++.        ++..|++|+.     
T Consensus       397 DGa~-----~~~Vdvilslv~a~~k~~~Gkq~~~~~~rkkkr~~~L~RPIICICNdL--------YaPaLR~Lr~-----  458 (877)
T KOG1969|consen  397 DGAP-----RAAVDVILSLVKATNKQATGKQAKKDKKRKKKRSKLLTRPIICICNDL--------YAPALRPLRP-----  458 (877)
T ss_pred             cCCc-----HHHHHHHHHHHHhhcchhhcCcccchhhhhhhccccccCCEEEEecCc--------cchhhhhccc-----
Confidence            9864     2334445544431                       135999999984        4567777776     


Q ss_pred             CeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCcHHHHHHHHHHHhcCCCCcccccccCCCCCCCcccc
Q 005987          327 GARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASGGDIRQAITSLQFSSLKQDPMLNLSLSISKPNFPEEKA  406 (666)
Q Consensus       327 r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~s~GDIR~AIn~LQf~~~~~~~~~~~~~~~~~~~~~k~~~  406 (666)
                      .|.+|.|.|++.+.+.++|+.||.+|++.++..+|..|++.+++|||+|||+|||++.+.......   +   ..     
T Consensus       459 ~A~ii~f~~p~~s~Lv~RL~~IC~rE~mr~d~~aL~~L~el~~~DIRsCINtLQfLa~~~~r~ds~---i---~~-----  527 (877)
T KOG1969|consen  459 FAEIIAFVPPSQSRLVERLNEICHRENMRADSKALNALCELTQNDIRSCINTLQFLASNVDRRDSS---I---SV-----  527 (877)
T ss_pred             ceEEEEecCCChhHHHHHHHHHHhhhcCCCCHHHHHHHHHHhcchHHHHHHHHHHHHHhccccccc---c---hh-----
Confidence            499999999999999999999999999999999999999999999999999999999876542110   0   00     


Q ss_pred             CCCCCcccccCCccccchHHHHhHHhhCCCCCCccccccccchhhhhccccCCCCCCChHHHHHhcCCChhHHHHHHHhh
Q 005987          407 DGHGGFSIQFGRDETLSLFHALGKFLHNKRETDNLVKMDQDAFVVKDKFSRLPLKMDAPEKVLSQAHGQARPVLDFLHEN  486 (666)
Q Consensus       407 ~~~~~~~~~~~RD~~l~lFhalGkil~~Kr~~~~~~~~~~~~~~~~~~~~r~pl~~~~pE~vl~~~~~~~~~~~~~LhEN  486 (666)
                       +.......+.+|.+.++|..+-.||.-.+......        ..+.+.      +  -.-....++..+++++.++.|
T Consensus       528 -~~i~a~~~~~k~~~~slf~~w~ei~ql~k~~~~r~--------~~~~l~------~--l~~~~~l~~~servlqg~f~~  590 (877)
T KOG1969|consen  528 -KLICAKNVGAKSNSDSLFSWWKEIFQLRKKDRHRS--------IDEQLY------G--LLNQVELHGNSERVLQGCFSI  590 (877)
T ss_pred             -hhhhhhhhcccccccchHHHHHHHHHHhhcccccc--------hHHHhh------h--hhhhhhccCchHHHHhhhhcc
Confidence             00011245678888899999988887665443110        111110      0  011234567788999999999


Q ss_pred             cCC-CCCcchHHHHHHHHHHhhHhhhccccccCccccccchhHHHHHHHHHHHHHHHhhhCCCCCCCCcccccCCcchhh
Q 005987          487 FLD-FISEDAIDDAWAVASYLSDADLLLASFRGRLVRYNEADNVLQSAAASVAARGVLFGNSHPVPPRWHAIRKPKLWRV  565 (666)
Q Consensus       487 y~~-f~~d~~i~~~~~~~d~LS~aD~l~~~~~~~~~~~~~~~~~l~~~a~sva~RGv~~~n~~p~~~~~~~~~~P~~~~~  565 (666)
                      |+. .|.|-.|..++.+++||-+-|.+....+.. ++|.    ++.+.......+-++|+..++     .++-+|+.-+.
T Consensus       591 ~~~~~~~D~~i~~~~~~s~WL~F~D~l~~~~~s~-qn~e----LlrY~~~~~l~fh~l~at~~~-----~~i~~p~~~q~  660 (877)
T KOG1969|consen  591 FLRLKYSDLGIGKPANASDWLFFHDLLYQSMYSH-QNWE----LLRYSPSVPLHFHQLFATIAN-----KRIIRPKNSQY  660 (877)
T ss_pred             ccccccccccccchhhhhhHHHhhhHHHHHHHhc-CCee----ecccccchhHHHHHHhcccCC-----cccCCCchhHH
Confidence            998 567778999999999999999998876542 3443    233334445566788887776     36788888888


Q ss_pred             hhhhHHHHHHHHHhhhccccCCcccccccCCCCCchhhhhhhhhhhhHHhhcC
Q 005987          566 DQSSLQKKKELLKKKFMAWDGSISADVYNGSSSSDVSVLATEYAPALKWLGNR  618 (666)
Q Consensus       566 ~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~e~lP~l~~i~~~  618 (666)
                      .+..+.+.++.+.....++..      + .+.......+..+++++|-.|.++
T Consensus       661 ~~~kl~~~~e~i~s~is~i~s------~-~~~~~~~ksllldli~~iL~il~P  706 (877)
T KOG1969|consen  661 EQRKLKRANEDIVSLISRIIS------Y-QGPLAASKSLLLDLIFEILPILDP  706 (877)
T ss_pred             HHHHHHHHHHHHHHHHHhccc------c-cccccchHHHHHHHHHHHHHhcCC
Confidence            888888888888775554110      1 122222346888888888888766

>KOG0989 consensus Replication factor C, subunit RFC4 [Replication, recombination and repair]

Probab=99.97  E-value=3.3e-30  Score=259.76  Aligned_cols=208  Identities=23%  Similarity=0.395  Sum_probs=157.3

Q ss_pred             CCccccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCC------cEEEE
Q 005987          136 QQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGA------RLYEW  209 (666)
Q Consensus       136 ~~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~------~viE~  209 (666)
                      ...|++||||++++|++||+..+..|++.+.+      +..  .++|||||||||||++|+++|+++..      .+++.
T Consensus        23 ~~swteKYrPkt~de~~gQe~vV~~L~~a~~~------~~l--p~~LFyGPpGTGKTStalafar~L~~~~~~~~rvl~l   94 (346)
T KOG0989|consen   23 HRSWTEKYRPKTFDELAGQEHVVQVLKNALLR------RIL--PHYLFYGPPGTGKTSTALAFARALNCEQLFPCRVLEL   94 (346)
T ss_pred             ccchHHHhCCCcHHhhcchHHHHHHHHHHHhh------cCC--ceEEeeCCCCCcHhHHHHHHHHHhcCccccccchhhh
Confidence            45699999999999999999999999998886      233  38999999999999999999999965      57888


Q ss_pred             cCCCchhhhhhhhcccCCccc-cchhHHHHHHHHHHHhhcCCCCCCCCC-CCCceEEEEeCCCCCcchhHHHHHHHHHHH
Q 005987          210 DTPTPTIWQEYMHNCKTGLEY-TSKLDEFENFVERIRRYGSTSPSIPGE-SKSSAILLIDDLPVTNGRTAFERLRQCLLL  287 (666)
Q Consensus       210 nasd~~~~~e~l~~~~~g~~~-~s~~~~f~~fl~~a~~~~~l~~s~~~~-~~~~~IIlIDEid~l~~~~~~~~l~~~L~~  287 (666)
                      |+++           .+|+.. ..+...|........       ...+. ..+.+||||||+|.+...     .+.+|..
T Consensus        95 naSd-----------erGisvvr~Kik~fakl~~~~~-------~~~~~~~~~fKiiIlDEcdsmtsd-----aq~aLrr  151 (346)
T KOG0989|consen   95 NASD-----------ERGISVVREKIKNFAKLTVLLK-------RSDGYPCPPFKIIILDECDSMTSD-----AQAALRR  151 (346)
T ss_pred             cccc-----------cccccchhhhhcCHHHHhhccc-------cccCCCCCcceEEEEechhhhhHH-----HHHHHHH
Confidence            8887           345442 122222322211110       01121 234489999999987532     2334555


Q ss_pred             HHhc-CCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHH
Q 005987          288 LVRS-THIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQ  366 (666)
Q Consensus       288 l~~~-~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~  366 (666)
                      .++. .+.-.+|++++        +..+.+.++.+     ||..++|.++....+.++|+.||.+|++.+++++++.|+.
T Consensus       152 ~mE~~s~~trFiLIcn--------ylsrii~pi~S-----RC~KfrFk~L~d~~iv~rL~~Ia~~E~v~~d~~al~~I~~  218 (346)
T KOG0989|consen  152 TMEDFSRTTRFILICN--------YLSRIIRPLVS-----RCQKFRFKKLKDEDIVDRLEKIASKEGVDIDDDALKLIAK  218 (346)
T ss_pred             HHhccccceEEEEEcC--------ChhhCChHHHh-----hHHHhcCCCcchHHHHHHHHHHHHHhCCCCCHHHHHHHHH
Confidence            5554 33345666666        34566666655     5999999999999999999999999999999999999999


Q ss_pred             HcCCcHHHHHHHHHHHhcCCC
Q 005987          367 ASGGDIRQAITSLQFSSLKQD  387 (666)
Q Consensus       367 ~s~GDIR~AIn~LQf~~~~~~  387 (666)
                      .|+||+|.||+.||-++..+.
T Consensus       219 ~S~GdLR~Ait~Lqsls~~gk  239 (346)
T KOG0989|consen  219 ISDGDLRRAITTLQSLSLLGK  239 (346)
T ss_pred             HcCCcHHHHHHHHHHhhccCc
Confidence            999999999999999987543

>KOG0991 consensus Replication factor C, subunit RFC2 [Replication, recombination and repair]

Probab=99.96  E-value=2e-29  Score=244.05  Aligned_cols=206  Identities=20%  Similarity=0.390  Sum_probs=161.9

Q ss_pred             CCCccccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc-C----CcEEEE
Q 005987          135 TQQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL-G----ARLYEW  209 (666)
Q Consensus       135 ~~~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel-g----~~viE~  209 (666)
                      ...+|+|||||..+.|++|++..++.|.-+.++      |+.|  +++|+|||||||||.+.+||+++ |    --++|+
T Consensus        13 ~~l~wVeKYrP~~l~dIVGNe~tv~rl~via~~------gnmP--~liisGpPG~GKTTsi~~LAr~LLG~~~ke~vLEL   84 (333)
T KOG0991|consen   13 YQLPWVEKYRPSVLQDIVGNEDTVERLSVIAKE------GNMP--NLIISGPPGTGKTTSILCLARELLGDSYKEAVLEL   84 (333)
T ss_pred             ccchHHHhhCchHHHHhhCCHHHHHHHHHHHHc------CCCC--ceEeeCCCCCchhhHHHHHHHHHhChhhhhHhhhc
Confidence            356799999999999999999999999998887      7777  79999999999999999999998 3    247899


Q ss_pred             cCCCchhhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHH
Q 005987          210 DTPTPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLV  289 (666)
Q Consensus       210 nasd~~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~  289 (666)
                      |+||           .+|+.+.  ...++.|-++-   -.++      .++.+|||+||+|.+... +.+.++..++.+.
T Consensus        85 NASd-----------eRGIDvV--Rn~IK~FAQ~k---v~lp------~grhKIiILDEADSMT~g-AQQAlRRtMEiyS  141 (333)
T KOG0991|consen   85 NASD-----------ERGIDVV--RNKIKMFAQKK---VTLP------PGRHKIIILDEADSMTAG-AQQALRRTMEIYS  141 (333)
T ss_pred             cCcc-----------ccccHHH--HHHHHHHHHhh---ccCC------CCceeEEEeeccchhhhH-HHHHHHHHHHHHc
Confidence            9998           4565531  11233332221   1111      134579999999987543 3455666677776


Q ss_pred             hcCCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcC
Q 005987          290 RSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASG  369 (666)
Q Consensus       290 ~~~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~s~  369 (666)
                      ..+++   .++++        ...+.++++++     ||..++|..+++.++.++|..+++.|++.++++.+++|+..++
T Consensus       142 ~ttRF---alaCN--------~s~KIiEPIQS-----RCAiLRysklsd~qiL~Rl~~v~k~Ekv~yt~dgLeaiifta~  205 (333)
T KOG0991|consen  142 NTTRF---ALACN--------QSEKIIEPIQS-----RCAILRYSKLSDQQILKRLLEVAKAEKVNYTDDGLEAIIFTAQ  205 (333)
T ss_pred             ccchh---hhhhc--------chhhhhhhHHh-----hhHhhhhcccCHHHHHHHHHHHHHHhCCCCCcchHHHhhhhcc
Confidence            66664   33333        23467888887     6999999999999999999999999999999999999999999


Q ss_pred             CcHHHHHHHHHHHhcCCC
Q 005987          370 GDIRQAITSLQFSSLKQD  387 (666)
Q Consensus       370 GDIR~AIn~LQf~~~~~~  387 (666)
                      ||+|+|+|+||....+..
T Consensus       206 GDMRQalNnLQst~~g~g  223 (333)
T KOG0991|consen  206 GDMRQALNNLQSTVNGFG  223 (333)
T ss_pred             chHHHHHHHHHHHhcccc
Confidence            999999999999776543

>PLN03025 replication factor C subunit; Provisional

Probab=99.95  E-value=1.3e-26  Score=246.98  Aligned_cols=286  Identities=17%  Similarity=0.269  Sum_probs=186.6

Q ss_pred             CccccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcC-----CcEEEEcC
Q 005987          137 QLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLG-----ARLYEWDT  211 (666)
Q Consensus       137 ~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg-----~~viE~na  211 (666)
                      .+|++||||++++|++||+..++.|+.++..      ++.+  ++||+|||||||||+|+++|+++.     ..++|+|+
T Consensus         1 ~~w~~kyrP~~l~~~~g~~~~~~~L~~~~~~------~~~~--~lll~Gp~G~GKTtla~~la~~l~~~~~~~~~~eln~   72 (319)
T PLN03025          1 LPWVEKYRPTKLDDIVGNEDAVSRLQVIARD------GNMP--NLILSGPPGTGKTTSILALAHELLGPNYKEAVLELNA   72 (319)
T ss_pred             CChhhhcCCCCHHHhcCcHHHHHHHHHHHhc------CCCc--eEEEECCCCCCHHHHHHHHHHHHhcccCccceeeecc
Confidence            3799999999999999999999999988775      4554  699999999999999999999982     34788888


Q ss_pred             CCchhhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhc
Q 005987          212 PTPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRS  291 (666)
Q Consensus       212 sd~~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~  291 (666)
                      ++.+           |.      +.+++.+.........   ..  ....+||+|||+|.+... +    +++|+.+++.
T Consensus        73 sd~~-----------~~------~~vr~~i~~~~~~~~~---~~--~~~~kviiiDE~d~lt~~-a----q~aL~~~lE~  125 (319)
T PLN03025         73 SDDR-----------GI------DVVRNKIKMFAQKKVT---LP--PGRHKIVILDEADSMTSG-A----QQALRRTMEI  125 (319)
T ss_pred             cccc-----------cH------HHHHHHHHHHHhcccc---CC--CCCeEEEEEechhhcCHH-H----HHHHHHHHhc
Confidence            7621           21      2333333322211110   01  123579999999998643 2    2334444443


Q ss_pred             C-CCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCC
Q 005987          292 T-HIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASGG  370 (666)
Q Consensus       292 ~-~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~s~G  370 (666)
                      . ..-.++++++.        ..+.+++|++     ||..++|.+++.+++.++|.++|.+|++.+++++++.|+..++|
T Consensus       126 ~~~~t~~il~~n~--------~~~i~~~L~S-----Rc~~i~f~~l~~~~l~~~L~~i~~~egi~i~~~~l~~i~~~~~g  192 (319)
T PLN03025        126 YSNTTRFALACNT--------SSKIIEPIQS-----RCAIVRFSRLSDQEILGRLMKVVEAEKVPYVPEGLEAIIFTADG  192 (319)
T ss_pred             ccCCceEEEEeCC--------ccccchhHHH-----hhhcccCCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC
Confidence            2 11123344431        1234445554     58999999999999999999999999999999999999999999


Q ss_pred             cHHHHHHHHHHHhcCCCCcccccccCCCCCCCccccCCCCCcccccCCccccchHHHHhHHhhCCCCCCccccccccchh
Q 005987          371 DIRQAITSLQFSSLKQDPMLNLSLSISKPNFPEEKADGHGGFSIQFGRDETLSLFHALGKFLHNKRETDNLVKMDQDAFV  450 (666)
Q Consensus       371 DIR~AIn~LQf~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~~~~~RD~~l~lFhalGkil~~Kr~~~~~~~~~~~~~~  450 (666)
                      |+|.|+|.||.++.+......                  +.+..+.+......+|..+..+...... .           
T Consensus       193 DlR~aln~Lq~~~~~~~~i~~------------------~~v~~~~~~~~~~~i~~~i~~~~~~~~~-~-----------  242 (319)
T PLN03025        193 DMRQALNNLQATHSGFGFVNQ------------------ENVFKVCDQPHPLHVKNIVRNCLKGKFD-D-----------  242 (319)
T ss_pred             CHHHHHHHHHHHHhcCCCCCH------------------HHHHHHcCCCCHHHHHHHHHHHHcCCHH-H-----------
Confidence            999999999977653211000                  0011223445555677777666543210 0           


Q ss_pred             hhhccccCCCCCCChHHHHHhcCCChhHHHHHHHhhcCCC-CCcchHHHHHHHHHHhhHhhhccc
Q 005987          451 VKDKFSRLPLKMDAPEKVLSQAHGQARPVLDFLHENFLDF-ISEDAIDDAWAVASYLSDADLLLA  514 (666)
Q Consensus       451 ~~~~~~r~pl~~~~pE~vl~~~~~~~~~~~~~LhENy~~f-~~d~~i~~~~~~~d~LS~aD~l~~  514 (666)
                      ...          .-.+++ ..+.++..++..||+-.... +++   ..-..++.+++++|.-+.
T Consensus       243 a~~----------~l~~ll-~~g~~~~~Il~~l~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~  293 (319)
T PLN03025        243 ACD----------GLKQLY-DLGYSPTDIITTLFRVVKNYDMPE---FLKLEYLREIGFAHMRIC  293 (319)
T ss_pred             HHH----------HHHHHH-HcCCCHHHHHHHHHHHHHhcCCCH---HHHHHHHHHHHHHHHHHH
Confidence            000          012333 33777888888785433222 122   223457788888888665

>PRK14956 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.94  E-value=1.2e-25  Score=245.31  Aligned_cols=215  Identities=13%  Similarity=0.246  Sum_probs=151.2

Q ss_pred             CCccccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEE-EcCCCc
Q 005987          136 QQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYE-WDTPTP  214 (666)
Q Consensus       136 ~~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE-~nasd~  214 (666)
                      -++|++||||++|+|++||+..++.|+.++..      ++.+ +.+||+|||||||||+|+++|+.+++.-.. ......
T Consensus         5 ~~~L~~KyRP~~f~dvVGQe~iv~~L~~~i~~------~ri~-ha~Lf~GP~GtGKTTlAriLAk~Lnce~~~~~~pCg~   77 (484)
T PRK14956          5 HEVLSRKYRPQFFRDVIHQDLAIGALQNALKS------GKIG-HAYIFFGPRGVGKTTIARILAKRLNCENPIGNEPCNE   77 (484)
T ss_pred             cchhHHHhCCCCHHHHhChHHHHHHHHHHHHc------CCCC-eEEEEECCCCCCHHHHHHHHHHhcCcccccCccccCC
Confidence            57899999999999999999999999999986      5555 679999999999999999999999764210 000000


Q ss_pred             hhhhhhhhcc----cCCcc--ccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHH
Q 005987          215 TIWQEYMHNC----KTGLE--YTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLL  288 (666)
Q Consensus       215 ~~~~e~l~~~----~~g~~--~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l  288 (666)
                      +.....+...    ...+.  .....+.++++++.+. +...       .++.+|+||||++++... +    .++|+..
T Consensus        78 C~sC~~i~~g~~~dviEIdaas~~gVd~IReL~e~l~-~~p~-------~g~~KV~IIDEah~Ls~~-A----~NALLKt  144 (484)
T PRK14956         78 CTSCLEITKGISSDVLEIDAASNRGIENIRELRDNVK-FAPM-------GGKYKVYIIDEVHMLTDQ-S----FNALLKT  144 (484)
T ss_pred             CcHHHHHHccCCccceeechhhcccHHHHHHHHHHHH-hhhh-------cCCCEEEEEechhhcCHH-H----HHHHHHH
Confidence            0000000000    00000  0123456677766654 2111       124579999999988642 2    3445666


Q ss_pred             HhcCCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHc
Q 005987          289 VRSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQAS  368 (666)
Q Consensus       289 ~~~~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~s  368 (666)
                      ++.....++||.+.+.       ..+.+..|+   +  ||+.+.|.+++..++.++|+++|..+++.++++++..|++.+
T Consensus       145 LEEPp~~viFILaTte-------~~kI~~TI~---S--RCq~~~f~~ls~~~i~~~L~~i~~~Egi~~e~eAL~~Ia~~S  212 (484)
T PRK14956        145 LEEPPAHIVFILATTE-------FHKIPETIL---S--RCQDFIFKKVPLSVLQDYSEKLCKIENVQYDQEGLFWIAKKG  212 (484)
T ss_pred             hhcCCCceEEEeecCC-------hhhccHHHH---h--hhheeeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHc
Confidence            6776556666654432       122333333   3  599999999999999999999999999999999999999999


Q ss_pred             CCcHHHHHHHHHHH
Q 005987          369 GGDIRQAITSLQFS  382 (666)
Q Consensus       369 ~GDIR~AIn~LQf~  382 (666)
                      +||+|.|++.|+-+
T Consensus       213 ~Gd~RdAL~lLeq~  226 (484)
T PRK14956        213 DGSVRDMLSFMEQA  226 (484)
T ss_pred             CChHHHHHHHHHHH
Confidence            99999999999653

>PRK07003 DNA polymerase III subunits gamma and tau; Validated

Probab=99.94  E-value=1.3e-25  Score=253.01  Aligned_cols=214  Identities=21%  Similarity=0.321  Sum_probs=149.4

Q ss_pred             CCccccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCch
Q 005987          136 QQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPT  215 (666)
Q Consensus       136 ~~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~  215 (666)
                      -+.|++||||++|+||+||++.++.|++|+..      ++.+ +.+||+||+||||||+++.||+.++++.-.  ....+
T Consensus         3 Y~vLarKYRPqtFdEVIGQe~Vv~~L~~aL~~------gRL~-HAyLFtGPpGvGKTTlAriLAKaLnCe~~~--~~~PC   73 (830)
T PRK07003          3 YQVLARKWRPKDFASLVGQEHVVRALTHALDG------GRLH-HAYLFTGTRGVGKTTLSRIFAKALNCETGV--TSQPC   73 (830)
T ss_pred             cHhHHHHhCCCcHHHHcCcHHHHHHHHHHHhc------CCCC-eEEEEECCCCCCHHHHHHHHHHHhcCccCC--CCCCC
Confidence            45699999999999999999999999999985      5665 688999999999999999999999864210  01111


Q ss_pred             hhhhhhhcccCC-----c----cccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHH
Q 005987          216 IWQEYMHNCKTG-----L----EYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLL  286 (666)
Q Consensus       216 ~~~e~l~~~~~g-----~----~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~  286 (666)
                      ..+..+.....|     +    ......++++++++.+. |...       ..+.+||||||+|++... .++    .|+
T Consensus        74 G~C~sCr~I~~G~h~DviEIDAas~rgVDdIReLIe~a~-~~P~-------~gr~KVIIIDEah~LT~~-A~N----ALL  140 (830)
T PRK07003         74 GVCRACREIDEGRFVDYVEMDAASNRGVDEMAALLERAV-YAPV-------DARFKVYMIDEVHMLTNH-AFN----AML  140 (830)
T ss_pred             cccHHHHHHhcCCCceEEEecccccccHHHHHHHHHHHH-hccc-------cCCceEEEEeChhhCCHH-HHH----HHH
Confidence            100000000000     0    01234567777777664 3211       124579999999998643 334    355


Q ss_pred             HHHhcCCCce-EEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHH
Q 005987          287 LLVRSTHIPT-AVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVA  365 (666)
Q Consensus       287 ~l~~~~~~Pi-ViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia  365 (666)
                      +.++.....+ +|++++ +       ..+.+..|++     ||..|.|++++.++|.++|++||..|++.++++.+..|+
T Consensus       141 KtLEEPP~~v~FILaTt-d-------~~KIp~TIrS-----RCq~f~Fk~Ls~eeIv~~L~~Il~~EgI~id~eAL~lIA  207 (830)
T PRK07003        141 KTLEEPPPHVKFILATT-D-------PQKIPVTVLS-----RCLQFNLKQMPAGHIVSHLERILGEERIAFEPQALRLLA  207 (830)
T ss_pred             HHHHhcCCCeEEEEEEC-C-------hhhccchhhh-----heEEEecCCcCHHHHHHHHHHHHHHcCCCCCHHHHHHHH
Confidence            5555543223 333333 1       1233333443     599999999999999999999999999999999999999


Q ss_pred             HHcCCcHHHHHHHH-HHHhc
Q 005987          366 QASGGDIRQAITSL-QFSSL  384 (666)
Q Consensus       366 ~~s~GDIR~AIn~L-Qf~~~  384 (666)
                      ..++||+|.||+.| |.++.
T Consensus       208 ~~A~GsmRdALsLLdQAia~  227 (830)
T PRK07003        208 RAAQGSMRDALSLTDQAIAY  227 (830)
T ss_pred             HHcCCCHHHHHHHHHHHHHh
Confidence            99999999999985 55544

>PRK14960 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.93  E-value=6e-25  Score=245.52  Aligned_cols=247  Identities=20%  Similarity=0.300  Sum_probs=165.4

Q ss_pred             CccccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCchh
Q 005987          137 QLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTI  216 (666)
Q Consensus       137 ~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~~  216 (666)
                      +.|++||||++|+||+||+..++.|..|+..      ++.+ +.+||+||+||||||+|+++|+.+++.-  .....++.
T Consensus         3 ~~LarKyRPktFddVIGQe~vv~~L~~aI~~------grl~-HAyLF~GPpGvGKTTlAriLAK~LnC~~--~~~~~pCg   73 (702)
T PRK14960          3 QVLARKYRPRNFNELVGQNHVSRALSSALER------GRLH-HAYLFTGTRGVGKTTIARILAKCLNCET--GVTSTPCE   73 (702)
T ss_pred             hhHHHHhCCCCHHHhcCcHHHHHHHHHHHHc------CCCC-eEEEEECCCCCCHHHHHHHHHHHhCCCc--CCCCCCCc
Confidence            5699999999999999999999999999986      6666 7899999999999999999999997631  00111111


Q ss_pred             hhhhhhcccCCc---------cccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHH
Q 005987          217 WQEYMHNCKTGL---------EYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLL  287 (666)
Q Consensus       217 ~~e~l~~~~~g~---------~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~  287 (666)
                      .+..+.....|.         ......+.++++++.+. |...       .++.+|+||||+++++.. ++    ++|+.
T Consensus        74 ~C~sC~~I~~g~hpDviEIDAAs~~~VddIReli~~~~-y~P~-------~gk~KV~IIDEVh~LS~~-A~----NALLK  140 (702)
T PRK14960         74 VCATCKAVNEGRFIDLIEIDAASRTKVEDTRELLDNVP-YAPT-------QGRFKVYLIDEVHMLSTH-SF----NALLK  140 (702)
T ss_pred             cCHHHHHHhcCCCCceEEecccccCCHHHHHHHHHHHh-hhhh-------cCCcEEEEEechHhcCHH-HH----HHHHH
Confidence            100000000000         00234567788877664 3211       124579999999988653 23    34666


Q ss_pred             HHhcCCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHH
Q 005987          288 LVRSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQA  367 (666)
Q Consensus       288 l~~~~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~  367 (666)
                      +++.....+.||++...       ..+..   ..+++  ||..+.|.+++..++.++|.+||.++++.++++++..|+..
T Consensus       141 tLEEPP~~v~FILaTtd-------~~kIp---~TIlS--RCq~feFkpLs~eEI~k~L~~Il~kEgI~id~eAL~~IA~~  208 (702)
T PRK14960        141 TLEEPPEHVKFLFATTD-------PQKLP---ITVIS--RCLQFTLRPLAVDEITKHLGAILEKEQIAADQDAIWQIAES  208 (702)
T ss_pred             HHhcCCCCcEEEEEECC-------hHhhh---HHHHH--hhheeeccCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHH
Confidence            66664433333333211       11222   23333  59999999999999999999999999999999999999999


Q ss_pred             cCCcHHHHHHHH-HHHhcCCCCcccccccCCCCCCCccccCCCCCcccccCCccccchHHHHhHHhhCC
Q 005987          368 SGGDIRQAITSL-QFSSLKQDPMLNLSLSISKPNFPEEKADGHGGFSIQFGRDETLSLFHALGKFLHNK  435 (666)
Q Consensus       368 s~GDIR~AIn~L-Qf~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~~~~~RD~~l~lFhalGkil~~K  435 (666)
                      ++||+|.|+|.| |.++.+.+. ..                .+.-...++..|.. .+|+.+..|+.++
T Consensus       209 S~GdLRdALnLLDQaIayg~g~-IT----------------~edV~~lLG~~d~e-~IfdLldAI~k~d  259 (702)
T PRK14960        209 AQGSLRDALSLTDQAIAYGQGA-VH----------------HQDVKEMLGLIDRT-IIYDLILAVHQNQ  259 (702)
T ss_pred             cCCCHHHHHHHHHHHHHhcCCC-cC----------------HHHHHHHhccCCHH-HHHHHHHHHHhcC
Confidence            999999999997 444432211 10                00001123444544 5888888888764

>PRK14958 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.92  E-value=3.2e-24  Score=240.10  Aligned_cols=214  Identities=21%  Similarity=0.326  Sum_probs=150.4

Q ss_pred             CCccccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCch
Q 005987          136 QQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPT  215 (666)
Q Consensus       136 ~~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~  215 (666)
                      -+.|++||||++|+||+||+..++.|++++..      ++.+ +.+||+||+||||||+|+++|+.+++.--  ....++
T Consensus         3 y~~l~~kyRP~~f~divGq~~v~~~L~~~~~~------~~l~-ha~Lf~Gp~G~GKTt~A~~lAk~l~c~~~--~~~~pC   73 (509)
T PRK14958          3 HQVLARKWRPRCFQEVIGQAPVVRALSNALDQ------QYLH-HAYLFTGTRGVGKTTISRILAKCLNCEKG--VSANPC   73 (509)
T ss_pred             chhHHHHHCCCCHHHhcCCHHHHHHHHHHHHh------CCCC-eeEEEECCCCCCHHHHHHHHHHHhcCCCC--CCcccC
Confidence            46799999999999999999999999999986      6666 67999999999999999999999976410  000111


Q ss_pred             hhhhhhhcccCC---------ccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHH
Q 005987          216 IWQEYMHNCKTG---------LEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLL  286 (666)
Q Consensus       216 ~~~e~l~~~~~g---------~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~  286 (666)
                      ..+..+.....|         .......+.++++++.+. |...       .++.+|+||||+|+++.. +++    +|+
T Consensus        74 g~C~~C~~i~~g~~~d~~eidaas~~~v~~iR~l~~~~~-~~p~-------~~~~kV~iIDE~~~ls~~-a~n----aLL  140 (509)
T PRK14958         74 NDCENCREIDEGRFPDLFEVDAASRTKVEDTRELLDNIP-YAPT-------KGRFKVYLIDEVHMLSGH-SFN----ALL  140 (509)
T ss_pred             CCCHHHHHHhcCCCceEEEEcccccCCHHHHHHHHHHHh-hccc-------cCCcEEEEEEChHhcCHH-HHH----HHH
Confidence            100000000000         001234567777777664 3211       124679999999998653 334    455


Q ss_pred             HHHhcCCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHH
Q 005987          287 LLVRSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQ  366 (666)
Q Consensus       287 ~l~~~~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~  366 (666)
                      .+++.....++||+..+.       ..+.+..+.   +  ||..+.|.+++..++.+.|..++.++++.+++++++.|+.
T Consensus       141 k~LEepp~~~~fIlattd-------~~kl~~tI~---S--Rc~~~~f~~l~~~~i~~~l~~il~~egi~~~~~al~~ia~  208 (509)
T PRK14958        141 KTLEEPPSHVKFILATTD-------HHKLPVTVL---S--RCLQFHLAQLPPLQIAAHCQHLLKEENVEFENAALDLLAR  208 (509)
T ss_pred             HHHhccCCCeEEEEEECC-------hHhchHHHH---H--HhhhhhcCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHH
Confidence            566654333433333211       122333333   3  5999999999999999999999999999999999999999


Q ss_pred             HcCCcHHHHHHHHHHHh
Q 005987          367 ASGGDIRQAITSLQFSS  383 (666)
Q Consensus       367 ~s~GDIR~AIn~LQf~~  383 (666)
                      .++||+|.|++.|+-++
T Consensus       209 ~s~GslR~al~lLdq~i  225 (509)
T PRK14958        209 AANGSVRDALSLLDQSI  225 (509)
T ss_pred             HcCCcHHHHHHHHHHHH
Confidence            99999999999995433

>KOG1968 consensus Replication factor C, subunit RFC1 (large subunit) [Replication, recombination and repair]

Probab=99.92  E-value=1.1e-24  Score=252.47  Aligned_cols=398  Identities=18%  Similarity=0.246  Sum_probs=258.9

Q ss_pred             CCccccccCCCCccccccCHHHHHHHHHHHHHhhcCC--------CCCCCcc-EEEEECCCCchHHHHHHHHHHHcCCcE
Q 005987          136 QQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDS--------KDKFSTN-VLVITGQAGVGKTATVRQIASHLGARL  206 (666)
Q Consensus       136 ~~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~--------~g~~~~k-~LLL~GPpG~GKTtla~~LAkelg~~v  206 (666)
                      ...|+++|+|++..+++++......+..||..|-...        .+... . .++++||||+|||++++++|+++|+.+
T Consensus       307 ~~~~~~k~~p~~~k~~~~~~~~~~~~~~~l~~~k~~~~~sy~~~~~~ss~-~~~~l~~G~pGigKT~~~h~~~k~~g~~v  385 (871)
T KOG1968|consen  307 GAGWTEKYQPTSSKALEGNASSSKKASKWLAKSKDKEKSSYKENEPDSSK-KKALLLSGPPGIGKTTAAHKAAKELGFKV  385 (871)
T ss_pred             ccccccccccccHHhhhcccchhhhhhhHHHhhhccccccccccCcchhh-HHHHHhcCCCCCCchhhHhhhhhhcccce
Confidence            5789999999999999999999999999999883221        01111 2 579999999999999999999999999


Q ss_pred             EEEcCCCchhhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHH
Q 005987          207 YEWDTPTPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLL  286 (666)
Q Consensus       207 iE~nasd~~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~  286 (666)
                      +|.|+++.|.-....... ....-..   .+....   ..++.    -........|||+||+|.+++ .+.+ +...|-
T Consensus       386 ~E~Nas~~RSk~~l~~~~-~~~~~s~---si~~~~---~~~~~----~~~~~~~~~vil~devD~~~~-~dRg-~v~~l~  452 (871)
T KOG1968|consen  386 VEKNASDVRSKKELLNKL-GNATSSH---SIKGSK---KKKGN----RQSLNSDHFLILMDEVDGMFG-EDRG-GVSKLS  452 (871)
T ss_pred             eecCccccccccHHHhhh-hcccccc---chhhhh---ccccc----ccccccceeEEEEeccccccc-hhhh-hHHHHH
Confidence            999999865322111110 0000000   000000   00110    000112345999999999987 4433 444577


Q ss_pred             HHHhcCCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHH
Q 005987          287 LLVRSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQ  366 (666)
Q Consensus       287 ~l~~~~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~  366 (666)
                      .++.....|+|++|++.+.+.           .+.+.+  -|..|+|..|....+..+|..||..|++.+++..++.|++
T Consensus       453 ~l~~ks~~Piv~~cndr~~p~-----------sr~~~~--~~~~l~f~kP~~~~i~~ri~si~~se~~ki~~~~l~~~s~  519 (871)
T KOG1968|consen  453 SLCKKSSRPLVCTCNDRNLPK-----------SRALSR--ACSDLRFSKPSSELIRSRIMSICKSEGIKISDDVLEEISK  519 (871)
T ss_pred             HHHHhccCCeEEEecCCCCcc-----------ccchhh--hcceeeecCCcHHHHHhhhhhhhcccceecCcHHHHHHHH
Confidence            788888899999999976542           222221  3789999999999999999999999999999999999999


Q ss_pred             HcCCcHHHHHHHHHHHhcCCCCcccccccCCCCCCCccccCCCCCcccccCCccccchHHHHhHHhhCCCCCCccccccc
Q 005987          367 ASGGDIRQAITSLQFSSLKQDPMLNLSLSISKPNFPEEKADGHGGFSIQFGRDETLSLFHALGKFLHNKRETDNLVKMDQ  446 (666)
Q Consensus       367 ~s~GDIR~AIn~LQf~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~~~~~RD~~l~lFhalGkil~~Kr~~~~~~~~~~  446 (666)
                      .++||||.+|++|||++........         .++..      ......++..+..|++..++|...|.....     
T Consensus       520 ~~~~DiR~~i~~lq~~~~~~~~~~~---------~~~~~------~~~~~~~~~~~~~~d~~~~~L~~~~~~s~~-----  579 (871)
T KOG1968|consen  520 LSGGDIRQIIMQLQFWSLSKPAELP---------KKKGT------PIKTSKKNITVKDFDAAEGLLDISRVASEE-----  579 (871)
T ss_pred             hcccCHHHHHHHHhhhhccchhhhc---------cccCc------cccccccccccchhHHHhhhccHhhhhhhh-----
Confidence            9999999999999999865322111         00000      001123788889999999999833321100     


Q ss_pred             cchhhhhccccCCCCCCChHHHHHhcCCChhHHHHHHHhhcCCCCCc------chHHHHHHHHHHhhHhhhccccccCcc
Q 005987          447 DAFVVKDKFSRLPLKMDAPEKVLSQAHGQARPVLDFLHENFLDFISE------DAIDDAWAVASYLSDADLLLASFRGRL  520 (666)
Q Consensus       447 ~~~~~~~~~~r~pl~~~~pE~vl~~~~~~~~~~~~~LhENy~~f~~d------~~i~~~~~~~d~LS~aD~l~~~~~~~~  520 (666)
                        ....          .    -.+++..+......++.+||+..-.+      ..+++++++.|.+|..|+...++++..
T Consensus       580 --~~~~----------~----k~~~~~ed~~~~p~~v~~n~~~~~~~~~~~~~~~l~~~~~~ad~is~~d~~~~~~r~~~  643 (871)
T KOG1968|consen  580 --TSNQ----------S----KAELYFEDYSISPLKVQENYLQVLPRSMKQILDELEDVSEAADSISLGDLRPKSIRGPE  643 (871)
T ss_pred             --hhcc----------c----hHHHhccccccchhhcchhhhcccchhhhhhHHHHHHHhhhhhhhhhhhhcchhhcCcc
Confidence              0000          0    01122224566678889999886543      245688899999999999999888754


Q ss_pred             cccc--chhHHHHHHHHHHHHHHHhhhCCCCCCCCcccccCCcchhhhhhhHHHHHHHHHhhhccccCCcccccccCCCC
Q 005987          521 VRYN--EADNVLQSAAASVAARGVLFGNSHPVPPRWHAIRKPKLWRVDQSSLQKKKELLKKKFMAWDGSISADVYNGSSS  598 (666)
Q Consensus       521 ~~~~--~~~~~l~~~a~sva~RGv~~~n~~p~~~~~~~~~~P~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~  598 (666)
                      ..|.  ....+++..-..+++.|      +    .-+++.+|+|+..+.+... ...++.....+         ......
T Consensus       644 ~~~~L~~~~a~~s~~~p~~~~~~------~----~~~~i~f~~~~~~~sk~~~-~~~~l~el~~h---------~~~~~s  703 (871)
T KOG1968|consen  644 LDWKLNPLHAVDSKVLPASKVGG------H----LLFRLGFPQWLGENSKSGK-LKRFLQELLPH---------TRLKQS  703 (871)
T ss_pred             chhhhhhhhhhhhhhcchhhhhh------c----cccccccccccCccccccc-hhHHHHHhchh---------hhhhhc
Confidence            4342  22222222222222222      2    2357889999888776554 33455444433         111223


Q ss_pred             CchhhhhhhhhhhhHHhh
Q 005987          599 SDVSVLATEYAPALKWLG  616 (666)
Q Consensus       599 ~~~~~~~~e~lP~l~~i~  616 (666)
                      .+...++..|.|.++...
T Consensus       704 ~~~~~~~~~y~~i~~~~~  721 (871)
T KOG1968|consen  704 ANKARVRESYNPISRQFS  721 (871)
T ss_pred             cchhhhhhhhhhhhhhcc
Confidence            344568888988888765

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

Probab=99.92  E-value=4.2e-24  Score=223.08  Aligned_cols=200  Identities=26%  Similarity=0.394  Sum_probs=158.4

Q ss_pred             CccccccCCCCccccccCHHHHHH---HHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCC
Q 005987          137 QLWAEKYKPRSLEELAVQRKKVEE---VRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPT  213 (666)
Q Consensus       137 ~~W~eKY~P~sl~eLvg~~k~i~e---l~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd  213 (666)
                      +++.++.||++++|++||++.+.+   |++.++.      +..+  .++|||||||||||+|++||+..+..+.++++..
T Consensus        12 ~PLA~rmRP~~lde~vGQ~HLlg~~~~lrr~v~~------~~l~--SmIl~GPPG~GKTTlA~liA~~~~~~f~~~sAv~   83 (436)
T COG2256          12 MPLAERLRPKSLDEVVGQEHLLGEGKPLRRAVEA------GHLH--SMILWGPPGTGKTTLARLIAGTTNAAFEALSAVT   83 (436)
T ss_pred             cChHHHhCCCCHHHhcChHhhhCCCchHHHHHhc------CCCc--eeEEECCCCCCHHHHHHHHHHhhCCceEEecccc
Confidence            589999999999999999998855   5555554      5554  8999999999999999999999999999999853


Q ss_pred             chhhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcCC
Q 005987          214 PTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTH  293 (666)
Q Consensus       214 ~~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~~  293 (666)
                                        +..++++.+++++++...        .+++.||||||+++++..     -++.|+..++.+ 
T Consensus        84 ------------------~gvkdlr~i~e~a~~~~~--------~gr~tiLflDEIHRfnK~-----QQD~lLp~vE~G-  131 (436)
T COG2256          84 ------------------SGVKDLREIIEEARKNRL--------LGRRTILFLDEIHRFNKA-----QQDALLPHVENG-  131 (436)
T ss_pred             ------------------ccHHHHHHHHHHHHHHHh--------cCCceEEEEehhhhcChh-----hhhhhhhhhcCC-
Confidence                              345688999999866542        135689999999987542     245688888888 


Q ss_pred             CceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHh--CCC-----CCHHHHHHHHH
Q 005987          294 IPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQE--QYS-----LSTEQIDLVAQ  366 (666)
Q Consensus       294 ~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e--~i~-----v~~~~l~~Ia~  366 (666)
                        .|++++.++.+++.       +--..+++  ||.++.|.|++.+++.++|++.+..+  ++.     +++++++.|+.
T Consensus       132 --~iilIGATTENPsF-------~ln~ALlS--R~~vf~lk~L~~~di~~~l~ra~~~~~rgl~~~~~~i~~~a~~~l~~  200 (436)
T COG2256         132 --TIILIGATTENPSF-------ELNPALLS--RARVFELKPLSSEDIKKLLKRALLDEERGLGGQIIVLDEEALDYLVR  200 (436)
T ss_pred             --eEEEEeccCCCCCe-------eecHHHhh--hhheeeeecCCHHHHHHHHHHHHhhhhcCCCcccccCCHHHHHHHHH
Confidence              45666666655432       21233333  59999999999999999999955543  333     78999999999


Q ss_pred             HcCCcHHHHHHHHHHHhcCCC
Q 005987          367 ASGGDIRQAITSLQFSSLKQD  387 (666)
Q Consensus       367 ~s~GDIR~AIn~LQf~~~~~~  387 (666)
                      .++||.|.|+|.|+++.....
T Consensus       201 ~s~GD~R~aLN~LE~~~~~~~  221 (436)
T COG2256         201 LSNGDARRALNLLELAALSAE  221 (436)
T ss_pred             hcCchHHHHHHHHHHHHHhcC
Confidence            999999999999999986543

>PRK14949 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.92  E-value=6.5e-24  Score=243.49  Aligned_cols=213  Identities=20%  Similarity=0.300  Sum_probs=152.0

Q ss_pred             CCccccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCch
Q 005987          136 QQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPT  215 (666)
Q Consensus       136 ~~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~  215 (666)
                      -..|++||||++|+||+||++.++.|++++..      ++++ +.+||+|||||||||+|+++|+.+++.-. ++. .++
T Consensus         3 Y~~LaeKyRP~tFddIIGQe~Iv~~LknaI~~------~rl~-HAyLFtGPpGtGKTTLARiLAk~Lnce~~-~~~-~pC   73 (944)
T PRK14949          3 YQVLARKWRPATFEQMVGQSHVLHALTNALTQ------QRLH-HAYLFTGTRGVGKTSLARLFAKGLNCEQG-VTA-TPC   73 (944)
T ss_pred             chhHHHHhCCCCHHHhcCcHHHHHHHHHHHHh------CCCC-eEEEEECCCCCCHHHHHHHHHHhccCccC-CCC-CCC
Confidence            36799999999999999999999999999886      6666 67899999999999999999999987511 110 011


Q ss_pred             hhhhhhhcccCC-----c----cccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHH
Q 005987          216 IWQEYMHNCKTG-----L----EYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLL  286 (666)
Q Consensus       216 ~~~e~l~~~~~g-----~----~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~  286 (666)
                      ..+..+.....|     +    ......+.++++++.+.... .       .++.+|+||||++.+...     .+++|+
T Consensus        74 g~C~sC~~i~~g~~~DviEidAas~~kVDdIReLie~v~~~P-~-------~gk~KViIIDEAh~LT~e-----AqNALL  140 (944)
T PRK14949         74 GVCSSCVEIAQGRFVDLIEVDAASRTKVDDTRELLDNVQYRP-S-------RGRFKVYLIDEVHMLSRS-----SFNALL  140 (944)
T ss_pred             CCchHHHHHhcCCCceEEEeccccccCHHHHHHHHHHHHhhh-h-------cCCcEEEEEechHhcCHH-----HHHHHH
Confidence            100000000000     0    00234667788777664221 1       124679999999998532     234566


Q ss_pred             HHHhcCCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHH
Q 005987          287 LLVRSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQ  366 (666)
Q Consensus       287 ~l~~~~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~  366 (666)
                      +.++.....++||++.+..       .+.+   ..+++  ||.+++|++++.+++.++|++++..+++.+++++++.|+.
T Consensus       141 KtLEEPP~~vrFILaTTe~-------~kLl---~TIlS--RCq~f~fkpLs~eEI~~~L~~il~~EgI~~edeAL~lIA~  208 (944)
T PRK14949        141 KTLEEPPEHVKFLLATTDP-------QKLP---VTVLS--RCLQFNLKSLTQDEIGTQLNHILTQEQLPFEAEALTLLAK  208 (944)
T ss_pred             HHHhccCCCeEEEEECCCc-------hhch---HHHHH--hheEEeCCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHH
Confidence            6777655445555543221       1233   33343  5999999999999999999999999999999999999999


Q ss_pred             HcCCcHHHHHHHHHHH
Q 005987          367 ASGGDIRQAITSLQFS  382 (666)
Q Consensus       367 ~s~GDIR~AIn~LQf~  382 (666)
                      .++||+|.|++.|+.+
T Consensus       209 ~S~Gd~R~ALnLLdQa  224 (944)
T PRK14949        209 AANGSMRDALSLTDQA  224 (944)
T ss_pred             HcCCCHHHHHHHHHHH
Confidence            9999999999998543

>PRK12323 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.92  E-value=3.1e-24  Score=239.29  Aligned_cols=213  Identities=22%  Similarity=0.295  Sum_probs=149.8

Q ss_pred             CCccccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEE-Ec--CC
Q 005987          136 QQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYE-WD--TP  212 (666)
Q Consensus       136 ~~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE-~n--as  212 (666)
                      -+.|.+||||++|+||+||+..++.|++++..      ++.+ +.+||+||+||||||+++.||+.+++.--. ..  .+
T Consensus         3 y~vLarKYRPqtFddVIGQe~vv~~L~~al~~------gRLp-HA~LFtGP~GvGKTTLAriLAkaLnC~~p~~~~g~~~   75 (700)
T PRK12323          3 YQVLARKWRPRDFTTLVGQEHVVRALTHALEQ------QRLH-HAYLFTGTRGVGKTTLSRILAKSLNCTGADGEGGITA   75 (700)
T ss_pred             chhHHHHhCCCcHHHHcCcHHHHHHHHHHHHh------CCCc-eEEEEECCCCCCHHHHHHHHHHHhcCCCccccccCCC
Confidence            46799999999999999999999999999987      6666 789999999999999999999999873100 00  00


Q ss_pred             CchhhhhhhhcccCC-----cc----ccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHH
Q 005987          213 TPTIWQEYMHNCKTG-----LE----YTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQ  283 (666)
Q Consensus       213 d~~~~~e~l~~~~~g-----~~----~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~  283 (666)
                      .++..+..+.....|     +.    .....++++++++.+.... .       .++.+|+||||+|+++.. .++    
T Consensus        76 ~PCG~C~sC~~I~aG~hpDviEIdAas~~gVDdIReLie~~~~~P-~-------~gr~KViIIDEah~Ls~~-AaN----  142 (700)
T PRK12323         76 QPCGQCRACTEIDAGRFVDYIEMDAASNRGVDEMAQLLDKAVYAP-T-------AGRFKVYMIDEVHMLTNH-AFN----  142 (700)
T ss_pred             CCCcccHHHHHHHcCCCCcceEecccccCCHHHHHHHHHHHHhch-h-------cCCceEEEEEChHhcCHH-HHH----
Confidence            011111100000000     00    1234567777777664221 1       124679999999998643 334    


Q ss_pred             HHHHHHhcCCC-ceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHH
Q 005987          284 CLLLLVRSTHI-PTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQID  362 (666)
Q Consensus       284 ~L~~l~~~~~~-PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~  362 (666)
                      .|++.++.... -++|++++.        ..+.+..|++     ||..+.|++++.+++.++|++||..|++.+++++++
T Consensus       143 ALLKTLEEPP~~v~FILaTte--------p~kLlpTIrS-----RCq~f~f~~ls~eei~~~L~~Il~~Egi~~d~eAL~  209 (700)
T PRK12323        143 AMLKTLEEPPEHVKFILATTD--------PQKIPVTVLS-----RCLQFNLKQMPPGHIVSHLDAILGEEGIAHEVNALR  209 (700)
T ss_pred             HHHHhhccCCCCceEEEEeCC--------hHhhhhHHHH-----HHHhcccCCCChHHHHHHHHHHHHHcCCCCCHHHHH
Confidence            45555665432 234444431        2233334443     599999999999999999999999999999999999


Q ss_pred             HHHHHcCCcHHHHHHHHHH
Q 005987          363 LVAQASGGDIRQAITSLQF  381 (666)
Q Consensus       363 ~Ia~~s~GDIR~AIn~LQf  381 (666)
                      .|+..++|++|.|++.|+.
T Consensus       210 ~IA~~A~Gs~RdALsLLdQ  228 (700)
T PRK12323        210 LLAQAAQGSMRDALSLTDQ  228 (700)
T ss_pred             HHHHHcCCCHHHHHHHHHH
Confidence            9999999999999998754

>PRK14964 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.91  E-value=2e-23  Score=230.54  Aligned_cols=198  Identities=23%  Similarity=0.364  Sum_probs=150.7

Q ss_pred             ccccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCc------------
Q 005987          138 LWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGAR------------  205 (666)
Q Consensus       138 ~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~------------  205 (666)
                      .|..||||++|+||+||+..++.+++++..      ++.+ +.+||+||+|+||||+|+++|+.+++.            
T Consensus         2 ~la~KyRP~~f~dliGQe~vv~~L~~a~~~------~ri~-ha~Lf~Gp~G~GKTT~ArilAk~LnC~~~~~~~pCg~C~   74 (491)
T PRK14964          2 NLALKYRPSSFKDLVGQDVLVRILRNAFTL------NKIP-QSILLVGASGVGKTTCARIISLCLNCSNGPTSDPCGTCH   74 (491)
T ss_pred             ChhHHhCCCCHHHhcCcHHHHHHHHHHHHc------CCCC-ceEEEECCCCccHHHHHHHHHHHHcCcCCCCCCCccccH
Confidence            488999999999999999999999988875      6666 789999999999999999999988543            


Q ss_pred             ------------EEEEcCCCchhhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCc
Q 005987          206 ------------LYEWDTPTPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTN  273 (666)
Q Consensus       206 ------------viE~nasd~~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~  273 (666)
                                  ++|+++++                 ....++++++++.+...+ .    .   .+.+|+||||++++.
T Consensus        75 ~C~~i~~~~~~Dv~eidaas-----------------~~~vddIR~Iie~~~~~P-~----~---~~~KVvIIDEah~Ls  129 (491)
T PRK14964         75 NCISIKNSNHPDVIEIDAAS-----------------NTSVDDIKVILENSCYLP-I----S---SKFKVYIIDEVHMLS  129 (491)
T ss_pred             HHHHHhccCCCCEEEEeccc-----------------CCCHHHHHHHHHHHHhcc-c----c---CCceEEEEeChHhCC
Confidence                        23333221                 234567888887774332 1    1   246799999999886


Q ss_pred             chhHHHHHHHHHHHHHhcCCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhC
Q 005987          274 GRTAFERLRQCLLLLVRSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQ  353 (666)
Q Consensus       274 ~~~~~~~l~~~L~~l~~~~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~  353 (666)
                      .. +++    .|+.+++.....+++|+..+.       ..+...   .+.+  ||..+.|.+++..++.+.|.+++.+++
T Consensus       130 ~~-A~N----aLLK~LEePp~~v~fIlatte-------~~Kl~~---tI~S--Rc~~~~f~~l~~~el~~~L~~ia~~Eg  192 (491)
T PRK14964        130 NS-AFN----ALLKTLEEPAPHVKFILATTE-------VKKIPV---TIIS--RCQRFDLQKIPTDKLVEHLVDIAKKEN  192 (491)
T ss_pred             HH-HHH----HHHHHHhCCCCCeEEEEEeCC-------hHHHHH---HHHH--hheeeecccccHHHHHHHHHHHHHHcC
Confidence            42 333    466666665444444444321       112222   2333  599999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHcCCcHHHHHHHHHHHhc
Q 005987          354 YSLSTEQIDLVAQASGGDIRQAITSLQFSSL  384 (666)
Q Consensus       354 i~v~~~~l~~Ia~~s~GDIR~AIn~LQf~~~  384 (666)
                      +.+++++++.|++.++||+|.|++.|+-++.
T Consensus       193 i~i~~eAL~lIa~~s~GslR~alslLdqli~  223 (491)
T PRK14964        193 IEHDEESLKLIAENSSGSMRNALFLLEQAAI  223 (491)
T ss_pred             CCCCHHHHHHHHHHcCCCHHHHHHHHHHHHH
Confidence            9999999999999999999999999977664

>PRK14962 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.91  E-value=2.3e-23  Score=230.87  Aligned_cols=199  Identities=18%  Similarity=0.319  Sum_probs=146.1

Q ss_pred             CccccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCc-----------
Q 005987          137 QLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGAR-----------  205 (666)
Q Consensus       137 ~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~-----------  205 (666)
                      +.|.+||||++++|++||++.++.+..++..      ++.+ +.+||+|||||||||+|+++|+.+++.           
T Consensus         2 ~~l~~kyRP~~~~divGq~~i~~~L~~~i~~------~~l~-~~~Lf~GPpGtGKTTlA~~lA~~l~~~~~~~~~pc~~c   74 (472)
T PRK14962          2 EALYRKYRPKTFSEVVGQDHVKKLIINALKK------NSIS-HAYIFAGPRGTGKTTVARILAKSLNCENRKGVEPCNEC   74 (472)
T ss_pred             chhHHHHCCCCHHHccCcHHHHHHHHHHHHc------CCCC-eEEEEECCCCCCHHHHHHHHHHHhccccCCCCCCCccc
Confidence            3589999999999999999999999888875      5555 679999999999999999999998753           


Q ss_pred             -------------EEEEcCCCchhhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCC
Q 005987          206 -------------LYEWDTPTPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVT  272 (666)
Q Consensus       206 -------------viE~nasd~~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l  272 (666)
                                   +++++++.                 ....+.++.+.+.+.... .    .   ...+||||||++.+
T Consensus        75 ~~c~~i~~g~~~dv~el~aa~-----------------~~gid~iR~i~~~~~~~p-~----~---~~~kVvIIDE~h~L  129 (472)
T PRK14962         75 RACRSIDEGTFMDVIELDAAS-----------------NRGIDEIRKIRDAVGYRP-M----E---GKYKVYIIDEVHML  129 (472)
T ss_pred             HHHHHHhcCCCCccEEEeCcc-----------------cCCHHHHHHHHHHHhhCh-h----c---CCeEEEEEEChHHh
Confidence                         33333221                 122456666665553221 1    1   23579999999987


Q ss_pred             cchhHHHHHHHHHHHHHhcCCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHh
Q 005987          273 NGRTAFERLRQCLLLLVRSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQE  352 (666)
Q Consensus       273 ~~~~~~~~l~~~L~~l~~~~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e  352 (666)
                      ...     .++.|+..++.....+++|++.++.       .+    +...+.+ ||..+.|.+++..++.++|++++..+
T Consensus       130 t~~-----a~~~LLk~LE~p~~~vv~Ilattn~-------~k----l~~~L~S-R~~vv~f~~l~~~el~~~L~~i~~~e  192 (472)
T PRK14962        130 TKE-----AFNALLKTLEEPPSHVVFVLATTNL-------EK----VPPTIIS-RCQVIEFRNISDELIIKRLQEVAEAE  192 (472)
T ss_pred             HHH-----HHHHHHHHHHhCCCcEEEEEEeCCh-------Hh----hhHHHhc-CcEEEEECCccHHHHHHHHHHHHHHc
Confidence            432     2334555666543334444332211       11    2222222 69999999999999999999999999


Q ss_pred             CCCCCHHHHHHHHHHcCCcHHHHHHHHHHHhc
Q 005987          353 QYSLSTEQIDLVAQASGGDIRQAITSLQFSSL  384 (666)
Q Consensus       353 ~i~v~~~~l~~Ia~~s~GDIR~AIn~LQf~~~  384 (666)
                      ++.+++++++.|+..++||+|.|+|.|+.++.
T Consensus       193 gi~i~~eal~~Ia~~s~GdlR~aln~Le~l~~  224 (472)
T PRK14962        193 GIEIDREALSFIAKRASGGLRDALTMLEQVWK  224 (472)
T ss_pred             CCCCCHHHHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            99999999999999999999999999998664

>PRK14952 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.91  E-value=4e-23  Score=233.10  Aligned_cols=214  Identities=18%  Similarity=0.273  Sum_probs=153.0

Q ss_pred             ccccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCchhh
Q 005987          138 LWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTIW  217 (666)
Q Consensus       138 ~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~~~  217 (666)
                      .|++||||++|+||+||+..++.|+.++..      ++.+ +.+||+||+||||||+|+++|+.+++.--  ....++..
T Consensus         2 al~~kyRP~~f~eivGq~~i~~~L~~~i~~------~r~~-ha~Lf~Gp~G~GKTt~A~~lAk~l~c~~~--~~~~pCg~   72 (584)
T PRK14952          2 ALYRKYRPATFAEVVGQEHVTEPLSSALDA------GRIN-HAYLFSGPRGCGKTSSARILARSLNCAQG--PTATPCGV   72 (584)
T ss_pred             cHHHHhCCCcHHHhcCcHHHHHHHHHHHHc------CCCC-eEEEEECCCCCCHHHHHHHHHHHhccccC--CCCCcccc
Confidence            478999999999999999999999999986      6666 67899999999999999999999976310  00011111


Q ss_pred             hhhhhccc---CC--------ccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHH
Q 005987          218 QEYMHNCK---TG--------LEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLL  286 (666)
Q Consensus       218 ~e~l~~~~---~g--------~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~  286 (666)
                      +..+....   .+        .......+.++++++.+.....     .   ...+|+||||++.+... +    .++|+
T Consensus        73 C~~C~~i~~~~~~~~dvieidaas~~gvd~iRel~~~~~~~P~-----~---~~~KVvIIDEah~Lt~~-A----~NALL  139 (584)
T PRK14952         73 CESCVALAPNGPGSIDVVELDAASHGGVDDTRELRDRAFYAPA-----Q---SRYRIFIVDEAHMVTTA-G----FNALL  139 (584)
T ss_pred             cHHHHHhhcccCCCceEEEeccccccCHHHHHHHHHHHHhhhh-----c---CCceEEEEECCCcCCHH-H----HHHHH
Confidence            11000000   00        0012246677777776643221     1   24579999999998643 3    33566


Q ss_pred             HHHhcCCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHH
Q 005987          287 LLVRSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQ  366 (666)
Q Consensus       287 ~l~~~~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~  366 (666)
                      .+++.....++||+..+.       ..+.+..|++     ||..+.|.+++..++.+.|.++|.++++.++++++..|+.
T Consensus       140 K~LEEpp~~~~fIL~tte-------~~kll~TI~S-----Rc~~~~F~~l~~~~i~~~L~~i~~~egi~i~~~al~~Ia~  207 (584)
T PRK14952        140 KIVEEPPEHLIFIFATTE-------PEKVLPTIRS-----RTHHYPFRLLPPRTMRALIARICEQEGVVVDDAVYPLVIR  207 (584)
T ss_pred             HHHhcCCCCeEEEEEeCC-------hHhhHHHHHH-----hceEEEeeCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHH
Confidence            677765544555544322       1233333443     5999999999999999999999999999999999999999


Q ss_pred             HcCCcHHHHHHHHHHHhcC
Q 005987          367 ASGGDIRQAITSLQFSSLK  385 (666)
Q Consensus       367 ~s~GDIR~AIn~LQf~~~~  385 (666)
                      .++||+|.|+|.|+.++..
T Consensus       208 ~s~GdlR~aln~Ldql~~~  226 (584)
T PRK14952        208 AGGGSPRDTLSVLDQLLAG  226 (584)
T ss_pred             HcCCCHHHHHHHHHHHHhc
Confidence            9999999999999887654

>PRK00440 rfc replication factor C small subunit; Reviewed

Probab=99.91  E-value=1.4e-22  Score=215.44  Aligned_cols=289  Identities=17%  Similarity=0.311  Sum_probs=187.8

Q ss_pred             CCCccccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcC-----CcEEEE
Q 005987          135 TQQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLG-----ARLYEW  209 (666)
Q Consensus       135 ~~~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg-----~~viE~  209 (666)
                      .+.+|+|||||++++|++||+..++.+..|++.      +..+  +++|+||||+|||++++++++++.     ..++++
T Consensus         3 ~~~~w~~kyrP~~~~~~~g~~~~~~~l~~~i~~------~~~~--~~ll~G~~G~GKt~~~~~l~~~l~~~~~~~~~i~~   74 (319)
T PRK00440          3 MEEIWVEKYRPRTLDEIVGQEEIVERLKSYVKE------KNMP--HLLFAGPPGTGKTTAALALARELYGEDWRENFLEL   74 (319)
T ss_pred             ccCccchhhCCCcHHHhcCcHHHHHHHHHHHhC------CCCC--eEEEECCCCCCHHHHHHHHHHHHcCCccccceEEe
Confidence            367899999999999999999999999999875      4443  589999999999999999999973     245566


Q ss_pred             cCCCchhhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHH
Q 005987          210 DTPTPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLV  289 (666)
Q Consensus       210 nasd~~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~  289 (666)
                      ++++..           +      ...+.+.+........     .+. ..+++|+|||++.+... .    +..|..++
T Consensus        75 ~~~~~~-----------~------~~~~~~~i~~~~~~~~-----~~~-~~~~vviiDe~~~l~~~-~----~~~L~~~l  126 (319)
T PRK00440         75 NASDER-----------G------IDVIRNKIKEFARTAP-----VGG-APFKIIFLDEADNLTSD-A----QQALRRTM  126 (319)
T ss_pred             cccccc-----------c------hHHHHHHHHHHHhcCC-----CCC-CCceEEEEeCcccCCHH-H----HHHHHHHH
Confidence            554311           1      1112222222211110     111 13569999999988543 1    22344444


Q ss_pred             hcCC-CceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHc
Q 005987          290 RSTH-IPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQAS  368 (666)
Q Consensus       290 ~~~~-~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~s  368 (666)
                      +... ...++++++..        .+.++.+++     ||..+.|.+++..++.++|..++.++++.+++++++.|+..+
T Consensus       127 e~~~~~~~lIl~~~~~--------~~l~~~l~s-----r~~~~~~~~l~~~ei~~~l~~~~~~~~~~i~~~al~~l~~~~  193 (319)
T PRK00440        127 EMYSQNTRFILSCNYS--------SKIIDPIQS-----RCAVFRFSPLKKEAVAERLRYIAENEGIEITDDALEAIYYVS  193 (319)
T ss_pred             hcCCCCCeEEEEeCCc--------cccchhHHH-----HhheeeeCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHc
Confidence            4322 22333333311        122333333     488899999999999999999999999999999999999999


Q ss_pred             CCcHHHHHHHHHHHhcCCCCcccccccCCCCCCCccccCCCCCcccccCCccccchHHHHhHHhhCCCCCCccccccccc
Q 005987          369 GGDIRQAITSLQFSSLKQDPMLNLSLSISKPNFPEEKADGHGGFSIQFGRDETLSLFHALGKFLHNKRETDNLVKMDQDA  448 (666)
Q Consensus       369 ~GDIR~AIn~LQf~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~~~~~RD~~l~lFhalGkil~~Kr~~~~~~~~~~~~  448 (666)
                      +||+|.|++.||.++..+.....                  +.+..+..+....++|..+..++.++.. ..        
T Consensus       194 ~gd~r~~~~~l~~~~~~~~~it~------------------~~v~~~~~~~~~~~i~~l~~~~~~~~~~-~a--------  246 (319)
T PRK00440        194 EGDMRKAINALQAAAATGKEVTE------------------EAVYKITGTARPEEIREMIELALNGDFT-EA--------  246 (319)
T ss_pred             CCCHHHHHHHHHHHHHcCCCCCH------------------HHHHHHhCCCCHHHHHHHHHHHHcCCHH-HH--------
Confidence            99999999999998764211100                  0111233444455788877777643211 00        


Q ss_pred             hhhhhccccCCCCCCChHHHHHhcCCChhHHHHHHHhhcCCCCCcchHHHHHHHHHHhhHhhhccc
Q 005987          449 FVVKDKFSRLPLKMDAPEKVLSQAHGQARPVLDFLHENFLDFISEDAIDDAWAVASYLSDADLLLA  514 (666)
Q Consensus       449 ~~~~~~~~r~pl~~~~pE~vl~~~~~~~~~~~~~LhENy~~f~~d~~i~~~~~~~d~LS~aD~l~~  514 (666)
                         ..          .-.+++...+.++..++..+++....  ...+.+...+++++++++|..+.
T Consensus       247 ---~~----------~l~~ll~~~g~~~~~i~~~l~~~~~~--~~~~~~~l~~~~~~~~~~d~~~k  297 (319)
T PRK00440        247 ---RE----------KLRDLMIDYGLSGEDIIKQIHREVWS--LDIPEELKVELIDAIGEADFRIT  297 (319)
T ss_pred             ---HH----------HHHHHHHHcCCCHHHHHHHHHHHHHh--cCCCHHHHHHHHHHHHHHHHHHH
Confidence               00          01123333455566666667764433  12336788899999999999876

>PRK12402 replication factor C small subunit 2; Reviewed

Probab=99.91  E-value=8.5e-23  Score=218.95  Aligned_cols=303  Identities=21%  Similarity=0.276  Sum_probs=190.0

Q ss_pred             CCccccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcC-----CcEEEEc
Q 005987          136 QQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLG-----ARLYEWD  210 (666)
Q Consensus       136 ~~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg-----~~viE~n  210 (666)
                      ..+|++||+|+++++++|++..++.|..++..      ++.+  ++||+|||||||||+|+++|+++.     ..+++++
T Consensus         2 ~~~w~~ky~P~~~~~~~g~~~~~~~L~~~~~~------~~~~--~lll~Gp~GtGKT~la~~~~~~l~~~~~~~~~~~i~   73 (337)
T PRK12402          2 APLWTEKYRPALLEDILGQDEVVERLSRAVDS------PNLP--HLLVQGPPGSGKTAAVRALARELYGDPWENNFTEFN   73 (337)
T ss_pred             CCchHHhhCCCcHHHhcCCHHHHHHHHHHHhC------CCCc--eEEEECCCCCCHHHHHHHHHHHhcCcccccceEEec
Confidence            46899999999999999999999999998875      4433  699999999999999999999984     3457777


Q ss_pred             CCCchh-hhhhhhcccC-----C---ccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHH
Q 005987          211 TPTPTI-WQEYMHNCKT-----G---LEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERL  281 (666)
Q Consensus       211 asd~~~-~~e~l~~~~~-----g---~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l  281 (666)
                      +++... ....+.....     +   ....+..+.++.++.....+...    .   ..+++|||||++.+... .    
T Consensus        74 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~---~~~~vlilDe~~~l~~~-~----  141 (337)
T PRK12402         74 VADFFDQGKKYLVEDPRFAHFLGTDKRIRSSKIDNFKHVLKEYASYRPL----S---ADYKTILLDNAEALRED-A----  141 (337)
T ss_pred             hhhhhhcchhhhhcCcchhhhhhhhhhhccchHHHHHHHHHHHHhcCCC----C---CCCcEEEEeCcccCCHH-H----
Confidence            664210 0001100000     0   00112234555555544433221    1   12459999999987532 2    


Q ss_pred             HHHHHHHHhcCCC-ceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHH
Q 005987          282 RQCLLLLVRSTHI-PTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQ  360 (666)
Q Consensus       282 ~~~L~~l~~~~~~-PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~  360 (666)
                      ++.|..+++.... ..+|++++ ..       .+.+..|++     ||..+.|.|++.+++.++|.+++.++++.+++++
T Consensus       142 ~~~L~~~le~~~~~~~~Il~~~-~~-------~~~~~~L~s-----r~~~v~~~~~~~~~~~~~l~~~~~~~~~~~~~~a  208 (337)
T PRK12402        142 QQALRRIMEQYSRTCRFIIATR-QP-------SKLIPPIRS-----RCLPLFFRAPTDDELVDVLESIAEAEGVDYDDDG  208 (337)
T ss_pred             HHHHHHHHHhccCCCeEEEEeC-Ch-------hhCchhhcC-----CceEEEecCCCHHHHHHHHHHHHHHcCCCCCHHH
Confidence            2234444443222 23334433 11       122223332     5899999999999999999999999999999999


Q ss_pred             HHHHHHHcCCcHHHHHHHHHHHhcCCCCcccccccCCCCCCCccccCCCCCcccccCC-ccccchHHHHhHHhhCCCCCC
Q 005987          361 IDLVAQASGGDIRQAITSLQFSSLKQDPMLNLSLSISKPNFPEEKADGHGGFSIQFGR-DETLSLFHALGKFLHNKRETD  439 (666)
Q Consensus       361 l~~Ia~~s~GDIR~AIn~LQf~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~~~~~R-D~~l~lFhalGkil~~Kr~~~  439 (666)
                      ++.|+..++||+|.+++.|+.++........                  ..+..+..+ +...++|..+-.++..+. ..
T Consensus       209 l~~l~~~~~gdlr~l~~~l~~~~~~~~~It~------------------~~v~~~~~~~~~~~~i~~l~~ai~~~~~-~~  269 (337)
T PRK12402        209 LELIAYYAGGDLRKAILTLQTAALAAGEITM------------------EAAYEALGDVGTDEVIESLLDAAEAGDF-TD  269 (337)
T ss_pred             HHHHHHHcCCCHHHHHHHHHHHHHcCCCCCH------------------HHHHHHhCCCCCHHHHHHHHHHHHcCCH-HH
Confidence            9999999999999999999998743221100                  001112222 334577776666655421 11


Q ss_pred             ccccccccchhhhhccccCCCCCCChHHHHHhcCCChhHHHHHHHhhcCCCCCcchHHHHHHHHHHhhHhhhccc
Q 005987          440 NLVKMDQDAFVVKDKFSRLPLKMDAPEKVLSQAHGQARPVLDFLHENFLDFISEDAIDDAWAVASYLSDADLLLA  514 (666)
Q Consensus       440 ~~~~~~~~~~~~~~~~~r~pl~~~~pE~vl~~~~~~~~~~~~~LhENy~~f~~d~~i~~~~~~~d~LS~aD~l~~  514 (666)
                      .           ..          .-.+++...+.++..+...|.......|+   .+...+++++++++|..+.
T Consensus       270 a-----------~~----------~l~~l~~~~g~~~~~i~~~l~~~~~~~~~---~~~l~~~~~~l~~~d~~lk  320 (337)
T PRK12402        270 A-----------RK----------TLDDLLIDEGLSGGEVLEELLRVARSRYR---GDNLARLHRLAADADARLT  320 (337)
T ss_pred             H-----------HH----------HHHHHHHHcCCCHHHHHHHHHHHHHHHCC---HHHHHHHHHHHHHHHHHHH
Confidence            0           00          01122233445555555555544333343   6778889999999999876

>PRK06645 DNA polymerase III subunits gamma and tau; Validated

Probab=99.91  E-value=9.1e-23  Score=226.98  Aligned_cols=218  Identities=19%  Similarity=0.243  Sum_probs=153.4

Q ss_pred             CCCccccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCC--
Q 005987          135 TQQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTP--  212 (666)
Q Consensus       135 ~~~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nas--  212 (666)
                      .-.+|++||||++|+|++||+..++.++..+..      ++.+ +.+||+|||||||||+|+++|+.+++....-..+  
T Consensus         7 ~y~~la~kyRP~~f~dliGq~~vv~~L~~ai~~------~ri~-~a~Lf~Gp~G~GKTT~ArilAk~Lnc~~~~~~~~~~   79 (507)
T PRK06645          7 QYIPFARKYRPSNFAELQGQEVLVKVLSYTILN------DRLA-GGYLLTGIRGVGKTTSARIIAKAVNCSALITENTTI   79 (507)
T ss_pred             cccchhhhhCCCCHHHhcCcHHHHHHHHHHHHc------CCCC-ceEEEECCCCCCHHHHHHHHHHHhcCccccccCcCc
Confidence            468999999999999999999999999988875      5655 7899999999999999999999997642110000  


Q ss_pred             CchhhhhhhhcccCC---------ccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHH
Q 005987          213 TPTIWQEYMHNCKTG---------LEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQ  283 (666)
Q Consensus       213 d~~~~~e~l~~~~~g---------~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~  283 (666)
                      .++.....+.....+         .......+.++++++.+...+ .    .   .+.+|+||||++.+.. .+++    
T Consensus        80 ~~C~~C~~C~~i~~~~h~Dv~eidaas~~~vd~Ir~iie~a~~~P-~----~---~~~KVvIIDEa~~Ls~-~a~n----  146 (507)
T PRK06645         80 KTCEQCTNCISFNNHNHPDIIEIDAASKTSVDDIRRIIESAEYKP-L----Q---GKHKIFIIDEVHMLSK-GAFN----  146 (507)
T ss_pred             CCCCCChHHHHHhcCCCCcEEEeeccCCCCHHHHHHHHHHHHhcc-c----c---CCcEEEEEEChhhcCH-HHHH----
Confidence            011110100000000         011234667888887764332 1    1   2467999999998854 2333    


Q ss_pred             HHHHHHhcCCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHH
Q 005987          284 CLLLLVRSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDL  363 (666)
Q Consensus       284 ~L~~l~~~~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~  363 (666)
                      .|+.+++.....++||+..+.       ..+....++   +  ||..+.|.+++..++.++|.+++.++++.+++++++.
T Consensus       147 aLLk~LEepp~~~vfI~aTte-------~~kI~~tI~---S--Rc~~~ef~~ls~~el~~~L~~i~~~egi~ie~eAL~~  214 (507)
T PRK06645        147 ALLKTLEEPPPHIIFIFATTE-------VQKIPATII---S--RCQRYDLRRLSFEEIFKLLEYITKQENLKTDIEALRI  214 (507)
T ss_pred             HHHHHHhhcCCCEEEEEEeCC-------hHHhhHHHH---h--cceEEEccCCCHHHHHHHHHHHHHHcCCCCCHHHHHH
Confidence            355555655444555544321       112222232   2  6999999999999999999999999999999999999


Q ss_pred             HHHHcCCcHHHHHHHHHHHhc
Q 005987          364 VAQASGGDIRQAITSLQFSSL  384 (666)
Q Consensus       364 Ia~~s~GDIR~AIn~LQf~~~  384 (666)
                      |+..++||+|.|++.|+-++.
T Consensus       215 Ia~~s~GslR~al~~Ldkai~  235 (507)
T PRK06645        215 IAYKSEGSARDAVSILDQAAS  235 (507)
T ss_pred             HHHHcCCCHHHHHHHHHHHHH
Confidence            999999999999999987743

>PRK08691 DNA polymerase III subunits gamma and tau; Validated

Probab=99.91  E-value=2.9e-23  Score=234.18  Aligned_cols=217  Identities=17%  Similarity=0.276  Sum_probs=148.3

Q ss_pred             CCccccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEE-EcCCCc
Q 005987          136 QQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYE-WDTPTP  214 (666)
Q Consensus       136 ~~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE-~nasd~  214 (666)
                      -+.|++||||++|+||+||+..++.|+.|+..      ++.+ +.+||+||+||||||+|+++|+.+++.-.. ......
T Consensus         3 y~vLarKYRP~tFddIIGQe~vv~~L~~ai~~------~rl~-Ha~Lf~GP~GvGKTTlAriLAk~LnC~~~~~~~pCg~   75 (709)
T PRK08691          3 YQVLARKWRPKTFADLVGQEHVVKALQNALDE------GRLH-HAYLLTGTRGVGKTTIARILAKSLNCENAQHGEPCGV   75 (709)
T ss_pred             chhHHHHhCCCCHHHHcCcHHHHHHHHHHHHc------CCCC-eEEEEECCCCCcHHHHHHHHHHHhcccCCCCCCCCcc
Confidence            36799999999999999999999999999986      6665 789999999999999999999999764211 110000


Q ss_pred             hhhhhhhhcc-cCC-c----cccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHH
Q 005987          215 TIWQEYMHNC-KTG-L----EYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLL  288 (666)
Q Consensus       215 ~~~~e~l~~~-~~g-~----~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l  288 (666)
                      +..+..+... ... +    ......+.++++++.+.....     .   .+.+||||||++.+... +++    .|+.+
T Consensus        76 C~sCr~i~~g~~~DvlEidaAs~~gVd~IRelle~a~~~P~-----~---gk~KVIIIDEad~Ls~~-A~N----ALLKt  142 (709)
T PRK08691         76 CQSCTQIDAGRYVDLLEIDAASNTGIDNIREVLENAQYAPT-----A---GKYKVYIIDEVHMLSKS-AFN----AMLKT  142 (709)
T ss_pred             cHHHHHHhccCccceEEEeccccCCHHHHHHHHHHHHhhhh-----h---CCcEEEEEECccccCHH-HHH----HHHHH
Confidence            0000000000 000 0    012234567777766532221     1   23579999999987642 333    35555


Q ss_pred             HhcCCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHc
Q 005987          289 VRSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQAS  368 (666)
Q Consensus       289 ~~~~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~s  368 (666)
                      ++.....++||++...       ..+.+..++   +  ||..+.|.+++..++.++|.+++.++++.++++++..|++.+
T Consensus       143 LEEPp~~v~fILaTtd-------~~kL~~TIr---S--RC~~f~f~~Ls~eeI~~~L~~Il~kEgi~id~eAL~~Ia~~A  210 (709)
T PRK08691        143 LEEPPEHVKFILATTD-------PHKVPVTVL---S--RCLQFVLRNMTAQQVADHLAHVLDSEKIAYEPPALQLLGRAA  210 (709)
T ss_pred             HHhCCCCcEEEEEeCC-------ccccchHHH---H--HHhhhhcCCCCHHHHHHHHHHHHHHcCCCcCHHHHHHHHHHh
Confidence            5543222223322211       112333333   3  599999999999999999999999999999999999999999


Q ss_pred             CCcHHHHHHHHHHHhc
Q 005987          369 GGDIRQAITSLQFSSL  384 (666)
Q Consensus       369 ~GDIR~AIn~LQf~~~  384 (666)
                      +||+|.+++.|+.++.
T Consensus       211 ~GslRdAlnLLDqaia  226 (709)
T PRK08691        211 AGSMRDALSLLDQAIA  226 (709)
T ss_pred             CCCHHHHHHHHHHHHH
Confidence            9999999999965443

>PRK14957 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.90  E-value=7.2e-23  Score=229.09  Aligned_cols=214  Identities=21%  Similarity=0.256  Sum_probs=149.7

Q ss_pred             CCccccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCch
Q 005987          136 QQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPT  215 (666)
Q Consensus       136 ~~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~  215 (666)
                      ..+|++||||++|+|++||+..++.+..+++.      ++.+ +.+||+||+||||||+|+.+|+.+++.--  ...+++
T Consensus         3 y~~La~KyRP~~f~diiGq~~~v~~L~~~i~~------~rl~-ha~Lf~Gp~GvGKTTlAr~lAk~L~c~~~--~~~~pC   73 (546)
T PRK14957          3 YQALARKYRPQSFAEVAGQQHALNSLVHALET------QKVH-HAYLFTGTRGVGKTTLGRLLAKCLNCKTG--VTAEPC   73 (546)
T ss_pred             chhHHHHHCcCcHHHhcCcHHHHHHHHHHHHc------CCCC-eEEEEECCCCCCHHHHHHHHHHHhCCCCC--CCCCCC
Confidence            46799999999999999999999999999986      5555 67999999999999999999999875311  000011


Q ss_pred             hhh---hhhhc-ccCC-----ccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHH
Q 005987          216 IWQ---EYMHN-CKTG-----LEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLL  286 (666)
Q Consensus       216 ~~~---e~l~~-~~~g-----~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~  286 (666)
                      ..+   ..+.+ ....     .......+.++.+++.+.....     .   ...+|+||||++.++..     ..+.|+
T Consensus        74 g~C~sC~~i~~~~~~dlieidaas~~gvd~ir~ii~~~~~~p~-----~---g~~kViIIDEa~~ls~~-----a~naLL  140 (546)
T PRK14957         74 NKCENCVAINNNSFIDLIEIDAASRTGVEETKEILDNIQYMPS-----Q---GRYKVYLIDEVHMLSKQ-----SFNALL  140 (546)
T ss_pred             cccHHHHHHhcCCCCceEEeecccccCHHHHHHHHHHHHhhhh-----c---CCcEEEEEechhhccHH-----HHHHHH
Confidence            000   00000 0000     0011234566777776643221     1   24579999999988642     234566


Q ss_pred             HHHhcCCCceEEE-EecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHH
Q 005987          287 LLVRSTHIPTAVV-LTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVA  365 (666)
Q Consensus       287 ~l~~~~~~PiViI-it~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia  365 (666)
                      .+++.....++|| +++ .       ..+.+..|+   +  ||..+.|++++..++.+.|.+++.++++.+++++++.|+
T Consensus       141 K~LEepp~~v~fIL~Tt-d-------~~kil~tI~---S--Rc~~~~f~~Ls~~eI~~~L~~il~~egi~~e~~Al~~Ia  207 (546)
T PRK14957        141 KTLEEPPEYVKFILATT-D-------YHKIPVTIL---S--RCIQLHLKHISQADIKDQLKIILAKENINSDEQSLEYIA  207 (546)
T ss_pred             HHHhcCCCCceEEEEEC-C-------hhhhhhhHH---H--heeeEEeCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHH
Confidence            6777654333333 332 1       122232333   3  599999999999999999999999999999999999999


Q ss_pred             HHcCCcHHHHHHHHHHHhc
Q 005987          366 QASGGDIRQAITSLQFSSL  384 (666)
Q Consensus       366 ~~s~GDIR~AIn~LQf~~~  384 (666)
                      ..++||+|.|+|.|+.++.
T Consensus       208 ~~s~GdlR~alnlLek~i~  226 (546)
T PRK14957        208 YHAKGSLRDALSLLDQAIS  226 (546)
T ss_pred             HHcCCCHHHHHHHHHHHHH
Confidence            9999999999999987664

>PRK07994 DNA polymerase III subunits gamma and tau; Validated

Probab=99.90  E-value=5.1e-23  Score=233.40  Aligned_cols=213  Identities=19%  Similarity=0.301  Sum_probs=152.5

Q ss_pred             CCccccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCch
Q 005987          136 QQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPT  215 (666)
Q Consensus       136 ~~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~  215 (666)
                      -+.|.+||||++|+||+||+..++.|++.+..      ++.+ +.+||+||+||||||+|+++|+.+++....  ...++
T Consensus         3 y~~La~KyRP~~f~divGQe~vv~~L~~~l~~------~rl~-hAyLf~Gp~GvGKTTlAr~lAk~L~c~~~~--~~~pC   73 (647)
T PRK07994          3 YQVLARKWRPQTFAEVVGQEHVLTALANALDL------GRLH-HAYLFSGTRGVGKTTIARLLAKGLNCETGI--TATPC   73 (647)
T ss_pred             chhHHHHhCCCCHHHhcCcHHHHHHHHHHHHc------CCCC-eEEEEECCCCCCHHHHHHHHHHhhhhccCC--CCCCC
Confidence            46799999999999999999999999998886      6666 678999999999999999999999875211  11111


Q ss_pred             hhhhhhhcccCC---------ccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHH
Q 005987          216 IWQEYMHNCKTG---------LEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLL  286 (666)
Q Consensus       216 ~~~e~l~~~~~g---------~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~  286 (666)
                      ..+..+.....|         .......+.++++++.+.... .       .++.+|+||||++.++.. ++    ++|+
T Consensus        74 g~C~~C~~i~~g~~~D~ieidaas~~~VddiR~li~~~~~~p-~-------~g~~KV~IIDEah~Ls~~-a~----NALL  140 (647)
T PRK07994         74 GECDNCREIEQGRFVDLIEIDAASRTKVEDTRELLDNVQYAP-A-------RGRFKVYLIDEVHMLSRH-SF----NALL  140 (647)
T ss_pred             CCCHHHHHHHcCCCCCceeecccccCCHHHHHHHHHHHHhhh-h-------cCCCEEEEEechHhCCHH-HH----HHHH
Confidence            111111000000         000234667888887764221 1       124679999999988643 23    4566


Q ss_pred             HHHhcCCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHH
Q 005987          287 LLVRSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQ  366 (666)
Q Consensus       287 ~l~~~~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~  366 (666)
                      +.++.....++||++.+..       .+.+..|++     ||..++|++++.+++..+|.++|..+++.++++++..|+.
T Consensus       141 KtLEEPp~~v~FIL~Tt~~-------~kLl~TI~S-----RC~~~~f~~Ls~~ei~~~L~~il~~e~i~~e~~aL~~Ia~  208 (647)
T PRK07994        141 KTLEEPPEHVKFLLATTDP-------QKLPVTILS-----RCLQFHLKALDVEQIRQQLEHILQAEQIPFEPRALQLLAR  208 (647)
T ss_pred             HHHHcCCCCeEEEEecCCc-------cccchHHHh-----hheEeeCCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHH
Confidence            6777654444444443221       123333333     5999999999999999999999999999999999999999


Q ss_pred             HcCCcHHHHHHHHHHH
Q 005987          367 ASGGDIRQAITSLQFS  382 (666)
Q Consensus       367 ~s~GDIR~AIn~LQf~  382 (666)
                      .++||+|.|++.|+.+
T Consensus       209 ~s~Gs~R~Al~lldqa  224 (647)
T PRK07994        209 AADGSMRDALSLTDQA  224 (647)
T ss_pred             HcCCCHHHHHHHHHHH
Confidence            9999999999999543

>PRK14961 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.90  E-value=1.1e-22  Score=220.25  Aligned_cols=217  Identities=19%  Similarity=0.268  Sum_probs=148.9

Q ss_pred             CCccccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCC-c
Q 005987          136 QQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPT-P  214 (666)
Q Consensus       136 ~~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd-~  214 (666)
                      -.+|++||||++++|++||++.++.++.++..      ++.+ +.+||+||||+||||+|+++|+++++....-..+. .
T Consensus         3 ~~~l~~kyrP~~~~~iiGq~~~~~~l~~~~~~------~~~~-h~~L~~Gp~G~GKTtla~~la~~l~c~~~~~~~pc~~   75 (363)
T PRK14961          3 YQILARKWRPQYFRDIIGQKHIVTAISNGLSL------GRIH-HAWLLSGTRGVGKTTIARLLAKSLNCQNGITSNPCRK   75 (363)
T ss_pred             cHHHHHHhCCCchhhccChHHHHHHHHHHHHc------CCCC-eEEEEecCCCCCHHHHHHHHHHHhcCCCCCCCCCCCC
Confidence            35799999999999999999999999998875      5665 67899999999999999999999975321111110 0


Q ss_pred             hh-hhhhhhccc-----CCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHH
Q 005987          215 TI-WQEYMHNCK-----TGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLL  288 (666)
Q Consensus       215 ~~-~~e~l~~~~-----~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l  288 (666)
                      +. ..+......     .........+.++++++.+...+.        ....+|+||||++.+... ++    +.|+..
T Consensus        76 c~~c~~~~~~~~~d~~~~~~~~~~~v~~ir~i~~~~~~~p~--------~~~~kviIIDEa~~l~~~-a~----naLLk~  142 (363)
T PRK14961         76 CIICKEIEKGLCLDLIEIDAASRTKVEEMREILDNIYYSPS--------KSRFKVYLIDEVHMLSRH-SF----NALLKT  142 (363)
T ss_pred             CHHHHHHhcCCCCceEEecccccCCHHHHHHHHHHHhcCcc--------cCCceEEEEEChhhcCHH-HH----HHHHHH
Confidence            00 000000000     000011345667777766532210        123579999999988542 22    345555


Q ss_pred             HhcCCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHc
Q 005987          289 VRSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQAS  368 (666)
Q Consensus       289 ~~~~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~s  368 (666)
                      ++.....+.+|++...       ..+.++.+++     ||..+.|.|++.+++.++|.+++..+++.+++++++.|+..+
T Consensus       143 lEe~~~~~~fIl~t~~-------~~~l~~tI~S-----Rc~~~~~~~l~~~el~~~L~~~~~~~g~~i~~~al~~ia~~s  210 (363)
T PRK14961        143 LEEPPQHIKFILATTD-------VEKIPKTILS-----RCLQFKLKIISEEKIFNFLKYILIKESIDTDEYALKLIAYHA  210 (363)
T ss_pred             HhcCCCCeEEEEEcCC-------hHhhhHHHHh-----hceEEeCCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHc
Confidence            6654433433333211       1122223332     599999999999999999999999999999999999999999


Q ss_pred             CCcHHHHHHHHHHHhc
Q 005987          369 GGDIRQAITSLQFSSL  384 (666)
Q Consensus       369 ~GDIR~AIn~LQf~~~  384 (666)
                      +||+|.|++.|+.++.
T Consensus       211 ~G~~R~al~~l~~~~~  226 (363)
T PRK14961        211 HGSMRDALNLLEHAIN  226 (363)
T ss_pred             CCCHHHHHHHHHHHHH
Confidence            9999999999987754

>PRK14951 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.90  E-value=6.5e-23  Score=232.16  Aligned_cols=217  Identities=21%  Similarity=0.332  Sum_probs=151.0

Q ss_pred             CCccccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEE-c--CC
Q 005987          136 QQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEW-D--TP  212 (666)
Q Consensus       136 ~~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~-n--as  212 (666)
                      -+.|++||||++|+|++||+..++.|++++..      ++.+ +.+||+||+||||||+|+++|+.+++.--.. .  ..
T Consensus         3 y~vla~KyRP~~f~dviGQe~vv~~L~~~l~~------~rl~-ha~Lf~Gp~GvGKTtlAr~lAk~LnC~~~~~~~~~~~   75 (618)
T PRK14951          3 YLVLARKYRPRSFSEMVGQEHVVQALTNALTQ------QRLH-HAYLFTGTRGVGKTTVSRILAKSLNCQGPDGQGGITA   75 (618)
T ss_pred             hHHHHHHHCCCCHHHhcCcHHHHHHHHHHHHc------CCCC-eEEEEECCCCCCHHHHHHHHHHHhcCCCcccccCCCC
Confidence            46799999999999999999999999999986      5665 6889999999999999999999997632110 0  00


Q ss_pred             CchhhhhhhhcccCCc---------cccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHH
Q 005987          213 TPTIWQEYMHNCKTGL---------EYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQ  283 (666)
Q Consensus       213 d~~~~~e~l~~~~~g~---------~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~  283 (666)
                      .++..+..+.....|.         ......+.++++++.+. |...       .++.+|+||||+++++.. .++    
T Consensus        76 ~pCg~C~~C~~i~~g~h~D~~eldaas~~~Vd~iReli~~~~-~~p~-------~g~~KV~IIDEvh~Ls~~-a~N----  142 (618)
T PRK14951         76 TPCGVCQACRDIDSGRFVDYTELDAASNRGVDEVQQLLEQAV-YKPV-------QGRFKVFMIDEVHMLTNT-AFN----  142 (618)
T ss_pred             CCCCccHHHHHHHcCCCCceeecCcccccCHHHHHHHHHHHH-hCcc-------cCCceEEEEEChhhCCHH-HHH----
Confidence            1111111111000000         01234567788887663 3211       124579999999998653 334    


Q ss_pred             HHHHHHhcCCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHH
Q 005987          284 CLLLLVRSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDL  363 (666)
Q Consensus       284 ~L~~l~~~~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~  363 (666)
                      .|+..++.....++||+..+.       ..+.+   ..+++  ||..+.|.+++..++.+.|.+++.++|+.++++++..
T Consensus       143 aLLKtLEEPP~~~~fIL~Ttd-------~~kil---~TIlS--Rc~~~~f~~Ls~eei~~~L~~i~~~egi~ie~~AL~~  210 (618)
T PRK14951        143 AMLKTLEEPPEYLKFVLATTD-------PQKVP---VTVLS--RCLQFNLRPMAPETVLEHLTQVLAAENVPAEPQALRL  210 (618)
T ss_pred             HHHHhcccCCCCeEEEEEECC-------chhhh---HHHHH--hceeeecCCCCHHHHHHHHHHHHHHcCCCCCHHHHHH
Confidence            355556654433333333211       11222   33443  5999999999999999999999999999999999999


Q ss_pred             HHHHcCCcHHHHHHHHH-HHhc
Q 005987          364 VAQASGGDIRQAITSLQ-FSSL  384 (666)
Q Consensus       364 Ia~~s~GDIR~AIn~LQ-f~~~  384 (666)
                      |+..++||+|.+++.|. .++.
T Consensus       211 La~~s~GslR~al~lLdq~ia~  232 (618)
T PRK14951        211 LARAARGSMRDALSLTDQAIAF  232 (618)
T ss_pred             HHHHcCCCHHHHHHHHHHHHHh
Confidence            99999999999999985 4443

>PRK14963 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.90  E-value=2.1e-22  Score=224.96  Aligned_cols=215  Identities=17%  Similarity=0.212  Sum_probs=144.5

Q ss_pred             ccccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcE----EEEcCCC
Q 005987          138 LWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARL----YEWDTPT  213 (666)
Q Consensus       138 ~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~v----iE~nasd  213 (666)
                      +| +||||++++||+||++.++.|+.++..      ++.+ +.+||+|||||||||+|+++|+.+.+.-    ..+.+..
T Consensus         4 l~-~KyRP~~~~dvvGq~~v~~~L~~~i~~------~~l~-ha~Lf~GppGtGKTTlA~~lA~~l~c~~~~~~~cg~C~s   75 (504)
T PRK14963          4 LY-QRARPITFDEVVGQEHVKEVLLAALRQ------GRLG-HAYLFSGPRGVGKTTTARLIAMAVNCSGEDPKPCGECES   75 (504)
T ss_pred             HH-HhhCCCCHHHhcChHHHHHHHHHHHHc------CCCC-eEEEEECCCCCCHHHHHHHHHHHHhccCCCCCCCCcChh
Confidence            44 999999999999999999999999986      5555 6789999999999999999999986420    0000000


Q ss_pred             chhhhhhhhccc--CCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhc
Q 005987          214 PTIWQEYMHNCK--TGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRS  291 (666)
Q Consensus       214 ~~~~~e~l~~~~--~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~  291 (666)
                      .+......+...  .+.......+.++++.+.+.....     .   ..++||||||++.+.. .+    .+.|+..++.
T Consensus        76 c~~i~~~~h~dv~el~~~~~~~vd~iR~l~~~~~~~p~-----~---~~~kVVIIDEad~ls~-~a----~naLLk~LEe  142 (504)
T PRK14963         76 CLAVRRGAHPDVLEIDAASNNSVEDVRDLREKVLLAPL-----R---GGRKVYILDEAHMMSK-SA----FNALLKTLEE  142 (504)
T ss_pred             hHHHhcCCCCceEEecccccCCHHHHHHHHHHHhhccc-----c---CCCeEEEEECccccCH-HH----HHHHHHHHHh
Confidence            000000000000  000012234556666555543221     1   2457999999998743 22    2345555555


Q ss_pred             CCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCc
Q 005987          292 THIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASGGD  371 (666)
Q Consensus       292 ~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~s~GD  371 (666)
                      ....+++|+....       .......+++     ||..+.|.+++..++.+.|.+++.++|+.+++++++.|+..++||
T Consensus       143 p~~~t~~Il~t~~-------~~kl~~~I~S-----Rc~~~~f~~ls~~el~~~L~~i~~~egi~i~~~Al~~ia~~s~Gd  210 (504)
T PRK14963        143 PPEHVIFILATTE-------PEKMPPTILS-----RTQHFRFRRLTEEEIAGKLRRLLEAEGREAEPEALQLVARLADGA  210 (504)
T ss_pred             CCCCEEEEEEcCC-------hhhCChHHhc-----ceEEEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCC
Confidence            4333344433211       1122222332     599999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHhcC
Q 005987          372 IRQAITSLQFSSLK  385 (666)
Q Consensus       372 IR~AIn~LQf~~~~  385 (666)
                      +|.|+|.||.++..
T Consensus       211 lR~aln~Lekl~~~  224 (504)
T PRK14963        211 MRDAESLLERLLAL  224 (504)
T ss_pred             HHHHHHHHHHHHhc
Confidence            99999999998754

>PRK05896 DNA polymerase III subunits gamma and tau; Validated

Probab=99.90  E-value=1.5e-22  Score=226.51  Aligned_cols=215  Identities=14%  Similarity=0.221  Sum_probs=152.1

Q ss_pred             CCccccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCch
Q 005987          136 QQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPT  215 (666)
Q Consensus       136 ~~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~  215 (666)
                      ...|++||||++|+|++||+..++.+.+++..      ++.+ +.+||+||+|+||||+|+++|+.+.+.-  |...+++
T Consensus         3 ~~~~~~KyRP~~F~dIIGQe~iv~~L~~aI~~------~rl~-hA~Lf~GP~GvGKTTlA~~lAk~L~C~~--~~~~~~C   73 (605)
T PRK05896          3 EITFYRKYRPHNFKQIIGQELIKKILVNAILN------NKLT-HAYIFSGPRGIGKTSIAKIFAKAINCLN--PKDGDCC   73 (605)
T ss_pred             chhHHHHhCCCCHHHhcCcHHHHHHHHHHHHc------CCCC-ceEEEECCCCCCHHHHHHHHHHHhcCCC--CCCCCCC
Confidence            36899999999999999999999999999875      5555 7899999999999999999999986422  1111111


Q ss_pred             hhhhh---hhc----c---cCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHH
Q 005987          216 IWQEY---MHN----C---KTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCL  285 (666)
Q Consensus       216 ~~~e~---l~~----~---~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L  285 (666)
                      ..+..   +..    .   ..+.. ....+.++.+++.+...+.     .+   ..+|++|||++.+... +    .++|
T Consensus        74 g~C~sCr~i~~~~h~DiieIdaas-~igVd~IReIi~~~~~~P~-----~~---~~KVIIIDEad~Lt~~-A----~NaL  139 (605)
T PRK05896         74 NSCSVCESINTNQSVDIVELDAAS-NNGVDEIRNIIDNINYLPT-----TF---KYKVYIIDEAHMLSTS-A----WNAL  139 (605)
T ss_pred             cccHHHHHHHcCCCCceEEecccc-ccCHHHHHHHHHHHHhchh-----hC---CcEEEEEechHhCCHH-H----HHHH
Confidence            11110   000    0   00100 1345567777766643321     11   3569999999988643 2    3456


Q ss_pred             HHHHhcCCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHH
Q 005987          286 LLLVRSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVA  365 (666)
Q Consensus       286 ~~l~~~~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia  365 (666)
                      +.+++.....+++|+....       ..+.+..++   +  ||..+.|.+++..++..+|..++.++++.+++++++.|+
T Consensus       140 LKtLEEPp~~tvfIL~Tt~-------~~KLl~TI~---S--Rcq~ieF~~Ls~~eL~~~L~~il~kegi~Is~eal~~La  207 (605)
T PRK05896        140 LKTLEEPPKHVVFIFATTE-------FQKIPLTII---S--RCQRYNFKKLNNSELQELLKSIAKKEKIKIEDNAIDKIA  207 (605)
T ss_pred             HHHHHhCCCcEEEEEECCC-------hHhhhHHHH---h--hhhhcccCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHH
Confidence            6777765433444433311       122222333   2  599999999999999999999999999999999999999


Q ss_pred             HHcCCcHHHHHHHHHHHhcC
Q 005987          366 QASGGDIRQAITSLQFSSLK  385 (666)
Q Consensus       366 ~~s~GDIR~AIn~LQf~~~~  385 (666)
                      ..++||+|.|++.|+.++..
T Consensus       208 ~lS~GdlR~AlnlLekL~~y  227 (605)
T PRK05896        208 DLADGSLRDGLSILDQLSTF  227 (605)
T ss_pred             HHcCCcHHHHHHHHHHHHhh
Confidence            99999999999999987653

>PHA02544 44 clamp loader, small subunit; Provisional

Probab=99.90  E-value=6.9e-22  Score=210.36  Aligned_cols=279  Identities=14%  Similarity=0.201  Sum_probs=180.2

Q ss_pred             CCCccccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCc
Q 005987          135 TQQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTP  214 (666)
Q Consensus       135 ~~~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~  214 (666)
                      ...+|++||||++++|+++|+..++.++.|++.      ++.+ +.+||+||||+|||++++++|++++..++++++.+.
T Consensus         7 ~~~~w~~kyrP~~~~~~~~~~~~~~~l~~~~~~------~~~~-~~lll~G~~G~GKT~la~~l~~~~~~~~~~i~~~~~   79 (316)
T PHA02544          7 NEFMWEQKYRPSTIDECILPAADKETFKSIVKK------GRIP-NMLLHSPSPGTGKTTVAKALCNEVGAEVLFVNGSDC   79 (316)
T ss_pred             CCCcceeccCCCcHHHhcCcHHHHHHHHHHHhc------CCCC-eEEEeeCcCCCCHHHHHHHHHHHhCccceEeccCcc
Confidence            367899999999999999999999999999985      5555 678889999999999999999999999999987641


Q ss_pred             hhhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcC--
Q 005987          215 TIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRST--  292 (666)
Q Consensus       215 ~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~--  292 (666)
                      .                  .+.+++.+.........    .   ..+++|||||++.+.....    ++.|..+++..  
T Consensus        80 ~------------------~~~i~~~l~~~~~~~~~----~---~~~~vliiDe~d~l~~~~~----~~~L~~~le~~~~  130 (316)
T PHA02544         80 R------------------IDFVRNRLTRFASTVSL----T---GGGKVIIIDEFDRLGLADA----QRHLRSFMEAYSK  130 (316)
T ss_pred             c------------------HHHHHHHHHHHHHhhcc----c---CCCeEEEEECcccccCHHH----HHHHHHHHHhcCC
Confidence            0                  11122212111111100    1   1356999999998744332    23344444442  


Q ss_pred             CCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHH-------HHHHHHHhCCCCCHHHHHHHH
Q 005987          293 HIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRT-------LSKICRQEQYSLSTEQIDLVA  365 (666)
Q Consensus       293 ~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~ki-------L~~I~~~e~i~v~~~~l~~Ia  365 (666)
                      ..++| ++++.        ..+..+.|++     ||..+.|++|+..+...+       +..++..+++.++++++..++
T Consensus       131 ~~~~I-lt~n~--------~~~l~~~l~s-----R~~~i~~~~p~~~~~~~il~~~~~~~~~~~~~~~~~i~~~al~~l~  196 (316)
T PHA02544        131 NCSFI-ITANN--------KNGIIEPLRS-----RCRVIDFGVPTKEEQIEMMKQMIVRCKGILEAEGVEVDMKVLAALV  196 (316)
T ss_pred             CceEE-EEcCC--------hhhchHHHHh-----hceEEEeCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHH
Confidence            23333 33321        1123333333     588999999998876644       445566789999999999999


Q ss_pred             HHcCCcHHHHHHHHHHHhcCCCCcccccccCCCCCCCccccCCCCCcccccCCccccchHHHHhHHhhCCCCCCcccccc
Q 005987          366 QASGGDIRQAITSLQFSSLKQDPMLNLSLSISKPNFPEEKADGHGGFSIQFGRDETLSLFHALGKFLHNKRETDNLVKMD  445 (666)
Q Consensus       366 ~~s~GDIR~AIn~LQf~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~~~~~RD~~l~lFhalGkil~~Kr~~~~~~~~~  445 (666)
                      ..+.||+|.+++.|+.++.... ...                  ..+..+.    ...+|+.+..+ ..+ .. .     
T Consensus       197 ~~~~~d~r~~l~~l~~~~~~~~-i~~------------------~~l~~~~----~~~~~~l~~~l-~~~-d~-~-----  245 (316)
T PHA02544        197 KKNFPDFRRTINELQRYASTGK-IDA------------------GILSEVT----NSDIDDVVEAL-KAK-DF-K-----  245 (316)
T ss_pred             HhcCCCHHHHHHHHHHHHccCC-CCH------------------HHHHHhh----HHHHHHHHHHH-HcC-CH-H-----
Confidence            9999999999999998774321 000                  0000111    22344444332 221 00 0     


Q ss_pred             ccchhhhhccccCCCCCCChHHHHHhcCCChhHHHHHHHhhcCCCCCcchHHHHHHHHHHhhHhhhcccc
Q 005987          446 QDAFVVKDKFSRLPLKMDAPEKVLSQAHGQARPVLDFLHENFLDFISEDAIDDAWAVASYLSDADLLLAS  515 (666)
Q Consensus       446 ~~~~~~~~~~~r~pl~~~~pE~vl~~~~~~~~~~~~~LhENy~~f~~d~~i~~~~~~~d~LS~aD~l~~~  515 (666)
                          .+.              .+....+.+++.++..++++...-+.   ......+++.++.+|..+..
T Consensus       246 ----~~~--------------~~~~~~~~~~~~~l~~~~~~~~~~~~---~~~~~~~~~~l~~~~~~~~~  294 (316)
T PHA02544        246 ----AVR--------------ALAPNYANDYASFVGKLYDELYPQVT---PPSIIRLIEIIGENNQYHGF  294 (316)
T ss_pred             ----HHH--------------HHHHHhccCHHHHHHHHHHHHHHhCC---HHHHHHHHHHHHHHHHHHHh
Confidence                000              12233455677888888888876553   56777889999999988763

>PRK07764 DNA polymerase III subunits gamma and tau; Validated

Probab=99.90  E-value=2e-22  Score=235.41  Aligned_cols=215  Identities=19%  Similarity=0.290  Sum_probs=154.3

Q ss_pred             CccccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCchh
Q 005987          137 QLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTI  216 (666)
Q Consensus       137 ~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~~  216 (666)
                      ..|.+||||++|+||+||+..++.|+.++..      ++.+ +.+||+||+||||||+|++||+.|++.-  ......+.
T Consensus         3 ~~l~~KyRP~~f~eiiGqe~v~~~L~~~i~~------~ri~-Ha~Lf~Gp~G~GKTt~A~~lAr~L~C~~--~~~~~pCg   73 (824)
T PRK07764          3 LALYRRYRPATFAEVIGQEHVTEPLSTALDS------GRIN-HAYLFSGPRGCGKTSSARILARSLNCVE--GPTSTPCG   73 (824)
T ss_pred             hhHHHHhCCCCHHHhcCcHHHHHHHHHHHHh------CCCC-ceEEEECCCCCCHHHHHHHHHHHhCccc--CCCCCCCc
Confidence            4588999999999999999999999999986      6666 6799999999999999999999998641  11111111


Q ss_pred             hhhhhhcccCC----c-------cccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHH
Q 005987          217 WQEYMHNCKTG----L-------EYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCL  285 (666)
Q Consensus       217 ~~e~l~~~~~g----~-------~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L  285 (666)
                      .+..+.....|    .       .....+++++++.+++. +...       ..+.+|+||||++.+...     ..+.|
T Consensus        74 ~C~sC~~~~~g~~~~~dv~eidaas~~~Vd~iR~l~~~~~-~~p~-------~~~~KV~IIDEad~lt~~-----a~NaL  140 (824)
T PRK07764         74 ECDSCVALAPGGPGSLDVTEIDAASHGGVDDARELRERAF-FAPA-------ESRYKIFIIDEAHMVTPQ-----GFNAL  140 (824)
T ss_pred             ccHHHHHHHcCCCCCCcEEEecccccCCHHHHHHHHHHHH-hchh-------cCCceEEEEechhhcCHH-----HHHHH
Confidence            11111000000    0       00124567777666553 2211       124679999999998642     23457


Q ss_pred             HHHHhcCCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHH
Q 005987          286 LLLVRSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVA  365 (666)
Q Consensus       286 ~~l~~~~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia  365 (666)
                      +++++.....++||+..+.       ..+.+..|++     ||.+|.|.+++..+|.++|.++|.++++.++++++..|+
T Consensus       141 LK~LEEpP~~~~fIl~tt~-------~~kLl~TIrS-----Rc~~v~F~~l~~~~l~~~L~~il~~EGv~id~eal~lLa  208 (824)
T PRK07764        141 LKIVEEPPEHLKFIFATTE-------PDKVIGTIRS-----RTHHYPFRLVPPEVMRGYLERICAQEGVPVEPGVLPLVI  208 (824)
T ss_pred             HHHHhCCCCCeEEEEEeCC-------hhhhhHHHHh-----heeEEEeeCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHH
Confidence            7777776555555544321       1233334444     599999999999999999999999999999999999999


Q ss_pred             HHcCCcHHHHHHHHHHHhcC
Q 005987          366 QASGGDIRQAITSLQFSSLK  385 (666)
Q Consensus       366 ~~s~GDIR~AIn~LQf~~~~  385 (666)
                      ..++||+|.+++.|+-++..
T Consensus       209 ~~sgGdlR~Al~eLEKLia~  228 (824)
T PRK07764        209 RAGGGSVRDSLSVLDQLLAG  228 (824)
T ss_pred             HHcCCCHHHHHHHHHHHHhh
Confidence            99999999999999877643

>PRK08451 DNA polymerase III subunits gamma and tau; Validated

Probab=99.90  E-value=3.6e-22  Score=222.36  Aligned_cols=199  Identities=22%  Similarity=0.360  Sum_probs=147.6

Q ss_pred             CccccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCc-----------
Q 005987          137 QLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGAR-----------  205 (666)
Q Consensus       137 ~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~-----------  205 (666)
                      +.|++||||++++|++||+..++.++.++..      |+.+ +.+|||||+|+||||+|+++|+.+.+.           
T Consensus         2 ~~l~~KyRP~~fdeiiGqe~v~~~L~~~I~~------grl~-hayLf~Gp~G~GKTt~Ar~LAk~L~c~~~~~~~pC~~C   74 (535)
T PRK08451          2 QALALKYRPKHFDELIGQESVSKTLSLALDN------NRLA-HAYLFSGLRGSGKTSSARIFARALVCEQGPSSTPCDTC   74 (535)
T ss_pred             ccHHHHHCCCCHHHccCcHHHHHHHHHHHHc------CCCC-eeEEEECCCCCcHHHHHHHHHHHhcCCCCCCCCCCccc
Confidence            4699999999999999999999999999986      6666 788999999999999999999998432           


Q ss_pred             -------------EEEEcCCCchhhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCC
Q 005987          206 -------------LYEWDTPTPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVT  272 (666)
Q Consensus       206 -------------viE~nasd~~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l  272 (666)
                                   ++++++.+                 ....+.++++++.+...+.     .   ...+|+||||++++
T Consensus        75 ~~C~~~~~~~h~dv~eldaas-----------------~~gId~IRelie~~~~~P~-----~---~~~KVvIIDEad~L  129 (535)
T PRK08451         75 IQCQSALENRHIDIIEMDAAS-----------------NRGIDDIRELIEQTKYKPS-----M---ARFKIFIIDEVHML  129 (535)
T ss_pred             HHHHHHhhcCCCeEEEecccc-----------------ccCHHHHHHHHHHHhhCcc-----c---CCeEEEEEECcccC
Confidence                         22222111                 1235667777765432111     1   24579999999998


Q ss_pred             cchhHHHHHHHHHHHHHhcCCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHh
Q 005987          273 NGRTAFERLRQCLLLLVRSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQE  352 (666)
Q Consensus       273 ~~~~~~~~l~~~L~~l~~~~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e  352 (666)
                      ... +++    +|+.+++.....++||+....       ..+.+..|++     ||..++|.+++..++.++|.++|.++
T Consensus       130 t~~-A~N----ALLK~LEEpp~~t~FIL~ttd-------~~kL~~tI~S-----Rc~~~~F~~Ls~~ei~~~L~~Il~~E  192 (535)
T PRK08451        130 TKE-AFN----ALLKTLEEPPSYVKFILATTD-------PLKLPATILS-----RTQHFRFKQIPQNSIISHLKTILEKE  192 (535)
T ss_pred             CHH-HHH----HHHHHHhhcCCceEEEEEECC-------hhhCchHHHh-----hceeEEcCCCCHHHHHHHHHHHHHHc
Confidence            642 333    455666654333333333211       1233333443     59999999999999999999999999


Q ss_pred             CCCCCHHHHHHHHHHcCCcHHHHHHHHHHHhc
Q 005987          353 QYSLSTEQIDLVAQASGGDIRQAITSLQFSSL  384 (666)
Q Consensus       353 ~i~v~~~~l~~Ia~~s~GDIR~AIn~LQf~~~  384 (666)
                      |+.++++++..|+..++||+|.|++.|+-++.
T Consensus       193 Gi~i~~~Al~~Ia~~s~GdlR~alnlLdqai~  224 (535)
T PRK08451        193 GVSYEPEALEILARSGNGSLRDTLTLLDQAII  224 (535)
T ss_pred             CCCCCHHHHHHHHHHcCCcHHHHHHHHHHHHH
Confidence            99999999999999999999999999976553

>PRK14959 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.89  E-value=3.7e-22  Score=224.53  Aligned_cols=214  Identities=17%  Similarity=0.258  Sum_probs=146.2

Q ss_pred             CCccccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCch
Q 005987          136 QQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPT  215 (666)
Q Consensus       136 ~~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~  215 (666)
                      ..+|++||||++|+||+||+..++.|.++++.      ++.+ +.+||+||+||||||+|+++|+.+.+.--.  ...++
T Consensus         3 ~~~la~KyRP~sf~dIiGQe~v~~~L~~ai~~------~ri~-ha~Lf~GPpG~GKTtiArilAk~L~C~~~~--~~~pC   73 (624)
T PRK14959          3 HASLTARYRPQTFAEVAGQETVKAILSRAAQE------NRVA-PAYLFSGTRGVGKTTIARIFAKALNCETAP--TGEPC   73 (624)
T ss_pred             cchHHHHhCCCCHHHhcCCHHHHHHHHHHHHc------CCCC-ceEEEECCCCCCHHHHHHHHHHhccccCCC--CCCCC
Confidence            46899999999999999999999999999886      5555 689999999999999999999999763110  00011


Q ss_pred             hhhhhhhcccCCc---------cccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHH
Q 005987          216 IWQEYMHNCKTGL---------EYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLL  286 (666)
Q Consensus       216 ~~~e~l~~~~~g~---------~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~  286 (666)
                      ..++.+.....|.         .....++.++.+.+.+.... .       ....+||||||++.+... .    .+.|+
T Consensus        74 g~C~sC~~i~~g~hpDv~eId~a~~~~Id~iR~L~~~~~~~p-~-------~g~~kVIIIDEad~Lt~~-a----~naLL  140 (624)
T PRK14959         74 NTCEQCRKVTQGMHVDVVEIDGASNRGIDDAKRLKEAIGYAP-M-------EGRYKVFIIDEAHMLTRE-A----FNALL  140 (624)
T ss_pred             cccHHHHHHhcCCCCceEEEecccccCHHHHHHHHHHHHhhh-h-------cCCceEEEEEChHhCCHH-H----HHHHH
Confidence            0000000000000         00123455666555543221 1       123579999999988632 2    33455


Q ss_pred             HHHhcCCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHH
Q 005987          287 LLVRSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQ  366 (666)
Q Consensus       287 ~l~~~~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~  366 (666)
                      .+++.....+++|+....       ..+.+..|+   +  ||..|.|++++.+++.++|..++..+++.+++++++.|+.
T Consensus       141 k~LEEP~~~~ifILaTt~-------~~kll~TI~---S--Rcq~i~F~pLs~~eL~~~L~~il~~egi~id~eal~lIA~  208 (624)
T PRK14959        141 KTLEEPPARVTFVLATTE-------PHKFPVTIV---S--RCQHFTFTRLSEAGLEAHLTKVLGREGVDYDPAAVRLIAR  208 (624)
T ss_pred             HHhhccCCCEEEEEecCC-------hhhhhHHHH---h--hhhccccCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHH
Confidence            666654333333333211       112222233   2  5999999999999999999999999999999999999999


Q ss_pred             HcCCcHHHHHHHHHHHh
Q 005987          367 ASGGDIRQAITSLQFSS  383 (666)
Q Consensus       367 ~s~GDIR~AIn~LQf~~  383 (666)
                      .++||+|.|++.|+.++
T Consensus       209 ~s~GdlR~Al~lLeqll  225 (624)
T PRK14959        209 RAAGSVRDSMSLLGQVL  225 (624)
T ss_pred             HcCCCHHHHHHHHHHHH
Confidence            99999999999997544

>PRK14969 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.89  E-value=3.3e-22  Score=225.28  Aligned_cols=217  Identities=19%  Similarity=0.251  Sum_probs=151.1

Q ss_pred             CCccccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEE-EcCCCc
Q 005987          136 QQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYE-WDTPTP  214 (666)
Q Consensus       136 ~~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE-~nasd~  214 (666)
                      -+.|++||||++|+||+||+..++.+..++..      ++.+ +.+||+||||+||||+|+++|+.++++... ......
T Consensus         3 ~~~l~~k~rP~~f~divGq~~v~~~L~~~i~~------~~~~-ha~Lf~Gp~G~GKTt~A~~lAk~l~c~~~~~~~pcg~   75 (527)
T PRK14969          3 YQVLARKWRPKSFSELVGQEHVVRALTNALEQ------QRLH-HAYLFTGTRGVGKTTLARILAKSLNCETGVTATPCGV   75 (527)
T ss_pred             cHHHHHHhCCCcHHHhcCcHHHHHHHHHHHHc------CCCC-EEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCC
Confidence            35699999999999999999999999999986      5555 678999999999999999999999764211 011111


Q ss_pred             hhhhhhhhcc-c-----CCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHH
Q 005987          215 TIWQEYMHNC-K-----TGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLL  288 (666)
Q Consensus       215 ~~~~e~l~~~-~-----~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l  288 (666)
                      +.....+.+. .     .........+.++++++.+...+ .       ..+.+|+||||++++... ++    +.|+..
T Consensus        76 C~~C~~i~~~~~~d~~ei~~~~~~~vd~ir~l~~~~~~~p-~-------~~~~kVvIIDEad~ls~~-a~----naLLK~  142 (527)
T PRK14969         76 CSACLEIDSGRFVDLIEVDAASNTQVDAMRELLDNAQYAP-T-------RGRFKVYIIDEVHMLSKS-AF----NAMLKT  142 (527)
T ss_pred             CHHHHHHhcCCCCceeEeeccccCCHHHHHHHHHHHhhCc-c-------cCCceEEEEcCcccCCHH-HH----HHHHHH
Confidence            1111100000 0     00001234567777777664221 1       124679999999988643 23    346666


Q ss_pred             HhcCCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHc
Q 005987          289 VRSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQAS  368 (666)
Q Consensus       289 ~~~~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~s  368 (666)
                      ++.....++||+..+.       ..+.+..++   +  ||..+.|.+++..++.+.|.+++.+|++.++++++..|+..+
T Consensus       143 LEepp~~~~fIL~t~d-------~~kil~tI~---S--Rc~~~~f~~l~~~~i~~~L~~il~~egi~~~~~al~~la~~s  210 (527)
T PRK14969        143 LEEPPEHVKFILATTD-------PQKIPVTVL---S--RCLQFNLKQMPPPLIVSHLQHILEQENIPFDATALQLLARAA  210 (527)
T ss_pred             HhCCCCCEEEEEEeCC-------hhhCchhHH---H--HHHHHhcCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHc
Confidence            6665433434333221       112232333   3  499999999999999999999999999999999999999999


Q ss_pred             CCcHHHHHHHHHHHhc
Q 005987          369 GGDIRQAITSLQFSSL  384 (666)
Q Consensus       369 ~GDIR~AIn~LQf~~~  384 (666)
                      +||+|.|++.|+.++.
T Consensus       211 ~Gslr~al~lldqai~  226 (527)
T PRK14969        211 AGSMRDALSLLDQAIA  226 (527)
T ss_pred             CCCHHHHHHHHHHHHH
Confidence            9999999999965543

>PRK07133 DNA polymerase III subunits gamma and tau; Validated

Probab=99.89  E-value=8.5e-22  Score=224.48  Aligned_cols=215  Identities=20%  Similarity=0.298  Sum_probs=154.1

Q ss_pred             CCccccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCch
Q 005987          136 QQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPT  215 (666)
Q Consensus       136 ~~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~  215 (666)
                      -..|++||||++++||+||+..++.|+.++..      ++.+ +.+||+||+|+|||++|+++|+.+.+.-.. ....++
T Consensus         5 y~~l~~KyRP~~f~dIiGQe~~v~~L~~aI~~------~rl~-HAYLF~GP~GtGKTt~AriLAk~LnC~~~~-~~~~pC   76 (725)
T PRK07133          5 YKALYRKYRPKTFDDIVGQDHIVQTLKNIIKS------NKIS-HAYLFSGPRGTGKTSVAKIFANALNCSHKT-DLLEPC   76 (725)
T ss_pred             hhhHHHHhCCCCHHHhcCcHHHHHHHHHHHHc------CCCC-eEEEEECCCCCcHHHHHHHHHHHhcccccC-CCCCch
Confidence            57899999999999999999999999999986      6666 789999999999999999999999764210 001111


Q ss_pred             hhhhhhhccc------CCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHH
Q 005987          216 IWQEYMHNCK------TGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLV  289 (666)
Q Consensus       216 ~~~e~l~~~~------~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~  289 (666)
                      ..+.......      .+. .....+.++++++.+...+.        ....+|+||||++.+... +    .++|+..+
T Consensus        77 ~~C~~~~~~~~Dvieidaa-sn~~vd~IReLie~~~~~P~--------~g~~KV~IIDEa~~LT~~-A----~NALLKtL  142 (725)
T PRK07133         77 QECIENVNNSLDIIEMDAA-SNNGVDEIRELIENVKNLPT--------QSKYKIYIIDEVHMLSKS-A----FNALLKTL  142 (725)
T ss_pred             hHHHHhhcCCCcEEEEecc-ccCCHHHHHHHHHHHHhchh--------cCCCEEEEEEChhhCCHH-H----HHHHHHHh
Confidence            1111100000      000 01235667777777653321        124579999999988643 2    34566667


Q ss_pred             hcCCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcC
Q 005987          290 RSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASG  369 (666)
Q Consensus       290 ~~~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~s~  369 (666)
                      +.....+++|+....       ..+.+.   .+++  ||..+.|.+++..++.++|..++.++|+.++++++..|+..++
T Consensus       143 EEPP~~tifILaTte-------~~KLl~---TI~S--Rcq~ieF~~L~~eeI~~~L~~il~kegI~id~eAl~~LA~lS~  210 (725)
T PRK07133        143 EEPPKHVIFILATTE-------VHKIPL---TILS--RVQRFNFRRISEDEIVSRLEFILEKENISYEKNALKLIAKLSS  210 (725)
T ss_pred             hcCCCceEEEEEcCC-------hhhhhH---HHHh--hceeEEccCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcC
Confidence            766545555544321       112222   3333  5999999999999999999999999999999999999999999


Q ss_pred             CcHHHHHHHHHHHhc
Q 005987          370 GDIRQAITSLQFSSL  384 (666)
Q Consensus       370 GDIR~AIn~LQf~~~  384 (666)
                      ||+|.|++.|+-++.
T Consensus       211 GslR~AlslLekl~~  225 (725)
T PRK07133        211 GSLRDALSIAEQVSI  225 (725)
T ss_pred             CCHHHHHHHHHHHHH
Confidence            999999999987654

>PRK05563 DNA polymerase III subunits gamma and tau; Validated

Probab=99.89  E-value=7.4e-22  Score=223.86  Aligned_cols=214  Identities=19%  Similarity=0.284  Sum_probs=152.3

Q ss_pred             CccccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCchh
Q 005987          137 QLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTI  216 (666)
Q Consensus       137 ~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~~  216 (666)
                      +.|++||||++|+||+||+..++.+++++..      ++.+ +.+||+||+|||||++|+.+|+.+++.--  ....++.
T Consensus         4 ~al~~k~rP~~f~~viGq~~v~~~L~~~i~~------~~~~-hayLf~Gp~GtGKTt~Ak~lAkal~c~~~--~~~~pC~   74 (559)
T PRK05563          4 QALYRKWRPQTFEDVVGQEHITKTLKNAIKQ------GKIS-HAYLFSGPRGTGKTSAAKIFAKAVNCLNP--PDGEPCN   74 (559)
T ss_pred             HHHHHHhCCCcHHhccCcHHHHHHHHHHHHc------CCCC-eEEEEECCCCCCHHHHHHHHHHHhcCCCC--CCCCCCC
Confidence            5688999999999999999999999999986      5555 78999999999999999999999865311  0011111


Q ss_pred             hhhhhhcccCCc---------cccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHH
Q 005987          217 WQEYMHNCKTGL---------EYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLL  287 (666)
Q Consensus       217 ~~e~l~~~~~g~---------~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~  287 (666)
                      .+..+.....|.         ......+.++++++.+...+.        ..+.+|+||||++.+... +++    +|+.
T Consensus        75 ~C~~C~~i~~g~~~dv~eidaas~~~vd~ir~i~~~v~~~p~--------~~~~kViIIDE~~~Lt~~-a~n----aLLK  141 (559)
T PRK05563         75 ECEICKAITNGSLMDVIEIDAASNNGVDEIRDIRDKVKYAPS--------EAKYKVYIIDEVHMLSTG-AFN----ALLK  141 (559)
T ss_pred             ccHHHHHHhcCCCCCeEEeeccccCCHHHHHHHHHHHhhCcc--------cCCeEEEEEECcccCCHH-HHH----HHHH
Confidence            111111000110         012345677778777643221        124679999999988542 333    4556


Q ss_pred             HHhcCCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHH
Q 005987          288 LVRSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQA  367 (666)
Q Consensus       288 l~~~~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~  367 (666)
                      .++.....++||++.+..       .+.+..|++     ||..+.|.+++..++.++|..++.++|+.++++++..|+..
T Consensus       142 tLEepp~~~ifIlatt~~-------~ki~~tI~S-----Rc~~~~f~~~~~~ei~~~L~~i~~~egi~i~~~al~~ia~~  209 (559)
T PRK05563        142 TLEEPPAHVIFILATTEP-------HKIPATILS-----RCQRFDFKRISVEDIVERLKYILDKEGIEYEDEALRLIARA  209 (559)
T ss_pred             HhcCCCCCeEEEEEeCCh-------hhCcHHHHh-----HheEEecCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHH
Confidence            666654445555554221       223333333     59999999999999999999999999999999999999999


Q ss_pred             cCCcHHHHHHHHHHHhc
Q 005987          368 SGGDIRQAITSLQFSSL  384 (666)
Q Consensus       368 s~GDIR~AIn~LQf~~~  384 (666)
                      ++||+|.|++.|+.+..
T Consensus       210 s~G~~R~al~~Ldq~~~  226 (559)
T PRK05563        210 AEGGMRDALSILDQAIS  226 (559)
T ss_pred             cCCCHHHHHHHHHHHHH
Confidence            99999999999976543

>PRK09111 DNA polymerase III subunits gamma and tau; Validated

Probab=99.88  E-value=7.8e-22  Score=223.82  Aligned_cols=217  Identities=22%  Similarity=0.327  Sum_probs=155.1

Q ss_pred             CCccccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEc-CC--
Q 005987          136 QQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWD-TP--  212 (666)
Q Consensus       136 ~~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~n-as--  212 (666)
                      -..|.+||||++|+||+||+..++.|.+++..      |+.+ +.+||+||+|+||||+|+++|+.+++.....+ .+  
T Consensus        11 y~~la~KyRP~~f~dliGq~~~v~~L~~~~~~------gri~-ha~L~~Gp~GvGKTt~Ar~lAk~L~c~~~~~~~~~~~   83 (598)
T PRK09111         11 YRVLARKYRPQTFDDLIGQEAMVRTLTNAFET------GRIA-QAFMLTGVRGVGKTTTARILARALNYEGPDGDGGPTI   83 (598)
T ss_pred             chhHHhhhCCCCHHHhcCcHHHHHHHHHHHHc------CCCC-ceEEEECCCCCCHHHHHHHHHHhhCcCCccccCCCcc
Confidence            57899999999999999999999999999986      6766 78999999999999999999999987543222 11  


Q ss_pred             CchhhhhhhhcccCCcc---------ccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHH
Q 005987          213 TPTIWQEYMHNCKTGLE---------YTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQ  283 (666)
Q Consensus       213 d~~~~~e~l~~~~~g~~---------~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~  283 (666)
                      +.+..++.+.....|..         -....++++++++.+.....     .   ...+|+||||++.++.. +++    
T Consensus        84 ~~cg~c~~C~~i~~g~h~Dv~e~~a~s~~gvd~IReIie~~~~~P~-----~---a~~KVvIIDEad~Ls~~-a~n----  150 (598)
T PRK09111         84 DLCGVGEHCQAIMEGRHVDVLEMDAASHTGVDDIREIIESVRYRPV-----S---ARYKVYIIDEVHMLSTA-AFN----  150 (598)
T ss_pred             ccCcccHHHHHHhcCCCCceEEecccccCCHHHHHHHHHHHHhchh-----c---CCcEEEEEEChHhCCHH-HHH----
Confidence            12222222211111110         12346678888877643321     1   24579999999988643 333    


Q ss_pred             HHHHHHhcCCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHH
Q 005987          284 CLLLLVRSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDL  363 (666)
Q Consensus       284 ~L~~l~~~~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~  363 (666)
                      .|+.+++.....++||+....       ..+.+..|++     ||..|.|.+++..++.+.|.+++.++++.+++++++.
T Consensus       151 aLLKtLEePp~~~~fIl~tte-------~~kll~tI~S-----Rcq~~~f~~l~~~el~~~L~~i~~kegi~i~~eAl~l  218 (598)
T PRK09111        151 ALLKTLEEPPPHVKFIFATTE-------IRKVPVTVLS-----RCQRFDLRRIEADVLAAHLSRIAAKEGVEVEDEALAL  218 (598)
T ss_pred             HHHHHHHhCCCCeEEEEEeCC-------hhhhhHHHHh-----heeEEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHH
Confidence            455555654333333332211       1223333333     5999999999999999999999999999999999999


Q ss_pred             HHHHcCCcHHHHHHHHHHHhc
Q 005987          364 VAQASGGDIRQAITSLQFSSL  384 (666)
Q Consensus       364 Ia~~s~GDIR~AIn~LQf~~~  384 (666)
                      |+..++||+|.+++.|+-++.
T Consensus       219 Ia~~a~Gdlr~al~~Ldkli~  239 (598)
T PRK09111        219 IARAAEGSVRDGLSLLDQAIA  239 (598)
T ss_pred             HHHHcCCCHHHHHHHHHHHHh
Confidence            999999999999999965543

>KOG2035 consensus Replication factor C, subunit RFC3 [Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]

Probab=99.88  E-value=1.6e-21  Score=193.93  Aligned_cols=220  Identities=18%  Similarity=0.316  Sum_probs=157.8

Q ss_pred             CccccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc-CC-------cEEE
Q 005987          137 QLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL-GA-------RLYE  208 (666)
Q Consensus       137 ~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel-g~-------~viE  208 (666)
                      .+|++||+|++++.+.+|++.-.+++.....      +..|  ++++|||+|.||-|.+.+|.+++ |.       +..+
T Consensus         1 ~LWvdkyrpksl~~l~~~~e~~~~Lksl~~~------~d~P--Hll~yGPSGaGKKTrimclL~elYG~gveklki~~~t   72 (351)
T KOG2035|consen    1 MLWVDKYRPKSLDELIYHEELANLLKSLSST------GDFP--HLLVYGPSGAGKKTRIMCLLRELYGVGVEKLKIETRT   72 (351)
T ss_pred             CcchhhcCcchhhhcccHHHHHHHHHHhccc------CCCC--eEEEECCCCCCchhhHHHHHHHHhCCCchheeeeeEE
Confidence            3799999999999999999888888776543      5555  89999999999999999999998 21       2222


Q ss_pred             EcCCCchhh-------hhhhh--cccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHH
Q 005987          209 WDTPTPTIW-------QEYMH--NCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFE  279 (666)
Q Consensus       209 ~nasd~~~~-------~e~l~--~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~  279 (666)
                      |..+...-.       ..|+.  ....|...   .--+++++.++.+...+-   +...+.-+|++|-|+|.+.. ++..
T Consensus        73 ~~tpS~kklEistvsS~yHlEitPSDaG~~D---RvViQellKevAQt~qie---~~~qr~fKvvvi~ead~LT~-dAQ~  145 (351)
T KOG2035|consen   73 FTTPSKKKLEISTVSSNYHLEITPSDAGNYD---RVVIQELLKEVAQTQQIE---TQGQRPFKVVVINEADELTR-DAQH  145 (351)
T ss_pred             EecCCCceEEEEEecccceEEeChhhcCccc---HHHHHHHHHHHHhhcchh---hccccceEEEEEechHhhhH-HHHH
Confidence            322221100       00110  01112110   112455565554433221   22234567999999998743 3445


Q ss_pred             HHHHHHHHHHhcCCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHH
Q 005987          280 RLRQCLLLLVRSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTE  359 (666)
Q Consensus       280 ~l~~~L~~l~~~~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~  359 (666)
                      .++..++.+....+  +|++|+.         .++.++++++     ||..|+.+.|+++++..+|.++|++|++.++.+
T Consensus       146 aLRRTMEkYs~~~R--lIl~cns---------~SriIepIrS-----RCl~iRvpaps~eeI~~vl~~v~~kE~l~lp~~  209 (351)
T KOG2035|consen  146 ALRRTMEKYSSNCR--LILVCNS---------TSRIIEPIRS-----RCLFIRVPAPSDEEITSVLSKVLKKEGLQLPKE  209 (351)
T ss_pred             HHHHHHHHHhcCce--EEEEecC---------cccchhHHhh-----heeEEeCCCCCHHHHHHHHHHHHHHhcccCcHH
Confidence            67777888876664  4544443         4578888887     699999999999999999999999999999999


Q ss_pred             HHHHHHHHcCCcHHHHHHHHHHHhcCCC
Q 005987          360 QIDLVAQASGGDIRQAITSLQFSSLKQD  387 (666)
Q Consensus       360 ~l~~Ia~~s~GDIR~AIn~LQf~~~~~~  387 (666)
                      .+..||+.|+||+|.||-+|+..+....
T Consensus       210 ~l~rIa~kS~~nLRrAllmlE~~~~~n~  237 (351)
T KOG2035|consen  210 LLKRIAEKSNRNLRRALLMLEAVRVNNE  237 (351)
T ss_pred             HHHHHHHHhcccHHHHHHHHHHHHhccc
Confidence            9999999999999999999999998644

>PRK14953 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.88  E-value=1.7e-21  Score=217.03  Aligned_cols=214  Identities=22%  Similarity=0.298  Sum_probs=148.4

Q ss_pred             CCccccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCch
Q 005987          136 QQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPT  215 (666)
Q Consensus       136 ~~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~  215 (666)
                      -.+|++||||++|+|++||+..++.++.++..      ++.+ +.+|||||+|+||||+|+.+|+.+++.--  ...+++
T Consensus         3 y~~~~~kyRP~~f~diiGq~~i~~~L~~~i~~------~~i~-hayLf~Gp~G~GKTtlAr~lAk~L~c~~~--~~~~pc   73 (486)
T PRK14953          3 YIPFARKYRPKFFKEVIGQEIVVRILKNAVKL------QRVS-HAYIFAGPRGTGKTTIARILAKVLNCLNP--QEGEPC   73 (486)
T ss_pred             chHHHHhhCCCcHHHccChHHHHHHHHHHHHc------CCCC-eEEEEECCCCCCHHHHHHHHHHHhcCcCC--CCCCCC
Confidence            45899999999999999999999999999986      5555 67899999999999999999999975310  000111


Q ss_pred             hhhhhhhcccCC----c-----cccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHH
Q 005987          216 IWQEYMHNCKTG----L-----EYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLL  286 (666)
Q Consensus       216 ~~~e~l~~~~~g----~-----~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~  286 (666)
                      ..+..+.....|    +     ......+.++.+.+.+...+.     .   ..++|+||||++.+... ++    ++|+
T Consensus        74 ~~c~nc~~i~~g~~~d~~eidaas~~gvd~ir~I~~~~~~~P~-----~---~~~KVvIIDEad~Lt~~-a~----naLL  140 (486)
T PRK14953         74 GKCENCVEIDKGSFPDLIEIDAASNRGIDDIRALRDAVSYTPI-----K---GKYKVYIIDEAHMLTKE-AF----NALL  140 (486)
T ss_pred             CccHHHHHHhcCCCCcEEEEeCccCCCHHHHHHHHHHHHhCcc-----c---CCeeEEEEEChhhcCHH-HH----HHHH
Confidence            111100000000    0     011234556666665543221     1   24579999999987532 23    3455


Q ss_pred             HHHhcCCC-ceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHH
Q 005987          287 LLVRSTHI-PTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVA  365 (666)
Q Consensus       287 ~l~~~~~~-PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia  365 (666)
                      .+++.... .++|++++ .       ....+.   .+.+  ||..+.|++++..++.++|.+++..+|+.+++++++.|+
T Consensus       141 k~LEepp~~~v~Il~tt-~-------~~kl~~---tI~S--Rc~~i~f~~ls~~el~~~L~~i~k~egi~id~~al~~La  207 (486)
T PRK14953        141 KTLEEPPPRTIFILCTT-E-------YDKIPP---TILS--RCQRFIFSKPTKEQIKEYLKRICNEEKIEYEEKALDLLA  207 (486)
T ss_pred             HHHhcCCCCeEEEEEEC-C-------HHHHHH---HHHH--hceEEEcCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHH
Confidence            55665432 34444442 1       112222   2222  599999999999999999999999999999999999999


Q ss_pred             HHcCCcHHHHHHHHHHHhc
Q 005987          366 QASGGDIRQAITSLQFSSL  384 (666)
Q Consensus       366 ~~s~GDIR~AIn~LQf~~~  384 (666)
                      ..++||+|.|++.|+.++.
T Consensus       208 ~~s~G~lr~al~~Ldkl~~  226 (486)
T PRK14953        208 QASEGGMRDAASLLDQAST  226 (486)
T ss_pred             HHcCCCHHHHHHHHHHHHH
Confidence            9999999999999988764

>PRK14965 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.88  E-value=1.4e-21  Score=222.66  Aligned_cols=214  Identities=20%  Similarity=0.289  Sum_probs=149.8

Q ss_pred             CccccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEE-EEcCCCch
Q 005987          137 QLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLY-EWDTPTPT  215 (666)
Q Consensus       137 ~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~vi-E~nasd~~  215 (666)
                      +.|++||||++|+||+||++.++.|.++++.      ++.+ +.+|||||+|+||||+|+++|+.+++.-- .......+
T Consensus         4 ~~l~~k~RP~~f~~iiGq~~v~~~L~~~i~~------~~~~-hayLf~Gp~G~GKtt~A~~lak~l~c~~~~~~~~c~~c   76 (576)
T PRK14965          4 LVLARKYRPQTFSDLTGQEHVSRTLQNAIDT------GRVA-HAFLFTGARGVGKTSTARILAKALNCEQGLTAEPCNVC   76 (576)
T ss_pred             HHHHHHhCCCCHHHccCcHHHHHHHHHHHHc------CCCC-eEEEEECCCCCCHHHHHHHHHHhhcCCCCCCCCCCCcc
Confidence            5689999999999999999999999999986      6666 78899999999999999999999975310 00000000


Q ss_pred             hhhhhhhcc-------cCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHH
Q 005987          216 IWQEYMHNC-------KTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLL  288 (666)
Q Consensus       216 ~~~e~l~~~-------~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l  288 (666)
                      ..+..+...       ..|.. ....+.++++++.+...+.     .   .+.+|+||||+++++.. ++    ++|+.+
T Consensus        77 ~~c~~i~~g~~~d~~eid~~s-~~~v~~ir~l~~~~~~~p~-----~---~~~KVvIIdev~~Lt~~-a~----naLLk~  142 (576)
T PRK14965         77 PPCVEITEGRSVDVFEIDGAS-NTGVDDIRELRENVKYLPS-----R---SRYKIFIIDEVHMLSTN-AF----NALLKT  142 (576)
T ss_pred             HHHHHHhcCCCCCeeeeeccC-ccCHHHHHHHHHHHHhccc-----c---CCceEEEEEChhhCCHH-HH----HHHHHH
Confidence            000000000       00100 2345677777777643221     1   24579999999988643 33    356666


Q ss_pred             HhcCCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHc
Q 005987          289 VRSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQAS  368 (666)
Q Consensus       289 ~~~~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~s  368 (666)
                      ++.....++||+..+.       ..+.+..|++     ||..+.|++++..++.+.|..++.++++.++++++..|+..+
T Consensus       143 LEepp~~~~fIl~t~~-------~~kl~~tI~S-----Rc~~~~f~~l~~~~i~~~L~~i~~~egi~i~~~al~~la~~a  210 (576)
T PRK14965        143 LEEPPPHVKFIFATTE-------PHKVPITILS-----RCQRFDFRRIPLQKIVDRLRYIADQEGISISDAALALVARKG  210 (576)
T ss_pred             HHcCCCCeEEEEEeCC-------hhhhhHHHHH-----hhhhhhcCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHc
Confidence            6665433444433221       1223333333     599999999999999999999999999999999999999999


Q ss_pred             CCcHHHHHHHHHHHh
Q 005987          369 GGDIRQAITSLQFSS  383 (666)
Q Consensus       369 ~GDIR~AIn~LQf~~  383 (666)
                      +||+|.|++.|+-+.
T Consensus       211 ~G~lr~al~~Ldqli  225 (576)
T PRK14965        211 DGSMRDSLSTLDQVL  225 (576)
T ss_pred             CCCHHHHHHHHHHHH
Confidence            999999999996554

>TIGR02397 dnaX_nterm DNA polymerase III, subunit gamma and tau

Probab=99.88  E-value=4.4e-21  Score=207.37  Aligned_cols=216  Identities=18%  Similarity=0.286  Sum_probs=147.8

Q ss_pred             CccccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEE-EEcCCCch
Q 005987          137 QLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLY-EWDTPTPT  215 (666)
Q Consensus       137 ~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~vi-E~nasd~~  215 (666)
                      ++|++||+|+++++++||++.++.+..++..      |+.+ +.+||+||||+|||++++++|+.+.+.-. ...+...+
T Consensus         2 ~~~~~~~rp~~~~~iig~~~~~~~l~~~~~~------~~~~-~~~Ll~G~~G~GKt~~a~~la~~l~~~~~~~~~~c~~c   74 (355)
T TIGR02397         2 QVLARKYRPQTFEDVIGQEHIVQTLKNAIKN------GRIA-HAYLFSGPRGTGKTSIARIFAKALNCQNGPDGEPCNEC   74 (355)
T ss_pred             ccHHHHhCCCcHhhccCcHHHHHHHHHHHHc------CCCC-eEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCCC
Confidence            5899999999999999999999999999986      6655 68999999999999999999999865410 00000000


Q ss_pred             hhhhhhhc-cc------CCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHH
Q 005987          216 IWQEYMHN-CK------TGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLL  288 (666)
Q Consensus       216 ~~~e~l~~-~~------~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l  288 (666)
                      .....+.. ..      .+.. ....+.++++++.+...+.     .   ..++|++|||++.+... +    .+.|+..
T Consensus        75 ~~c~~~~~~~~~~~~~~~~~~-~~~~~~~~~l~~~~~~~p~-----~---~~~~vviidea~~l~~~-~----~~~Ll~~  140 (355)
T TIGR02397        75 ESCKEINSGSSLDVIEIDAAS-NNGVDDIREILDNVKYAPS-----S---GKYKVYIIDEVHMLSKS-A----FNALLKT  140 (355)
T ss_pred             HHHHHHhcCCCCCEEEeeccc-cCCHHHHHHHHHHHhcCcc-----c---CCceEEEEeChhhcCHH-H----HHHHHHH
Confidence            00000000 00      0000 1234456777776643221     1   23569999999987542 2    2335555


Q ss_pred             HhcCCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHc
Q 005987          289 VRSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQAS  368 (666)
Q Consensus       289 ~~~~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~s  368 (666)
                      ++.....+++|++..+       ..+.+..+++     ||..+.|.+++..++.++|..++..+++.+++++++.|+..+
T Consensus       141 le~~~~~~~lIl~~~~-------~~~l~~~l~s-----r~~~~~~~~~~~~~l~~~l~~~~~~~g~~i~~~a~~~l~~~~  208 (355)
T TIGR02397       141 LEEPPEHVVFILATTE-------PHKIPATILS-----RCQRFDFKRIPLEDIVERLKKILDKEGIKIEDEALELIARAA  208 (355)
T ss_pred             HhCCccceeEEEEeCC-------HHHHHHHHHh-----heeEEEcCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHc
Confidence            5554333444433211       1122222332     589999999999999999999999999999999999999999


Q ss_pred             CCcHHHHHHHHHHHhcC
Q 005987          369 GGDIRQAITSLQFSSLK  385 (666)
Q Consensus       369 ~GDIR~AIn~LQf~~~~  385 (666)
                      +||+|.|++.|+.++..
T Consensus       209 ~g~~~~a~~~lekl~~~  225 (355)
T TIGR02397       209 DGSLRDALSLLDQLISF  225 (355)
T ss_pred             CCChHHHHHHHHHHHhh
Confidence            99999999999887653

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.

>PRK14970 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.87  E-value=6.4e-21  Score=207.19  Aligned_cols=212  Identities=18%  Similarity=0.305  Sum_probs=147.2

Q ss_pred             CCccccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCch
Q 005987          136 QQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPT  215 (666)
Q Consensus       136 ~~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~  215 (666)
                      ...|.+||||++++|++||+..++.+..+++.      |..+ +.+|||||||+|||++++++|+.++.....-...+ .
T Consensus         4 ~~~~~~k~rP~~~~~iig~~~~~~~l~~~i~~------~~~~-~~~L~~G~~G~GKt~~a~~la~~l~~~~~~~~~~~-~   75 (367)
T PRK14970          4 FVVSARKYRPQTFDDVVGQSHITNTLLNAIEN------NHLA-QALLFCGPRGVGKTTCARILARKINQPGYDDPNED-F   75 (367)
T ss_pred             hHHHHHHHCCCcHHhcCCcHHHHHHHHHHHHc------CCCC-eEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCC-C
Confidence            46799999999999999999999999999986      5555 68999999999999999999999854211100000 0


Q ss_pred             hhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcCCCc
Q 005987          216 IWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHIP  295 (666)
Q Consensus       216 ~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~~~P  295 (666)
                      .+ . +... .+. .....+.+.+.++.+...+.     .   ..++||+|||++.+... .    .+.|..+++.....
T Consensus        76 ~~-~-~~~l-~~~-~~~~~~~i~~l~~~~~~~p~-----~---~~~kiviIDE~~~l~~~-~----~~~ll~~le~~~~~  138 (367)
T PRK14970         76 SF-N-IFEL-DAA-SNNSVDDIRNLIDQVRIPPQ-----T---GKYKIYIIDEVHMLSSA-A----FNAFLKTLEEPPAH  138 (367)
T ss_pred             Cc-c-eEEe-ccc-cCCCHHHHHHHHHHHhhccc-----c---CCcEEEEEeChhhcCHH-H----HHHHHHHHhCCCCc
Confidence            00 0 0000 000 01223566666666532221     1   13569999999987542 2    23455555554333


Q ss_pred             eEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCcHHHH
Q 005987          296 TAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASGGDIRQA  375 (666)
Q Consensus       296 iViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~s~GDIR~A  375 (666)
                      .++|++...       ..+.++.+++     ||..+.|.+++..++..+|..++.++++.+++++++.|+..++||+|.+
T Consensus       139 ~~~Il~~~~-------~~kl~~~l~s-----r~~~v~~~~~~~~~l~~~l~~~~~~~g~~i~~~al~~l~~~~~gdlr~~  206 (367)
T PRK14970        139 AIFILATTE-------KHKIIPTILS-----RCQIFDFKRITIKDIKEHLAGIAVKEGIKFEDDALHIIAQKADGALRDA  206 (367)
T ss_pred             eEEEEEeCC-------cccCCHHHHh-----cceeEecCCccHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhCCCCHHHH
Confidence            333333211       1233333433     5889999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhc
Q 005987          376 ITSLQFSSL  384 (666)
Q Consensus       376 In~LQf~~~  384 (666)
                      ++.|+.++.
T Consensus       207 ~~~lekl~~  215 (367)
T PRK14970        207 LSIFDRVVT  215 (367)
T ss_pred             HHHHHHHHH
Confidence            999999875

>PRK14948 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.87  E-value=8.4e-21  Score=216.79  Aligned_cols=218  Identities=22%  Similarity=0.286  Sum_probs=155.2

Q ss_pred             CCccccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCch
Q 005987          136 QQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPT  215 (666)
Q Consensus       136 ~~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~  215 (666)
                      ..+|.+||||++|++++||+..++.|..++..      ++.. +.+||+||+|+||||+|+++|+.+++....-....++
T Consensus         3 ~~pl~~kyRP~~f~~liGq~~i~~~L~~~l~~------~rl~-~a~Lf~Gp~G~GKttlA~~lAk~L~c~~~~~~~~~~C   75 (620)
T PRK14948          3 YEPLHHKYRPQRFDELVGQEAIATTLKNALIS------NRIA-PAYLFTGPRGTGKTSSARILAKSLNCLNSDKPTPEPC   75 (620)
T ss_pred             cchHHHHhCCCcHhhccChHHHHHHHHHHHHc------CCCC-ceEEEECCCCCChHHHHHHHHHHhcCCCcCCCCCCCC
Confidence            46899999999999999999999999999986      5554 6899999999999999999999997742211000111


Q ss_pred             hhhhhhhcccCCc---------cccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHH
Q 005987          216 IWQEYMHNCKTGL---------EYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLL  286 (666)
Q Consensus       216 ~~~e~l~~~~~g~---------~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~  286 (666)
                      ..++.+.....|.         ......+.++++++.+.....     .   ...+||||||++.+...     ..+.|+
T Consensus        76 g~C~~C~~i~~g~h~D~~ei~~~~~~~vd~IReii~~a~~~p~-----~---~~~KViIIDEad~Lt~~-----a~naLL  142 (620)
T PRK14948         76 GKCELCRAIAAGNALDVIEIDAASNTGVDNIRELIERAQFAPV-----Q---ARWKVYVIDECHMLSTA-----AFNALL  142 (620)
T ss_pred             cccHHHHHHhcCCCccEEEEeccccCCHHHHHHHHHHHhhChh-----c---CCceEEEEECccccCHH-----HHHHHH
Confidence            1111110000010         012345678888877642221     1   23579999999988642     234566


Q ss_pred             HHHhcCCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHH
Q 005987          287 LLVRSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQ  366 (666)
Q Consensus       287 ~l~~~~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~  366 (666)
                      .+++.....++||+....       ..+.+..|++     ||..+.|.+++..++.++|..++.++++.++++++..|++
T Consensus       143 K~LEePp~~tvfIL~t~~-------~~~llpTIrS-----Rc~~~~f~~l~~~ei~~~L~~ia~kegi~is~~al~~La~  210 (620)
T PRK14948        143 KTLEEPPPRVVFVLATTD-------PQRVLPTIIS-----RCQRFDFRRIPLEAMVQHLSEIAEKESIEIEPEALTLVAQ  210 (620)
T ss_pred             HHHhcCCcCeEEEEEeCC-------hhhhhHHHHh-----heeEEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHH
Confidence            677765444555543321       1233333433     5999999999999999999999999999999999999999


Q ss_pred             HcCCcHHHHHHHHHHHhcC
Q 005987          367 ASGGDIRQAITSLQFSSLK  385 (666)
Q Consensus       367 ~s~GDIR~AIn~LQf~~~~  385 (666)
                      .++||+|.|++.|+..++.
T Consensus       211 ~s~G~lr~A~~lLeklsL~  229 (620)
T PRK14948        211 RSQGGLRDAESLLDQLSLL  229 (620)
T ss_pred             HcCCCHHHHHHHHHHHHhc
Confidence            9999999999999987653

>PRK06305 DNA polymerase III subunits gamma and tau; Validated

Probab=99.87  E-value=6.2e-21  Score=211.29  Aligned_cols=216  Identities=19%  Similarity=0.218  Sum_probs=149.3

Q ss_pred             CCccccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcC--CC
Q 005987          136 QQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDT--PT  213 (666)
Q Consensus       136 ~~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~na--sd  213 (666)
                      .+.|.+||||++++|++||+..++.++.+++.      ++.+ +.+||+||||+|||++|+++|+.+.+.-..-+.  ..
T Consensus         4 ~~~~~~kyRP~~~~diiGq~~~v~~L~~~i~~------~~i~-ha~Lf~Gp~G~GKtt~A~~lAk~l~c~~~~~~~~~c~   76 (451)
T PRK06305          4 YQVSSRKYRPQTFSEILGQDAVVAVLKNALRF------NRAA-HAYLFSGIRGTGKTTLARIFAKALNCQNPTEDQEPCN   76 (451)
T ss_pred             hHHHHHHhCCCCHHHhcCcHHHHHHHHHHHHc------CCCc-eEEEEEcCCCCCHHHHHHHHHHHhcCCCcccCCCCCc
Confidence            46799999999999999999999999999986      6665 789999999999999999999998653110000  00


Q ss_pred             chhhhhhhhcc-------cCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHH
Q 005987          214 PTIWQEYMHNC-------KTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLL  286 (666)
Q Consensus       214 ~~~~~e~l~~~-------~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~  286 (666)
                      .+..+..+...       ..|.. ....+.++.+.+.+.... .       ...++||||||++.+...     ..+.|+
T Consensus        77 ~c~~C~~i~~~~~~d~~~i~g~~-~~gid~ir~i~~~l~~~~-~-------~~~~kvvIIdead~lt~~-----~~n~LL  142 (451)
T PRK06305         77 QCASCKEISSGTSLDVLEIDGAS-HRGIEDIRQINETVLFTP-S-------KSRYKIYIIDEVHMLTKE-----AFNSLL  142 (451)
T ss_pred             ccHHHHHHhcCCCCceEEeeccc-cCCHHHHHHHHHHHHhhh-h-------cCCCEEEEEecHHhhCHH-----HHHHHH
Confidence            00000000000       01111 112455555554443211 1       124579999999987542     234566


Q ss_pred             HHHhcCCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHH
Q 005987          287 LLVRSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQ  366 (666)
Q Consensus       287 ~l~~~~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~  366 (666)
                      .+++.....+++|+....       ..+.+..|++     ||..+.|++++..++.+.|..++.++++.+++++++.|+.
T Consensus       143 k~lEep~~~~~~Il~t~~-------~~kl~~tI~s-----Rc~~v~f~~l~~~el~~~L~~~~~~eg~~i~~~al~~L~~  210 (451)
T PRK06305        143 KTLEEPPQHVKFFLATTE-------IHKIPGTILS-----RCQKMHLKRIPEETIIDKLALIAKQEGIETSREALLPIAR  210 (451)
T ss_pred             HHhhcCCCCceEEEEeCC-------hHhcchHHHH-----hceEEeCCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHH
Confidence            677765434444433211       1233334443     5999999999999999999999999999999999999999


Q ss_pred             HcCCcHHHHHHHHHHHhc
Q 005987          367 ASGGDIRQAITSLQFSSL  384 (666)
Q Consensus       367 ~s~GDIR~AIn~LQf~~~  384 (666)
                      .++||+|.|++.|+..+.
T Consensus       211 ~s~gdlr~a~~~Lekl~~  228 (451)
T PRK06305        211 AAQGSLRDAESLYDYVVG  228 (451)
T ss_pred             HcCCCHHHHHHHHHHHHH
Confidence            999999999999998764

>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=2.4e-21  Score=190.95  Aligned_cols=200  Identities=21%  Similarity=0.293  Sum_probs=129.9

Q ss_pred             CCCccccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCc
Q 005987          135 TQQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTP  214 (666)
Q Consensus       135 ~~~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~  214 (666)
                      ...++.++.||++++|++||++.+..++-+++...... ..+  .++|||||||+||||+|+.+|++++..+...+++..
T Consensus        10 ~~~~l~~~lRP~~L~efiGQ~~l~~~l~i~i~aa~~r~-~~l--~h~lf~GPPG~GKTTLA~IIA~e~~~~~~~~sg~~i   86 (233)
T PF05496_consen   10 EEAPLAERLRPKSLDEFIGQEHLKGNLKILIRAAKKRG-EAL--DHMLFYGPPGLGKTTLARIIANELGVNFKITSGPAI   86 (233)
T ss_dssp             --S-HHHHTS-SSCCCS-S-HHHHHHHHHHHHHHHCTT-S-----EEEEESSTTSSHHHHHHHHHHHCT--EEEEECCC-
T ss_pred             cchhhHHhcCCCCHHHccCcHHHHhhhHHHHHHHHhcC-CCc--ceEEEECCCccchhHHHHHHHhccCCCeEeccchhh
Confidence            46789999999999999999999999999988764321 222  489999999999999999999999999988887541


Q ss_pred             hhhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcCCC
Q 005987          215 TIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHI  294 (666)
Q Consensus       215 ~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~~~  294 (666)
                                       ....++..++...              +.+.||||||++.++.     ..+++|+..++....
T Consensus        87 -----------------~k~~dl~~il~~l--------------~~~~ILFIDEIHRlnk-----~~qe~LlpamEd~~i  130 (233)
T PF05496_consen   87 -----------------EKAGDLAAILTNL--------------KEGDILFIDEIHRLNK-----AQQEILLPAMEDGKI  130 (233)
T ss_dssp             ------------------SCHHHHHHHHT----------------TT-EEEECTCCC--H-----HHHHHHHHHHHCSEE
T ss_pred             -----------------hhHHHHHHHHHhc--------------CCCcEEEEechhhccH-----HHHHHHHHHhccCeE
Confidence                             1122333344322              1346999999998853     245678888886531


Q ss_pred             -----------------ceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCC
Q 005987          295 -----------------PTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLS  357 (666)
Q Consensus       295 -----------------PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~  357 (666)
                                       |-+-++++++...          .|.+-|+.+.....+++.++.+++.+++.+-+...++.++
T Consensus       131 diiiG~g~~ar~~~~~l~~FTligATTr~g----------~ls~pLrdRFgi~~~l~~Y~~~el~~Iv~r~a~~l~i~i~  200 (233)
T PF05496_consen  131 DIIIGKGPNARSIRINLPPFTLIGATTRAG----------LLSSPLRDRFGIVLRLEFYSEEELAKIVKRSARILNIEID  200 (233)
T ss_dssp             EEEBSSSSS-BEEEEE----EEEEEESSGC----------CTSHCCCTTSSEEEE----THHHHHHHHHHCCHCTT-EE-
T ss_pred             EEEeccccccceeeccCCCceEeeeecccc----------ccchhHHhhcceecchhcCCHHHHHHHHHHHHHHhCCCcC
Confidence                             1122222222111          1222222212334589999999999999999999999999


Q ss_pred             HHHHHHHHHHcCCcHHHHHHHHHHHh
Q 005987          358 TEQIDLVAQASGGDIRQAITSLQFSS  383 (666)
Q Consensus       358 ~~~l~~Ia~~s~GDIR~AIn~LQf~~  383 (666)
                      +++..+||..|.|+.|-|.+.|...-
T Consensus       201 ~~~~~~Ia~rsrGtPRiAnrll~rvr  226 (233)
T PF05496_consen  201 EDAAEEIARRSRGTPRIANRLLRRVR  226 (233)
T ss_dssp             HHHHHHHHHCTTTSHHHHHHHHHHHC
T ss_pred             HHHHHHHHHhcCCChHHHHHHHHHHH
Confidence            99999999999999999999998753

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.

>PRK14971 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.87  E-value=7.8e-21  Score=217.09  Aligned_cols=215  Identities=17%  Similarity=0.258  Sum_probs=152.3

Q ss_pred             CCccccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEE--EcCCC
Q 005987          136 QQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYE--WDTPT  213 (666)
Q Consensus       136 ~~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE--~nasd  213 (666)
                      -..|++||||++|+||+||+..++.|..+++.      ++.+ +.+|||||+|+||||+|+++|+.+.+....  ..+..
T Consensus         4 ~~~~~~kyRP~~f~~viGq~~~~~~L~~~i~~------~~l~-hayLf~Gp~G~GKtt~A~~lAk~l~c~~~~~~~~~Cg   76 (614)
T PRK14971          4 YIVSARKYRPSTFESVVGQEALTTTLKNAIAT------NKLA-HAYLFCGPRGVGKTTCARIFAKTINCQNLTADGEACN   76 (614)
T ss_pred             hHHHHHHHCCCCHHHhcCcHHHHHHHHHHHHc------CCCC-eeEEEECCCCCCHHHHHHHHHHHhCCCCCCCCCCCCC
Confidence            35799999999999999999999999999986      6666 789999999999999999999999754210  00000


Q ss_pred             chhhhhhhhcc-------cCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHH
Q 005987          214 PTIWQEYMHNC-------KTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLL  286 (666)
Q Consensus       214 ~~~~~e~l~~~-------~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~  286 (666)
                      .+..+..+...       ..+.. ....+.++++++.+...+.     .+   ..+|+||||++.+...     ..+.|+
T Consensus        77 ~C~sC~~~~~~~~~n~~~ld~~~-~~~vd~Ir~li~~~~~~P~-----~~---~~KVvIIdea~~Ls~~-----a~naLL  142 (614)
T PRK14971         77 ECESCVAFNEQRSYNIHELDAAS-NNSVDDIRNLIEQVRIPPQ-----IG---KYKIYIIDEVHMLSQA-----AFNAFL  142 (614)
T ss_pred             cchHHHHHhcCCCCceEEecccc-cCCHHHHHHHHHHHhhCcc-----cC---CcEEEEEECcccCCHH-----HHHHHH
Confidence            00000000000       00110 1235677777776643331     11   3579999999998642     234566


Q ss_pred             HHHhcCCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHH
Q 005987          287 LLVRSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQ  366 (666)
Q Consensus       287 ~l~~~~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~  366 (666)
                      .+++.....++||+..+.       ..+.+..|++     ||..+.|.+++..++.+.|.+++.++|+.+++++++.|+.
T Consensus       143 K~LEepp~~tifIL~tt~-------~~kIl~tI~S-----Rc~iv~f~~ls~~ei~~~L~~ia~~egi~i~~~al~~La~  210 (614)
T PRK14971        143 KTLEEPPSYAIFILATTE-------KHKILPTILS-----RCQIFDFNRIQVADIVNHLQYVASKEGITAEPEALNVIAQ  210 (614)
T ss_pred             HHHhCCCCCeEEEEEeCC-------chhchHHHHh-----hhheeecCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHH
Confidence            677765433444433321       1234444443     5999999999999999999999999999999999999999


Q ss_pred             HcCCcHHHHHHHHHHHh
Q 005987          367 ASGGDIRQAITSLQFSS  383 (666)
Q Consensus       367 ~s~GDIR~AIn~LQf~~  383 (666)
                      .++||+|.|++.|+-.+
T Consensus       211 ~s~gdlr~al~~Lekl~  227 (614)
T PRK14971        211 KADGGMRDALSIFDQVV  227 (614)
T ss_pred             HcCCCHHHHHHHHHHHH
Confidence            99999999999997764

>PRK14955 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.86  E-value=6.9e-21  Score=208.59  Aligned_cols=216  Identities=17%  Similarity=0.273  Sum_probs=149.0

Q ss_pred             CccccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEE------c
Q 005987          137 QLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEW------D  210 (666)
Q Consensus       137 ~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~------n  210 (666)
                      ...++||||++++|++||+..++.|+.++++      |+.+ +.+||+|||||||||+|+++|+.+.+.-..-      +
T Consensus         4 ~~l~~k~RP~~~~eiiGq~~~~~~L~~~~~~------~~~~-ha~lf~Gp~G~GKtt~A~~~a~~l~c~~~~~~~~~~~~   76 (397)
T PRK14955          4 QVIARKYRPKKFADITAQEHITRTIQNSLRM------GRVG-HGYIFSGLRGVGKTTAARVFAKAVNCQRMIDDADYLQE   76 (397)
T ss_pred             HHHHHhcCCCcHhhccChHHHHHHHHHHHHh------CCcc-eeEEEECCCCCCHHHHHHHHHHHhcCCCCcCccccccc
Confidence            4578999999999999999999999999986      6666 6799999999999999999999997742100      0


Q ss_pred             CCCchhhhhhhhcccCCcc---------ccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHH
Q 005987          211 TPTPTIWQEYMHNCKTGLE---------YTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERL  281 (666)
Q Consensus       211 asd~~~~~e~l~~~~~g~~---------~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l  281 (666)
                      ...++.....+.....|..         .....+.++++.+.+...+.     .   ...+|+||||++.+... +    
T Consensus        77 ~~~~c~~c~~c~~~~~~~~~n~~~~~~~~~~~id~Ir~l~~~~~~~p~-----~---~~~kvvIIdea~~l~~~-~----  143 (397)
T PRK14955         77 VTEPCGECESCRDFDAGTSLNISEFDAASNNSVDDIRLLRENVRYGPQ-----K---GRYRVYIIDEVHMLSIA-A----  143 (397)
T ss_pred             CCCCCCCCHHHHHHhcCCCCCeEeecccccCCHHHHHHHHHHHhhchh-----c---CCeEEEEEeChhhCCHH-H----
Confidence            0111111110000000000         01235667777666642221     1   23579999999988642 2    


Q ss_pred             HHHHHHHHhcCCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHH
Q 005987          282 RQCLLLLVRSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQI  361 (666)
Q Consensus       282 ~~~L~~l~~~~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l  361 (666)
                      ++.|+.+++.....+++|+....       ..+.+..|++     ||..+.|.+++.+++.+.|..++..+++.++++++
T Consensus       144 ~~~LLk~LEep~~~t~~Il~t~~-------~~kl~~tl~s-----R~~~v~f~~l~~~ei~~~l~~~~~~~g~~i~~~al  211 (397)
T PRK14955        144 FNAFLKTLEEPPPHAIFIFATTE-------LHKIPATIAS-----RCQRFNFKRIPLEEIQQQLQGICEAEGISVDADAL  211 (397)
T ss_pred             HHHHHHHHhcCCCCeEEEEEeCC-------hHHhHHHHHH-----HHHHhhcCCCCHHHHHHHHHHHHHHcCCCCCHHHH
Confidence            23456666665433444433211       1222233333     58899999999999999999999999999999999


Q ss_pred             HHHHHHcCCcHHHHHHHHHHHhc
Q 005987          362 DLVAQASGGDIRQAITSLQFSSL  384 (666)
Q Consensus       362 ~~Ia~~s~GDIR~AIn~LQf~~~  384 (666)
                      +.|+..++||+|.|++.|+-++.
T Consensus       212 ~~l~~~s~g~lr~a~~~L~kl~~  234 (397)
T PRK14955        212 QLIGRKAQGSMRDAQSILDQVIA  234 (397)
T ss_pred             HHHHHHcCCCHHHHHHHHHHHHH
Confidence            99999999999999999997643

>PRK14950 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.86  E-value=1.1e-20  Score=216.33  Aligned_cols=215  Identities=20%  Similarity=0.298  Sum_probs=149.3

Q ss_pred             CccccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCchh
Q 005987          137 QLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTI  216 (666)
Q Consensus       137 ~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~~  216 (666)
                      +.|.+||||++|+||+||++.++.|+.++..      ++.+ +.+||+||+|+||||+|+.+|+.+++.... ....++.
T Consensus         4 ~~l~~kyRP~~~~eiiGq~~~~~~L~~~i~~------~~i~-~a~Lf~Gp~G~GKTtlA~~lA~~l~c~~~~-~~~~~c~   75 (585)
T PRK14950          4 QVLYRKWRSQTFAELVGQEHVVQTLRNAIAE------GRVA-HAYLFTGPRGVGKTSTARILAKAVNCTTND-PKGRPCG   75 (585)
T ss_pred             HHHHHHhCCCCHHHhcCCHHHHHHHHHHHHh------CCCc-eEEEEECCCCCCHHHHHHHHHHHhcCCCCC-CCCCCCc
Confidence            4588999999999999999999999999986      5554 678999999999999999999999753210 0001111


Q ss_pred             hhhhhhcccCCc--c-------ccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHH
Q 005987          217 WQEYMHNCKTGL--E-------YTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLL  287 (666)
Q Consensus       217 ~~e~l~~~~~g~--~-------~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~  287 (666)
                      .+..+.....|.  .       .....+.++++++.+.....     .   ...+||||||++.+... ++    +.|+.
T Consensus        76 ~c~~c~~i~~~~~~d~~~i~~~~~~~vd~ir~ii~~~~~~p~-----~---~~~kVvIIDEa~~L~~~-a~----naLLk  142 (585)
T PRK14950         76 TCEMCRAIAEGSAVDVIEMDAASHTSVDDAREIIERVQFRPA-----L---ARYKVYIIDEVHMLSTA-AF----NALLK  142 (585)
T ss_pred             cCHHHHHHhcCCCCeEEEEeccccCCHHHHHHHHHHHhhCcc-----c---CCeEEEEEeChHhCCHH-HH----HHHHH
Confidence            111110000010  0       12335667777766543221     1   23579999999988642 22    34566


Q ss_pred             HHhcCCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHH
Q 005987          288 LVRSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQA  367 (666)
Q Consensus       288 l~~~~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~  367 (666)
                      +++.....++||+....       ..+.+..|++     ||..+.|.+++..++.++|..++.++++.++++++..|+..
T Consensus       143 ~LEepp~~tv~Il~t~~-------~~kll~tI~S-----R~~~i~f~~l~~~el~~~L~~~a~~egl~i~~eal~~La~~  210 (585)
T PRK14950        143 TLEEPPPHAIFILATTE-------VHKVPATILS-----RCQRFDFHRHSVADMAAHLRKIAAAEGINLEPGALEAIARA  210 (585)
T ss_pred             HHhcCCCCeEEEEEeCC-------hhhhhHHHHh-----ccceeeCCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHH
Confidence            66665433444433311       1222223332     59999999999999999999999999999999999999999


Q ss_pred             cCCcHHHHHHHHHHHhc
Q 005987          368 SGGDIRQAITSLQFSSL  384 (666)
Q Consensus       368 s~GDIR~AIn~LQf~~~  384 (666)
                      ++||+|.|++.|+-++.
T Consensus       211 s~Gdlr~al~~LekL~~  227 (585)
T PRK14950        211 ATGSMRDAENLLQQLAT  227 (585)
T ss_pred             cCCCHHHHHHHHHHHHH
Confidence            99999999999998765

>PRK14954 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.86  E-value=1.6e-20  Score=213.53  Aligned_cols=216  Identities=18%  Similarity=0.297  Sum_probs=151.3

Q ss_pred             CccccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEE----Ec--
Q 005987          137 QLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYE----WD--  210 (666)
Q Consensus       137 ~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE----~n--  210 (666)
                      +..++||||++|+|++||+..++.|++++..      ++.+ +.+||+||+||||||+|+++|+.+.+....    |.  
T Consensus         4 ~~l~~kyRP~~f~eivGQe~i~~~L~~~i~~------~ri~-ha~Lf~Gp~GvGKttlA~~lAk~L~c~~~~~~~~~~~~   76 (620)
T PRK14954          4 QVIARKYRPSKFADITAQEHITHTIQNSLRM------DRVG-HGYIFSGLRGVGKTTAARVFAKAVNCQRMIDDPVYLQE   76 (620)
T ss_pred             HHHHHHHCCCCHHHhcCcHHHHHHHHHHHHc------CCCC-eeEEEECCCCCCHHHHHHHHHHHhCCCCcCCccccccc
Confidence            4568999999999999999999999999876      6666 679999999999999999999999874210    00  


Q ss_pred             CCCchhhhhhhhcccCCcc---------ccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHH
Q 005987          211 TPTPTIWQEYMHNCKTGLE---------YTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERL  281 (666)
Q Consensus       211 asd~~~~~e~l~~~~~g~~---------~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l  281 (666)
                      ...++..+..+.....|..         -....++++++++.+...+ .    .   ..++|+||||++.+... +    
T Consensus        77 ~~~~Cg~C~sC~~~~~g~~~n~~~~d~~s~~~vd~Ir~l~e~~~~~P-~----~---~~~KVvIIdEad~Lt~~-a----  143 (620)
T PRK14954         77 VTEPCGECESCRDFDAGTSLNISEFDAASNNSVDDIRQLRENVRYGP-Q----K---GRYRVYIIDEVHMLSTA-A----  143 (620)
T ss_pred             cCCCCccCHHHHHHhccCCCCeEEecccccCCHHHHHHHHHHHHhhh-h----c---CCCEEEEEeChhhcCHH-H----
Confidence            0011111111110011100         0123567777777664222 1    1   13579999999988643 2    


Q ss_pred             HHHHHHHHhcCCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHH
Q 005987          282 RQCLLLLVRSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQI  361 (666)
Q Consensus       282 ~~~L~~l~~~~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l  361 (666)
                      .+.|+.+++.....+++|+....       ..+.+..|++     ||..|.|.+++..++.+.|.+++..+++.++++++
T Consensus       144 ~naLLK~LEePp~~tv~IL~t~~-------~~kLl~TI~S-----Rc~~vef~~l~~~ei~~~L~~i~~~egi~I~~eal  211 (620)
T PRK14954        144 FNAFLKTLEEPPPHAIFIFATTE-------LHKIPATIAS-----RCQRFNFKRIPLDEIQSQLQMICRAEGIQIDADAL  211 (620)
T ss_pred             HHHHHHHHhCCCCCeEEEEEeCC-------hhhhhHHHHh-----hceEEecCCCCHHHHHHHHHHHHHHcCCCCCHHHH
Confidence            34567777775443444433211       1233333333     59999999999999999999999999999999999


Q ss_pred             HHHHHHcCCcHHHHHHHHHHHhc
Q 005987          362 DLVAQASGGDIRQAITSLQFSSL  384 (666)
Q Consensus       362 ~~Ia~~s~GDIR~AIn~LQf~~~  384 (666)
                      +.|+..++||+|.|++.|+-++.
T Consensus       212 ~~La~~s~Gdlr~al~eLeKL~~  234 (620)
T PRK14954        212 QLIARKAQGSMRDAQSILDQVIA  234 (620)
T ss_pred             HHHHHHhCCCHHHHHHHHHHHHH
Confidence            99999999999999999986553

>PRK13342 recombination factor protein RarA; Reviewed

Probab=99.86  E-value=1.5e-20  Score=207.15  Aligned_cols=197  Identities=23%  Similarity=0.376  Sum_probs=145.1

Q ss_pred             ccccccCCCCccccccCHHHHHH---HHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCc
Q 005987          138 LWAEKYKPRSLEELAVQRKKVEE---VRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTP  214 (666)
Q Consensus       138 ~W~eKY~P~sl~eLvg~~k~i~e---l~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~  214 (666)
                      +|++||||++++|++|+++.+..   +..+++.      +..  ..+||+|||||||||+|+++|+.++..++++++...
T Consensus         1 pla~~~RP~~l~d~vGq~~~v~~~~~L~~~i~~------~~~--~~ilL~GppGtGKTtLA~~ia~~~~~~~~~l~a~~~   72 (413)
T PRK13342          1 PLAERMRPKTLDEVVGQEHLLGPGKPLRRMIEA------GRL--SSMILWGPPGTGKTTLARIIAGATDAPFEALSAVTS   72 (413)
T ss_pred             ChhhhhCCCCHHHhcCcHHHhCcchHHHHHHHc------CCC--ceEEEECCCCCCHHHHHHHHHHHhCCCEEEEecccc
Confidence            69999999999999999999887   8888865      333  379999999999999999999999999999987541


Q ss_pred             hhhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcCCC
Q 005987          215 TIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHI  294 (666)
Q Consensus       215 ~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~~~  294 (666)
                                        ..+.++.+++.+.....        .+.+.||+|||++.+...     .++.|+..++.+. 
T Consensus        73 ------------------~~~~ir~ii~~~~~~~~--------~g~~~vL~IDEi~~l~~~-----~q~~LL~~le~~~-  120 (413)
T PRK13342         73 ------------------GVKDLREVIEEARQRRS--------AGRRTILFIDEIHRFNKA-----QQDALLPHVEDGT-  120 (413)
T ss_pred             ------------------cHHHHHHHHHHHHHhhh--------cCCceEEEEechhhhCHH-----HHHHHHHHhhcCc-
Confidence                              12344555555532210        123579999999987532     2344666666543 


Q ss_pred             ceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHh--CC-CCCHHHHHHHHHHcCCc
Q 005987          295 PTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQE--QY-SLSTEQIDLVAQASGGD  371 (666)
Q Consensus       295 PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e--~i-~v~~~~l~~Ia~~s~GD  371 (666)
                       +++|.+.+...     .....   ..+++  ||..+.|.+++.+++..+|.+++...  ++ .+++++++.|+..++||
T Consensus       121 -iilI~att~n~-----~~~l~---~aL~S--R~~~~~~~~ls~e~i~~lL~~~l~~~~~~~i~i~~~al~~l~~~s~Gd  189 (413)
T PRK13342        121 -ITLIGATTENP-----SFEVN---PALLS--RAQVFELKPLSEEDIEQLLKRALEDKERGLVELDDEALDALARLANGD  189 (413)
T ss_pred             -EEEEEeCCCCh-----hhhcc---HHHhc--cceeeEeCCCCHHHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHhCCCC
Confidence             33443322111     11111   23333  58999999999999999999988763  44 78999999999999999


Q ss_pred             HHHHHHHHHHHhcC
Q 005987          372 IRQAITSLQFSSLK  385 (666)
Q Consensus       372 IR~AIn~LQf~~~~  385 (666)
                      +|.++|.|+.++..
T Consensus       190 ~R~aln~Le~~~~~  203 (413)
T PRK13342        190 ARRALNLLELAALG  203 (413)
T ss_pred             HHHHHHHHHHHHHc
Confidence            99999999998754

>PRK06647 DNA polymerase III subunits gamma and tau; Validated

Probab=99.86  E-value=2.2e-20  Score=211.14  Aligned_cols=213  Identities=21%  Similarity=0.267  Sum_probs=150.6

Q ss_pred             CccccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCchh
Q 005987          137 QLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTI  216 (666)
Q Consensus       137 ~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~~  216 (666)
                      ..|+.||||++|+|++||+..++.++.++..      ++.+ +.+|||||+|+||||+|+++|+.+++.--  ....++.
T Consensus         4 ~~l~~kyRP~~f~diiGqe~iv~~L~~~i~~------~~i~-hayLf~Gp~G~GKTt~Ar~lAk~L~c~~~--~~~~pC~   74 (563)
T PRK06647          4 RGTATKRRPRDFNSLEGQDFVVETLKHSIES------NKIA-NAYIFSGPRGVGKTSSARAFARCLNCVNG--PTPMPCG   74 (563)
T ss_pred             HHHHHHhCCCCHHHccCcHHHHHHHHHHHHc------CCCC-eEEEEECCCCCCHHHHHHHHHHhhccccC--CCCCCCc
Confidence            5689999999999999999999999999986      6665 78999999999999999999999976410  0000111


Q ss_pred             hhhhhhccc----------CCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHH
Q 005987          217 WQEYMHNCK----------TGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLL  286 (666)
Q Consensus       217 ~~e~l~~~~----------~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~  286 (666)
                      ....+....          .|.. ....+.++++.+.+...+.        ....+|+||||++.+...     ..++|+
T Consensus        75 ~C~~C~~i~~~~~~dv~~idgas-~~~vddIr~l~e~~~~~p~--------~~~~KVvIIDEa~~Ls~~-----a~naLL  140 (563)
T PRK06647         75 ECSSCKSIDNDNSLDVIEIDGAS-NTSVQDVRQIKEEIMFPPA--------SSRYRVYIIDEVHMLSNS-----AFNALL  140 (563)
T ss_pred             cchHHHHHHcCCCCCeEEecCcc-cCCHHHHHHHHHHHHhchh--------cCCCEEEEEEChhhcCHH-----HHHHHH
Confidence            100000000          0110 1335567666666542221        124679999999988542     234466


Q ss_pred             HHHhcCCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHH
Q 005987          287 LLVRSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQ  366 (666)
Q Consensus       287 ~l~~~~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~  366 (666)
                      .+++.....+++|.+.+.       ..+.+..|++     ||..+.|.+++.+++.++|.+++..+++.++++++..|+.
T Consensus       141 K~LEepp~~~vfI~~tte-------~~kL~~tI~S-----Rc~~~~f~~l~~~el~~~L~~i~~~egi~id~eAl~lLa~  208 (563)
T PRK06647        141 KTIEEPPPYIVFIFATTE-------VHKLPATIKS-----RCQHFNFRLLSLEKIYNMLKKVCLEDQIKYEDEALKWIAY  208 (563)
T ss_pred             HhhccCCCCEEEEEecCC-------hHHhHHHHHH-----hceEEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHH
Confidence            666765444555554421       1222233333     5999999999999999999999999999999999999999


Q ss_pred             HcCCcHHHHHHHHHHHhc
Q 005987          367 ASGGDIRQAITSLQFSSL  384 (666)
Q Consensus       367 ~s~GDIR~AIn~LQf~~~  384 (666)
                      .++||+|.|++.|+-++.
T Consensus       209 ~s~GdlR~alslLdklis  226 (563)
T PRK06647        209 KSTGSVRDAYTLFDQVVS  226 (563)
T ss_pred             HcCCCHHHHHHHHHHHHh
Confidence            999999999999975443

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

Probab=99.86  E-value=4e-21  Score=196.99  Aligned_cols=199  Identities=22%  Similarity=0.341  Sum_probs=151.9

Q ss_pred             CCccccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcCC
Q 005987          136 QQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL---GARLYEWDTP  212 (666)
Q Consensus       136 ~~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~nas  212 (666)
                      ..++.|+-||++++|.+||.+.+.+ ...|.+.+..  ++.|  .++|+|||||||||+|+.||+.-   .|.++|+.+.
T Consensus       125 h~PLaermRPktL~dyvGQ~hlv~q-~gllrs~ieq--~~ip--SmIlWGppG~GKTtlArlia~tsk~~SyrfvelSAt  199 (554)
T KOG2028|consen  125 HKPLAERMRPKTLDDYVGQSHLVGQ-DGLLRSLIEQ--NRIP--SMILWGPPGTGKTTLARLIASTSKKHSYRFVELSAT  199 (554)
T ss_pred             cCChhhhcCcchHHHhcchhhhcCc-chHHHHHHHc--CCCC--ceEEecCCCCchHHHHHHHHhhcCCCceEEEEEecc
Confidence            4589999999999999999999877 4444443332  5665  89999999999999999999876   4668888765


Q ss_pred             CchhhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHH-HHHHHHHhc
Q 005987          213 TPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLR-QCLLLLVRS  291 (666)
Q Consensus       213 d~~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~-~~L~~l~~~  291 (666)
                      .                  ....+++.+++.++++..+.       +++.||||||+++.      ++.+ +.++..++.
T Consensus       200 ~------------------a~t~dvR~ife~aq~~~~l~-------krkTilFiDEiHRF------NksQQD~fLP~VE~  248 (554)
T KOG2028|consen  200 N------------------AKTNDVRDIFEQAQNEKSLT-------KRKTILFIDEIHRF------NKSQQDTFLPHVEN  248 (554)
T ss_pred             c------------------cchHHHHHHHHHHHHHHhhh-------cceeEEEeHHhhhh------hhhhhhcccceecc
Confidence            3                  23457888899988776542       46789999999865      3333 556667776


Q ss_pred             CCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHH----hC---------CCCCH
Q 005987          292 THIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQ----EQ---------YSLST  358 (666)
Q Consensus       292 ~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~----e~---------i~v~~  358 (666)
                      +   .|++++.++.+.+.       .-...+++  ||.++.+++++.+.+..+|.+....    +.         +.+++
T Consensus       249 G---~I~lIGATTENPSF-------qln~aLlS--RC~VfvLekL~~n~v~~iL~raia~l~dser~~~~l~n~s~~ve~  316 (554)
T KOG2028|consen  249 G---DITLIGATTENPSF-------QLNAALLS--RCRVFVLEKLPVNAVVTILMRAIASLGDSERPTDPLPNSSMFVED  316 (554)
T ss_pred             C---ceEEEecccCCCcc-------chhHHHHh--ccceeEeccCCHHHHHHHHHHHHHhhccccccCCCCCCcchhhhH
Confidence            6   45666776665532       22234444  5999999999999999999995442    11         34788


Q ss_pred             HHHHHHHHHcCCcHHHHHHHHHHH
Q 005987          359 EQIDLVAQASGGDIRQAITSLQFS  382 (666)
Q Consensus       359 ~~l~~Ia~~s~GDIR~AIn~LQf~  382 (666)
                      .+|+.|+..|.||.|.|+|.||+.
T Consensus       317 siidyla~lsdGDaR~aLN~Lems  340 (554)
T KOG2028|consen  317 SIIDYLAYLSDGDARAALNALEMS  340 (554)
T ss_pred             HHHHHHHHhcCchHHHHHHHHHHH
Confidence            999999999999999999999998

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

Probab=99.85  E-value=1.1e-20  Score=208.04  Aligned_cols=215  Identities=20%  Similarity=0.374  Sum_probs=162.1

Q ss_pred             CccccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCchh
Q 005987          137 QLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTI  216 (666)
Q Consensus       137 ~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~~  216 (666)
                      +..+.||||++|+|++||+..++.|++.+..      ++.. +.+||+||.||||||+||.+|+.+++.--  ...+++.
T Consensus         4 q~L~rKyRP~~F~evvGQe~v~~~L~nal~~------~ri~-hAYlfsG~RGvGKTt~Ari~AkalNC~~~--~~~ePC~   74 (515)
T COG2812           4 QVLARKYRPKTFDDVVGQEHVVKTLSNALEN------GRIA-HAYLFSGPRGVGKTTIARILAKALNCENG--PTAEPCG   74 (515)
T ss_pred             HHHHHHhCcccHHHhcccHHHHHHHHHHHHh------Ccch-hhhhhcCCCCcCchhHHHHHHHHhcCCCC--CCCCcch
Confidence            4578899999999999999999999999987      6666 78999999999999999999999987631  1112222


Q ss_pred             hhhhhhcccCC--c-------cccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHH
Q 005987          217 WQEYMHNCKTG--L-------EYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLL  287 (666)
Q Consensus       217 ~~e~l~~~~~g--~-------~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~  287 (666)
                      -+..+.+...|  +       .....+++++++++++. |...       ..+.+|++|||++++... +|+    +|++
T Consensus        75 ~C~~Ck~I~~g~~~DviEiDaASn~gVddiR~i~e~v~-y~P~-------~~ryKVyiIDEvHMLS~~-afN----ALLK  141 (515)
T COG2812          75 KCISCKEINEGSLIDVIEIDAASNTGVDDIREIIEKVN-YAPS-------EGRYKVYIIDEVHMLSKQ-AFN----ALLK  141 (515)
T ss_pred             hhhhhHhhhcCCcccchhhhhhhccChHHHHHHHHHhc-cCCc-------cccceEEEEecHHhhhHH-HHH----HHhc
Confidence            22222222222  1       12456778999998884 4322       235689999999988543 444    4556


Q ss_pred             HHhcCCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHH
Q 005987          288 LVRSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQA  367 (666)
Q Consensus       288 l~~~~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~  367 (666)
                      .++.....++||..++...       +.   +..+++  ||+.+.|++++.++|.+.|..|+.+|++.++++++..|+..
T Consensus       142 TLEEPP~hV~FIlATTe~~-------Ki---p~TIlS--Rcq~f~fkri~~~~I~~~L~~i~~~E~I~~e~~aL~~ia~~  209 (515)
T COG2812         142 TLEEPPSHVKFILATTEPQ-------KI---PNTILS--RCQRFDFKRLDLEEIAKHLAAILDKEGINIEEDALSLIARA  209 (515)
T ss_pred             ccccCccCeEEEEecCCcC-------cC---chhhhh--ccccccccCCCHHHHHHHHHHHHHhcCCccCHHHHHHHHHH
Confidence            6676665677776665432       22   234555  59999999999999999999999999999999999999999


Q ss_pred             cCCcHHHHHHHHH-HHhcC
Q 005987          368 SGGDIRQAITSLQ-FSSLK  385 (666)
Q Consensus       368 s~GDIR~AIn~LQ-f~~~~  385 (666)
                      ++|.+|-+++.|. +.+.+
T Consensus       210 a~Gs~RDalslLDq~i~~~  228 (515)
T COG2812         210 AEGSLRDALSLLDQAIAFG  228 (515)
T ss_pred             cCCChhhHHHHHHHHHHcc
Confidence            9999999999995 44443

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

Probab=99.84  E-value=4.7e-20  Score=213.27  Aligned_cols=199  Identities=22%  Similarity=0.353  Sum_probs=142.4

Q ss_pred             CCccccccCCCCccccccCHHHHH---HHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCC
Q 005987          136 QQLWAEKYKPRSLEELAVQRKKVE---EVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTP  212 (666)
Q Consensus       136 ~~~W~eKY~P~sl~eLvg~~k~i~---el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nas  212 (666)
                      ..+|++||||++++|++|++..+.   .++.+++.      ++.+  .+||+|||||||||+|+++|+.++..++++++.
T Consensus        15 ~~PLaek~RP~tldd~vGQe~ii~~~~~L~~~i~~------~~~~--slLL~GPpGtGKTTLA~aIA~~~~~~f~~lna~   86 (725)
T PRK13341         15 EAPLADRLRPRTLEEFVGQDHILGEGRLLRRAIKA------DRVG--SLILYGPPGVGKTTLARIIANHTRAHFSSLNAV   86 (725)
T ss_pred             cCChHHhcCCCcHHHhcCcHHHhhhhHHHHHHHhc------CCCc--eEEEECCCCCCHHHHHHHHHHHhcCcceeehhh
Confidence            468999999999999999999985   45565553      4443  789999999999999999999999888888865


Q ss_pred             CchhhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcC
Q 005987          213 TPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRST  292 (666)
Q Consensus       213 d~~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~  292 (666)
                      ..            +      .+.++..++.+......       .+...+|||||++.++..     .++.|...++.+
T Consensus        87 ~~------------~------i~dir~~i~~a~~~l~~-------~~~~~IL~IDEIh~Ln~~-----qQdaLL~~lE~g  136 (725)
T PRK13341         87 LA------------G------VKDLRAEVDRAKERLER-------HGKRTILFIDEVHRFNKA-----QQDALLPWVENG  136 (725)
T ss_pred             hh------------h------hHHHHHHHHHHHHHhhh-------cCCceEEEEeChhhCCHH-----HHHHHHHHhcCc
Confidence            31            1      12233334433221100       013469999999987542     233456666654


Q ss_pred             CCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHH-------HhCCCCCHHHHHHHH
Q 005987          293 HIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICR-------QEQYSLSTEQIDLVA  365 (666)
Q Consensus       293 ~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~-------~e~i~v~~~~l~~Ia  365 (666)
                      .  + +++++++.+.       ...-...+++  ||..+.|+|++.+++..+|++++.       .+++.+++++++.|+
T Consensus       137 ~--I-iLI~aTTenp-------~~~l~~aL~S--R~~v~~l~pLs~edi~~IL~~~l~~~~~~~g~~~v~I~deaL~~La  204 (725)
T PRK13341        137 T--I-TLIGATTENP-------YFEVNKALVS--RSRLFRLKSLSDEDLHQLLKRALQDKERGYGDRKVDLEPEAEKHLV  204 (725)
T ss_pred             e--E-EEEEecCCCh-------HhhhhhHhhc--cccceecCCCCHHHHHHHHHHHHHHHHhhcCCcccCCCHHHHHHHH
Confidence            2  3 3444332221       1111123333  588999999999999999999998       467889999999999


Q ss_pred             HHcCCcHHHHHHHHHHHhc
Q 005987          366 QASGGDIRQAITSLQFSSL  384 (666)
Q Consensus       366 ~~s~GDIR~AIn~LQf~~~  384 (666)
                      ..+.||+|.++|.|+.++.
T Consensus       205 ~~s~GD~R~lln~Le~a~~  223 (725)
T PRK13341        205 DVANGDARSLLNALELAVE  223 (725)
T ss_pred             HhCCCCHHHHHHHHHHHHH
Confidence            9999999999999998764

>KOG0990 consensus Replication factor C, subunit RFC5 [Replication, recombination and repair]

Probab=99.84  E-value=3.7e-21  Score=195.40  Aligned_cols=207  Identities=21%  Similarity=0.261  Sum_probs=149.7

Q ss_pred             CCCCccccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcC------CcEE
Q 005987          134 STQQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLG------ARLY  207 (666)
Q Consensus       134 ~~~~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg------~~vi  207 (666)
                      ...++|++||+|..+.|+++|+..+..+.++...      ++.|  ++|+|||||+|||+++.+.|+.+.      ..+.
T Consensus        26 ~~~~pwvekyrP~~l~dv~~~~ei~st~~~~~~~------~~lP--h~L~YgPPGtGktsti~a~a~~ly~~~~~~~m~l   97 (360)
T KOG0990|consen   26 QYPQPWVEKYRPPFLGIVIKQEPIWSTENRYSGM------PGLP--HLLFYGPPGTGKTSTILANARDFYSPHPTTSMLL   97 (360)
T ss_pred             ccCCCCccCCCCchhhhHhcCCchhhHHHHhccC------CCCC--cccccCCCCCCCCCchhhhhhhhcCCCCchhHHH
Confidence            4578999999999999999999998888777332      5555  899999999999999999999983      2367


Q ss_pred             EEcCCCchhhhhhhhcccCCccccc-hhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHH
Q 005987          208 EWDTPTPTIWQEYMHNCKTGLEYTS-KLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLL  286 (666)
Q Consensus       208 E~nasd~~~~~e~l~~~~~g~~~~s-~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~  286 (666)
                      |+|++++           +|..... +...|. +......|.        .....+++|+||+|.+.. ++.+.++..++
T Consensus        98 elnaSd~-----------rgid~vr~qi~~fa-st~~~~~fs--------t~~~fKlvILDEADaMT~-~AQnALRRvie  156 (360)
T KOG0990|consen   98 ELNASDD-----------RGIDPVRQQIHLFA-STQQPTTYS--------THAAFKLVILDEADAMTR-DAQNALRRVIE  156 (360)
T ss_pred             HhhccCc-----------cCCcchHHHHHHHH-hhccceecc--------ccCceeEEEecchhHhhH-HHHHHHHHHHH
Confidence            8888773           4444321 111111 111111111        112357999999998743 33445555555


Q ss_pred             HHHhcCCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHH
Q 005987          287 LLVRSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQ  366 (666)
Q Consensus       287 ~l~~~~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~  366 (666)
                      .+..+.   .++++++.        .....+.+++     ||+.++|.|++.+.+..++..+|..|....+++....++.
T Consensus       157 k~t~n~---rF~ii~n~--------~~ki~pa~qs-----Rctrfrf~pl~~~~~~~r~shi~e~e~~~~~~~~~~a~~r  220 (360)
T KOG0990|consen  157 KYTANT---RFATISNP--------PQKIHPAQQS-----RCTRFRFAPLTMAQQTERQSHIRESEQKETNPEGYSALGR  220 (360)
T ss_pred             Hhccce---EEEEeccC--------hhhcCchhhc-----ccccCCCCCCChhhhhhHHHHHHhcchhhcCHHHHHHHHH
Confidence            554444   34455542        2333334443     6999999999999999999999999999999999999999


Q ss_pred             HcCCcHHHHHHHHHHHhcC
Q 005987          367 ASGGDIRQAITSLQFSSLK  385 (666)
Q Consensus       367 ~s~GDIR~AIn~LQf~~~~  385 (666)
                      .+.||+|.|+|.||..+..
T Consensus       221 ~s~gDmr~a~n~Lqs~~~~  239 (360)
T KOG0990|consen  221 LSVGDMRVALNYLQSILKK  239 (360)
T ss_pred             HhHHHHHHHHHHHHHHHHH
Confidence            9999999999999998764

>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed

Probab=99.80  E-value=1.7e-18  Score=185.35  Aligned_cols=203  Identities=18%  Similarity=0.218  Sum_probs=140.5

Q ss_pred             CCCccccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCc
Q 005987          135 TQQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTP  214 (666)
Q Consensus       135 ~~~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~  214 (666)
                      ...+|-.+|||+++++++|+++.++.+..++..+...  +. +.+++||+||||||||++|+++|++++..+...+.+..
T Consensus        11 ~~~~~~~~~rP~~~~~~vG~~~~~~~l~~~l~~~~~~--~~-~~~~~ll~GppG~GKT~la~~ia~~l~~~~~~~~~~~~   87 (328)
T PRK00080         11 EEDEIERSLRPKSLDEFIGQEKVKENLKIFIEAAKKR--GE-ALDHVLLYGPPGLGKTTLANIIANEMGVNIRITSGPAL   87 (328)
T ss_pred             ccchhhhhcCcCCHHHhcCcHHHHHHHHHHHHHHHhc--CC-CCCcEEEECCCCccHHHHHHHHHHHhCCCeEEEecccc
Confidence            3567889999999999999999999999999865432  22 23689999999999999999999999988776654421


Q ss_pred             hhhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHH-----
Q 005987          215 TIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLV-----  289 (666)
Q Consensus       215 ~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~-----  289 (666)
                                       .....+..++...              ..+.||+|||++.+... ..+.+...+....     
T Consensus        88 -----------------~~~~~l~~~l~~l--------------~~~~vl~IDEi~~l~~~-~~e~l~~~~e~~~~~~~l  135 (328)
T PRK00080         88 -----------------EKPGDLAAILTNL--------------EEGDVLFIDEIHRLSPV-VEEILYPAMEDFRLDIMI  135 (328)
T ss_pred             -----------------cChHHHHHHHHhc--------------ccCCEEEEecHhhcchH-HHHHHHHHHHhcceeeee
Confidence                             0112333343322              12459999999987542 1122222222210     


Q ss_pred             hcC--------CCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHH
Q 005987          290 RST--------HIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQI  361 (666)
Q Consensus       290 ~~~--------~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l  361 (666)
                      ...        ..|-++++..++...      ....+|++   | ....+.|.+++.+++.++|.+.+...++.++++++
T Consensus       136 ~~~~~~~~~~~~l~~~~li~at~~~~------~l~~~L~s---R-f~~~~~l~~~~~~e~~~il~~~~~~~~~~~~~~~~  205 (328)
T PRK00080        136 GKGPAARSIRLDLPPFTLIGATTRAG------LLTSPLRD---R-FGIVQRLEFYTVEELEKIVKRSARILGVEIDEEGA  205 (328)
T ss_pred             ccCccccceeecCCCceEEeecCCcc------cCCHHHHH---h-cCeeeecCCCCHHHHHHHHHHHHHHcCCCcCHHHH
Confidence            000        112223333322211      11122333   2 24679999999999999999999999999999999


Q ss_pred             HHHHHHcCCcHHHHHHHHHHH
Q 005987          362 DLVAQASGGDIRQAITSLQFS  382 (666)
Q Consensus       362 ~~Ia~~s~GDIR~AIn~LQf~  382 (666)
                      +.|+..|+|+.|.|.+.|+..
T Consensus       206 ~~ia~~~~G~pR~a~~~l~~~  226 (328)
T PRK00080        206 LEIARRSRGTPRIANRLLRRV  226 (328)
T ss_pred             HHHHHHcCCCchHHHHHHHHH
Confidence            999999999999999999864

>PRK04132 replication factor C small subunit; Provisional

Probab=99.77  E-value=1.4e-17  Score=193.68  Aligned_cols=250  Identities=17%  Similarity=0.230  Sum_probs=173.6

Q ss_pred             EEEEEC--CCCchHHHHHHHHHHHc-----CCcEEEEcCCCchhhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCC
Q 005987          180 VLVITG--QAGVGKTATVRQIASHL-----GARLYEWDTPTPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSP  252 (666)
Q Consensus       180 ~LLL~G--PpG~GKTtla~~LAkel-----g~~viE~nasd~~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~  252 (666)
                      .-+..|  |.++||||+|++||+++     +.+++|+|+++.+           |      .+.+++++..+..+..+. 
T Consensus       566 ~~~~~G~lPh~lGKTT~A~ala~~l~g~~~~~~~lElNASd~r-----------g------id~IR~iIk~~a~~~~~~-  627 (846)
T PRK04132        566 HNFIGGNLPTVLHNTTAALALARELFGENWRHNFLELNASDER-----------G------INVIREKVKEFARTKPIG-  627 (846)
T ss_pred             hhhhcCCCCCcccHHHHHHHHHHhhhcccccCeEEEEeCCCcc-----------c------HHHHHHHHHHHHhcCCcC-
Confidence            356678  99999999999999998     5689999999732           2      346666776655443221 


Q ss_pred             CCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhc--CCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeE
Q 005987          253 SIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRS--THIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARK  330 (666)
Q Consensus       253 s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~--~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~  330 (666)
                           ..+.+|+||||+|.++..     .+++|+.+++.  ...++|++|++         ..+.+++|++     ||+.
T Consensus       628 -----~~~~KVvIIDEaD~Lt~~-----AQnALLk~lEep~~~~~FILi~N~---------~~kIi~tIrS-----RC~~  683 (846)
T PRK04132        628 -----GASFKIIFLDEADALTQD-----AQQALRRTMEMFSSNVRFILSCNY---------SSKIIEPIQS-----RCAI  683 (846)
T ss_pred             -----CCCCEEEEEECcccCCHH-----HHHHHHHHhhCCCCCeEEEEEeCC---------hhhCchHHhh-----hceE
Confidence                 123579999999998642     34457777775  34455555443         2344455554     6999


Q ss_pred             EEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCcHHHHHHHHHHHhcCCCCcccccccCCCCCCCccccCCCC
Q 005987          331 VALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASGGDIRQAITSLQFSSLKQDPMLNLSLSISKPNFPEEKADGHG  410 (666)
Q Consensus       331 I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~s~GDIR~AIn~LQf~~~~~~~~~~~~~~~~~~~~~k~~~~~~~  410 (666)
                      +.|.+++.+++.++|.++|.+|++.++++++..|+..|+||+|.|||.||.++.......                  .+
T Consensus       684 i~F~~ls~~~i~~~L~~I~~~Egi~i~~e~L~~Ia~~s~GDlR~AIn~Lq~~~~~~~~It------------------~~  745 (846)
T PRK04132        684 FRFRPLRDEDIAKRLRYIAENEGLELTEEGLQAILYIAEGDMRRAINILQAAAALDDKIT------------------DE  745 (846)
T ss_pred             EeCCCCCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhcCCCC------------------HH
Confidence            999999999999999999999999999999999999999999999999999876432110                  01


Q ss_pred             CcccccCCccccchHHHHhHHhhCCCCCCccccccccchhhhhccccCCCCCCChHHHHHhcCCChhHHHHHHHhhcCCC
Q 005987          411 GFSIQFGRDETLSLFHALGKFLHNKRETDNLVKMDQDAFVVKDKFSRLPLKMDAPEKVLSQAHGQARPVLDFLHENFLDF  490 (666)
Q Consensus       411 ~~~~~~~RD~~l~lFhalGkil~~Kr~~~~~~~~~~~~~~~~~~~~r~pl~~~~pE~vl~~~~~~~~~~~~~LhENy~~f  490 (666)
                      .+..+.+++..-.++..+..++.++ ...           ..+          .-.+++...+.++..++.-+++.+...
T Consensus       746 ~V~~~~~~~~~~~I~~il~~~l~~~-~~~-----------ar~----------~l~ell~~~G~~~~~iL~~l~~~l~~~  803 (846)
T PRK04132        746 NVFLVASRARPEDIREMMLLALKGN-FLK-----------ARE----------KLREILLKQGLSGEDVLVQMHREVFNL  803 (846)
T ss_pred             HHHHHhCCCCHHHHHHHHHHHhcCc-HHH-----------HHH----------HHHHHHHHhCCCHHHHHHHHHHHHHhc
Confidence            1123345666667888888777643 100           000          012345566778888888888887543


Q ss_pred             -CCcchHHHHHHHHHHhhHhhhccc
Q 005987          491 -ISEDAIDDAWAVASYLSDADLLLA  514 (666)
Q Consensus       491 -~~d~~i~~~~~~~d~LS~aD~l~~  514 (666)
                       .++   ......++.++++|..+.
T Consensus       804 ~i~~---~~k~~ll~~lae~e~rl~  825 (846)
T PRK04132        804 PIDE---PKKVELADKIGEYNFRLV  825 (846)
T ss_pred             CCCH---HHHHHHHHHHHHHhHHHH
Confidence             332   233456788888888765

>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit

Probab=99.72  E-value=2.3e-16  Score=167.09  Aligned_cols=192  Identities=19%  Similarity=0.188  Sum_probs=127.8

Q ss_pred             CCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCchhhhhhhhccc
Q 005987          146 RSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTIWQEYMHNCK  225 (666)
Q Consensus       146 ~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~~~~e~l~~~~  225 (666)
                      ++|+|++|+++.++.|..|+...... .+.  .++++|+||||||||++++++|++++..+.....+..           
T Consensus         1 ~~~~~~iG~~~~~~~l~~~l~~~~~~-~~~--~~~~ll~Gp~G~GKT~la~~ia~~~~~~~~~~~~~~~-----------   66 (305)
T TIGR00635         1 KLLAEFIGQEKVKEQLQLFIEAAKMR-QEA--LDHLLLYGPPGLGKTTLAHIIANEMGVNLKITSGPAL-----------   66 (305)
T ss_pred             CCHHHHcCHHHHHHHHHHHHHHHHhc-CCC--CCeEEEECCCCCCHHHHHHHHHHHhCCCEEEeccchh-----------
Confidence            47899999999999999999865432 122  2579999999999999999999999887665543320           


Q ss_pred             CCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHH-----hc---------
Q 005987          226 TGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLV-----RS---------  291 (666)
Q Consensus       226 ~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~-----~~---------  291 (666)
                            .....+..++...              +.+.+|+|||++.+.... .+.+...+....     ..         
T Consensus        67 ------~~~~~l~~~l~~~--------------~~~~vl~iDEi~~l~~~~-~e~l~~~~~~~~~~~v~~~~~~~~~~~~  125 (305)
T TIGR00635        67 ------EKPGDLAAILTNL--------------EEGDVLFIDEIHRLSPAV-EELLYPAMEDFRLDIVIGKGPSARSVRL  125 (305)
T ss_pred             ------cCchhHHHHHHhc--------------ccCCEEEEehHhhhCHHH-HHHhhHHHhhhheeeeeccCccccceee
Confidence                  0112233333221              123599999999876432 222322222111     00         


Q ss_pred             CCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCc
Q 005987          292 THIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASGGD  371 (666)
Q Consensus       292 ~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~s~GD  371 (666)
                      ...|.+ ++..++...      .....++   +| ....+.|.+++.+++.++|++++...++.+++++++.|++.++||
T Consensus       126 ~~~~~~-li~~t~~~~------~l~~~l~---sR-~~~~~~l~~l~~~e~~~il~~~~~~~~~~~~~~al~~ia~~~~G~  194 (305)
T TIGR00635       126 DLPPFT-LVGATTRAG------MLTSPLR---DR-FGIILRLEFYTVEELAEIVSRSAGLLNVEIEPEAALEIARRSRGT  194 (305)
T ss_pred             cCCCeE-EEEecCCcc------ccCHHHH---hh-cceEEEeCCCCHHHHHHHHHHHHHHhCCCcCHHHHHHHHHHhCCC
Confidence            011233 333222111      1111222   22 235789999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHh
Q 005987          372 IRQAITSLQFSS  383 (666)
Q Consensus       372 IR~AIn~LQf~~  383 (666)
                      +|.+++.+..+.
T Consensus       195 pR~~~~ll~~~~  206 (305)
T TIGR00635       195 PRIANRLLRRVR  206 (305)
T ss_pred             cchHHHHHHHHH
Confidence            999998887653

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.

>PTZ00112 origin recognition complex 1 protein; Provisional

Probab=99.71  E-value=4.1e-16  Score=176.89  Aligned_cols=218  Identities=18%  Similarity=0.284  Sum_probs=139.0

Q ss_pred             ccccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc----------CCcEE
Q 005987          138 LWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL----------GARLY  207 (666)
Q Consensus       138 ~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel----------g~~vi  207 (666)
                      .+-.-|.|   +.|.++++.+++|..+|..++..   ..+.++|+|+||||||||++++.+++++          .+.++
T Consensus       747 vL~~DYVP---D~LPhREeEIeeLasfL~paIkg---sgpnnvLYIyG~PGTGKTATVK~VLrELqeeaeqk~lp~f~vV  820 (1164)
T PTZ00112        747 MMQLDVVP---KYLPCREKEIKEVHGFLESGIKQ---SGSNQILYISGMPGTGKTATVYSVIQLLQHKTKQKLLPSFNVF  820 (1164)
T ss_pred             HcCcccCC---CcCCChHHHHHHHHHHHHHHHhc---CCCCceEEEECCCCCCHHHHHHHHHHHHHHHHhhccCCCceEE
Confidence            45667888   56799999999999999988763   3333567899999999999999998877          36788


Q ss_pred             EEcCCCch----hhhhhhhcccCCccc---cchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHH
Q 005987          208 EWDTPTPT----IWQEYMHNCKTGLEY---TSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFER  280 (666)
Q Consensus       208 E~nasd~~----~~~e~l~~~~~g~~~---~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~  280 (666)
                      ++|+....    .+...... ..+...   .+..+.+..++..+..          ..+...||+|||+|.+....    
T Consensus       821 YINCm~Lstp~sIYqvI~qq-L~g~~P~~GlsS~evLerLF~~L~k----------~~r~v~IIILDEID~L~kK~----  885 (1164)
T PTZ00112        821 EINGMNVVHPNAAYQVLYKQ-LFNKKPPNALNSFKILDRLFNQNKK----------DNRNVSILIIDEIDYLITKT----  885 (1164)
T ss_pred             EEeCCccCCHHHHHHHHHHH-HcCCCCCccccHHHHHHHHHhhhhc----------ccccceEEEeehHhhhCccH----
Confidence            99985421    12221111 111111   1122333333333211          11224599999999886532    


Q ss_pred             HHHHHHHHHhc---CCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCC
Q 005987          281 LRQCLLLLVRS---THIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLS  357 (666)
Q Consensus       281 l~~~L~~l~~~---~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~  357 (666)
                       +++|..+++.   ....++ +++.++.   .+...+..+.+++.   .+...|.|.|++.+++..+|...+......++
T Consensus       886 -QDVLYnLFR~~~~s~SKLi-LIGISNd---lDLperLdPRLRSR---Lg~eeIvF~PYTaEQL~dILk~RAe~A~gVLd  957 (1164)
T PTZ00112        886 -QKVLFTLFDWPTKINSKLV-LIAISNT---MDLPERLIPRCRSR---LAFGRLVFSPYKGDEIEKIIKERLENCKEIID  957 (1164)
T ss_pred             -HHHHHHHHHHhhccCCeEE-EEEecCc---hhcchhhhhhhhhc---cccccccCCCCCHHHHHHHHHHHHHhCCCCCC
Confidence             1223333321   112222 2222221   12223333444443   23456999999999999999999886555689


Q ss_pred             HHHHHHHHH---HcCCcHHHHHHHHHHHhc
Q 005987          358 TEQIDLVAQ---ASGGDIRQAITSLQFSSL  384 (666)
Q Consensus       358 ~~~l~~Ia~---~s~GDIR~AIn~LQf~~~  384 (666)
                      +++|+.||.   ...||+|.||+.|..+..
T Consensus       958 DdAIELIArkVAq~SGDARKALDILRrAgE  987 (1164)
T PTZ00112        958 HTAIQLCARKVANVSGDIRKALQICRKAFE  987 (1164)
T ss_pred             HHHHHHHHHhhhhcCCHHHHHHHHHHHHHh
Confidence            999999998   678999999999998764

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

Probab=99.71  E-value=3.7e-16  Score=156.95  Aligned_cols=194  Identities=18%  Similarity=0.242  Sum_probs=140.6

Q ss_pred             cccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCchhhh
Q 005987          139 WAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTIWQ  218 (666)
Q Consensus       139 W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~~~~  218 (666)
                      .-...||++++|++||++..+.+.-+++.....  +. ..-++||+||||.||||+|+.+|+|+|..+.....|.     
T Consensus        16 ~e~~lRP~~l~efiGQ~~vk~~L~ifI~AAk~r--~e-~lDHvLl~GPPGlGKTTLA~IIA~Emgvn~k~tsGp~-----   87 (332)
T COG2255          16 IERSLRPKTLDEFIGQEKVKEQLQIFIKAAKKR--GE-ALDHVLLFGPPGLGKTTLAHIIANELGVNLKITSGPA-----   87 (332)
T ss_pred             hhcccCcccHHHhcChHHHHHHHHHHHHHHHhc--CC-CcCeEEeeCCCCCcHHHHHHHHHHHhcCCeEeccccc-----
Confidence            445679999999999999999999999976542  22 2258999999999999999999999998876555442     


Q ss_pred             hhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcC------
Q 005987          219 EYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRST------  292 (666)
Q Consensus       219 e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~------  292 (666)
                                  -.+..++..++..+              ...-|+||||++.++..     +.+.|+..++.-      
T Consensus        88 ------------leK~gDlaaiLt~L--------------e~~DVLFIDEIHrl~~~-----vEE~LYpaMEDf~lDI~I  136 (332)
T COG2255          88 ------------LEKPGDLAAILTNL--------------EEGDVLFIDEIHRLSPA-----VEEVLYPAMEDFRLDIII  136 (332)
T ss_pred             ------------ccChhhHHHHHhcC--------------CcCCeEEEehhhhcChh-----HHHHhhhhhhheeEEEEE
Confidence                        11222333333322              13459999999988642     223444444331      


Q ss_pred             -----------CCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHH
Q 005987          293 -----------HIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQI  361 (666)
Q Consensus       293 -----------~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l  361 (666)
                                 ..|-+-++++++....      .-.+|+..    .....+++-++.+++.+++.+-+...++.+++++.
T Consensus       137 G~gp~Arsv~ldLppFTLIGATTr~G~------lt~PLrdR----FGi~~rlefY~~~eL~~Iv~r~a~~l~i~i~~~~a  206 (332)
T COG2255         137 GKGPAARSIRLDLPPFTLIGATTRAGM------LTNPLRDR----FGIIQRLEFYTVEELEEIVKRSAKILGIEIDEEAA  206 (332)
T ss_pred             ccCCccceEeccCCCeeEeeecccccc------ccchhHHh----cCCeeeeecCCHHHHHHHHHHHHHHhCCCCChHHH
Confidence                       2244445555443221      22345553    35578999999999999999999999999999999


Q ss_pred             HHHHHHcCCcHHHHHHHHHH
Q 005987          362 DLVAQASGGDIRQAITSLQF  381 (666)
Q Consensus       362 ~~Ia~~s~GDIR~AIn~LQf  381 (666)
                      ..||..|.|-.|-|.+.|.-
T Consensus       207 ~eIA~rSRGTPRIAnRLLrR  226 (332)
T COG2255         207 LEIARRSRGTPRIANRLLRR  226 (332)
T ss_pred             HHHHHhccCCcHHHHHHHHH
Confidence            99999999999999998854

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

Probab=99.69  E-value=1.6e-16  Score=169.24  Aligned_cols=199  Identities=18%  Similarity=0.256  Sum_probs=140.2

Q ss_pred             cccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcC------------------------C
Q 005987          149 EELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLG------------------------A  204 (666)
Q Consensus       149 ~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg------------------------~  204 (666)
                      +++++++..+.++..|...+     ++.+ +.+||+||||+||||+|.++|+++.                        .
T Consensus         1 ~~~~~~~~~~~~l~~~~~~~-----~~~~-halL~~Gp~G~Gktt~a~~lA~~l~~~~~~~~~~~~~~~~~~~~~~~~~~   74 (325)
T COG0470           1 DELVPWQEAVKRLLVQALES-----GRLP-HALLFYGPPGVGKTTAALALAKELLCENPTGLLPCGHCRSCKLIPAGNHP   74 (325)
T ss_pred             CCcccchhHHHHHHHHHHhc-----CCCC-ceeeeeCCCCCCHHHHHHHHHHHHhCCCcccCCcccchhhhhHHhhcCCC
Confidence            46789999999999999975     4444 4699999999999999999999997                        6


Q ss_pred             cEEEEcCCCchhhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHH
Q 005987          205 RLYEWDTPTPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQC  284 (666)
Q Consensus       205 ~viE~nasd~~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~  284 (666)
                      +++|+++++.+.           ..  -..+.++++.+.....        +.....+||||||+|.+...     ..++
T Consensus        75 d~lel~~s~~~~-----------~~--i~~~~vr~~~~~~~~~--------~~~~~~kviiidead~mt~~-----A~na  128 (325)
T COG0470          75 DFLELNPSDLRK-----------ID--IIVEQVRELAEFLSES--------PLEGGYKVVIIDEADKLTED-----AANA  128 (325)
T ss_pred             ceEEecccccCC-----------Cc--chHHHHHHHHHHhccC--------CCCCCceEEEeCcHHHHhHH-----HHHH
Confidence            888888887331           10  1223344444333211        11234679999999988642     2344


Q ss_pred             HHHHHhcCC--CceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHH
Q 005987          285 LLLLVRSTH--IPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQID  362 (666)
Q Consensus       285 L~~l~~~~~--~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~  362 (666)
                      ++..++...  .|+|++++.         ..+.+++|++     ||..|.|+|      .+.+..|+..+     ++.+.
T Consensus       129 llk~lEep~~~~~~il~~n~---------~~~il~tI~S-----Rc~~i~f~~------~~~~~~i~~~e-----~~~l~  183 (325)
T COG0470         129 LLKTLEEPPKNTRFILITND---------PSKILPTIRS-----RCQRIRFKP------PSRLEAIAWLE-----DQGLE  183 (325)
T ss_pred             HHHHhccCCCCeEEEEEcCC---------hhhccchhhh-----cceeeecCC------chHHHHHHHhh-----ccchh
Confidence            555555543  344444332         2345555665     699999999      45666676666     77889


Q ss_pred             HHHHHcCCcHHHHHHHHHHHhcCCCCcccccccCCCCCCCccccCCCCCcccccCCccccchHHHHhHHhhCCC
Q 005987          363 LVAQASGGDIRQAITSLQFSSLKQDPMLNLSLSISKPNFPEEKADGHGGFSIQFGRDETLSLFHALGKFLHNKR  436 (666)
Q Consensus       363 ~Ia~~s~GDIR~AIn~LQf~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~~~~~RD~~l~lFhalGkil~~Kr  436 (666)
                      .++..+.||+|++||.||..+..                                ++.....|+++..+++...
T Consensus       184 ~i~~~~~gd~r~~i~~lq~~~~~--------------------------------~~~~~~~~~~~~~~~~~~~  225 (325)
T COG0470         184 EIAAVAEGDARKAINPLQALAAL--------------------------------EIGEESIYEALLLALPESL  225 (325)
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHh--------------------------------cccHHHHHHHHHhhChhhc
Confidence            99999999999999999999863                                3345678888888888654

>PRK06893 DNA replication initiation factor; Validated

Probab=99.67  E-value=2.3e-15  Score=152.93  Aligned_cols=194  Identities=14%  Similarity=0.168  Sum_probs=123.6

Q ss_pred             CCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcCCCchhhhhh
Q 005987          144 KPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL---GARLYEWDTPTPTIWQEY  220 (666)
Q Consensus       144 ~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~nasd~~~~~e~  220 (666)
                      .|.+|+++++++.. ..+..+.+.+ .   .... +.++|+||||||||++++++|+++   +..+..++....      
T Consensus        11 ~~~~fd~f~~~~~~-~~~~~~~~~~-~---~~~~-~~l~l~G~~G~GKThL~~ai~~~~~~~~~~~~y~~~~~~------   78 (229)
T PRK06893         11 DDETLDNFYADNNL-LLLDSLRKNF-I---DLQQ-PFFYIWGGKSSGKSHLLKAVSNHYLLNQRTAIYIPLSKS------   78 (229)
T ss_pred             CcccccccccCChH-HHHHHHHHHh-h---ccCC-CeEEEECCCCCCHHHHHHHHHHHHHHcCCCeEEeeHHHh------
Confidence            46789999977643 2333333332 2   1111 468999999999999999999986   334443332110      


Q ss_pred             hhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHH-HHHHHHHHHHhcCCCceEEE
Q 005987          221 MHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFE-RLRQCLLLLVRSTHIPTAVV  299 (666)
Q Consensus       221 l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~-~l~~~L~~l~~~~~~PiViI  299 (666)
                                   ......+++...              ...+|+|||++.+.+..... .+...+....+.+ .+++++
T Consensus        79 -------------~~~~~~~~~~~~--------------~~dlLilDDi~~~~~~~~~~~~l~~l~n~~~~~~-~~illi  130 (229)
T PRK06893         79 -------------QYFSPAVLENLE--------------QQDLVCLDDLQAVIGNEEWELAIFDLFNRIKEQG-KTLLLI  130 (229)
T ss_pred             -------------hhhhHHHHhhcc--------------cCCEEEEeChhhhcCChHHHHHHHHHHHHHHHcC-CcEEEE
Confidence                         000012222221              23499999999875433222 2334344443333 344444


Q ss_pred             EecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCcHHHHHHHH
Q 005987          300 LTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASGGDIRQAITSL  379 (666)
Q Consensus       300 it~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~s~GDIR~AIn~L  379 (666)
                      .++.. +..++   -.++.|++++..  +..+++++|+.+++.++|++.+..+++.++++++++|+..+.||+|.+++.|
T Consensus       131 ts~~~-p~~l~---~~~~~L~sRl~~--g~~~~l~~pd~e~~~~iL~~~a~~~~l~l~~~v~~~L~~~~~~d~r~l~~~l  204 (229)
T PRK06893        131 SADCS-PHALS---IKLPDLASRLTW--GEIYQLNDLTDEQKIIVLQRNAYQRGIELSDEVANFLLKRLDRDMHTLFDAL  204 (229)
T ss_pred             eCCCC-hHHcc---ccchhHHHHHhc--CCeeeCCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhccCCHHHHHHHH
Confidence            44432 22111   123456665442  5688999999999999999999999999999999999999999999999999


Q ss_pred             HHHh
Q 005987          380 QFSS  383 (666)
Q Consensus       380 Qf~~  383 (666)
                      +-+.
T Consensus       205 ~~l~  208 (229)
T PRK06893        205 DLLD  208 (229)
T ss_pred             HHHH
Confidence            8653

>PRK09112 DNA polymerase III subunit delta'; Validated

Probab=99.67  E-value=3.7e-15  Score=159.97  Aligned_cols=205  Identities=16%  Similarity=0.246  Sum_probs=133.6

Q ss_pred             ccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcE------EEEc-CCCc
Q 005987          142 KYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARL------YEWD-TPTP  214 (666)
Q Consensus       142 KY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~v------iE~n-asd~  214 (666)
                      ...|+.+.+|+||++.++.+...+..      |+.+ +.+||+||+|+||||+|+.+|+.+.+.-      .... +...
T Consensus        16 ~~~P~~~~~l~Gh~~a~~~L~~a~~~------grl~-ha~L~~G~~G~GKttlA~~lA~~Llc~~~~~~~~~~~~~~~~~   88 (351)
T PRK09112         16 VPSPSENTRLFGHEEAEAFLAQAYRE------GKLH-HALLFEGPEGIGKATLAFHLANHILSHPDPAEAPETLADPDPA   88 (351)
T ss_pred             CCCCCchhhccCcHHHHHHHHHHHHc------CCCC-eeEeeECCCCCCHHHHHHHHHHHHcCCCccccCccccCCCCCC
Confidence            37899999999999999999999886      7766 7899999999999999999999996521      1111 1111


Q ss_pred             hhhhhhhh-cccCCc--------------cccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHH
Q 005987          215 TIWQEYMH-NCKTGL--------------EYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFE  279 (666)
Q Consensus       215 ~~~~e~l~-~~~~g~--------------~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~  279 (666)
                      +.....+. ....++              ...-.+++++.+.+......        ..+..+|+||||++.++... .+
T Consensus        89 c~~c~~i~~~~hPdl~~l~~~~~~~~~~~~~~I~vd~iR~l~~~l~~~~--------~~g~~rVviIDeAd~l~~~a-an  159 (351)
T PRK09112         89 SPVWRQIAQGAHPNLLHITRPFDEKTGKFKTAITVDEIRRVGHFLSQTS--------GDGNWRIVIIDPADDMNRNA-AN  159 (351)
T ss_pred             CHHHHHHHcCCCCCEEEeecccccccccccccCCHHHHHHHHHHhhhcc--------ccCCceEEEEEchhhcCHHH-HH
Confidence            11111110 000000              00111344444333222110        11245799999999986432 23


Q ss_pred             HHHHHHHHHHhcCC-CceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCH
Q 005987          280 RLRQCLLLLVRSTH-IPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLST  358 (666)
Q Consensus       280 ~l~~~L~~l~~~~~-~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~  358 (666)
                          +|+..++... ..+++++++.        ..+.++.+++     ||..++|.|++.+++.++|...+...+  +++
T Consensus       160 ----aLLk~LEEpp~~~~fiLit~~--------~~~llptIrS-----Rc~~i~l~pl~~~~~~~~L~~~~~~~~--~~~  220 (351)
T PRK09112        160 ----AILKTLEEPPARALFILISHS--------SGRLLPTIRS-----RCQPISLKPLDDDELKKALSHLGSSQG--SDG  220 (351)
T ss_pred             ----HHHHHHhcCCCCceEEEEECC--------hhhccHHHHh-----hccEEEecCCCHHHHHHHHHHhhcccC--CCH
Confidence                3555555532 3455555541        1233444443     599999999999999999998664444  778


Q ss_pred             HHHHHHHHHcCCcHHHHHHHHHH
Q 005987          359 EQIDLVAQASGGDIRQAITSLQF  381 (666)
Q Consensus       359 ~~l~~Ia~~s~GDIR~AIn~LQf  381 (666)
                      +++..|+..++|++|.|++.|+.
T Consensus       221 ~~~~~i~~~s~G~pr~Al~ll~~  243 (351)
T PRK09112        221 EITEALLQRSKGSVRKALLLLNY  243 (351)
T ss_pred             HHHHHHHHHcCCCHHHHHHHHhc
Confidence            99999999999999999988754

>PRK08084 DNA replication initiation factor; Provisional

Probab=99.66  E-value=8.1e-15  Score=149.49  Aligned_cols=189  Identities=10%  Similarity=0.149  Sum_probs=126.5

Q ss_pred             Cccccc--cCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcCCCchhhhhhh
Q 005987          147 SLEELA--VQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL---GARLYEWDTPTPTIWQEYM  221 (666)
Q Consensus       147 sl~eLv--g~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~nasd~~~~~e~l  221 (666)
                      +|++++  .+...+..+..|...+      .  .+.++|+||||||||++++++|+++   |..+..++....       
T Consensus        20 ~fd~f~~~~n~~a~~~l~~~~~~~------~--~~~l~l~Gp~G~GKThLl~a~~~~~~~~~~~v~y~~~~~~-------   84 (235)
T PRK08084         20 TFASFYPGDNDSLLAALQNALRQE------H--SGYIYLWSREGAGRSHLLHAACAELSQRGRAVGYVPLDKR-------   84 (235)
T ss_pred             CccccccCccHHHHHHHHHHHhCC------C--CCeEEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEEHHHH-------
Confidence            566666  4666777777766432      1  1479999999999999999999976   344444443110       


Q ss_pred             hcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhH-HHHHHHHHHHHHhcCCCceEEEE
Q 005987          222 HNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTA-FERLRQCLLLLVRSTHIPTAVVL  300 (666)
Q Consensus       222 ~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~-~~~l~~~L~~l~~~~~~PiViIi  300 (666)
                               ..   ...++++....              ..+|+|||++.+.+... ...+...+....+.++. .++++
T Consensus        85 ---------~~---~~~~~~~~~~~--------------~dlliiDdi~~~~~~~~~~~~lf~l~n~~~e~g~~-~li~t  137 (235)
T PRK08084         85 ---------AW---FVPEVLEGMEQ--------------LSLVCIDNIECIAGDELWEMAIFDLYNRILESGRT-RLLIT  137 (235)
T ss_pred             ---------hh---hhHHHHHHhhh--------------CCEEEEeChhhhcCCHHHHHHHHHHHHHHHHcCCC-eEEEe
Confidence                     00   01122222211              13899999998765332 23344555566555443 34455


Q ss_pred             ecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCcHHHHHHHHH
Q 005987          301 TECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASGGDIRQAITSLQ  380 (666)
Q Consensus       301 t~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~s~GDIR~AIn~LQ  380 (666)
                      ++ ..+..+   ...++.|++++..  +.++.+.+|+.+++.++|++.+..+++.++++++++|+..+.||+|.+++.|+
T Consensus       138 s~-~~p~~l---~~~~~~L~SRl~~--g~~~~l~~~~~~~~~~~l~~~a~~~~~~l~~~v~~~L~~~~~~d~r~l~~~l~  211 (235)
T PRK08084        138 GD-RPPRQL---NLGLPDLASRLDW--GQIYKLQPLSDEEKLQALQLRARLRGFELPEDVGRFLLKRLDREMRTLFMTLD  211 (235)
T ss_pred             CC-CChHHc---CcccHHHHHHHhC--CceeeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhhcCCHHHHHHHHH
Confidence            54 222111   1134567776543  58999999999999999999898899999999999999999999999999998


Q ss_pred             HHh
Q 005987          381 FSS  383 (666)
Q Consensus       381 f~~  383 (666)
                      .+-
T Consensus       212 ~l~  214 (235)
T PRK08084        212 QLD  214 (235)
T ss_pred             HHH
Confidence            753

>TIGR02881 spore_V_K stage V sporulation protein K

Probab=99.66  E-value=4.5e-15  Score=153.88  Aligned_cols=206  Identities=12%  Similarity=0.145  Sum_probs=124.9

Q ss_pred             CccccccCHHHHHHHH---HHHHHhhc----CCCCCCCccEEEEECCCCchHHHHHHHHHHHc---C----CcEEEEcCC
Q 005987          147 SLEELAVQRKKVEEVR---AWFEERLG----DSKDKFSTNVLVITGQAGVGKTATVRQIASHL---G----ARLYEWDTP  212 (666)
Q Consensus       147 sl~eLvg~~k~i~el~---~wL~~~~~----~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel---g----~~viE~nas  212 (666)
                      .+++|+|.+.+.+.|+   .|++....    +........++||+|||||||||+|+++|+++   +    ..+++++++
T Consensus         4 ~l~~~~Gl~~vk~~i~~~~~~~~~~~~~~~~g~~~~~~~~~vll~GppGtGKTtlA~~ia~~l~~~~~~~~~~~v~~~~~   83 (261)
T TIGR02881         4 ELSRMVGLDEVKALIKEIYAWIQINEKRKEEGLKTSKQVLHMIFKGNPGTGKTTVARILGKLFKEMNVLSKGHLIEVERA   83 (261)
T ss_pred             HHHHhcChHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCcceEEEEcCCCCCHHHHHHHHHHHHHhcCcccCCceEEecHH
Confidence            3577889877766665   44432111    11111122479999999999999999999986   2    245555443


Q ss_pred             CchhhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcch--hHHH-HHHHHHHHHH
Q 005987          213 TPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGR--TAFE-RLRQCLLLLV  289 (666)
Q Consensus       213 d~~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~--~~~~-~l~~~L~~l~  289 (666)
                      +.           .+..+........++++++.               +.||||||++.+...  ..+. ...+.|...+
T Consensus        84 ~l-----------~~~~~g~~~~~~~~~~~~a~---------------~~VL~IDE~~~L~~~~~~~~~~~~i~~Ll~~~  137 (261)
T TIGR02881        84 DL-----------VGEYIGHTAQKTREVIKKAL---------------GGVLFIDEAYSLARGGEKDFGKEAIDTLVKGM  137 (261)
T ss_pred             Hh-----------hhhhccchHHHHHHHHHhcc---------------CCEEEEechhhhccCCccchHHHHHHHHHHHH
Confidence            31           11111112233344444331               249999999987421  1111 2334455666


Q ss_pred             hcCCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHH--
Q 005987          290 RSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQA--  367 (666)
Q Consensus       290 ~~~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~--  367 (666)
                      +..+..+++|++....  ..+.....-   +.+.+| ....|.|++++.+++.+++++++...++.++++++..|++.  
T Consensus       138 e~~~~~~~vila~~~~--~~~~~~~~~---p~L~sR-f~~~i~f~~~~~~el~~Il~~~~~~~~~~l~~~a~~~l~~~~~  211 (261)
T TIGR02881       138 EDNRNEFVLILAGYSD--EMDYFLSLN---PGLRSR-FPISIDFPDYTVEELMEIAERMVKEREYKLTEEAKWKLREHLY  211 (261)
T ss_pred             hccCCCEEEEecCCcc--hhHHHHhcC---hHHHhc-cceEEEECCCCHHHHHHHHHHHHHHcCCccCHHHHHHHHHHHH
Confidence            6555555555543221  111111111   222222 13679999999999999999999999999999999888653  


Q ss_pred             --------cCCcHHHHHHHHHHHhc
Q 005987          368 --------SGGDIRQAITSLQFSSL  384 (666)
Q Consensus       368 --------s~GDIR~AIn~LQf~~~  384 (666)
                              +.||.|.+.|.++.+..
T Consensus       212 ~~~~~~~~~~gn~R~~~n~~e~a~~  236 (261)
T TIGR02881       212 KVDQLSSREFSNARYVRNIIEKAIR  236 (261)
T ss_pred             HHHhccCCCCchHHHHHHHHHHHHH
Confidence                    36999999999998764

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.

>TIGR02902 spore_lonB ATP-dependent protease LonB

Probab=99.65  E-value=1.6e-15  Score=171.74  Aligned_cols=221  Identities=19%  Similarity=0.297  Sum_probs=134.9

Q ss_pred             CCccccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc----------CCc
Q 005987          136 QQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL----------GAR  205 (666)
Q Consensus       136 ~~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel----------g~~  205 (666)
                      +++|.+||||++|++++|++..++.++..+..      .. + .++||+||||||||++|+++.++.          +..
T Consensus        52 ~~~~~~~~rp~~f~~iiGqs~~i~~l~~al~~------~~-~-~~vLi~Ge~GtGKt~lAr~i~~~~~~~~~s~~~~~~~  123 (531)
T TIGR02902        52 TEPLSEKTRPKSFDEIIGQEEGIKALKAALCG------PN-P-QHVIIYGPPGVGKTAAARLVLEEAKKNPASPFKEGAA  123 (531)
T ss_pred             cchHHHhhCcCCHHHeeCcHHHHHHHHHHHhC------CC-C-ceEEEECCCCCCHHHHHHHHHHHhhhccCCCcCCCCC
Confidence            67899999999999999999999999876532      22 2 479999999999999999998753          246


Q ss_pred             EEEEcCCCchhhhhhhhcccCCccccchhHHHHHHHHHHHhhc--CCCCCCCC--CCCCceEEEEeCCCCCcchhHHHHH
Q 005987          206 LYEWDTPTPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYG--STSPSIPG--ESKSSAILLIDDLPVTNGRTAFERL  281 (666)
Q Consensus       206 viE~nasd~~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~--~l~~s~~~--~~~~~~IIlIDEid~l~~~~~~~~l  281 (666)
                      ++++++...+.....+.+...|..    .+-   +...+..++  ..+....|  ......+|+|||++.++.. ..+.+
T Consensus       124 fi~id~~~~~~~~~~~~~~li~~~----~~p---~~~~~~~~g~~g~~~~~~G~l~~a~gG~L~IdEI~~L~~~-~q~~L  195 (531)
T TIGR02902       124 FVEIDATTARFDERGIADPLIGSV----HDP---IYQGAGPLGIAGIPQPKPGAVTRAHGGVLFIDEIGELHPV-QMNKL  195 (531)
T ss_pred             EEEEccccccCCccccchhhcCCc----ccc---hhccccccccCCcccccCchhhccCCcEEEEechhhCCHH-HHHHH
Confidence            788886531100000000000000    000   000000000  00000000  0112459999999998653 23444


Q ss_pred             HHHHHHH---Hh-----c--------------CCCc--eEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCC
Q 005987          282 RQCLLLL---VR-----S--------------THIP--TAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPIT  337 (666)
Q Consensus       282 ~~~L~~l---~~-----~--------------~~~P--iViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s  337 (666)
                      ...|..-   +.     .              ...|  +.+|++++....      ...+.+++     ||..|.|.+++
T Consensus       196 L~~Le~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~rlI~ATt~~p~------~L~paLrs-----R~~~I~f~pL~  264 (531)
T TIGR02902       196 LKVLEDRKVFLDSAYYNSENPNIPSHIHDIFQNGLPADFRLIGATTRNPE------EIPPALRS-----RCVEIFFRPLL  264 (531)
T ss_pred             HHHHHhCeeeeccccccccCcccccchhhhcccCcccceEEEEEecCCcc------cCChHHhh-----hhheeeCCCCC
Confidence            3333220   00     0              0111  223333222111      12223332     58999999999


Q ss_pred             HHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCcHHHHHHHHHHHhc
Q 005987          338 NGSIKRTLSKICRQEQYSLSTEQIDLVAQASGGDIRQAITSLQFSSL  384 (666)
Q Consensus       338 ~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~s~GDIR~AIn~LQf~~~  384 (666)
                      .+++..++++.+.+.++.+++++++.|+..+. |.|.++|.+|.++.
T Consensus       265 ~eei~~Il~~~a~k~~i~is~~al~~I~~y~~-n~Rel~nll~~Aa~  310 (531)
T TIGR02902       265 DEEIKEIAKNAAEKIGINLEKHALELIVKYAS-NGREAVNIVQLAAG  310 (531)
T ss_pred             HHHHHHHHHHHHHHcCCCcCHHHHHHHHHhhh-hHHHHHHHHHHHHH
Confidence            99999999999999999999999999988774 99999999999874

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.

>PRK08727 hypothetical protein; Validated

Probab=99.65  E-value=1.5e-14  Score=147.41  Aligned_cols=189  Identities=14%  Similarity=0.165  Sum_probs=121.3

Q ss_pred             CCccccccCHH-HHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcCCCchhhhhhh
Q 005987          146 RSLEELAVQRK-KVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL---GARLYEWDTPTPTIWQEYM  221 (666)
Q Consensus       146 ~sl~eLvg~~k-~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~nasd~~~~~e~l  221 (666)
                      .+|+++++.+. .+..+..+..       +.. .+.++|+||+|||||+++++++.++   |..++.++..+        
T Consensus        16 ~~f~~f~~~~~n~~~~~~~~~~-------~~~-~~~l~l~G~~G~GKThL~~a~~~~~~~~~~~~~y~~~~~--------   79 (233)
T PRK08727         16 QRFDSYIAAPDGLLAQLQALAA-------GQS-SDWLYLSGPAGTGKTHLALALCAAAEQAGRSSAYLPLQA--------   79 (233)
T ss_pred             CChhhccCCcHHHHHHHHHHHh-------ccC-CCeEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEEeHHH--------
Confidence            36777776543 3333332221       222 2579999999999999999998775   55555554321        


Q ss_pred             hcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHH-HHHHHHHHHHHhcCCCceEEEE
Q 005987          222 HNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAF-ERLRQCLLLLVRSTHIPTAVVL  300 (666)
Q Consensus       222 ~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~-~~l~~~L~~l~~~~~~PiViIi  300 (666)
                                 ....+.++++....              .-+|+|||++.+.+.... ..+...+....+ .+.+ ++++
T Consensus        80 -----------~~~~~~~~~~~l~~--------------~dlLiIDDi~~l~~~~~~~~~lf~l~n~~~~-~~~~-vI~t  132 (233)
T PRK08727         80 -----------AAGRLRDALEALEG--------------RSLVALDGLESIAGQREDEVALFDFHNRARA-AGIT-LLYT  132 (233)
T ss_pred             -----------hhhhHHHHHHHHhc--------------CCEEEEeCcccccCChHHHHHHHHHHHHHHH-cCCe-EEEE
Confidence                       01122333333322              238999999987643221 122232222222 2233 4444


Q ss_pred             ecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCcHHHHHHHHH
Q 005987          301 TECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASGGDIRQAITSLQ  380 (666)
Q Consensus       301 t~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~s~GDIR~AIn~LQ  380 (666)
                      ++.. +..   ....++.|++.+..  +..+.|++|+.+++..+|+++|..+++.+++++++.|++.++||+|.+++.|+
T Consensus       133 s~~~-p~~---l~~~~~dL~SRl~~--~~~~~l~~~~~e~~~~iL~~~a~~~~l~l~~e~~~~La~~~~rd~r~~l~~L~  206 (233)
T PRK08727        133 ARQM-PDG---LALVLPDLRSRLAQ--CIRIGLPVLDDVARAAVLRERAQRRGLALDEAAIDWLLTHGERELAGLVALLD  206 (233)
T ss_pred             CCCC-hhh---hhhhhHHHHHHHhc--CceEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhCCCCHHHHHHHHH
Confidence            4422 111   12234566666543  78999999999999999999999999999999999999999999999999998


Q ss_pred             HHh
Q 005987          381 FSS  383 (666)
Q Consensus       381 f~~  383 (666)
                      .+-
T Consensus       207 ~l~  209 (233)
T PRK08727        207 RLD  209 (233)
T ss_pred             HHH
Confidence            653

>PRK07940 DNA polymerase III subunit delta'; Validated

Probab=99.63  E-value=1.2e-14  Score=158.15  Aligned_cols=202  Identities=20%  Similarity=0.210  Sum_probs=127.4

Q ss_pred             CccccccCHHHHHHHHHHHHHhhcC---CCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCchhhhhhhh-
Q 005987          147 SLEELAVQRKKVEEVRAWFEERLGD---SKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTIWQEYMH-  222 (666)
Q Consensus       147 sl~eLvg~~k~i~el~~wL~~~~~~---~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~~~~e~l~-  222 (666)
                      .+++|+||++.++.+++++......   ..++.+ +.+||+||||+|||++|+.+|+.+.+.-....+...+..+..+. 
T Consensus         3 ~f~~IiGq~~~~~~L~~~i~~~~~~~~~~~~~l~-ha~Lf~Gp~G~GKt~lA~~lA~~l~c~~~~~~~Cg~C~~C~~~~~   81 (394)
T PRK07940          3 VWDDLVGQEAVVAELRAAARAARADVAAAGSGMT-HAWLFTGPPGSGRSVAARAFAAALQCTDPDEPGCGECRACRTVLA   81 (394)
T ss_pred             hhhhccChHHHHHHHHHHHHhccccccccCCCCC-eEEEEECCCCCcHHHHHHHHHHHhCCCCCCCCCCCCCHHHHHHhc
Confidence            5789999999999999999874311   001234 78999999999999999999999866421100000110000000 


Q ss_pred             cccCCc------cccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcCCCce
Q 005987          223 NCKTGL------EYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHIPT  296 (666)
Q Consensus       223 ~~~~g~------~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~~~Pi  296 (666)
                      .....+      ...-..++++++++.+...+.        ....+|+||||+|.+....     .+.|+..++......
T Consensus        82 ~~hpD~~~i~~~~~~i~i~~iR~l~~~~~~~p~--------~~~~kViiIDead~m~~~a-----anaLLk~LEep~~~~  148 (394)
T PRK07940         82 GTHPDVRVVAPEGLSIGVDEVRELVTIAARRPS--------TGRWRIVVIEDADRLTERA-----ANALLKAVEEPPPRT  148 (394)
T ss_pred             CCCCCEEEeccccccCCHHHHHHHHHHHHhCcc--------cCCcEEEEEechhhcCHHH-----HHHHHHHhhcCCCCC
Confidence            000000      012235667777776643221        1246799999999986432     245666667654444


Q ss_pred             EEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCcHHHHH
Q 005987          297 AVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASGGDIRQAI  376 (666)
Q Consensus       297 ViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~s~GDIR~AI  376 (666)
                      ++|++.++.       ...++.|++     ||..|.|.+|+.+++.+.|.+   ..  .++++.+..++..++|+++.|+
T Consensus       149 ~fIL~a~~~-------~~llpTIrS-----Rc~~i~f~~~~~~~i~~~L~~---~~--~~~~~~a~~la~~s~G~~~~A~  211 (394)
T PRK07940        149 VWLLCAPSP-------EDVLPTIRS-----RCRHVALRTPSVEAVAEVLVR---RD--GVDPETARRAARASQGHIGRAR  211 (394)
T ss_pred             eEEEEECCh-------HHChHHHHh-----hCeEEECCCCCHHHHHHHHHH---hc--CCCHHHHHHHHHHcCCCHHHHH
Confidence            444443221       123333333     599999999999999988873   22  3678889999999999999886


Q ss_pred             HHH
Q 005987          377 TSL  379 (666)
Q Consensus       377 n~L  379 (666)
                      ..+
T Consensus       212 ~l~  214 (394)
T PRK07940        212 RLA  214 (394)
T ss_pred             HHh
Confidence            553

>KOG0733 consensus Nuclear AAA ATPase (VCP subfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=99.62  E-value=1.1e-14  Score=158.48  Aligned_cols=200  Identities=18%  Similarity=0.270  Sum_probs=139.1

Q ss_pred             CccccccCHHHHHHHHHHHHHhhcC----CCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCchhhhhhhh
Q 005987          147 SLEELAVQRKKVEEVRAWFEERLGD----SKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTIWQEYMH  222 (666)
Q Consensus       147 sl~eLvg~~k~i~el~~wL~~~~~~----~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~~~~e~l~  222 (666)
                      +|.+|-|.++.+.+|...+-.....    .-|-.|++.+|||||||||||.+|+++|.+++..++.++++..        
T Consensus       188 ~f~diGG~d~~~~el~~li~~i~~Pe~~~~lGv~PprGvLlHGPPGCGKT~lA~AiAgel~vPf~~isApei--------  259 (802)
T KOG0733|consen  188 SFSDIGGLDKTLAELCELIIHIKHPEVFSSLGVRPPRGVLLHGPPGCGKTSLANAIAGELGVPFLSISAPEI--------  259 (802)
T ss_pred             chhhccChHHHHHHHHHHHHHhcCchhHhhcCCCCCCceeeeCCCCccHHHHHHHHhhhcCCceEeecchhh--------
Confidence            5899999999999999988753221    1255566899999999999999999999999999999999862        


Q ss_pred             cccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchh-----HH-HHHHHHHHHHHhcC----
Q 005987          223 NCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRT-----AF-ERLRQCLLLLVRST----  292 (666)
Q Consensus       223 ~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~-----~~-~~l~~~L~~l~~~~----  292 (666)
                        ..|+. ....+.++++++++..+            .|+|+||||+|-+..+.     .. +++...|+..++.-    
T Consensus       260 --vSGvS-GESEkkiRelF~~A~~~------------aPcivFiDeIDAI~pkRe~aqreMErRiVaQLlt~mD~l~~~~  324 (802)
T KOG0733|consen  260 --VSGVS-GESEKKIRELFDQAKSN------------APCIVFIDEIDAITPKREEAQREMERRIVAQLLTSMDELSNEK  324 (802)
T ss_pred             --hcccC-cccHHHHHHHHHHHhcc------------CCeEEEeecccccccchhhHHHHHHHHHHHHHHHhhhcccccc
Confidence              23332 34567788889888654            37999999999875431     11 12222333333321    


Q ss_pred             --CCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCC
Q 005987          293 --HIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASGG  370 (666)
Q Consensus       293 --~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~s~G  370 (666)
                        .-| |+++++++.+++.|...|+...        .-..|.+.-|+.+...++|+.+|....+.- +-....||..+.|
T Consensus       325 ~~g~~-VlVIgATnRPDslDpaLRRaGR--------FdrEI~l~vP~e~aR~~IL~~~~~~lrl~g-~~d~~qlA~lTPG  394 (802)
T KOG0733|consen  325 TKGDP-VLVIGATNRPDSLDPALRRAGR--------FDREICLGVPSETAREEILRIICRGLRLSG-DFDFKQLAKLTPG  394 (802)
T ss_pred             cCCCC-eEEEecCCCCcccCHHHhcccc--------ccceeeecCCchHHHHHHHHHHHhhCCCCC-CcCHHHHHhcCCC
Confidence              135 5566777777765543332211        134699999999999999999998655443 3345778888877


Q ss_pred             cHHHHHHHH
Q 005987          371 DIRQAITSL  379 (666)
Q Consensus       371 DIR~AIn~L  379 (666)
                      -+-.-+..|
T Consensus       395 fVGADL~AL  403 (802)
T KOG0733|consen  395 FVGADLMAL  403 (802)
T ss_pred             ccchhHHHH
Confidence            655544444

>PRK06620 hypothetical protein; Validated

Probab=99.62  E-value=4.7e-14  Score=141.62  Aligned_cols=188  Identities=14%  Similarity=0.112  Sum_probs=126.0

Q ss_pred             CccccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCchh
Q 005987          137 QLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTI  216 (666)
Q Consensus       137 ~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~~  216 (666)
                      ..|..+|.+.+|-.--.+......++.|.+.|-    ..+..+.++||||||||||++++++|+..+..++.  ...   
T Consensus         7 ~~~~~~~tfd~Fvvg~~N~~a~~~~~~~~~~~~----~~~~~~~l~l~Gp~G~GKThLl~a~~~~~~~~~~~--~~~---   77 (214)
T PRK06620          7 FTTSSKYHPDEFIVSSSNDQAYNIIKNWQCGFG----VNPYKFTLLIKGPSSSGKTYLTKIWQNLSNAYIIK--DIF---   77 (214)
T ss_pred             CCCCCCCCchhhEecccHHHHHHHHHHHHHccc----cCCCcceEEEECCCCCCHHHHHHHHHhccCCEEcc--hhh---
Confidence            345666755555333345667777777776441    11212579999999999999999999987642221  000   


Q ss_pred             hhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcCCCce
Q 005987          217 WQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHIPT  296 (666)
Q Consensus       217 ~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~~~Pi  296 (666)
                                         ....+      +.           ...+++|||++....    ..+...+..+.+.++  .
T Consensus        78 -------------------~~~~~------~~-----------~~d~lliDdi~~~~~----~~lf~l~N~~~e~g~--~  115 (214)
T PRK06620         78 -------------------FNEEI------LE-----------KYNAFIIEDIENWQE----PALLHIFNIINEKQK--Y  115 (214)
T ss_pred             -------------------hchhH------Hh-----------cCCEEEEeccccchH----HHHHHHHHHHHhcCC--E
Confidence                               00011      11           124899999996522    123344444445553  3


Q ss_pred             EEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCcHHHHH
Q 005987          297 AVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASGGDIRQAI  376 (666)
Q Consensus       297 ViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~s~GDIR~AI  376 (666)
                      +++++++.+. .    .. ++.|++++..  +..+.+++|+.+.+..+|++.+...++.+++++++.|+..+.||+|.++
T Consensus       116 ilits~~~p~-~----l~-l~~L~SRl~~--gl~~~l~~pd~~~~~~~l~k~~~~~~l~l~~ev~~~L~~~~~~d~r~l~  187 (214)
T PRK06620        116 LLLTSSDKSR-N----FT-LPDLSSRIKS--VLSILLNSPDDELIKILIFKHFSISSVTISRQIIDFLLVNLPREYSKII  187 (214)
T ss_pred             EEEEcCCCcc-c----cc-hHHHHHHHhC--CceEeeCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHccCCHHHHH
Confidence            4455544332 1    11 3567776653  6689999999999999999999989999999999999999999999999


Q ss_pred             HHHHHHh
Q 005987          377 TSLQFSS  383 (666)
Q Consensus       377 n~LQf~~  383 (666)
                      +.|+.+.
T Consensus       188 ~~l~~l~  194 (214)
T PRK06620        188 EILENIN  194 (214)
T ss_pred             HHHHHHH
Confidence            9998864

>TIGR02928 orc1/cdc6 family replication initiation protein

Probab=99.61  E-value=1.9e-14  Score=156.17  Aligned_cols=220  Identities=17%  Similarity=0.223  Sum_probs=131.1

Q ss_pred             CccccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcC---------CcEE
Q 005987          137 QLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLG---------ARLY  207 (666)
Q Consensus       137 ~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg---------~~vi  207 (666)
                      ......|.|.   +++++++.+++|..+|..+..   +..+ ..++|+||||||||++++.+++++.         +.++
T Consensus         6 ~~l~~~~~p~---~l~gRe~e~~~l~~~l~~~~~---~~~~-~~i~I~G~~GtGKT~l~~~~~~~l~~~~~~~~~~~~~v   78 (365)
T TIGR02928         6 DLLEPDYVPD---RIVHRDEQIEELAKALRPILR---GSRP-SNVFIYGKTGTGKTAVTKYVMKELEEAAEDRDVRVVTV   78 (365)
T ss_pred             hhCCCCCCCC---CCCCcHHHHHHHHHHHHHHHc---CCCC-CcEEEECCCCCCHHHHHHHHHHHHHHHhhccCCceEEE
Confidence            4567889997   569999999999999998765   3222 5799999999999999999998763         5688


Q ss_pred             EEcCCCchhh----hhhhhcccC-Cccc----cchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHH
Q 005987          208 EWDTPTPTIW----QEYMHNCKT-GLEY----TSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAF  278 (666)
Q Consensus       208 E~nasd~~~~----~e~l~~~~~-g~~~----~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~  278 (666)
                      ++|+......    ...+..... |...    .+..+.+..+.+.+...           +++.||+|||+|.+....  
T Consensus        79 ~in~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~l~~~-----------~~~~vlvIDE~d~L~~~~--  145 (365)
T TIGR02928        79 YVNCQILDTLYQVLVELANQLRGSGEEVPTTGLSTSEVFRRLYKELNER-----------GDSLIIVLDEIDYLVGDD--  145 (365)
T ss_pred             EEECCCCCCHHHHHHHHHHHHhhcCCCCCCCCCCHHHHHHHHHHHHHhc-----------CCeEEEEECchhhhccCC--
Confidence            8887653221    111111100 1111    01112233333333211           246799999999885221  


Q ss_pred             HHHHHHHHHHH--hc-CCCceEEE-EecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHH--h
Q 005987          279 ERLRQCLLLLV--RS-THIPTAVV-LTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQ--E  352 (666)
Q Consensus       279 ~~l~~~L~~l~--~~-~~~PiViI-it~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~--e  352 (666)
                      ..+...|..+.  .. ...++++| +++.  ..   ...+....+.   ++.....|.|+|++.+++..+|+..+..  .
T Consensus       146 ~~~L~~l~~~~~~~~~~~~~v~lI~i~n~--~~---~~~~l~~~~~---s~~~~~~i~f~p~~~~e~~~il~~r~~~~~~  217 (365)
T TIGR02928       146 DDLLYQLSRARSNGDLDNAKVGVIGISND--LK---FRENLDPRVK---SSLCEEEIIFPPYDAEELRDILENRAEKAFY  217 (365)
T ss_pred             cHHHHhHhccccccCCCCCeEEEEEEECC--cc---hHhhcCHHHh---ccCCcceeeeCCCCHHHHHHHHHHHHHhhcc
Confidence            11211122221  11 11233322 3321  11   1111111122   2222357999999999999999998863  2


Q ss_pred             CCCCCHHHHHHHH---HHcCCcHHHHHHHHHHHhc
Q 005987          353 QYSLSTEQIDLVA---QASGGDIRQAITSLQFSSL  384 (666)
Q Consensus       353 ~i~v~~~~l~~Ia---~~s~GDIR~AIn~LQf~~~  384 (666)
                      ...+++++++.++   ..+.||+|.|++.|+.++.
T Consensus       218 ~~~~~~~~l~~i~~~~~~~~Gd~R~al~~l~~a~~  252 (365)
T TIGR02928       218 DGVLDDGVIPLCAALAAQEHGDARKAIDLLRVAGE  252 (365)
T ss_pred             CCCCChhHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Confidence            3347888776655   4557999999999987653

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.

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

Probab=99.61  E-value=6.5e-15  Score=145.83  Aligned_cols=199  Identities=15%  Similarity=0.239  Sum_probs=130.8

Q ss_pred             ccccCCCCccccccCHHHHHH---HHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCchh
Q 005987          140 AEKYKPRSLEELAVQRKKVEE---VRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTI  216 (666)
Q Consensus       140 ~eKY~P~sl~eLvg~~k~i~e---l~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~~  216 (666)
                      .+-.+--+++|++||+...+.   |..+|++--.  =|...++.+|||||||+|||.+|++||++....++.++++.   
T Consensus       112 ~e~~~~it~ddViGqEeAK~kcrli~~yLenPe~--Fg~WAPknVLFyGppGTGKTm~Akalane~kvp~l~vkat~---  186 (368)
T COG1223         112 REIISDITLDDVIGQEEAKRKCRLIMEYLENPER--FGDWAPKNVLFYGPPGTGKTMMAKALANEAKVPLLLVKATE---  186 (368)
T ss_pred             hhhhccccHhhhhchHHHHHHHHHHHHHhhChHH--hcccCcceeEEECCCCccHHHHHHHHhcccCCceEEechHH---
Confidence            355566799999999877665   4455543111  14555689999999999999999999999999999998864   


Q ss_pred             hhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHH-------HHHHHHHHH
Q 005987          217 WQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFER-------LRQCLLLLV  289 (666)
Q Consensus       217 ~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~-------l~~~L~~l~  289 (666)
                              ..|-.+.....++.+..+++.+..            |+|++|||+|.+.-...++.       ..++|+.-+
T Consensus       187 --------liGehVGdgar~Ihely~rA~~~a------------PcivFiDE~DAiaLdRryQelRGDVsEiVNALLTel  246 (368)
T COG1223         187 --------LIGEHVGDGARRIHELYERARKAA------------PCIVFIDELDAIALDRRYQELRGDVSEIVNALLTEL  246 (368)
T ss_pred             --------HHHHHhhhHHHHHHHHHHHHHhcC------------CeEEEehhhhhhhhhhhHHHhcccHHHHHHHHHHhc
Confidence                    123333344567888888887653            78999999997643222222       223333332


Q ss_pred             hcCC-CceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHc
Q 005987          290 RSTH-IPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQAS  368 (666)
Q Consensus       290 ~~~~-~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~s  368 (666)
                      +..+ .--|+.++.++.+...|      ..+++.    .-..|.|.-|+.++...+|..-++...+.++.. ++.++..+
T Consensus       247 Dgi~eneGVvtIaaTN~p~~LD------~aiRsR----FEeEIEF~LP~~eEr~~ile~y~k~~Plpv~~~-~~~~~~~t  315 (368)
T COG1223         247 DGIKENEGVVTIAATNRPELLD------PAIRSR----FEEEIEFKLPNDEERLEILEYYAKKFPLPVDAD-LRYLAAKT  315 (368)
T ss_pred             cCcccCCceEEEeecCChhhcC------HHHHhh----hhheeeeeCCChHHHHHHHHHHHHhCCCccccC-HHHHHHHh
Confidence            2211 12234444444433222      123332    345799999999999999999998877776654 67777664


Q ss_pred             ----CCcHHH
Q 005987          369 ----GGDIRQ  374 (666)
Q Consensus       369 ----~GDIR~  374 (666)
                          +.||-.
T Consensus       316 ~g~SgRdike  325 (368)
T COG1223         316 KGMSGRDIKE  325 (368)
T ss_pred             CCCCchhHHH
Confidence                446643

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

Probab=99.59  E-value=1.8e-14  Score=149.15  Aligned_cols=213  Identities=18%  Similarity=0.278  Sum_probs=141.6

Q ss_pred             CccccccCCCCccccccCHHHHHHHHHHHHHhhcCC-----CCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcC
Q 005987          137 QLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDS-----KDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDT  211 (666)
Q Consensus       137 ~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~-----~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~na  211 (666)
                      .+=+++-.-.+++|+-|-++.+++|++.++--+..+     -|--|++.+|||||||||||.+|+++|++.+..++.+..
T Consensus       139 ~M~v~e~PdvtY~dIGGL~~Qi~EirE~VELPL~~PElF~~~GI~PPKGVLLYGPPGTGKTLLAkAVA~~T~AtFIrvvg  218 (406)
T COG1222         139 VMEVEEKPDVTYEDIGGLDEQIQEIREVVELPLKNPELFEELGIDPPKGVLLYGPPGTGKTLLAKAVANQTDATFIRVVG  218 (406)
T ss_pred             eeeeccCCCCChhhccCHHHHHHHHHHHhcccccCHHHHHHcCCCCCCceEeeCCCCCcHHHHHHHHHhccCceEEEecc
Confidence            455666666789999999999999999987544321     144455899999999999999999999999999999988


Q ss_pred             CCchhhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcch------hHHHHHHHHH
Q 005987          212 PTPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGR------TAFERLRQCL  285 (666)
Q Consensus       212 sd~~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~------~~~~~l~~~L  285 (666)
                      |.  ..++++...         ....+++++-|+.            +.|.||||||+|.+.+.      ..-+.++.+|
T Consensus       219 SE--lVqKYiGEG---------aRlVRelF~lAre------------kaPsIIFiDEIDAIg~kR~d~~t~gDrEVQRTm  275 (406)
T COG1222         219 SE--LVQKYIGEG---------ARLVRELFELARE------------KAPSIIFIDEIDAIGAKRFDSGTSGDREVQRTM  275 (406)
T ss_pred             HH--HHHHHhccc---------hHHHHHHHHHHhh------------cCCeEEEEechhhhhcccccCCCCchHHHHHHH
Confidence            75  344444331         1234555555543            35789999999965321      1123466666


Q ss_pred             HHHHhcC------CCceEEEEecCCCCCCccchhhhhhHHHHHHhhcC--eeEEEeCCCCHHHHHHHHHHHHHHhCCCCC
Q 005987          286 LLLVRST------HIPTAVVLTECGKADSVDSTAQSFEELQSILVDAG--ARKVALNPITNGSIKRTLSKICRQEQYSLS  357 (666)
Q Consensus       286 ~~l~~~~------~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r--~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~  357 (666)
                      .+++..-      ..--||.+||  ..+          .|.+.|-|++  -..|.|+.|+.....++|+-.+.+..+. +
T Consensus       276 leLL~qlDGFD~~~nvKVI~ATN--R~D----------~LDPALLRPGR~DRkIEfplPd~~gR~~Il~IHtrkM~l~-~  342 (406)
T COG1222         276 LELLNQLDGFDPRGNVKVIMATN--RPD----------ILDPALLRPGRFDRKIEFPLPDEEGRAEILKIHTRKMNLA-D  342 (406)
T ss_pred             HHHHHhccCCCCCCCeEEEEecC--Ccc----------ccChhhcCCCcccceeecCCCCHHHHHHHHHHHhhhccCc-c
Confidence            6666541      1223444444  222          2333333332  3479999999999999999888776543 1


Q ss_pred             HHHHHHHHHH----cCCcHHHHHHHHHHHhcC
Q 005987          358 TEQIDLVAQA----SGGDIRQAITSLQFSSLK  385 (666)
Q Consensus       358 ~~~l~~Ia~~----s~GDIR~AIn~LQf~~~~  385 (666)
                      +--++.||..    |+-||++...-.-++|..
T Consensus       343 dvd~e~la~~~~g~sGAdlkaictEAGm~AiR  374 (406)
T COG1222         343 DVDLELLARLTEGFSGADLKAICTEAGMFAIR  374 (406)
T ss_pred             CcCHHHHHHhcCCCchHHHHHHHHHHhHHHHH
Confidence            2234555555    445788777666666654

>PRK07471 DNA polymerase III subunit delta'; Validated

Probab=99.59  E-value=3.7e-14  Score=153.07  Aligned_cols=201  Identities=15%  Similarity=0.206  Sum_probs=129.1

Q ss_pred             cCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEE-EEc----------C
Q 005987          143 YKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLY-EWD----------T  211 (666)
Q Consensus       143 Y~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~vi-E~n----------a  211 (666)
                      .+|+++++|+||++.++.+.+.+.+      ++.+ +.+||+||+|+||+++|..+|+.+-++-- .-.          .
T Consensus        13 ~~P~~~~~iiGq~~~~~~L~~~~~~------~rl~-HA~Lf~Gp~G~GK~~lA~~~A~~Llc~~~~~~~~~~~~~~~l~~   85 (365)
T PRK07471         13 PHPRETTALFGHAAAEAALLDAYRS------GRLH-HAWLIGGPQGIGKATLAYRMARFLLATPPPGGDGAVPPPTSLAI   85 (365)
T ss_pred             CCCCchhhccChHHHHHHHHHHHHc------CCCC-ceEEEECCCCCCHHHHHHHHHHHHhCCCCCCCCccccccccccC
Confidence            6899999999999999999998886      7776 78999999999999999999999854220 000          0


Q ss_pred             CCchhhhhhh----hc----c-----cCCcc--ccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchh
Q 005987          212 PTPTIWQEYM----HN----C-----KTGLE--YTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRT  276 (666)
Q Consensus       212 sd~~~~~e~l----~~----~-----~~g~~--~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~  276 (666)
                      ...+.....+    +.    .     ..+..  -.-.+++++++...+...        .....++|+||||++.++.. 
T Consensus        86 ~~~c~~c~~i~~~~HPDl~~i~~~~~~~~~~~~~~I~VdqiR~l~~~~~~~--------~~~~~~kVviIDead~m~~~-  156 (365)
T PRK07471         86 DPDHPVARRIAAGAHGGLLTLERSWNEKGKRLRTVITVDEVRELISFFGLT--------AAEGGWRVVIVDTADEMNAN-  156 (365)
T ss_pred             CCCChHHHHHHccCCCCeEEEecccccccccccccccHHHHHHHHHHhCcC--------cccCCCEEEEEechHhcCHH-
Confidence            0000001100    00    0     00100  011244555554443211        11234679999999988643 


Q ss_pred             HHHHHHHHHHHHHhcCC-CceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCC
Q 005987          277 AFERLRQCLLLLVRSTH-IPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYS  355 (666)
Q Consensus       277 ~~~~l~~~L~~l~~~~~-~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~  355 (666)
                          ..++|++.++... .+++|+++...        .+.+..++     .||..|.|.+++.+++.+.|....    ..
T Consensus       157 ----aanaLLK~LEepp~~~~~IL~t~~~--------~~llpti~-----SRc~~i~l~~l~~~~i~~~L~~~~----~~  215 (365)
T PRK07471        157 ----AANALLKVLEEPPARSLFLLVSHAP--------ARLLPTIR-----SRCRKLRLRPLAPEDVIDALAAAG----PD  215 (365)
T ss_pred             ----HHHHHHHHHhcCCCCeEEEEEECCc--------hhchHHhh-----ccceEEECCCCCHHHHHHHHHHhc----cc
Confidence                2234666666653 44566665521        12222232     269999999999999999988643    33


Q ss_pred             CCHHHHHHHHHHcCCcHHHHHHHHH
Q 005987          356 LSTEQIDLVAQASGGDIRQAITSLQ  380 (666)
Q Consensus       356 v~~~~l~~Ia~~s~GDIR~AIn~LQ  380 (666)
                      .++..+..++..++|+++.|++.++
T Consensus       216 ~~~~~~~~l~~~s~Gsp~~Al~ll~  240 (365)
T PRK07471        216 LPDDPRAALAALAEGSVGRALRLAG  240 (365)
T ss_pred             CCHHHHHHHHHHcCCCHHHHHHHhc
Confidence            4566668899999999999988764

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=99.59  E-value=6.4e-14  Score=153.73  Aligned_cols=218  Identities=19%  Similarity=0.193  Sum_probs=132.7

Q ss_pred             CccccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc-----CCcEEEEcC
Q 005987          137 QLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL-----GARLYEWDT  211 (666)
Q Consensus       137 ~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel-----g~~viE~na  211 (666)
                      .++...|.|.   .++++++.+++|..++..+..   +..+ ..++|+||||+|||++++.+++++     ++.++.+|+
T Consensus        21 ~~l~~~~~P~---~l~~Re~e~~~l~~~l~~~~~---~~~~-~~~lI~G~~GtGKT~l~~~v~~~l~~~~~~~~~v~in~   93 (394)
T PRK00411         21 EVLEPDYVPE---NLPHREEQIEELAFALRPALR---GSRP-LNVLIYGPPGTGKTTTVKKVFEELEEIAVKVVYVYINC   93 (394)
T ss_pred             hhCCCCCcCC---CCCCHHHHHHHHHHHHHHHhC---CCCC-CeEEEECCCCCCHHHHHHHHHHHHHHhcCCcEEEEEEC
Confidence            3466667774   469999999999999988764   2222 468999999999999999999987     577888988


Q ss_pred             CCchhh----hhhhhcccCCccc----cchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHH
Q 005987          212 PTPTIW----QEYMHNCKTGLEY----TSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQ  283 (666)
Q Consensus       212 sd~~~~----~e~l~~~~~g~~~----~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~  283 (666)
                      ......    ...+... .+...    .+..+.+..+.+.+..           .+.+.||+|||+|.+........+..
T Consensus        94 ~~~~~~~~~~~~i~~~l-~~~~~~~~~~~~~~~~~~~~~~l~~-----------~~~~~viviDE~d~l~~~~~~~~l~~  161 (394)
T PRK00411         94 QIDRTRYAIFSEIARQL-FGHPPPSSGLSFDELFDKIAEYLDE-----------RDRVLIVALDDINYLFEKEGNDVLYS  161 (394)
T ss_pred             CcCCCHHHHHHHHHHHh-cCCCCCCCCCCHHHHHHHHHHHHHh-----------cCCEEEEEECCHhHhhccCCchHHHH
Confidence            653321    1111111 11000    0111122222222221           12457999999998751111111222


Q ss_pred             HHHHHHhc-CCCc--eEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHh--CCCCCH
Q 005987          284 CLLLLVRS-THIP--TAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQE--QYSLST  358 (666)
Q Consensus       284 ~L~~l~~~-~~~P--iViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e--~i~v~~  358 (666)
                       |..+... ...+  +|++.++...      ....-..+++   +.+...|.|.|++.+++.++|+..+...  ...+++
T Consensus       162 -l~~~~~~~~~~~v~vI~i~~~~~~------~~~l~~~~~s---~~~~~~i~f~py~~~e~~~il~~r~~~~~~~~~~~~  231 (394)
T PRK00411        162 -LLRAHEEYPGARIGVIGISSDLTF------LYILDPRVKS---VFRPEEIYFPPYTADEIFDILKDRVEEGFYPGVVDD  231 (394)
T ss_pred             -HHHhhhccCCCeEEEEEEECCcch------hhhcCHHHHh---cCCcceeecCCCCHHHHHHHHHHHHHhhcccCCCCH
Confidence             2222222 2223  3333332211      1111112232   2345689999999999999999988643  235789


Q ss_pred             HHHHHHHHHc---CCcHHHHHHHHHHHh
Q 005987          359 EQIDLVAQAS---GGDIRQAITSLQFSS  383 (666)
Q Consensus       359 ~~l~~Ia~~s---~GDIR~AIn~LQf~~  383 (666)
                      ++++.|++.+   .||+|.|++.|..++
T Consensus       232 ~~l~~i~~~~~~~~Gd~r~a~~ll~~a~  259 (394)
T PRK00411        232 EVLDLIADLTAREHGDARVAIDLLRRAG  259 (394)
T ss_pred             hHHHHHHHHHHHhcCcHHHHHHHHHHHH
Confidence            9999998887   899999999997654

>PRK05642 DNA replication initiation factor; Validated

Probab=99.58  E-value=1.4e-13  Score=140.28  Aligned_cols=193  Identities=13%  Similarity=0.181  Sum_probs=122.6

Q ss_pred             CccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcCCCchhhhhhhhc
Q 005987          147 SLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL---GARLYEWDTPTPTIWQEYMHN  223 (666)
Q Consensus       147 sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~nasd~~~~~e~l~~  223 (666)
                      +|++++...  ......+++.|.... +....+.++|+||+|+|||++++++|+++   +..++.++..+.      .  
T Consensus        17 tfdnF~~~~--~~~a~~~~~~~~~~~-~~~~~~~l~l~G~~G~GKTHLl~a~~~~~~~~~~~v~y~~~~~~------~--   85 (234)
T PRK05642         17 TFANYYPGA--NAAALGYVERLCEAD-AGWTESLIYLWGKDGVGRSHLLQAACLRFEQRGEPAVYLPLAEL------L--   85 (234)
T ss_pred             cccccCcCC--hHHHHHHHHHHhhcc-ccCCCCeEEEECCCCCCHHHHHHHHHHHHHhCCCcEEEeeHHHH------H--
Confidence            566665322  133444454443211 12223679999999999999999999875   566666654220      0  


Q ss_pred             ccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhH-HHHHHHHHHHHHhcCCCceEEEEec
Q 005987          224 CKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTA-FERLRQCLLLLVRSTHIPTAVVLTE  302 (666)
Q Consensus       224 ~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~-~~~l~~~L~~l~~~~~~PiViIit~  302 (666)
                                 .....+++....+              -+|+|||++...+... ...+..++..+.+.++ + +++.++
T Consensus        86 -----------~~~~~~~~~~~~~--------------d~LiiDDi~~~~~~~~~~~~Lf~l~n~~~~~g~-~-ilits~  138 (234)
T PRK05642         86 -----------DRGPELLDNLEQY--------------ELVCLDDLDVIAGKADWEEALFHLFNRLRDSGR-R-LLLAAS  138 (234)
T ss_pred             -----------hhhHHHHHhhhhC--------------CEEEEechhhhcCChHHHHHHHHHHHHHHhcCC-E-EEEeCC
Confidence                       0011233333211              2899999997754322 2234444444444443 3 344444


Q ss_pred             CCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCcHHHHHHHHHHH
Q 005987          303 CGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASGGDIRQAITSLQFS  382 (666)
Q Consensus       303 ~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~s~GDIR~AIn~LQf~  382 (666)
                      .... .   .....+.|++++..  +..+.+.+++.+++.++|+..+...++.+++++++.|++.+.||+|.+++.|+.+
T Consensus       139 ~~p~-~---l~~~~~~L~SRl~~--gl~~~l~~~~~e~~~~il~~ka~~~~~~l~~ev~~~L~~~~~~d~r~l~~~l~~l  212 (234)
T PRK05642        139 KSPR-E---LPIKLPDLKSRLTL--ALVFQMRGLSDEDKLRALQLRASRRGLHLTDEVGHFILTRGTRSMSALFDLLERL  212 (234)
T ss_pred             CCHH-H---cCccCccHHHHHhc--CeeeecCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHH
Confidence            3321 1   11123556776543  6789999999999999999888888999999999999999999999999988876


Q ss_pred             h
Q 005987          383 S  383 (666)
Q Consensus       383 ~  383 (666)
                      -
T Consensus       213 ~  213 (234)
T PRK05642        213 D  213 (234)
T ss_pred             H
Confidence            4

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=99.58  E-value=2.2e-13  Score=138.23  Aligned_cols=187  Identities=13%  Similarity=0.161  Sum_probs=123.8

Q ss_pred             CCCCccccc--cCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcCCCchhhh
Q 005987          144 KPRSLEELA--VQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL---GARLYEWDTPTPTIWQ  218 (666)
Q Consensus       144 ~P~sl~eLv--g~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~nasd~~~~~  218 (666)
                      +|.++++++  .+...+..++.|...      . ...+.++|+||+|||||++++++++++   +..++.+++...    
T Consensus        13 ~~~~~d~f~~~~~~~~~~~l~~~~~~------~-~~~~~~~l~G~~G~GKT~La~ai~~~~~~~~~~~~~i~~~~~----   81 (227)
T PRK08903         13 PPPTFDNFVAGENAELVARLRELAAG------P-VADRFFYLWGEAGSGRSHLLQALVADASYGGRNARYLDAASP----   81 (227)
T ss_pred             ChhhhcccccCCcHHHHHHHHHHHhc------c-CCCCeEEEECCCCCCHHHHHHHHHHHHHhCCCcEEEEehHHh----
Confidence            456788877  356667777777652      1 122589999999999999999999986   556666654320    


Q ss_pred             hhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcCCCceEE
Q 005987          219 EYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHIPTAV  298 (666)
Q Consensus       219 e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~~~PiVi  298 (666)
                                         ...+   . +.          ....+|+|||++.+.... ...+...+..... ...++++
T Consensus        82 -------------------~~~~---~-~~----------~~~~~liiDdi~~l~~~~-~~~L~~~~~~~~~-~~~~~vl  126 (227)
T PRK08903         82 -------------------LLAF---D-FD----------PEAELYAVDDVERLDDAQ-QIALFNLFNRVRA-HGQGALL  126 (227)
T ss_pred             -------------------HHHH---h-hc----------ccCCEEEEeChhhcCchH-HHHHHHHHHHHHH-cCCcEEE
Confidence                               0000   0 10          113489999999875432 2333333333322 2233444


Q ss_pred             EEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCcHHHHHHH
Q 005987          299 VLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASGGDIRQAITS  378 (666)
Q Consensus       299 Iit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~s~GDIR~AIn~  378 (666)
                      ++++. .+.    .......|.+.+.  .+..|.++|++......+|.+++..+++.+++++++.|+..+.||+|.+++.
T Consensus       127 ~~~~~-~~~----~~~l~~~L~sr~~--~~~~i~l~pl~~~~~~~~l~~~~~~~~v~l~~~al~~L~~~~~gn~~~l~~~  199 (227)
T PRK08903        127 VAGPA-APL----ALPLREDLRTRLG--WGLVYELKPLSDADKIAALKAAAAERGLQLADEVPDYLLTHFRRDMPSLMAL  199 (227)
T ss_pred             EeCCC-CHH----hCCCCHHHHHHHh--cCeEEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhccCCHHHHHHH
Confidence            44432 111    1111233444443  2689999999999999999999999999999999999999999999999888


Q ss_pred             HHHHh
Q 005987          379 LQFSS  383 (666)
Q Consensus       379 LQf~~  383 (666)
                      |+.+.
T Consensus       200 l~~l~  204 (227)
T PRK08903        200 LDALD  204 (227)
T ss_pred             HHHHH
Confidence            88764

>PRK07399 DNA polymerase III subunit delta'; Validated

Probab=99.57  E-value=1.2e-13  Score=146.45  Aligned_cols=200  Identities=15%  Similarity=0.219  Sum_probs=130.1

Q ss_pred             CccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCc----------EEEEcCCCchh
Q 005987          147 SLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGAR----------LYEWDTPTPTI  216 (666)
Q Consensus       147 sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~----------viE~nasd~~~  216 (666)
                      .|++|+||+..++.+...+..      ++.+ +.+||+||+|+||+++|.++|+.+.+.          +...+.||...
T Consensus         2 ~f~~iiGq~~~~~~L~~~i~~------~rl~-ha~Lf~G~~G~Gk~~~A~~~a~~llc~~~c~~c~~~~~~~~~hPDl~~   74 (314)
T PRK07399          2 LFANLIGQPLAIELLTAAIKQ------NRIA-PAYLFAGPEGVGRKLAALCFIEGLLSQGSPSKNIRRRLEEGNHPDLLW   74 (314)
T ss_pred             cHHHhCCHHHHHHHHHHHHHh------CCCC-ceEEEECCCCCCHHHHHHHHHHHHcCCCCCCCcHhcccccCCCCCEEE
Confidence            478999999999999999987      7776 799999999999999999999998433          22334444211


Q ss_pred             hhhh-hhcc---------cCCc--c--ccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHH
Q 005987          217 WQEY-MHNC---------KTGL--E--YTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLR  282 (666)
Q Consensus       217 ~~e~-l~~~---------~~g~--~--~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~  282 (666)
                      .... ....         ..|.  .  ..-.++.++++.+.+...+     ..   ...+|+|||+++.++..     ..
T Consensus        75 i~p~~~~~g~~~~~~~~~~~~~~~~~~~~I~id~ir~i~~~l~~~p-----~~---~~~kVvII~~ae~m~~~-----aa  141 (314)
T PRK07399         75 VEPTYQHQGKLITASEAEEAGLKRKAPPQIRLEQIREIKRFLSRPP-----LE---APRKVVVIEDAETMNEA-----AA  141 (314)
T ss_pred             EeccccccccccchhhhhhccccccccccCcHHHHHHHHHHHccCc-----cc---CCceEEEEEchhhcCHH-----HH
Confidence            0000 0000         0000  0  0112344555444432211     11   23579999999988643     23


Q ss_pred             HHHHHHHhcCCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHH
Q 005987          283 QCLLLLVRSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQID  362 (666)
Q Consensus       283 ~~L~~l~~~~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~  362 (666)
                      ++|+++++.....++|++++ .       ..+.++.|++     ||..|.|.+++.+++.++|.+.+..++..   ..+.
T Consensus       142 NaLLK~LEEPp~~~fILi~~-~-------~~~Ll~TI~S-----Rcq~i~f~~l~~~~~~~~L~~~~~~~~~~---~~~~  205 (314)
T PRK07399        142 NALLKTLEEPGNGTLILIAP-S-------PESLLPTIVS-----RCQIIPFYRLSDEQLEQVLKRLGDEEILN---INFP  205 (314)
T ss_pred             HHHHHHHhCCCCCeEEEEEC-C-------hHhCcHHHHh-----hceEEecCCCCHHHHHHHHHHhhccccch---hHHH
Confidence            45666667665334455554 1       2345555554     69999999999999999999886544322   2357


Q ss_pred             HHHHHcCCcHHHHHHHHHHH
Q 005987          363 LVAQASGGDIRQAITSLQFS  382 (666)
Q Consensus       363 ~Ia~~s~GDIR~AIn~LQf~  382 (666)
                      .++..++||.|.|++.++..
T Consensus       206 ~l~~~a~Gs~~~al~~l~~~  225 (314)
T PRK07399        206 ELLALAQGSPGAAIANIEQL  225 (314)
T ss_pred             HHHHHcCCCHHHHHHHHHHH
Confidence            88899999999999988754

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=99.57  E-value=1.8e-13  Score=138.41  Aligned_cols=189  Identities=12%  Similarity=0.163  Sum_probs=122.4

Q ss_pred             CCCccccc--cCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcCCCchhhhh
Q 005987          145 PRSLEELA--VQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL---GARLYEWDTPTPTIWQE  219 (666)
Q Consensus       145 P~sl~eLv--g~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~nasd~~~~~e  219 (666)
                      |.++++++  +++..++.++.|+..+      .  .+.++|+||+|||||++|+.+++++   +..++.+++....    
T Consensus        11 ~~~~~~~~~~~~~~~~~~l~~~~~~~------~--~~~lll~G~~G~GKT~la~~~~~~~~~~~~~~~~i~~~~~~----   78 (226)
T TIGR03420        11 DPTFDNFYAGGNAELLAALRQLAAGK------G--DRFLYLWGESGSGKSHLLQAACAAAEERGKSAIYLPLAELA----   78 (226)
T ss_pred             chhhcCcCcCCcHHHHHHHHHHHhcC------C--CCeEEEECCCCCCHHHHHHHHHHHHHhcCCcEEEEeHHHHH----
Confidence            45667766  3667888888887531      1  2589999999999999999999987   4556666543210    


Q ss_pred             hhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchh-HHHHHHHHHHHHHhcCCCceEE
Q 005987          220 YMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRT-AFERLRQCLLLLVRSTHIPTAV  298 (666)
Q Consensus       220 ~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~-~~~~l~~~L~~l~~~~~~PiVi  298 (666)
                                     .....+++..              ....+|+|||++.+.... ..+.+...+..+.... .+ ++
T Consensus        79 ---------------~~~~~~~~~~--------------~~~~lLvIDdi~~l~~~~~~~~~L~~~l~~~~~~~-~~-iI  127 (226)
T TIGR03420        79 ---------------QADPEVLEGL--------------EQADLVCLDDVEAIAGQPEWQEALFHLYNRVREAG-GR-LL  127 (226)
T ss_pred             ---------------HhHHHHHhhc--------------ccCCEEEEeChhhhcCChHHHHHHHHHHHHHHHcC-Ce-EE
Confidence                           0111222211              112489999999875431 1233434343333322 23 33


Q ss_pred             EEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCcHHHHHHH
Q 005987          299 VLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASGGDIRQAITS  378 (666)
Q Consensus       299 Iit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~s~GDIR~AIn~  378 (666)
                      ++++... ...   ....+.|.+.+.  .+..|.+.+++.+++..+|...+.+.++.+++++++.|+..++|++|.+.+.
T Consensus       128 its~~~~-~~~---~~~~~~L~~r~~--~~~~i~l~~l~~~e~~~~l~~~~~~~~~~~~~~~l~~L~~~~~gn~r~L~~~  201 (226)
T TIGR03420       128 IAGRAAP-AQL---PLRLPDLRTRLA--WGLVFQLPPLSDEEKIAALQSRAARRGLQLPDEVADYLLRHGSRDMGSLMAL  201 (226)
T ss_pred             EECCCCh-HHC---CcccHHHHHHHh--cCeeEecCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhccCCHHHHHHH
Confidence            3333221 100   011133444332  2578999999999999999999988899999999999999999999999988


Q ss_pred             HHHH
Q 005987          379 LQFS  382 (666)
Q Consensus       379 LQf~  382 (666)
                      |+-+
T Consensus       202 l~~~  205 (226)
T TIGR03420       202 LDAL  205 (226)
T ss_pred             HHHH
Confidence            7654

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.

>PRK05564 DNA polymerase III subunit delta'; Validated

Probab=99.53  E-value=3.7e-13  Score=143.21  Aligned_cols=189  Identities=13%  Similarity=0.193  Sum_probs=126.9

Q ss_pred             CccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCchhhhhhhhcccC
Q 005987          147 SLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTIWQEYMHNCKT  226 (666)
Q Consensus       147 sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~~~~e~l~~~~~  226 (666)
                      +|+|++||++.++.+..+++.      ++.+ +.+||+||+|+|||++|+.+|+.+.+....-+.+|...+.     ...
T Consensus         2 ~~~~i~g~~~~~~~l~~~~~~------~~~~-ha~Lf~G~~G~Gk~~la~~~a~~l~c~~~~~~h~D~~~~~-----~~~   69 (313)
T PRK05564          2 SFHTIIGHENIKNRIKNSIIK------NRFS-HAHIIVGEDGIGKSLLAKEIALKILGKSQQREYVDIIEFK-----PIN   69 (313)
T ss_pred             ChhhccCcHHHHHHHHHHHHc------CCCC-ceEEeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCeEEec-----ccc
Confidence            689999999999999999975      6666 7899999999999999999999885432211222211110     001


Q ss_pred             CccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcCCCceEEEEecCCCC
Q 005987          227 GLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHIPTAVVLTECGKA  306 (666)
Q Consensus       227 g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~~~PiViIit~~~~~  306 (666)
                      |.  .-..++++++++.+...+     ..   ...+|+|||+++.++..     ..++|+.+++....-+++|+...+  
T Consensus        70 ~~--~i~v~~ir~~~~~~~~~p-----~~---~~~kv~iI~~ad~m~~~-----a~naLLK~LEepp~~t~~il~~~~--  132 (313)
T PRK05564         70 KK--SIGVDDIRNIIEEVNKKP-----YE---GDKKVIIIYNSEKMTEQ-----AQNAFLKTIEEPPKGVFIILLCEN--  132 (313)
T ss_pred             CC--CCCHHHHHHHHHHHhcCc-----cc---CCceEEEEechhhcCHH-----HHHHHHHHhcCCCCCeEEEEEeCC--
Confidence            11  123456777666553222     11   24679999999987543     234567777765433333333221  


Q ss_pred             CCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCcHHHHHHH
Q 005987          307 DSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASGGDIRQAITS  378 (666)
Q Consensus       307 ~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~s~GDIR~AIn~  378 (666)
                           ..+.++.+++     ||..+.|.+++..++.+.|.+...    .++++.++.++..++|....|+..
T Consensus       133 -----~~~ll~TI~S-----Rc~~~~~~~~~~~~~~~~l~~~~~----~~~~~~~~~l~~~~~g~~~~a~~~  190 (313)
T PRK05564        133 -----LEQILDTIKS-----RCQIYKLNRLSKEEIEKFISYKYN----DIKEEEKKSAIAFSDGIPGKVEKF  190 (313)
T ss_pred             -----hHhCcHHHHh-----hceeeeCCCcCHHHHHHHHHHHhc----CCCHHHHHHHHHHcCCCHHHHHHH
Confidence                 1244444554     599999999999999988876542    467888999999999988888644

>CHL00181 cbbX CbbX; Provisional

Probab=99.52  E-value=8.5e-13  Score=138.33  Aligned_cols=204  Identities=16%  Similarity=0.163  Sum_probs=121.5

Q ss_pred             ccccCHHHHHHHHHHHHH---h-hcCCCCC---CCccEEEEECCCCchHHHHHHHHHHHc---CC----cEEEEcCCCch
Q 005987          150 ELAVQRKKVEEVRAWFEE---R-LGDSKDK---FSTNVLVITGQAGVGKTATVRQIASHL---GA----RLYEWDTPTPT  215 (666)
Q Consensus       150 eLvg~~k~i~el~~wL~~---~-~~~~~g~---~~~k~LLL~GPpG~GKTtla~~LAkel---g~----~viE~nasd~~  215 (666)
                      +++|.+...++|++++.-   . .....|.   .+..++||+||||||||++|+++|+.+   |+    .+++++.++  
T Consensus        24 ~l~Gl~~vK~~i~e~~~~~~~~~~~~~~g~~~~~~~~~ill~G~pGtGKT~lAr~la~~~~~~g~~~~~~~~~v~~~~--  101 (287)
T CHL00181         24 ELVGLAPVKTRIREIAALLLIDRLRKNLGLTSSNPGLHMSFTGSPGTGKTTVALKMADILYKLGYIKKGHLLTVTRDD--  101 (287)
T ss_pred             hcCCcHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCCceEEEECCCCCCHHHHHHHHHHHHHHcCCCCCCceEEecHHH--
Confidence            688887777766665421   0 0000111   122469999999999999999999986   22    356666432  


Q ss_pred             hhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcch----hHHHHHHHHHHHHHhc
Q 005987          216 IWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGR----TAFERLRQCLLLLVRS  291 (666)
Q Consensus       216 ~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~----~~~~~l~~~L~~l~~~  291 (666)
                      ....+     .|.    .......+++++               .+.||||||++.+...    ..-...++.|..+++.
T Consensus       102 l~~~~-----~g~----~~~~~~~~l~~a---------------~ggVLfIDE~~~l~~~~~~~~~~~e~~~~L~~~me~  157 (287)
T CHL00181        102 LVGQY-----IGH----TAPKTKEVLKKA---------------MGGVLFIDEAYYLYKPDNERDYGSEAIEILLQVMEN  157 (287)
T ss_pred             HHHHH-----hcc----chHHHHHHHHHc---------------cCCEEEEEccchhccCCCccchHHHHHHHHHHHHhc
Confidence            10001     111    111223344432               1249999999976321    1112344566676766


Q ss_pred             CCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHH----
Q 005987          292 THIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQA----  367 (666)
Q Consensus       292 ~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~----  367 (666)
                      ....+++|++.+..  ..   ...+..-+.+.+| ....|.|++++.+++.+++.+.+.+.+..++++.+..++..    
T Consensus       158 ~~~~~~vI~ag~~~--~~---~~~~~~np~L~sR-~~~~i~F~~~t~~el~~I~~~~l~~~~~~l~~~~~~~L~~~i~~~  231 (287)
T CHL00181        158 QRDDLVVIFAGYKD--RM---DKFYESNPGLSSR-IANHVDFPDYTPEELLQIAKIMLEEQQYQLTPEAEKALLDYIKKR  231 (287)
T ss_pred             CCCCEEEEEeCCcH--HH---HHHHhcCHHHHHh-CCceEEcCCcCHHHHHHHHHHHHHHhcCCCChhHHHHHHHHHHHh
Confidence            54445555554211  01   1111101222333 35689999999999999999999999999998877666653    


Q ss_pred             ----cCCcHHHHHHHHHHHhcC
Q 005987          368 ----SGGDIRQAITSLQFSSLK  385 (666)
Q Consensus       368 ----s~GDIR~AIn~LQf~~~~  385 (666)
                          .-|+.|.+.|.++.+...
T Consensus       232 ~~~~~~GNaR~vrn~ve~~~~~  253 (287)
T CHL00181        232 MEQPLFANARSVRNALDRARMR  253 (287)
T ss_pred             CCCCCCccHHHHHHHHHHHHHH
Confidence                238889998988877653

>CHL00195 ycf46 Ycf46; Provisional

Probab=99.51  E-value=3.7e-13  Score=149.98  Aligned_cols=205  Identities=15%  Similarity=0.158  Sum_probs=128.4

Q ss_pred             CCCccccccCHHHHHHHHHHHHHhhc--CCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCchhhhhhhh
Q 005987          145 PRSLEELAVQRKKVEEVRAWFEERLG--DSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTIWQEYMH  222 (666)
Q Consensus       145 P~sl~eLvg~~k~i~el~~wL~~~~~--~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~~~~e~l~  222 (666)
                      +.++++|.|.+...+.+......+..  ...|-.+++.+||+||||||||.+|+++|++++..++.++.+.       +.
T Consensus       224 ~~~~~dvgGl~~lK~~l~~~~~~~~~~~~~~gl~~pkGILL~GPpGTGKTllAkaiA~e~~~~~~~l~~~~-------l~  296 (489)
T CHL00195        224 NEKISDIGGLDNLKDWLKKRSTSFSKQASNYGLPTPRGLLLVGIQGTGKSLTAKAIANDWQLPLLRLDVGK-------LF  296 (489)
T ss_pred             CCCHHHhcCHHHHHHHHHHHHHHhhHHHHhcCCCCCceEEEECCCCCcHHHHHHHHHHHhCCCEEEEEhHH-------hc
Confidence            46789999976665555443221110  0113334589999999999999999999999999999988643       11


Q ss_pred             cccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcch-------hHHHHHHHHHHHHHhcCCCc
Q 005987          223 NCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGR-------TAFERLRQCLLLLVRSTHIP  295 (666)
Q Consensus       223 ~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~-------~~~~~l~~~L~~l~~~~~~P  295 (666)
                          +..+......+++++..+...            .|+||+|||+|.+...       ....++...+...+.....|
T Consensus       297 ----~~~vGese~~l~~~f~~A~~~------------~P~IL~IDEID~~~~~~~~~~d~~~~~rvl~~lL~~l~~~~~~  360 (489)
T CHL00195        297 ----GGIVGESESRMRQMIRIAEAL------------SPCILWIDEIDKAFSNSESKGDSGTTNRVLATFITWLSEKKSP  360 (489)
T ss_pred             ----ccccChHHHHHHHHHHHHHhc------------CCcEEEehhhhhhhccccCCCCchHHHHHHHHHHHHHhcCCCc
Confidence                111122334566666655432            3689999999965321       12334444555556655566


Q ss_pred             eEEEEecCCCCCCccchhhhhhHHHHHHhh-cC-eeEEEeCCCCHHHHHHHHHHHHHHhCCC-CCHHHHHHHHHH----c
Q 005987          296 TAVVLTECGKADSVDSTAQSFEELQSILVD-AG-ARKVALNPITNGSIKRTLSKICRQEQYS-LSTEQIDLVAQA----S  368 (666)
Q Consensus       296 iViIit~~~~~~s~d~~~r~l~~L~s~L~r-~r-~~~I~F~p~s~~~i~kiL~~I~~~e~i~-v~~~~l~~Ia~~----s  368 (666)
                      +++|+++ +...          .|...+.| .| -..|.|..|+..+..++++..+.+.+.. ..+..++.|+..    +
T Consensus       361 V~vIaTT-N~~~----------~Ld~allR~GRFD~~i~v~lP~~~eR~~Il~~~l~~~~~~~~~~~dl~~La~~T~GfS  429 (489)
T CHL00195        361 VFVVATA-NNID----------LLPLEILRKGRFDEIFFLDLPSLEEREKIFKIHLQKFRPKSWKKYDIKKLSKLSNKFS  429 (489)
T ss_pred             eEEEEec-CChh----------hCCHHHhCCCcCCeEEEeCCcCHHHHHHHHHHHHhhcCCCcccccCHHHHHhhcCCCC
Confidence            7665554 3222          12222222 12 3578999999999999999888775432 335557788877    4


Q ss_pred             CCcHHHHHHHHHHHh
Q 005987          369 GGDIRQAITSLQFSS  383 (666)
Q Consensus       369 ~GDIR~AIn~LQf~~  383 (666)
                      ++||+.+++..-+.+
T Consensus       430 GAdI~~lv~eA~~~A  444 (489)
T CHL00195        430 GAEIEQSIIEAMYIA  444 (489)
T ss_pred             HHHHHHHHHHHHHHH
Confidence            568888876554444

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX

Probab=99.51  E-value=9.2e-13  Score=138.05  Aligned_cols=204  Identities=18%  Similarity=0.165  Sum_probs=125.7

Q ss_pred             ccccCHHHHHHHHHHHHH---h-hcCCCCC---CCccEEEEECCCCchHHHHHHHHHHHcC---C----cEEEEcCCCch
Q 005987          150 ELAVQRKKVEEVRAWFEE---R-LGDSKDK---FSTNVLVITGQAGVGKTATVRQIASHLG---A----RLYEWDTPTPT  215 (666)
Q Consensus       150 eLvg~~k~i~el~~wL~~---~-~~~~~g~---~~~k~LLL~GPpG~GKTtla~~LAkelg---~----~viE~nasd~~  215 (666)
                      +|+|.+...++|.++..-   . .....|-   .+..++||+||||||||++|+++|+.+.   +    .++++++++. 
T Consensus        23 ~l~Gl~~vk~~i~e~~~~~~~~~~r~~~g~~~~~~~~~vll~G~pGTGKT~lA~~ia~~l~~~g~~~~~~~v~v~~~~l-  101 (284)
T TIGR02880        23 ELIGLKPVKTRIREIAALLLVERLRQRLGLASAAPTLHMSFTGNPGTGKTTVALRMAQILHRLGYVRKGHLVSVTRDDL-  101 (284)
T ss_pred             hccCHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCCCceEEEEcCCCCCHHHHHHHHHHHHHHcCCcccceEEEecHHHH-
Confidence            577877776666554331   0 0000111   1234799999999999999999999872   2    4666665431 


Q ss_pred             hhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcch----hHHHHHHHHHHHHHhc
Q 005987          216 IWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGR----TAFERLRQCLLLLVRS  291 (666)
Q Consensus       216 ~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~----~~~~~l~~~L~~l~~~  291 (666)
                       ...     ..|.    ....+..+++++.               +.+|+|||++.+...    ..-...++.|..+++.
T Consensus       102 -~~~-----~~g~----~~~~~~~~~~~a~---------------~gvL~iDEi~~L~~~~~~~~~~~~~~~~Ll~~le~  156 (284)
T TIGR02880       102 -VGQ-----YIGH----TAPKTKEILKRAM---------------GGVLFIDEAYYLYRPDNERDYGQEAIEILLQVMEN  156 (284)
T ss_pred             -hHh-----hccc----chHHHHHHHHHcc---------------CcEEEEechhhhccCCCccchHHHHHHHHHHHHhc
Confidence             100     1111    1123344444431               248999999976311    1112344567777766


Q ss_pred             CCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHH----
Q 005987          292 THIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQA----  367 (666)
Q Consensus       292 ~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~----  367 (666)
                      .+..+++|++.+..  ..+    .+..+...+.++....|.|++++.+++..++...+.+.+..+++++++.+...    
T Consensus       157 ~~~~~~vI~a~~~~--~~~----~~~~~np~L~sR~~~~i~fp~l~~edl~~I~~~~l~~~~~~l~~~a~~~L~~~l~~~  230 (284)
T TIGR02880       157 QRDDLVVILAGYKD--RMD----SFFESNPGFSSRVAHHVDFPDYSEAELLVIAGLMLKEQQYRFSAEAEEAFADYIALR  230 (284)
T ss_pred             CCCCEEEEEeCCcH--HHH----HHHhhCHHHHhhCCcEEEeCCcCHHHHHHHHHHHHHHhccccCHHHHHHHHHHHHHh
Confidence            55445555554321  011    11112222333234689999999999999999999999889999999888775    


Q ss_pred             ----cCCcHHHHHHHHHHHhcC
Q 005987          368 ----SGGDIRQAITSLQFSSLK  385 (666)
Q Consensus       368 ----s~GDIR~AIn~LQf~~~~  385 (666)
                          -.|++|.+.|.++.+...
T Consensus       231 ~~~~~~GN~R~lrn~ve~~~~~  252 (284)
T TIGR02880       231 RTQPHFANARSIRNAIDRARLR  252 (284)
T ss_pred             CCCCCCChHHHHHHHHHHHHHH
Confidence                349999999999988764

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.

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

Probab=99.51  E-value=7.8e-13  Score=142.64  Aligned_cols=213  Identities=18%  Similarity=0.275  Sum_probs=139.2

Q ss_pred             cccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcC-----CcEEEEcCCC
Q 005987          139 WAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLG-----ARLYEWDTPT  213 (666)
Q Consensus       139 W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg-----~~viE~nasd  213 (666)
                      .-+-|-|..   |.+++..++.+...|..++.   |..| ..++++||||||||++++.+++++.     ..++++|+..
T Consensus        10 l~~~~iP~~---l~~Re~ei~~l~~~l~~~~~---~~~p-~n~~iyG~~GTGKT~~~~~v~~~l~~~~~~~~~~yINc~~   82 (366)
T COG1474          10 LLEDYIPEE---LPHREEEINQLASFLAPALR---GERP-SNIIIYGPTGTGKTATVKFVMEELEESSANVEVVYINCLE   82 (366)
T ss_pred             cCCCCCccc---ccccHHHHHHHHHHHHHHhc---CCCC-ccEEEECCCCCCHhHHHHHHHHHHHhhhccCceEEEeeee
Confidence            445567766   79999999999999998886   4444 4599999999999999999999983     3388898875


Q ss_pred             chhhh----hhhh----cccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHH
Q 005987          214 PTIWQ----EYMH----NCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCL  285 (666)
Q Consensus       214 ~~~~~----e~l~----~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L  285 (666)
                      .....    +.+.    -...|...   .+.+..+.+.....           +...||++||+|.+.....     +.|
T Consensus        83 ~~t~~~i~~~i~~~~~~~p~~g~~~---~~~~~~l~~~~~~~-----------~~~~IvvLDEid~L~~~~~-----~~L  143 (366)
T COG1474          83 LRTPYQVLSKILNKLGKVPLTGDSS---LEILKRLYDNLSKK-----------GKTVIVILDEVDALVDKDG-----EVL  143 (366)
T ss_pred             CCCHHHHHHHHHHHcCCCCCCCCch---HHHHHHHHHHHHhc-----------CCeEEEEEcchhhhccccc-----hHH
Confidence            43221    1111    12233322   22333333333221           2457999999999866532     446


Q ss_pred             HHHHhcCCCc---e-EEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHh--CCCCCHH
Q 005987          286 LLLVRSTHIP---T-AVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQE--QYSLSTE  359 (666)
Q Consensus       286 ~~l~~~~~~P---i-ViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e--~i~v~~~  359 (666)
                      ..++.....+   + ++.+++  .   .+......+.+++.+   +...|.|+|++.+++..+|...+...  .-.++++
T Consensus       144 Y~L~r~~~~~~~~v~vi~i~n--~---~~~~~~ld~rv~s~l---~~~~I~F~pY~a~el~~Il~~R~~~~~~~~~~~~~  215 (366)
T COG1474         144 YSLLRAPGENKVKVSIIAVSN--D---DKFLDYLDPRVKSSL---GPSEIVFPPYTAEELYDILRERVEEGFSAGVIDDD  215 (366)
T ss_pred             HHHHhhccccceeEEEEEEec--c---HHHHHHhhhhhhhcc---CcceeeeCCCCHHHHHHHHHHHHHhhccCCCcCcc
Confidence            6665544433   2 222222  1   111112223344443   45569999999999999999988742  3457888


Q ss_pred             HHHHHHH---HcCCcHHHHHHHHHHHhcC
Q 005987          360 QIDLVAQ---ASGGDIRQAITSLQFSSLK  385 (666)
Q Consensus       360 ~l~~Ia~---~s~GDIR~AIn~LQf~~~~  385 (666)
                      +++.++.   ..+||.|.||..|..++..
T Consensus       216 vl~lia~~~a~~~GDAR~aidilr~A~ei  244 (366)
T COG1474         216 VLKLIAALVAAESGDARKAIDILRRAGEI  244 (366)
T ss_pred             HHHHHHHHHHHcCccHHHHHHHHHHHHHH
Confidence            8887774   4668999999999888753

>PRK09087 hypothetical protein; Validated

Probab=99.51  E-value=6.8e-13  Score=134.39  Aligned_cols=176  Identities=15%  Similarity=0.132  Sum_probs=116.8

Q ss_pred             Ccccccc---CHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCchhhhhhhhc
Q 005987          147 SLEELAV---QRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTIWQEYMHN  223 (666)
Q Consensus       147 sl~eLvg---~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~~~~e~l~~  223 (666)
                      +++++++   +...+.    +++.|.    +. +.+.++|+||+|||||++++++|+..+..++...  +          
T Consensus        19 ~~~~Fi~~~~N~~a~~----~l~~~~----~~-~~~~l~l~G~~GsGKThLl~~~~~~~~~~~i~~~--~----------   77 (226)
T PRK09087         19 GRDDLLVTESNRAAVS----LVDHWP----NW-PSPVVVLAGPVGSGKTHLASIWREKSDALLIHPN--E----------   77 (226)
T ss_pred             ChhceeecCchHHHHH----HHHhcc----cC-CCCeEEEECCCCCCHHHHHHHHHHhcCCEEecHH--H----------
Confidence            6777775   444444    444432    11 1246999999999999999999998765533211  0          


Q ss_pred             ccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcCCCceEEEEecC
Q 005987          224 CKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHIPTAVVLTEC  303 (666)
Q Consensus       224 ~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~~~PiViIit~~  303 (666)
                                  --..++..+.               ..+|+|||++.+...  ...+...+..+.+.+ .+ ++++++.
T Consensus        78 ------------~~~~~~~~~~---------------~~~l~iDDi~~~~~~--~~~lf~l~n~~~~~g-~~-ilits~~  126 (226)
T PRK09087         78 ------------IGSDAANAAA---------------EGPVLIEDIDAGGFD--ETGLFHLINSVRQAG-TS-LLMTSRL  126 (226)
T ss_pred             ------------cchHHHHhhh---------------cCeEEEECCCCCCCC--HHHHHHHHHHHHhCC-Ce-EEEECCC
Confidence                        0011222111               127899999976432  133545455555544 33 3444443


Q ss_pred             CCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCcHHHHHHHHH
Q 005987          304 GKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASGGDIRQAITSLQ  380 (666)
Q Consensus       304 ~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~s~GDIR~AIn~LQ  380 (666)
                      .. ..+   ...++.|++++..  +..+.+.+|+.+.+.++|++.+...++.++++++++|+..+.||+|.++..|.
T Consensus       127 ~p-~~~---~~~~~dL~SRl~~--gl~~~l~~pd~e~~~~iL~~~~~~~~~~l~~ev~~~La~~~~r~~~~l~~~l~  197 (226)
T PRK09087        127 WP-SSW---NVKLPDLKSRLKA--ATVVEIGEPDDALLSQVIFKLFADRQLYVDPHVVYYLVSRMERSLFAAQTIVD  197 (226)
T ss_pred             Ch-HHh---ccccccHHHHHhC--CceeecCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhhhhHHHHHHHHH
Confidence            22 111   1224567877664  78999999999999999999999999999999999999999999999986443

>KOG0733 consensus Nuclear AAA ATPase (VCP subfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=99.51  E-value=2.3e-13  Score=148.44  Aligned_cols=247  Identities=17%  Similarity=0.284  Sum_probs=152.1

Q ss_pred             cccCCCCCc---hhhhchhhhhhccccCCccccccCCCCCCCCccCCCCCCccccccCCCCccccccCHHHHHHHHHHHH
Q 005987           90 WTNKNKPCS---LEEHAIQKENVGRFLTPSRFEGLVNPDHDSASASSSTQQLWAEKYKPRSLEELAVQRKKVEEVRAWFE  166 (666)
Q Consensus        90 w~~~~~~~s---~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~W~eKY~P~sl~eLvg~~k~i~el~~wL~  166 (666)
                      |.+.+.|||   ........+||...+.  .|    +|.++.....-..+..|         +|+-+.++...++...+.
T Consensus       464 i~~~~d~~S~E~~~~L~i~~eDF~~Al~--~i----QPSakREGF~tVPdVtW---------~dIGaL~~vR~eL~~aI~  528 (802)
T KOG0733|consen  464 ILNNPDPLSKELLEGLSIKFEDFEEALS--KI----QPSAKREGFATVPDVTW---------DDIGALEEVRLELNMAIL  528 (802)
T ss_pred             HHhCCCCcChHHhccceecHHHHHHHHH--hc----CcchhcccceecCCCCh---------hhcccHHHHHHHHHHHHh
Confidence            556666777   3344456667776665  44    44443333222233444         667777777777776665


Q ss_pred             HhhcCC-----CCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCchhhhhhhhcccCCccccchhHHHHHHH
Q 005987          167 ERLGDS-----KDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTIWQEYMHNCKTGLEYTSKLDEFENFV  241 (666)
Q Consensus       167 ~~~~~~-----~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~~~~e~l~~~~~g~~~~s~~~~f~~fl  241 (666)
                      .-.+..     -|-.++..+||+||||||||.+|+++|+|.|.+++.+..|.  .+..++         ......+++++
T Consensus       529 ~PiK~pd~~k~lGi~~PsGvLL~GPPGCGKTLlAKAVANEag~NFisVKGPE--LlNkYV---------GESErAVR~vF  597 (802)
T KOG0733|consen  529 APIKRPDLFKALGIDAPSGVLLCGPPGCGKTLLAKAVANEAGANFISVKGPE--LLNKYV---------GESERAVRQVF  597 (802)
T ss_pred             hhccCHHHHHHhCCCCCCceEEeCCCCccHHHHHHHHhhhccCceEeecCHH--HHHHHh---------hhHHHHHHHHH
Confidence            322211     13333468999999999999999999999999999998875  222222         23345677888


Q ss_pred             HHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcch------hHHHHHHHHHHHHHhcC-CCceEEEEecCCCCCCccchhh
Q 005987          242 ERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGR------TAFERLRQCLLLLVRST-HIPTAVVLTECGKADSVDSTAQ  314 (666)
Q Consensus       242 ~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~------~~~~~l~~~L~~l~~~~-~~PiViIit~~~~~~s~d~~~r  314 (666)
                      .+++..            .|+|||+||+|.+..+      ..-.++.+.|+.-++.. .+--|+++++++.++..|.   
T Consensus       598 qRAR~s------------aPCVIFFDEiDaL~p~R~~~~s~~s~RvvNqLLtElDGl~~R~gV~viaATNRPDiIDp---  662 (802)
T KOG0733|consen  598 QRARAS------------APCVIFFDEIDALVPRRSDEGSSVSSRVVNQLLTELDGLEERRGVYVIAATNRPDIIDP---  662 (802)
T ss_pred             HHhhcC------------CCeEEEecchhhcCcccCCCCchhHHHHHHHHHHHhcccccccceEEEeecCCCcccch---
Confidence            888532            4799999999976432      22334544444333332 2334677777777765442   


Q ss_pred             hhhHHHHHHhhc-C-eeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHH-HHHHHHHH------cCCcHHHHHHHHHHHhc
Q 005987          315 SFEELQSILVDA-G-ARKVALNPITNGSIKRTLSKICRQEQYSLSTE-QIDLVAQA------SGGDIRQAITSLQFSSL  384 (666)
Q Consensus       315 ~l~~L~s~L~r~-r-~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~-~l~~Ia~~------s~GDIR~AIn~LQf~~~  384 (666)
                            ++| |+ | -..+....|+.++...+|+.+.+..+..++++ -++.||..      ++.|+-..+.---++++
T Consensus       663 ------AiL-RPGRlDk~LyV~lPn~~eR~~ILK~~tkn~k~pl~~dVdl~eia~~~~c~gftGADLaaLvreAsi~AL  734 (802)
T KOG0733|consen  663 ------AIL-RPGRLDKLLYVGLPNAEERVAILKTITKNTKPPLSSDVDLDEIARNTKCEGFTGADLAALVREASILAL  734 (802)
T ss_pred             ------hhc-CCCccCceeeecCCCHHHHHHHHHHHhccCCCCCCcccCHHHHhhcccccCCchhhHHHHHHHHHHHHH
Confidence                  122 22 2 23567778899999999999988655555543 36667654      45677665554444443

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=99.50  E-value=8.5e-13  Score=147.34  Aligned_cols=197  Identities=21%  Similarity=0.276  Sum_probs=122.5

Q ss_pred             Ccccccc---CHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc-----CCcEEEEcCCCchhhh
Q 005987          147 SLEELAV---QRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL-----GARLYEWDTPTPTIWQ  218 (666)
Q Consensus       147 sl~eLvg---~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel-----g~~viE~nasd~~~~~  218 (666)
                      +|+++++   +......++.|.+.     ++.. .+.++||||||||||++++++|+++     +..++.+++.+.  ..
T Consensus       120 tfd~fv~g~~n~~a~~~~~~~~~~-----~~~~-~~~l~l~G~~G~GKThL~~ai~~~~~~~~~~~~v~yi~~~~~--~~  191 (450)
T PRK00149        120 TFDNFVVGKSNRLAHAAALAVAEN-----PGKA-YNPLFIYGGVGLGKTHLLHAIGNYILEKNPNAKVVYVTSEKF--TN  191 (450)
T ss_pred             cccccccCCCcHHHHHHHHHHHhC-----cCcc-CCeEEEECCCCCCHHHHHHHHHHHHHHhCCCCeEEEEEHHHH--HH
Confidence            5666553   33345555555442     1222 2579999999999999999999998     566777775431  11


Q ss_pred             hhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhH-HHHHHHHHHHHHhcCCCceE
Q 005987          219 EYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTA-FERLRQCLLLLVRSTHIPTA  297 (666)
Q Consensus       219 e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~-~~~l~~~L~~l~~~~~~PiV  297 (666)
                      +......     ..   ....|.+...              ...+|+|||++.+.+... .+.+...+..+.+.++ ++ 
T Consensus       192 ~~~~~~~-----~~---~~~~~~~~~~--------------~~dlLiiDDi~~l~~~~~~~~~l~~~~n~l~~~~~-~i-  247 (450)
T PRK00149        192 DFVNALR-----NN---TMEEFKEKYR--------------SVDVLLIDDIQFLAGKERTQEEFFHTFNALHEAGK-QI-  247 (450)
T ss_pred             HHHHHHH-----cC---cHHHHHHHHh--------------cCCEEEEehhhhhcCCHHHHHHHHHHHHHHHHCCC-cE-
Confidence            1111100     00   1122333222              124899999998765432 2334444555555543 43 


Q ss_pred             EEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCcHHHHHH
Q 005987          298 VVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASGGDIRQAIT  377 (666)
Q Consensus       298 iIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~s~GDIR~AIn  377 (666)
                      +++++.... ..   ....+.|.+++.  .+..+.|.+|+.+.+.++|++.+...++.+++++++.|+..+.||+|.++.
T Consensus       248 iits~~~p~-~l---~~l~~~l~SRl~--~gl~v~i~~pd~~~r~~il~~~~~~~~~~l~~e~l~~ia~~~~~~~R~l~~  321 (450)
T PRK00149        248 VLTSDRPPK-EL---PGLEERLRSRFE--WGLTVDIEPPDLETRIAILKKKAEEEGIDLPDEVLEFIAKNITSNVRELEG  321 (450)
T ss_pred             EEECCCCHH-HH---HHHHHHHHhHhc--CCeeEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHcCcCCCHHHHHH
Confidence            445543211 00   111233455443  257899999999999999999999999999999999999999999998554


Q ss_pred             HHHH
Q 005987          378 SLQF  381 (666)
Q Consensus       378 ~LQf  381 (666)
                      .|..
T Consensus       322 ~l~~  325 (450)
T PRK00149        322 ALNR  325 (450)
T ss_pred             HHHH
Confidence            4443

>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=99.50  E-value=1.5e-12  Score=131.29  Aligned_cols=198  Identities=23%  Similarity=0.345  Sum_probs=120.3

Q ss_pred             Ccccccc---CHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc-----CCcEEEEcCCCchhhh
Q 005987          147 SLEELAV---QRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL-----GARLYEWDTPTPTIWQ  218 (666)
Q Consensus       147 sl~eLvg---~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel-----g~~viE~nasd~~~~~  218 (666)
                      ||+.++.   ++.....+....+.     ++. ..+.++||||+|+|||++++++++++     +..++.+++.+  ...
T Consensus         6 tFdnfv~g~~N~~a~~~~~~ia~~-----~~~-~~~~l~l~G~~G~GKTHLL~Ai~~~~~~~~~~~~v~y~~~~~--f~~   77 (219)
T PF00308_consen    6 TFDNFVVGESNELAYAAAKAIAEN-----PGE-RYNPLFLYGPSGLGKTHLLQAIANEAQKQHPGKRVVYLSAEE--FIR   77 (219)
T ss_dssp             SCCCS--TTTTHHHHHHHHHHHHS-----TTT-SSSEEEEEESTTSSHHHHHHHHHHHHHHHCTTS-EEEEEHHH--HHH
T ss_pred             ccccCCcCCcHHHHHHHHHHHHhc-----CCC-CCCceEEECCCCCCHHHHHHHHHHHHHhccccccceeecHHH--HHH
Confidence            5666653   44445555544433     122 22579999999999999999999886     56677776532  111


Q ss_pred             hhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhH-HHHHHHHHHHHHhcCCCceE
Q 005987          219 EYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTA-FERLRQCLLLLVRSTHIPTA  297 (666)
Q Consensus       219 e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~-~~~l~~~L~~l~~~~~~PiV  297 (666)
                      +.......        ....+|.++...              .-+|+|||++.+.+... ...+...+..+.+.++ + +
T Consensus        78 ~~~~~~~~--------~~~~~~~~~~~~--------------~DlL~iDDi~~l~~~~~~q~~lf~l~n~~~~~~k-~-l  133 (219)
T PF00308_consen   78 EFADALRD--------GEIEEFKDRLRS--------------ADLLIIDDIQFLAGKQRTQEELFHLFNRLIESGK-Q-L  133 (219)
T ss_dssp             HHHHHHHT--------TSHHHHHHHHCT--------------SSEEEEETGGGGTTHHHHHHHHHHHHHHHHHTTS-E-E
T ss_pred             HHHHHHHc--------ccchhhhhhhhc--------------CCEEEEecchhhcCchHHHHHHHHHHHHHHhhCC-e-E
Confidence            11111000        112334443322              23999999998876532 2334455555555543 3 4


Q ss_pred             EEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCcHHHHHH
Q 005987          298 VVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASGGDIRQAIT  377 (666)
Q Consensus       298 iIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~s~GDIR~AIn  377 (666)
                      +++++..+..    .....++|.+++..  +..+.+.+|+.+...++|++.+...++.+++++++.|+....+|+|....
T Consensus       134 i~ts~~~P~~----l~~~~~~L~SRl~~--Gl~~~l~~pd~~~r~~il~~~a~~~~~~l~~~v~~~l~~~~~~~~r~L~~  207 (219)
T PF00308_consen  134 ILTSDRPPSE----LSGLLPDLRSRLSW--GLVVELQPPDDEDRRRILQKKAKERGIELPEEVIEYLARRFRRDVRELEG  207 (219)
T ss_dssp             EEEESS-TTT----TTTS-HHHHHHHHC--SEEEEE----HHHHHHHHHHHHHHTT--S-HHHHHHHHHHTTSSHHHHHH
T ss_pred             EEEeCCCCcc----ccccChhhhhhHhh--cchhhcCCCCHHHHHHHHHHHHHHhCCCCcHHHHHHHHHhhcCCHHHHHH
Confidence            5556544322    12234567888864  78899999999999999999999999999999999999999999998766


Q ss_pred             HHHHH
Q 005987          378 SLQFS  382 (666)
Q Consensus       378 ~LQf~  382 (666)
                      .|.-+
T Consensus       208 ~l~~l  212 (219)
T PF00308_consen  208 ALNRL  212 (219)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            66543

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.

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

Probab=99.50  E-value=2.7e-13  Score=159.55  Aligned_cols=211  Identities=20%  Similarity=0.246  Sum_probs=145.2

Q ss_pred             CCCccccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc----------CC
Q 005987          135 TQQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL----------GA  204 (666)
Q Consensus       135 ~~~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel----------g~  204 (666)
                      ...+++++.+|..+++++|+++.++.+...|...      .  .+.+||+||||||||++|+.+|+.+          +.
T Consensus       168 ~~~~l~~~~r~~~l~~~igr~~ei~~~~~~L~~~------~--~~n~lL~G~pG~GKT~l~~~la~~~~~~~~p~~l~~~  239 (731)
T TIGR02639       168 YTVDLTEKAKNGKIDPLIGREDELERTIQVLCRR------K--KNNPLLVGEPGVGKTAIAEGLALRIAEGKVPENLKNA  239 (731)
T ss_pred             HhhhHHHHHhcCCCCcccCcHHHHHHHHHHHhcC------C--CCceEEECCCCCCHHHHHHHHHHHHHhCCCchhhcCC
Confidence            4567999999999999999999999988877642      1  2478999999999999999999998          56


Q ss_pred             cEEEEcCCCchhhhhhhhcccCCcccc-chhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchh----HHH
Q 005987          205 RLYEWDTPTPTIWQEYMHNCKTGLEYT-SKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRT----AFE  279 (666)
Q Consensus       205 ~viE~nasd~~~~~e~l~~~~~g~~~~-s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~----~~~  279 (666)
                      .+++++...          ...|..|. .....++.+++.+...            .+.||+|||++.+.+..    .-.
T Consensus       240 ~~~~~~~~~----------l~a~~~~~g~~e~~l~~i~~~~~~~------------~~~ILfiDEih~l~~~g~~~~~~~  297 (731)
T TIGR02639       240 KIYSLDMGS----------LLAGTKYRGDFEERLKAVVSEIEKE------------PNAILFIDEIHTIVGAGATSGGSM  297 (731)
T ss_pred             eEEEecHHH----------HhhhccccchHHHHHHHHHHHHhcc------------CCeEEEEecHHHHhccCCCCCccH
Confidence            666665322          11222221 2234566667666432            25799999999764321    001


Q ss_pred             HHHHHHHHHHhcCCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHH----hCCC
Q 005987          280 RLRQCLLLLVRSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQ----EQYS  355 (666)
Q Consensus       280 ~l~~~L~~l~~~~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~----e~i~  355 (666)
                      ...+.|...+..+.  +.+| +.++..    .+.+.++ +...|.| |+..|.+.+|+.+++.++|+.+...    .++.
T Consensus       298 ~~~~~L~~~l~~g~--i~~I-gaTt~~----e~~~~~~-~d~al~r-Rf~~i~v~~p~~~~~~~il~~~~~~~e~~~~v~  368 (731)
T TIGR02639       298 DASNLLKPALSSGK--LRCI-GSTTYE----EYKNHFE-KDRALSR-RFQKIDVGEPSIEETVKILKGLKEKYEEFHHVK  368 (731)
T ss_pred             HHHHHHHHHHhCCC--eEEE-EecCHH----HHHHHhh-hhHHHHH-hCceEEeCCCCHHHHHHHHHHHHHHHHhccCcc
Confidence            23455667766653  3333 333321    1223333 3444444 5889999999999999999988765    3577


Q ss_pred             CCHHHHHHHHHHcCC---c---HHHHHHHHHHHhc
Q 005987          356 LSTEQIDLVAQASGG---D---IRQAITSLQFSSL  384 (666)
Q Consensus       356 v~~~~l~~Ia~~s~G---D---IR~AIn~LQf~~~  384 (666)
                      ++++++..++..++.   |   .++||..|.-+|.
T Consensus       369 i~~~al~~~~~ls~ryi~~r~~P~kai~lld~a~a  403 (731)
T TIGR02639       369 YSDEALEAAVELSARYINDRFLPDKAIDVIDEAGA  403 (731)
T ss_pred             cCHHHHHHHHHhhhcccccccCCHHHHHHHHHhhh
Confidence            999999999998864   3   6788988876654

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

Probab=99.50  E-value=2.4e-13  Score=149.30  Aligned_cols=214  Identities=15%  Similarity=0.231  Sum_probs=130.5

Q ss_pred             CCccccccCCCCccccccCHHHHHHHHHHHHHhhcCC-----CCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEc
Q 005987          136 QQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDS-----KDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWD  210 (666)
Q Consensus       136 ~~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~-----~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~n  210 (666)
                      ..++++++.+.+++||.|.+..++++++++.-.+...     -|-.+++.+||+||||||||++|+++|++++..++.+.
T Consensus       170 ~~~~~~~~p~~~~~DIgGl~~qi~~l~e~v~lpl~~p~~~~~~gi~~p~gVLL~GPPGTGKT~LAraIA~el~~~fi~V~  249 (438)
T PTZ00361        170 SVMKVDKAPLESYADIGGLEQQIQEIKEAVELPLTHPELYDDIGIKPPKGVILYGPPGTGKTLLAKAVANETSATFLRVV  249 (438)
T ss_pred             hhcccccCCCCCHHHhcCHHHHHHHHHHHHHhhhhCHHHHHhcCCCCCcEEEEECCCCCCHHHHHHHHHHhhCCCEEEEe
Confidence            4578999999999999999999999999987443321     13334478999999999999999999999999999887


Q ss_pred             CCCchhhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchh------HHHHHHHH
Q 005987          211 TPTPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRT------AFERLRQC  284 (666)
Q Consensus       211 asd~~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~------~~~~l~~~  284 (666)
                      .++.  ...+     .|    .....+..++..+...            .+.||+|||+|.+....      .-...+..
T Consensus       250 ~seL--~~k~-----~G----e~~~~vr~lF~~A~~~------------~P~ILfIDEID~l~~kR~~~~sgg~~e~qr~  306 (438)
T PTZ00361        250 GSEL--IQKY-----LG----DGPKLVRELFRVAEEN------------APSIVFIDEIDAIGTKRYDATSGGEKEIQRT  306 (438)
T ss_pred             cchh--hhhh-----cc----hHHHHHHHHHHHHHhC------------CCcEEeHHHHHHHhccCCCCCCcccHHHHHH
Confidence            6541  1111     11    1122344555544321            36799999998653210      00111122


Q ss_pred             HHHHH---hc--CCCceEEEEecCCCCCCccchhhhhhHHHHHHhhc--CeeEEEeCCCCHHHHHHHHHHHHHHhCCCCC
Q 005987          285 LLLLV---RS--THIPTAVVLTECGKADSVDSTAQSFEELQSILVDA--GARKVALNPITNGSIKRTLSKICRQEQYSLS  357 (666)
Q Consensus       285 L~~l~---~~--~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~--r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~  357 (666)
                      +..++   +.  ....+++|+++ +.          +..+...+.|+  .-..|.|.+|+..+...+|+..+.+..+.- 
T Consensus       307 ll~LL~~Ldg~~~~~~V~VI~AT-Nr----------~d~LDpaLlRpGRfd~~I~~~~Pd~~~R~~Il~~~~~k~~l~~-  374 (438)
T PTZ00361        307 MLELLNQLDGFDSRGDVKVIMAT-NR----------IESLDPALIRPGRIDRKIEFPNPDEKTKRRIFEIHTSKMTLAE-  374 (438)
T ss_pred             HHHHHHHHhhhcccCCeEEEEec-CC----------hHHhhHHhccCCeeEEEEEeCCCCHHHHHHHHHHHHhcCCCCc-
Confidence            22222   11  11223333332 21          12234433332  245799999999999999998776554321 


Q ss_pred             HHHHHHHHH----HcCCcHHHHHHHHHHHhc
Q 005987          358 TEQIDLVAQ----ASGGDIRQAITSLQFSSL  384 (666)
Q Consensus       358 ~~~l~~Ia~----~s~GDIR~AIn~LQf~~~  384 (666)
                      +..+..++.    .++.||+.++...-+.|.
T Consensus       375 dvdl~~la~~t~g~sgAdI~~i~~eA~~~Al  405 (438)
T PTZ00361        375 DVDLEEFIMAKDELSGADIKAICTEAGLLAL  405 (438)
T ss_pred             CcCHHHHHHhcCCCCHHHHHHHHHHHHHHHH
Confidence            123445553    466788877766555554

>CHL00176 ftsH cell division protein; Validated

Probab=99.49  E-value=8.2e-13  Score=151.62  Aligned_cols=205  Identities=15%  Similarity=0.202  Sum_probs=128.8

Q ss_pred             CCCccccccCHHHHHHHHHHHHHhhcCCC----CCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCchhhhhh
Q 005987          145 PRSLEELAVQRKKVEEVRAWFEERLGDSK----DKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTIWQEY  220 (666)
Q Consensus       145 P~sl~eLvg~~k~i~el~~wL~~~~~~~~----g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~~~~e~  220 (666)
                      ..+++|++|.++..+++...+.-......    |...++.+||+||||||||++|+++|.+++..++.+++++..   + 
T Consensus       179 ~~~f~dv~G~~~~k~~l~eiv~~lk~~~~~~~~g~~~p~gVLL~GPpGTGKT~LAralA~e~~~p~i~is~s~f~---~-  254 (638)
T CHL00176        179 GITFRDIAGIEEAKEEFEEVVSFLKKPERFTAVGAKIPKGVLLVGPPGTGKTLLAKAIAGEAEVPFFSISGSEFV---E-  254 (638)
T ss_pred             CCCHHhccChHHHHHHHHHHHHHHhCHHHHhhccCCCCceEEEECCCCCCHHHHHHHHHHHhCCCeeeccHHHHH---H-
Confidence            36899999998888888776643211111    223347899999999999999999999999999988876411   0 


Q ss_pred             hhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcch---------hHHHHHHHHHHHHHhc
Q 005987          221 MHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGR---------TAFERLRQCLLLLVRS  291 (666)
Q Consensus       221 l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~---------~~~~~l~~~L~~l~~~  291 (666)
                         ...|.    ....++.++.++...            .|+||+|||+|.+...         .........|+..++.
T Consensus       255 ---~~~g~----~~~~vr~lF~~A~~~------------~P~ILfIDEID~l~~~r~~~~~~~~~e~~~~L~~LL~~~dg  315 (638)
T CHL00176        255 ---MFVGV----GAARVRDLFKKAKEN------------SPCIVFIDEIDAVGRQRGAGIGGGNDEREQTLNQLLTEMDG  315 (638)
T ss_pred             ---Hhhhh----hHHHHHHHHHHHhcC------------CCcEEEEecchhhhhcccCCCCCCcHHHHHHHHHHHhhhcc
Confidence               01111    123456666666432            3679999999976311         1112222222222221


Q ss_pred             --CCCceEEEEecCCCCCCccchhhhhhHHHHHHhhc--CeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHH
Q 005987          292 --THIPTAVVLTECGKADSVDSTAQSFEELQSILVDA--GARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQA  367 (666)
Q Consensus       292 --~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~--r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~  367 (666)
                        ....+++|++ ++..+          .+...+.|+  ....|.|.+|+.++...+|+..+....+ .++..+..|+..
T Consensus       316 ~~~~~~ViVIaa-TN~~~----------~LD~ALlRpGRFd~~I~v~lPd~~~R~~IL~~~l~~~~~-~~d~~l~~lA~~  383 (638)
T CHL00176        316 FKGNKGVIVIAA-TNRVD----------ILDAALLRPGRFDRQITVSLPDREGRLDILKVHARNKKL-SPDVSLELIARR  383 (638)
T ss_pred             ccCCCCeeEEEe-cCchH----------hhhhhhhccccCceEEEECCCCHHHHHHHHHHHHhhccc-chhHHHHHHHhc
Confidence              1223444433 33221          233333332  2367999999999999999998877432 346678899988


Q ss_pred             cCC----cHHHHHHHHHHHhc
Q 005987          368 SGG----DIRQAITSLQFSSL  384 (666)
Q Consensus       368 s~G----DIR~AIn~LQf~~~  384 (666)
                      +.|    ||+.++|..-+.+.
T Consensus       384 t~G~sgaDL~~lvneAal~a~  404 (638)
T CHL00176        384 TPGFSGADLANLLNEAAILTA  404 (638)
T ss_pred             CCCCCHHHHHHHHHHHHHHHH
Confidence            777    99999987655443

>TIGR01241 FtsH_fam ATP-dependent metalloprotease FtsH

Probab=99.49  E-value=3.4e-13  Score=152.26  Aligned_cols=211  Identities=17%  Similarity=0.253  Sum_probs=131.0

Q ss_pred             CccccccCCCCccccccCHHHHHHHHHHHHHhhcCC-----CCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcC
Q 005987          137 QLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDS-----KDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDT  211 (666)
Q Consensus       137 ~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~-----~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~na  211 (666)
                      ..+.+.....+++|++|.+...+++++++.- +...     .|..+++.+||+||||||||++|+++|++++..++.++.
T Consensus        43 ~~~~~~~~~~~~~di~g~~~~k~~l~~~~~~-l~~~~~~~~~g~~~~~giLL~GppGtGKT~la~alA~~~~~~~~~i~~  121 (495)
T TIGR01241        43 KLLNEEKPKVTFKDVAGIDEAKEELMEIVDF-LKNPSKFTKLGAKIPKGVLLVGPPGTGKTLLAKAVAGEAGVPFFSISG  121 (495)
T ss_pred             ccccCCCCCCCHHHhCCHHHHHHHHHHHHHH-HHCHHHHHhcCCCCCCcEEEECCCCCCHHHHHHHHHHHcCCCeeeccH
Confidence            3455666778999999999988888877662 2210     123334789999999999999999999999999998886


Q ss_pred             CCchhhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcch---------hHHHHHH
Q 005987          212 PTPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGR---------TAFERLR  282 (666)
Q Consensus       212 sd~~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~---------~~~~~l~  282 (666)
                      ++..   .    ...|    .....++.+++.+...            .|.||+|||+|.+...         .......
T Consensus       122 ~~~~---~----~~~g----~~~~~l~~~f~~a~~~------------~p~Il~iDEid~l~~~r~~~~~~~~~~~~~~~  178 (495)
T TIGR01241       122 SDFV---E----MFVG----VGASRVRDLFEQAKKN------------APCIIFIDEIDAVGRQRGAGLGGGNDEREQTL  178 (495)
T ss_pred             HHHH---H----HHhc----ccHHHHHHHHHHHHhc------------CCCEEEEechhhhhhccccCcCCccHHHHHHH
Confidence            5411   0    0111    1233566666666432            3579999999976321         1111222


Q ss_pred             HHHHHHHhc--CCCceEEEEecCCCCCCccchhhhhhHHHHHHhhc--CeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCH
Q 005987          283 QCLLLLVRS--THIPTAVVLTECGKADSVDSTAQSFEELQSILVDA--GARKVALNPITNGSIKRTLSKICRQEQYSLST  358 (666)
Q Consensus       283 ~~L~~l~~~--~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~--r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~  358 (666)
                      ..|+..++.  ....+++| ..++.++.          |...+.|+  .-..|.|..|+.++..++|+..+...... ++
T Consensus       179 ~~lL~~~d~~~~~~~v~vI-~aTn~~~~----------ld~al~r~gRfd~~i~i~~Pd~~~R~~il~~~l~~~~~~-~~  246 (495)
T TIGR01241       179 NQLLVEMDGFGTNTGVIVI-AATNRPDV----------LDPALLRPGRFDRQVVVDLPDIKGREEILKVHAKNKKLA-PD  246 (495)
T ss_pred             HHHHhhhccccCCCCeEEE-EecCChhh----------cCHHHhcCCcceEEEEcCCCCHHHHHHHHHHHHhcCCCC-cc
Confidence            223322221  11224333 33333221          22233221  23579999999999999999887665443 34


Q ss_pred             HHHHHHHHH----cCCcHHHHHHHHHHHh
Q 005987          359 EQIDLVAQA----SGGDIRQAITSLQFSS  383 (666)
Q Consensus       359 ~~l~~Ia~~----s~GDIR~AIn~LQf~~  383 (666)
                      ..+..|+..    +++||+.+++..-+.+
T Consensus       247 ~~l~~la~~t~G~sgadl~~l~~eA~~~a  275 (495)
T TIGR01241       247 VDLKAVARRTPGFSGADLANLLNEAALLA  275 (495)
T ss_pred             hhHHHHHHhCCCCCHHHHHHHHHHHHHHH
Confidence            456777776    4578998888654443

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.

>TIGR02903 spore_lon_C ATP-dependent protease, Lon family

Probab=99.49  E-value=1.1e-12  Score=150.90  Aligned_cols=224  Identities=16%  Similarity=0.171  Sum_probs=131.1

Q ss_pred             CCccccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc----------CCc
Q 005987          136 QQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL----------GAR  205 (666)
Q Consensus       136 ~~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel----------g~~  205 (666)
                      ..+..+.|||+++++++|+...++.+..-+..      +. + ..++|+|||||||||+|+++++..          +..
T Consensus       141 ~~~~~~~~rp~~~~~iiGqs~~~~~l~~~ia~------~~-~-~~vlL~Gp~GtGKTTLAr~i~~~~~~~~~~~~~~~~~  212 (615)
T TIGR02903       141 HKSAQSLLRPRAFSEIVGQERAIKALLAKVAS------PF-P-QHIILYGPPGVGKTTAARLALEEAKKLKHTPFAEDAP  212 (615)
T ss_pred             hhHHhhhcCcCcHHhceeCcHHHHHHHHHHhc------CC-C-CeEEEECCCCCCHHHHHHHHHHhhhhccCCcccCCCC
Confidence            35577889999999999999999987655532      22 2 479999999999999999998765          235


Q ss_pred             EEEEcCCCchhhh-hhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHH
Q 005987          206 LYEWDTPTPTIWQ-EYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQC  284 (666)
Q Consensus       206 viE~nasd~~~~~-e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~  284 (666)
                      ++++++.... +. ..+.+...|.............+....-..........  -...+|||||++.++... ...+...
T Consensus       213 fv~i~~~~l~-~d~~~i~~~llg~~~~~~~~~a~~~l~~~gl~~~~~g~v~~--asgGvL~LDEi~~Ld~~~-Q~~Ll~~  288 (615)
T TIGR02903       213 FVEVDGTTLR-WDPREVTNPLLGSVHDPIYQGARRDLAETGVPEPKTGLVTD--AHGGVLFIDEIGELDPLL-QNKLLKV  288 (615)
T ss_pred             eEEEechhcc-CCHHHHhHHhcCCccHHHHHHHHHHHHHcCCCchhcCchhh--cCCCeEEEeccccCCHHH-HHHHHHH
Confidence            6777765421 00 00000001100000000001111110000000000000  112499999999886532 2333333


Q ss_pred             HHHH-----------------------Hhc-CCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHH
Q 005987          285 LLLL-----------------------VRS-THIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGS  340 (666)
Q Consensus       285 L~~l-----------------------~~~-~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~  340 (666)
                      |..-                       +.. .+..++++++++....      ...+.|++     ||..+.|.|++.++
T Consensus       289 Le~~~v~~~~~~~~~~~~~~~~~ik~~~~~~~~~~~VLI~aTt~~~~------~l~~aLrS-----R~~~i~~~pls~ed  357 (615)
T TIGR02903       289 LEDKRVEFSSSYYDPDDPNVPKYIKKLFEEGAPADFVLIGATTRDPE------EINPALRS-----RCAEVFFEPLTPED  357 (615)
T ss_pred             HhhCeEEeecceeccCCcccchhhhhhcccCccceEEEEEecccccc------ccCHHHHh-----ceeEEEeCCCCHHH
Confidence            3210                       000 1112444444332211      11122332     58899999999999


Q ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHHHHcCCcHHHHHHHHHHHh
Q 005987          341 IKRTLSKICRQEQYSLSTEQIDLVAQASGGDIRQAITSLQFSS  383 (666)
Q Consensus       341 i~kiL~~I~~~e~i~v~~~~l~~Ia~~s~GDIR~AIn~LQf~~  383 (666)
                      +..++++++.+.++.+++++++.|+..+ ++.|.++|.|+-++
T Consensus       358 i~~Il~~~a~~~~v~ls~eal~~L~~ys-~~gRraln~L~~~~  399 (615)
T TIGR02903       358 IALIVLNAAEKINVHLAAGVEELIARYT-IEGRKAVNILADVY  399 (615)
T ss_pred             HHHHHHHHHHHcCCCCCHHHHHHHHHCC-CcHHHHHHHHHHHH
Confidence            9999999999888889999999999876 58899999998764

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.

>TIGR00678 holB DNA polymerase III, delta' subunit

Probab=99.48  E-value=1.7e-12  Score=127.81  Aligned_cols=169  Identities=17%  Similarity=0.236  Sum_probs=102.2

Q ss_pred             CCCCccEEEEECCCCchHHHHHHHHHHHcCCcE-EEEcCCCchhhhhhhhc-ccCCcc------ccchhHHHHHHHHHHH
Q 005987          174 DKFSTNVLVITGQAGVGKTATVRQIASHLGARL-YEWDTPTPTIWQEYMHN-CKTGLE------YTSKLDEFENFVERIR  245 (666)
Q Consensus       174 g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~v-iE~nasd~~~~~e~l~~-~~~g~~------~~s~~~~f~~fl~~a~  245 (666)
                      ++.+ +.+||+||+|+|||++++.+|+.+...- ........+.....+.. ...+..      -....+.++++++.+.
T Consensus        11 ~~~~-~~~L~~G~~G~gkt~~a~~~~~~l~~~~~~~~~~c~~~~~c~~~~~~~~~d~~~~~~~~~~~~~~~i~~i~~~~~   89 (188)
T TIGR00678        11 GRLA-HAYLFAGPEGVGKELLALALAKALLCEQPGGGEPCGECPSCRLIEAGNHPDLHRLEPEGQSIKVDQVRELVEFLS   89 (188)
T ss_pred             CCCC-eEEEEECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHHcCCCCcEEEeccccCcCCHHHHHHHHHHHc
Confidence            5555 6899999999999999999999985430 00000000000000000 000000      0123456766676664


Q ss_pred             hhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcCC-CceEEEEecCCCCCCccchhhhhhHHHHHHh
Q 005987          246 RYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTH-IPTAVVLTECGKADSVDSTAQSFEELQSILV  324 (666)
Q Consensus       246 ~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~~-~PiViIit~~~~~~s~d~~~r~l~~L~s~L~  324 (666)
                      ..+.     .   ..++||||||++.+...     .++.|+.+++... ..+++++++ .       ..+.++.+++   
T Consensus        90 ~~~~-----~---~~~kviiide~~~l~~~-----~~~~Ll~~le~~~~~~~~il~~~-~-------~~~l~~~i~s---  145 (188)
T TIGR00678        90 RTPQ-----E---SGRRVVIIEDAERMNEA-----AANALLKTLEEPPPNTLFILITP-S-------PEKLLPTIRS---  145 (188)
T ss_pred             cCcc-----c---CCeEEEEEechhhhCHH-----HHHHHHHHhcCCCCCeEEEEEEC-C-------hHhChHHHHh---
Confidence            3321     1   24579999999988643     2234556666533 223334433 1       1223333333   


Q ss_pred             hcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCcHHHH
Q 005987          325 DAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASGGDIRQA  375 (666)
Q Consensus       325 r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~s~GDIR~A  375 (666)
                        ||..+.|.|++..++.++|.+.    +  +++++++.|+..++||+|.|
T Consensus       146 --r~~~~~~~~~~~~~~~~~l~~~----g--i~~~~~~~i~~~~~g~~r~~  188 (188)
T TIGR00678       146 --RCQVLPFPPLSEEALLQWLIRQ----G--ISEEAAELLLALAGGSPGAA  188 (188)
T ss_pred             --hcEEeeCCCCCHHHHHHHHHHc----C--CCHHHHHHHHHHcCCCcccC
Confidence              5899999999999999998875    4  78999999999999999975

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.

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=99.48  E-value=2.2e-12  Score=142.16  Aligned_cols=173  Identities=22%  Similarity=0.299  Sum_probs=110.9

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc-----CCcEEEEcCCCchhhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL-----GARLYEWDTPTPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPS  253 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel-----g~~viE~nasd~~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s  253 (666)
                      +.++||||+|+|||++++++++++     +..++.+++.+.  ..+.......     ..   +..|.+....       
T Consensus       137 n~l~l~G~~G~GKThL~~ai~~~l~~~~~~~~v~yi~~~~~--~~~~~~~~~~-----~~---~~~~~~~~~~-------  199 (405)
T TIGR00362       137 NPLFIYGGVGLGKTHLLHAIGNEILENNPNAKVVYVSSEKF--TNDFVNALRN-----NK---MEEFKEKYRS-------  199 (405)
T ss_pred             CeEEEECCCCCcHHHHHHHHHHHHHHhCCCCcEEEEEHHHH--HHHHHHHHHc-----CC---HHHHHHHHHh-------
Confidence            579999999999999999999987     567777775431  1111111000     01   2223332221       


Q ss_pred             CCCCCCCceEEEEeCCCCCcchhH-HHHHHHHHHHHHhcCCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEE
Q 005987          254 IPGESKSSAILLIDDLPVTNGRTA-FERLRQCLLLLVRSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVA  332 (666)
Q Consensus       254 ~~~~~~~~~IIlIDEid~l~~~~~-~~~l~~~L~~l~~~~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~  332 (666)
                             ..+|+|||++.+.+... ...+...+..+.+.+ .++ +++++.... .   .....+.|.+++.  .+..+.
T Consensus       200 -------~dlLiiDDi~~l~~~~~~~~~l~~~~n~~~~~~-~~i-iits~~~p~-~---l~~l~~~l~SRl~--~g~~v~  264 (405)
T TIGR00362       200 -------VDLLLIDDIQFLAGKERTQEEFFHTFNALHENG-KQI-VLTSDRPPK-E---LPGLEERLRSRFE--WGLVVD  264 (405)
T ss_pred             -------CCEEEEehhhhhcCCHHHHHHHHHHHHHHHHCC-CCE-EEecCCCHH-H---Hhhhhhhhhhhcc--CCeEEE
Confidence                   23899999998765422 223444455554444 344 444442211 0   1111233444443  256899


Q ss_pred             eCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCcHHH---HHHHHHHHh
Q 005987          333 LNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASGGDIRQ---AITSLQFSS  383 (666)
Q Consensus       333 F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~s~GDIR~---AIn~LQf~~  383 (666)
                      |.+|+.+.+..+|+..+...++.+++++++.|++...||+|.   ||+.|..++
T Consensus       265 i~~pd~~~r~~il~~~~~~~~~~l~~e~l~~ia~~~~~~~r~l~~~l~~l~~~a  318 (405)
T TIGR00362       265 IEPPDLETRLAILQKKAEEEGLELPDEVLEFIAKNIRSNVRELEGALNRLLAYA  318 (405)
T ss_pred             eCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHHHHHHHHHH
Confidence            999999999999999999999999999999999999999998   555555544

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).

>PRK14087 dnaA chromosomal replication initiation protein; Provisional

Probab=99.47  E-value=1.4e-12  Score=144.82  Aligned_cols=202  Identities=14%  Similarity=0.176  Sum_probs=127.8

Q ss_pred             CCCccccccCHH---HHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc-----CCcEEEEcCCCchh
Q 005987          145 PRSLEELAVQRK---KVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL-----GARLYEWDTPTPTI  216 (666)
Q Consensus       145 P~sl~eLvg~~k---~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel-----g~~viE~nasd~~~  216 (666)
                      +.+|+.++..+.   ....+..+.+.     ++.. .+.++||||+|+|||++++++++++     +..++.+++.+  .
T Consensus       111 ~~tFdnFv~g~~n~~A~~aa~~~a~~-----~~~~-~npl~i~G~~G~GKTHLl~Ai~~~l~~~~~~~~v~yv~~~~--f  182 (450)
T PRK14087        111 ENTFENFVIGSSNEQAFIAVQTVSKN-----PGIS-YNPLFIYGESGMGKTHLLKAAKNYIESNFSDLKVSYMSGDE--F  182 (450)
T ss_pred             ccchhcccCCCcHHHHHHHHHHHHhC-----cCcc-cCceEEECCCCCcHHHHHHHHHHHHHHhCCCCeEEEEEHHH--H
Confidence            457888775432   33334444321     1322 2579999999999999999999965     46777776543  1


Q ss_pred             hhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchh-HHHHHHHHHHHHHhcCCCc
Q 005987          217 WQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRT-AFERLRQCLLLLVRSTHIP  295 (666)
Q Consensus       217 ~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~-~~~~l~~~L~~l~~~~~~P  295 (666)
                      ..+......      ...+.+..|..+.   .           ...+|||||++.+.+.. ..+.+...+..+...++ +
T Consensus       183 ~~~~~~~l~------~~~~~~~~~~~~~---~-----------~~dvLiIDDiq~l~~k~~~~e~lf~l~N~~~~~~k-~  241 (450)
T PRK14087        183 ARKAVDILQ------KTHKEIEQFKNEI---C-----------QNDVLIIDDVQFLSYKEKTNEIFFTIFNNFIENDK-Q  241 (450)
T ss_pred             HHHHHHHHH------HhhhHHHHHHHHh---c-----------cCCEEEEeccccccCCHHHHHHHHHHHHHHHHcCC-c
Confidence            111111000      0001223333322   1           12489999999876542 23444455555555554 3


Q ss_pred             eEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCC--CCCHHHHHHHHHHcCCcHH
Q 005987          296 TAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQY--SLSTEQIDLVAQASGGDIR  373 (666)
Q Consensus       296 iViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i--~v~~~~l~~Ia~~s~GDIR  373 (666)
                       ++++++.....    .....+.|.+++..  ...+.+.+|+.+++.++|++.+...++  .+++++++.|+..++||+|
T Consensus       242 -iIltsd~~P~~----l~~l~~rL~SR~~~--Gl~~~L~~pd~e~r~~iL~~~~~~~gl~~~l~~evl~~Ia~~~~gd~R  314 (450)
T PRK14087        242 -LFFSSDKSPEL----LNGFDNRLITRFNM--GLSIAIQKLDNKTATAIIKKEIKNQNIKQEVTEEAINFISNYYSDDVR  314 (450)
T ss_pred             -EEEECCCCHHH----HhhccHHHHHHHhC--CceeccCCcCHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHccCCCHH
Confidence             45555533211    11122456666553  678999999999999999999998875  6999999999999999999


Q ss_pred             HHHHHHHHH
Q 005987          374 QAITSLQFS  382 (666)
Q Consensus       374 ~AIn~LQf~  382 (666)
                      .+.+.|.-+
T Consensus       315 ~L~gaL~~l  323 (450)
T PRK14087        315 KIKGSVSRL  323 (450)
T ss_pred             HHHHHHHHH
Confidence            999888654

>KOG0730 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=99.47  E-value=5.7e-13  Score=147.33  Aligned_cols=209  Identities=16%  Similarity=0.271  Sum_probs=140.2

Q ss_pred             ccCCCCccccccCHHHHHHHHHHHHHhhcCC-----CCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCchh
Q 005987          142 KYKPRSLEELAVQRKKVEEVRAWFEERLGDS-----KDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTI  216 (666)
Q Consensus       142 KY~P~sl~eLvg~~k~i~el~~wL~~~~~~~-----~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~~  216 (666)
                      .-...+++|+-|.+...++++..++--.+.+     =|-.|++.+|||||||||||++|+++|++.+.+++.+..+.  .
T Consensus       427 e~p~v~W~dIGGlE~lK~elq~~V~~p~~~pe~F~r~Gi~ppkGVLlyGPPGC~KT~lAkalAne~~~nFlsvkgpE--L  504 (693)
T KOG0730|consen  427 EMPNVSWDDIGGLEELKRELQQAVEWPLKHPEKFARFGISPPKGVLLYGPPGCGKTLLAKALANEAGMNFLSVKGPE--L  504 (693)
T ss_pred             cCCCCChhhccCHHHHHHHHHHHHhhhhhchHHHHHhcCCCCceEEEECCCCcchHHHHHHHhhhhcCCeeeccCHH--H
Confidence            3445678999999999999887766222110     14344589999999999999999999999999999988775  2


Q ss_pred             hhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcch------hHHHHHHHHHHHHHh
Q 005987          217 WQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGR------TAFERLRQCLLLLVR  290 (666)
Q Consensus       217 ~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~------~~~~~l~~~L~~l~~  290 (666)
                      +..+         +......+++++.+++..            .|.||++||+|.+...      ....++...|+.-++
T Consensus       505 ~sk~---------vGeSEr~ir~iF~kAR~~------------aP~IiFfDEiDsi~~~R~g~~~~v~~RVlsqLLtEmD  563 (693)
T KOG0730|consen  505 FSKY---------VGESERAIREVFRKARQV------------APCIIFFDEIDALAGSRGGSSSGVTDRVLSQLLTEMD  563 (693)
T ss_pred             HHHh---------cCchHHHHHHHHHHHhhc------------CCeEEehhhHHhHhhccCCCccchHHHHHHHHHHHcc
Confidence            2222         233445677788887644            3689999999976332      123455544444443


Q ss_pred             cCC-CceEEEEecCCCCCCccchhhhhhHHHHHHhhcC--eeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHH-HHHHHHH
Q 005987          291 STH-IPTAVVLTECGKADSVDSTAQSFEELQSILVDAG--ARKVALNPITNGSIKRTLSKICRQEQYSLSTE-QIDLVAQ  366 (666)
Q Consensus       291 ~~~-~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r--~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~-~l~~Ia~  366 (666)
                      ... .--|+|++.+|.++.          |...|.||+  -..|.+++|+.+....+|+..+++.  .++++ .++.||+
T Consensus       564 G~e~~k~V~ViAATNRpd~----------ID~ALlRPGRlD~iiyVplPD~~aR~~Ilk~~~kkm--p~~~~vdl~~La~  631 (693)
T KOG0730|consen  564 GLEALKNVLVIAATNRPDM----------IDPALLRPGRLDRIIYVPLPDLEARLEILKQCAKKM--PFSEDVDLEELAQ  631 (693)
T ss_pred             cccccCcEEEEeccCChhh----------cCHHHcCCcccceeEeecCccHHHHHHHHHHHHhcC--CCCccccHHHHHH
Confidence            221 224667777776553          333333322  4578999999999999998776654  44444 6788887


Q ss_pred             H----cCCcHHHHHHHHHHHhcC
Q 005987          367 A----SGGDIRQAITSLQFSSLK  385 (666)
Q Consensus       367 ~----s~GDIR~AIn~LQf~~~~  385 (666)
                      .    |+-||+...+---..|..
T Consensus       632 ~T~g~SGAel~~lCq~A~~~a~~  654 (693)
T KOG0730|consen  632 ATEGYSGAEIVAVCQEAALLALR  654 (693)
T ss_pred             HhccCChHHHHHHHHHHHHHHHH
Confidence            5    566888777766555553

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

Probab=99.47  E-value=9.6e-13  Score=143.58  Aligned_cols=210  Identities=17%  Similarity=0.211  Sum_probs=128.1

Q ss_pred             ccccCCCCccccccCHHHHHHHHHHHHHhhcCC-----CCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCc
Q 005987          140 AEKYKPRSLEELAVQRKKVEEVRAWFEERLGDS-----KDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTP  214 (666)
Q Consensus       140 ~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~-----~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~  214 (666)
                      ++....-+++||.|.+..+++|++++.-.+...     .|-.+++.+||+||||||||++|+++|++++..++.+..+..
T Consensus       136 ~~~~p~v~~~digGl~~~k~~l~~~v~~pl~~~~~~~~~Gl~~pkgvLL~GppGTGKT~LAkalA~~l~~~fi~i~~s~l  215 (398)
T PTZ00454        136 MSEKPDVTYSDIGGLDIQKQEIREAVELPLTCPELYEQIGIDPPRGVLLYGPPGTGKTMLAKAVAHHTTATFIRVVGSEF  215 (398)
T ss_pred             ccCCCCCCHHHcCCHHHHHHHHHHHHHHHhcCHHHHHhcCCCCCceEEEECCCCCCHHHHHHHHHHhcCCCEEEEehHHH
Confidence            344455789999999999999999887444321     133445899999999999999999999999999888865431


Q ss_pred             hhhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchh------HHHHHHHHHHHH
Q 005987          215 TIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRT------AFERLRQCLLLL  288 (666)
Q Consensus       215 ~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~------~~~~l~~~L~~l  288 (666)
                        ...++     |    .....+++++..+..            ..|.||+|||+|.+....      .-...+..+..+
T Consensus       216 --~~k~~-----g----e~~~~lr~lf~~A~~------------~~P~ILfIDEID~i~~~r~~~~~~~d~~~~r~l~~L  272 (398)
T PTZ00454        216 --VQKYL-----G----EGPRMVRDVFRLARE------------NAPSIIFIDEVDSIATKRFDAQTGADREVQRILLEL  272 (398)
T ss_pred             --HHHhc-----c----hhHHHHHHHHHHHHh------------cCCeEEEEECHhhhccccccccCCccHHHHHHHHHH
Confidence              11111     1    112234555555432            246799999999753210      001122222222


Q ss_pred             H---hc--CCCceEEEEecCCCCCCccchhhhhhHHHHHHhhc--CeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHH
Q 005987          289 V---RS--THIPTAVVLTECGKADSVDSTAQSFEELQSILVDA--GARKVALNPITNGSIKRTLSKICRQEQYSLSTEQI  361 (666)
Q Consensus       289 ~---~~--~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~--r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l  361 (666)
                      +   +.  ....+++|+++ +..+          .+.+.+.|+  .-..|.|++|+..+...+++.++...++. .+-.+
T Consensus       273 L~~ld~~~~~~~v~VI~aT-N~~d----------~LDpAllR~GRfd~~I~~~~P~~~~R~~Il~~~~~~~~l~-~dvd~  340 (398)
T PTZ00454        273 LNQMDGFDQTTNVKVIMAT-NRAD----------TLDPALLRPGRLDRKIEFPLPDRRQKRLIFQTITSKMNLS-EEVDL  340 (398)
T ss_pred             HHHhhccCCCCCEEEEEec-CCch----------hCCHHHcCCCcccEEEEeCCcCHHHHHHHHHHHHhcCCCC-cccCH
Confidence            2   21  12234444332 2222          222222221  23569999999999999999887765543 22345


Q ss_pred             HHHHHH----cCCcHHHHHHHHHHHhc
Q 005987          362 DLVAQA----SGGDIRQAITSLQFSSL  384 (666)
Q Consensus       362 ~~Ia~~----s~GDIR~AIn~LQf~~~  384 (666)
                      ..++..    ++.||...++...+.|.
T Consensus       341 ~~la~~t~g~sgaDI~~l~~eA~~~A~  367 (398)
T PTZ00454        341 EDFVSRPEKISAADIAAICQEAGMQAV  367 (398)
T ss_pred             HHHHHHcCCCCHHHHHHHHHHHHHHHH
Confidence            666665    45688887777666665

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=99.47  E-value=5.9e-13  Score=158.02  Aligned_cols=212  Identities=16%  Similarity=0.180  Sum_probs=142.6

Q ss_pred             CCCccccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcC----------C
Q 005987          135 TQQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLG----------A  204 (666)
Q Consensus       135 ~~~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg----------~  204 (666)
                      .....+++.+|.++++++|+++.++.+..+|.+.      .  .+.+||+||||||||++|+.||+.+.          .
T Consensus       173 ~~~~L~~~~r~~~ld~~iGr~~ei~~~i~~l~r~------~--~~n~lLvG~pGvGKTal~~~La~~i~~~~v~~~l~~~  244 (852)
T TIGR03345       173 YTTDLTAQAREGKIDPVLGRDDEIRQMIDILLRR------R--QNNPILTGEAGVGKTAVVEGLALRIAAGDVPPALRNV  244 (852)
T ss_pred             HhhhHHHHhcCCCCCcccCCHHHHHHHHHHHhcC------C--cCceeEECCCCCCHHHHHHHHHHHHhhCCCCccccCC
Confidence            3457888899999999999999999998888652      2  14789999999999999999999873          2


Q ss_pred             cEEEEcCCCchhhhhhhhcccCCcccc-chhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchh---HHHH
Q 005987          205 RLYEWDTPTPTIWQEYMHNCKTGLEYT-SKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRT---AFER  280 (666)
Q Consensus       205 ~viE~nasd~~~~~e~l~~~~~g~~~~-s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~---~~~~  280 (666)
                      .++.++..          ....|..|. .....++.+++.+...+           .+.||+|||++.+.+..   ....
T Consensus       245 ~i~~l~l~----------~l~ag~~~~ge~e~~lk~ii~e~~~~~-----------~~~ILfIDEih~l~~~g~~~~~~d  303 (852)
T TIGR03345       245 RLLSLDLG----------LLQAGASVKGEFENRLKSVIDEVKASP-----------QPIILFIDEAHTLIGAGGQAGQGD  303 (852)
T ss_pred             eEEEeehh----------hhhcccccchHHHHHHHHHHHHHHhcC-----------CCeEEEEeChHHhccCCCcccccc
Confidence            33333221          111232332 23356677777764322           35799999999875311   1112


Q ss_pred             HHHHHHHHHhcCCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHH----hCCCC
Q 005987          281 LRQCLLLLVRSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQ----EQYSL  356 (666)
Q Consensus       281 l~~~L~~l~~~~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~----e~i~v  356 (666)
                      ..+.|...+..+.  +.| ++.++..    .+.+.++ +...|.| |+..|.+++|+.++..++|+.+...    .++.+
T Consensus       304 ~~n~Lkp~l~~G~--l~~-IgaTT~~----e~~~~~~-~d~AL~r-Rf~~i~v~eps~~~~~~iL~~~~~~~e~~~~v~i  374 (852)
T TIGR03345       304 AANLLKPALARGE--LRT-IAATTWA----EYKKYFE-KDPALTR-RFQVVKVEEPDEETAIRMLRGLAPVLEKHHGVLI  374 (852)
T ss_pred             HHHHhhHHhhCCC--eEE-EEecCHH----HHhhhhh-ccHHHHH-hCeEEEeCCCCHHHHHHHHHHHHHhhhhcCCCee
Confidence            2345667777664  233 3333321    1223333 2333444 5899999999999999998766653    35889


Q ss_pred             CHHHHHHHHHHcCCc------HHHHHHHHHHHhc
Q 005987          357 STEQIDLVAQASGGD------IRQAITSLQFSSL  384 (666)
Q Consensus       357 ~~~~l~~Ia~~s~GD------IR~AIn~LQf~~~  384 (666)
                      +++++..++..|.+=      ..+||..|.-+|.
T Consensus       375 ~d~al~~~~~ls~ryi~~r~LPDKAIdlldea~a  408 (852)
T TIGR03345       375 LDEAVVAAVELSHRYIPGRQLPDKAVSLLDTACA  408 (852)
T ss_pred             CHHHHHHHHHHcccccccccCccHHHHHHHHHHH
Confidence            999999999998754      4678988887664

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.

>PRK12422 chromosomal replication initiation protein; Provisional

Probab=99.44  E-value=5.8e-12  Score=139.52  Aligned_cols=204  Identities=17%  Similarity=0.256  Sum_probs=124.8

Q ss_pred             CCcccccc---CHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcCCCchhhhh
Q 005987          146 RSLEELAV---QRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL---GARLYEWDTPTPTIWQE  219 (666)
Q Consensus       146 ~sl~eLvg---~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~nasd~~~~~e  219 (666)
                      .+|+.++.   +......++.|.+.. ...++. ..+.++||||+|+|||++++++|+++   +..++.+++.+.  ..+
T Consensus       108 ~tFdnFv~g~~N~~a~~~a~~~a~~~-~~~~~~-~~npl~L~G~~G~GKTHLl~Ai~~~l~~~~~~v~yi~~~~f--~~~  183 (445)
T PRK12422        108 MTFANFLVTPENDLPHRILQEFTKVS-EQGKGF-PFNPIYLFGPEGSGKTHLMQAAVHALRESGGKILYVRSELF--TEH  183 (445)
T ss_pred             ccccceeeCCcHHHHHHHHHHHHhcc-ccccCC-CCceEEEEcCCCCCHHHHHHHHHHHHHHcCCCEEEeeHHHH--HHH
Confidence            36777764   233334455554321 111122 23679999999999999999999987   677777765321  001


Q ss_pred             hhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhH-HHHHHHHHHHHHhcCCCceEE
Q 005987          220 YMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTA-FERLRQCLLLLVRSTHIPTAV  298 (666)
Q Consensus       220 ~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~-~~~l~~~L~~l~~~~~~PiVi  298 (666)
                      .......     .   ....|...   |.           ...+|+|||++.+.+... .+.+...+..+...+ .++ +
T Consensus       184 ~~~~l~~-----~---~~~~f~~~---~~-----------~~dvLiIDDiq~l~~k~~~qeelf~l~N~l~~~~-k~I-I  239 (445)
T PRK12422        184 LVSAIRS-----G---EMQRFRQF---YR-----------NVDALFIEDIEVFSGKGATQEEFFHTFNSLHTEG-KLI-V  239 (445)
T ss_pred             HHHHHhc-----c---hHHHHHHH---cc-----------cCCEEEEcchhhhcCChhhHHHHHHHHHHHHHCC-CcE-E
Confidence            1100000     0   11112111   11           234999999998765322 233333344444443 334 4


Q ss_pred             EEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCcHHHHHHH
Q 005987          299 VLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASGGDIRQAITS  378 (666)
Q Consensus       299 Iit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~s~GDIR~AIn~  378 (666)
                      ++++.....    .....+.|.+++.  ....+.+.+|+.+++.++|++.+...++.+++++++.|+....||+|..++.
T Consensus       240 lts~~~p~~----l~~l~~rL~SR~~--~Gl~~~l~~pd~e~r~~iL~~k~~~~~~~l~~evl~~la~~~~~dir~L~g~  313 (445)
T PRK12422        240 ISSTCAPQD----LKAMEERLISRFE--WGIAIPLHPLTKEGLRSFLERKAEALSIRIEETALDFLIEALSSNVKSLLHA  313 (445)
T ss_pred             EecCCCHHH----HhhhHHHHHhhhc--CCeEEecCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHH
Confidence            455432110    1111233444332  1478999999999999999999999999999999999999999999999999


Q ss_pred             HHHHh
Q 005987          379 LQFSS  383 (666)
Q Consensus       379 LQf~~  383 (666)
                      |+.++
T Consensus       314 l~~l~  318 (445)
T PRK12422        314 LTLLA  318 (445)
T ss_pred             HHHHH
Confidence            99886

>PRK14088 dnaA chromosomal replication initiation protein; Provisional

Probab=99.43  E-value=5.1e-12  Score=140.19  Aligned_cols=197  Identities=20%  Similarity=0.260  Sum_probs=121.2

Q ss_pred             CccccccCH---HHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc-----CCcEEEEcCCCchhhh
Q 005987          147 SLEELAVQR---KKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL-----GARLYEWDTPTPTIWQ  218 (666)
Q Consensus       147 sl~eLvg~~---k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel-----g~~viE~nasd~~~~~  218 (666)
                      +|+++++.+   ........+.+.     ++.  .+.++||||||||||++++++|+++     +..++.+++.+  ...
T Consensus       103 tFdnFv~g~~n~~a~~~~~~~~~~-----~~~--~n~l~lyG~~G~GKTHLl~ai~~~l~~~~~~~~v~yi~~~~--f~~  173 (440)
T PRK14088        103 TFENFVVGPGNSFAYHAALEVAKN-----PGR--YNPLFIYGGVGLGKTHLLQSIGNYVVQNEPDLRVMYITSEK--FLN  173 (440)
T ss_pred             cccccccCCchHHHHHHHHHHHhC-----cCC--CCeEEEEcCCCCcHHHHHHHHHHHHHHhCCCCeEEEEEHHH--HHH
Confidence            677777433   233344444332     233  2579999999999999999999986     45677776533  111


Q ss_pred             hhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhH-HHHHHHHHHHHHhcCCCceE
Q 005987          219 EYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTA-FERLRQCLLLLVRSTHIPTA  297 (666)
Q Consensus       219 e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~-~~~l~~~L~~l~~~~~~PiV  297 (666)
                      +......     ..   .+..|.++..             ....+|||||++.+.+... ...+...+..+.+.++  .+
T Consensus       174 ~~~~~~~-----~~---~~~~f~~~~~-------------~~~dvLlIDDi~~l~~~~~~q~elf~~~n~l~~~~k--~i  230 (440)
T PRK14088        174 DLVDSMK-----EG---KLNEFREKYR-------------KKVDVLLIDDVQFLIGKTGVQTELFHTFNELHDSGK--QI  230 (440)
T ss_pred             HHHHHHh-----cc---cHHHHHHHHH-------------hcCCEEEEechhhhcCcHHHHHHHHHHHHHHHHcCC--eE
Confidence            1111100     01   1222332221             0134999999997654321 2334444555555543  34


Q ss_pred             EEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCcHHHHHH
Q 005987          298 VVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASGGDIRQAIT  377 (666)
Q Consensus       298 iIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~s~GDIR~AIn  377 (666)
                      +++++... .   ......+.+.+++..  ...+.|.+|+.+.+.++|++.+..+++.+++++++.|++.+.||+|....
T Consensus       231 Iitsd~~p-~---~l~~l~~rL~SR~~~--gl~v~i~~pd~e~r~~IL~~~~~~~~~~l~~ev~~~Ia~~~~~~~R~L~g  304 (440)
T PRK14088        231 VICSDREP-Q---KLSEFQDRLVSRFQM--GLVAKLEPPDEETRKKIARKMLEIEHGELPEEVLNFVAENVDDNLRRLRG  304 (440)
T ss_pred             EEECCCCH-H---HHHHHHHHHhhHHhc--CceEeeCCCCHHHHHHHHHHHHHhcCCCCCHHHHHHHHhccccCHHHHHH
Confidence            44554221 1   111222344554432  56899999999999999999999999999999999999999999988665


Q ss_pred             HHHH
Q 005987          378 SLQF  381 (666)
Q Consensus       378 ~LQf  381 (666)
                      .|.-
T Consensus       305 ~l~~  308 (440)
T PRK14088        305 AIIK  308 (440)
T ss_pred             HHHH
Confidence            5543

>PRK03992 proteasome-activating nucleotidase; Provisional

Probab=99.43  E-value=2.4e-12  Score=140.82  Aligned_cols=206  Identities=16%  Similarity=0.208  Sum_probs=124.6

Q ss_pred             CCCCccccccCHHHHHHHHHHHHHhhcC-----CCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCchhhh
Q 005987          144 KPRSLEELAVQRKKVEEVRAWFEERLGD-----SKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTIWQ  218 (666)
Q Consensus       144 ~P~sl~eLvg~~k~i~el~~wL~~~~~~-----~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~~~~  218 (666)
                      ...++++|.|.+..+++|+..+...+..     .-|-.+++.+||+||||||||++|+++|++++..++.+++++..  .
T Consensus       126 p~~~~~di~Gl~~~~~~l~~~i~~pl~~~~~~~~~g~~~p~gvLL~GppGtGKT~lAkaia~~~~~~~i~v~~~~l~--~  203 (389)
T PRK03992        126 PNVTYEDIGGLEEQIREVREAVELPLKKPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAHETNATFIRVVGSELV--Q  203 (389)
T ss_pred             CCCCHHHhCCcHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCceEEECCCCCChHHHHHHHHHHhCCCEEEeehHHHh--H
Confidence            3457889999999999999988643321     11333447899999999999999999999999999988765411  1


Q ss_pred             hhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchh------HHHHHHHHHHHHHhc-
Q 005987          219 EYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRT------AFERLRQCLLLLVRS-  291 (666)
Q Consensus       219 e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~------~~~~l~~~L~~l~~~-  291 (666)
                      .     ..|    .....++.+++.+...            .+.||+|||+|.+....      .-..++..+..++.. 
T Consensus       204 ~-----~~g----~~~~~i~~~f~~a~~~------------~p~IlfiDEiD~l~~~r~~~~~~~~~~~~~~l~~lL~~l  262 (389)
T PRK03992        204 K-----FIG----EGARLVRELFELAREK------------APSIIFIDEIDAIAAKRTDSGTSGDREVQRTLMQLLAEM  262 (389)
T ss_pred             h-----hcc----chHHHHHHHHHHHHhc------------CCeEEEEechhhhhcccccCCCCccHHHHHHHHHHHHhc
Confidence            1     111    1122344455555332            36799999999763210      001122233333321 


Q ss_pred             ----CCCceEEEEecCCCCCCccchhhhhhHHHHHHhhc--CeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHH
Q 005987          292 ----THIPTAVVLTECGKADSVDSTAQSFEELQSILVDA--GARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVA  365 (666)
Q Consensus       292 ----~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~--r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia  365 (666)
                          ...++++|++. +..+          .+...+.|+  .-..|.|++|+.++..++|+..+....+. .+..+..|+
T Consensus       263 d~~~~~~~v~VI~aT-n~~~----------~ld~allRpgRfd~~I~v~~P~~~~R~~Il~~~~~~~~~~-~~~~~~~la  330 (389)
T PRK03992        263 DGFDPRGNVKIIAAT-NRID----------ILDPAILRPGRFDRIIEVPLPDEEGRLEILKIHTRKMNLA-DDVDLEELA  330 (389)
T ss_pred             cccCCCCCEEEEEec-CChh----------hCCHHHcCCccCceEEEECCCCHHHHHHHHHHHhccCCCC-CcCCHHHHH
Confidence                11234444333 2211          122223221  13579999999999999999877654432 123456677


Q ss_pred             HH----cCCcHHHHHHHHHHHhc
Q 005987          366 QA----SGGDIRQAITSLQFSSL  384 (666)
Q Consensus       366 ~~----s~GDIR~AIn~LQf~~~  384 (666)
                      ..    +++||+..++..-+.+.
T Consensus       331 ~~t~g~sgadl~~l~~eA~~~a~  353 (389)
T PRK03992        331 ELTEGASGADLKAICTEAGMFAI  353 (389)
T ss_pred             HHcCCCCHHHHHHHHHHHHHHHH
Confidence            66    44688887776666554

>PLN00020 ribulose bisphosphate carboxylase/oxygenase activase -RuBisCO activase (RCA); Provisional

Probab=99.41  E-value=5.8e-12  Score=132.70  Aligned_cols=164  Identities=15%  Similarity=0.139  Sum_probs=103.2

Q ss_pred             CCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCchhhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCC
Q 005987          176 FSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIP  255 (666)
Q Consensus       176 ~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~  255 (666)
                      .++++|+||||||||||.+++++|+++|..++.+++++           ..+..+......+++.+..+.....      
T Consensus       146 k~PlgllL~GPPGcGKTllAraiA~elg~~~i~vsa~e-----------L~sk~vGEsEk~IR~~F~~A~~~a~------  208 (413)
T PLN00020        146 KVPLILGIWGGKGQGKSFQCELVFKKMGIEPIVMSAGE-----------LESENAGEPGKLIRQRYREAADIIK------  208 (413)
T ss_pred             CCCeEEEeeCCCCCCHHHHHHHHHHHcCCCeEEEEHHH-----------hhcCcCCcHHHHHHHHHHHHHHHhh------
Confidence            34489999999999999999999999999999998875           1122223445567777776654310      


Q ss_pred             CCCCCceEEEEeCCCCCcchh-----HH-HHHH-HHHHHHHhc-------------CCCceEEEEecCCCCCCccchhhh
Q 005987          256 GESKSSAILLIDDLPVTNGRT-----AF-ERLR-QCLLLLVRS-------------THIPTAVVLTECGKADSVDSTAQS  315 (666)
Q Consensus       256 ~~~~~~~IIlIDEid~l~~~~-----~~-~~l~-~~L~~l~~~-------------~~~PiViIit~~~~~~s~d~~~r~  315 (666)
                       ....++||+|||+|.+.++.     .. .++. ..|..+++.             ...+-|+|+..++.++        
T Consensus       209 -~~~aPcVLFIDEIDA~~g~r~~~~~tv~~qiV~~tLLnl~D~p~~v~l~G~w~~~~~~~~V~VIaTTNrpd--------  279 (413)
T PLN00020        209 -KKGKMSCLFINDLDAGAGRFGTTQYTVNNQMVNGTLMNIADNPTNVSLGGDWREKEEIPRVPIIVTGNDFS--------  279 (413)
T ss_pred             -ccCCCeEEEEehhhhcCCCCCCCCcchHHHHHHHHHHHHhcCCccccccccccccccCCCceEEEeCCCcc--------
Confidence             01257899999999654321     11 1222 334444321             1122233333333332        


Q ss_pred             hhHHHHHHhhc-CeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCC
Q 005987          316 FEELQSILVDA-GARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASGG  370 (666)
Q Consensus       316 l~~L~s~L~r~-r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~s~G  370 (666)
                        .|.+.|.|+ |+.. .|..|+.++...+|+.++...+  ++...+..|+....|
T Consensus       280 --~LDpALlRpGRfDk-~i~lPd~e~R~eIL~~~~r~~~--l~~~dv~~Lv~~f~g  330 (413)
T PLN00020        280 --TLYAPLIRDGRMEK-FYWAPTREDRIGVVHGIFRDDG--VSREDVVKLVDTFPG  330 (413)
T ss_pred             --cCCHhHcCCCCCCc-eeCCCCHHHHHHHHHHHhccCC--CCHHHHHHHHHcCCC
Confidence              233333333 3333 3558999999999999988765  567888899988766

>KOG0738 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=99.40  E-value=5.1e-12  Score=131.82  Aligned_cols=202  Identities=15%  Similarity=0.219  Sum_probs=125.5

Q ss_pred             CCccccccCHHHHHHHHHHHH------HhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCchhhhh
Q 005987          146 RSLEELAVQRKKVEEVRAWFE------ERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTIWQE  219 (666)
Q Consensus       146 ~sl~eLvg~~k~i~el~~wL~------~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~~~~e  219 (666)
                      -.++||+|...+++-|++.+-      ..++.  .+-|=+.+|+.||||+|||.+|+++|.|++-.++.+.+++-.  . 
T Consensus       209 ikW~DIagl~~AK~lL~EAVvlPi~mPe~F~G--irrPWkgvLm~GPPGTGKTlLAKAvATEc~tTFFNVSsstlt--S-  283 (491)
T KOG0738|consen  209 IKWDDIAGLHEAKKLLKEAVVLPIWMPEFFKG--IRRPWKGVLMVGPPGTGKTLLAKAVATECGTTFFNVSSSTLT--S-  283 (491)
T ss_pred             cChHhhcchHHHHHHHHHHHhhhhhhHHHHhh--cccccceeeeeCCCCCcHHHHHHHHHHhhcCeEEEechhhhh--h-
Confidence            467899999888888877654      22221  233447899999999999999999999999888877766521  1 


Q ss_pred             hhhcccCCccccchhHHH-HHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcch-------hHHHHHHHHHHHHHhc
Q 005987          220 YMHNCKTGLEYTSKLDEF-ENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGR-------TAFERLRQCLLLLVRS  291 (666)
Q Consensus       220 ~l~~~~~g~~~~s~~~~f-~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~-------~~~~~l~~~L~~l~~~  291 (666)
                               .|....+.+ +-+++.++.|.            |.+|||||||.+..+       ++-+++...|+..++.
T Consensus       284 ---------KwRGeSEKlvRlLFemARfyA------------PStIFiDEIDslcs~RG~s~EHEaSRRvKsELLvQmDG  342 (491)
T KOG0738|consen  284 ---------KWRGESEKLVRLLFEMARFYA------------PSTIFIDEIDSLCSQRGGSSEHEASRRVKSELLVQMDG  342 (491)
T ss_pred             ---------hhccchHHHHHHHHHHHHHhC------------CceeehhhHHHHHhcCCCccchhHHHHHHHHHHHHhhc
Confidence                     122222333 44556665554            568999999976321       3445666556555543


Q ss_pred             CC-----CceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHH
Q 005987          292 TH-----IPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQ  366 (666)
Q Consensus       292 ~~-----~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~  366 (666)
                      ..     .-+|+++..++.+  ||        |.+.|+|+.-..|.++-|+.+.....| +++-.+-...++-.++.|++
T Consensus       343 ~~~t~e~~k~VmVLAATN~P--Wd--------iDEAlrRRlEKRIyIPLP~~~~R~~Li-~~~l~~~~~~~~~~~~~lae  411 (491)
T KOG0738|consen  343 VQGTLENSKVVMVLAATNFP--WD--------IDEALRRRLEKRIYIPLPDAEARSALI-KILLRSVELDDPVNLEDLAE  411 (491)
T ss_pred             cccccccceeEEEEeccCCC--cc--------hHHHHHHHHhhheeeeCCCHHHHHHHH-HHhhccccCCCCccHHHHHH
Confidence            21     2467777777654  33        333443322235666666665555544 45544433344555667776


Q ss_pred             H----cCCcHHHHHHHHHHHhc
Q 005987          367 A----SGGDIRQAITSLQFSSL  384 (666)
Q Consensus       367 ~----s~GDIR~AIn~LQf~~~  384 (666)
                      .    |+-||+.+....-+.++
T Consensus       412 ~~eGySGaDI~nvCreAsm~~m  433 (491)
T KOG0738|consen  412 RSEGYSGADITNVCREASMMAM  433 (491)
T ss_pred             HhcCCChHHHHHHHHHHHHHHH
Confidence            6    55589988776666554

>TIGR03689 pup_AAA proteasome ATPase

Probab=99.39  E-value=7.3e-12  Score=139.55  Aligned_cols=194  Identities=14%  Similarity=0.218  Sum_probs=113.8

Q ss_pred             CCccccccCCCCccccccCHHHHHHHHHHHHHhhcC-----CCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEE--
Q 005987          136 QQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGD-----SKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYE--  208 (666)
Q Consensus       136 ~~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~-----~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE--  208 (666)
                      ..+-.+++.+.++++|.|.+..+++++..+...+..     .-|-.+++.+|||||||||||++++++|++++..+..  
T Consensus       169 ~~l~~~~~p~v~~~dIgGl~~~i~~i~~~v~lp~~~~~l~~~~gl~~p~GILLyGPPGTGKT~LAKAlA~eL~~~i~~~~  248 (512)
T TIGR03689       169 EDLVLEEVPDVTYADIGGLDSQIEQIRDAVELPFLHPELYREYDLKPPKGVLLYGPPGCGKTLIAKAVANSLAQRIGAET  248 (512)
T ss_pred             hcceeecCCCCCHHHcCChHHHHHHHHHHHHHHhhCHHHHHhccCCCCcceEEECCCCCcHHHHHHHHHHhhcccccccc
Confidence            345668888899999999999999999988643221     1133345789999999999999999999999765332  


Q ss_pred             ------EcCCCchhhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcch------h
Q 005987          209 ------WDTPTPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGR------T  276 (666)
Q Consensus       209 ------~nasd~~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~------~  276 (666)
                            ++......    +     ..........++.+++.+.....        .+.++||||||+|.+...      .
T Consensus       249 ~~~~~fl~v~~~eL----l-----~kyvGete~~ir~iF~~Ar~~a~--------~g~p~IIfIDEiD~L~~~R~~~~s~  311 (512)
T TIGR03689       249 GDKSYFLNIKGPEL----L-----NKYVGETERQIRLIFQRAREKAS--------DGRPVIVFFDEMDSIFRTRGSGVSS  311 (512)
T ss_pred             CCceeEEeccchhh----c-----ccccchHHHHHHHHHHHHHHHhh--------cCCCceEEEehhhhhhcccCCCccc
Confidence                  11111000    0     00111222344555555543221        124689999999976421      1


Q ss_pred             HH-HHHHHHHHHHHhcCC-CceEEEEecCCCCCCccchhhhhhHHHHHHhhc-C-eeEEEeCCCCHHHHHHHHHHHHHHh
Q 005987          277 AF-ERLRQCLLLLVRSTH-IPTAVVLTECGKADSVDSTAQSFEELQSILVDA-G-ARKVALNPITNGSIKRTLSKICRQE  352 (666)
Q Consensus       277 ~~-~~l~~~L~~l~~~~~-~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~-r-~~~I~F~p~s~~~i~kiL~~I~~~e  352 (666)
                      .. ..+...|+..++... .+-|+++..++..+.          |.+.+.|+ | -..|.|.+|+..+...+|+..+.. 
T Consensus       312 d~e~~il~~LL~~LDgl~~~~~ViVI~ATN~~d~----------LDpALlRpGRfD~~I~~~~Pd~e~r~~Il~~~l~~-  380 (512)
T TIGR03689       312 DVETTVVPQLLSELDGVESLDNVIVIGASNREDM----------IDPAILRPGRLDVKIRIERPDAEAAADIFSKYLTD-  380 (512)
T ss_pred             hHHHHHHHHHHHHhcccccCCceEEEeccCChhh----------CCHhhcCccccceEEEeCCCCHHHHHHHHHHHhhc-
Confidence            11 122233444433211 123344444443322          33333331 2 346999999999999999988753 


Q ss_pred             CCCCC
Q 005987          353 QYSLS  357 (666)
Q Consensus       353 ~i~v~  357 (666)
                      .+.++
T Consensus       381 ~l~l~  385 (512)
T TIGR03689       381 SLPLD  385 (512)
T ss_pred             cCCch
Confidence            34443

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.

>PRK14086 dnaA chromosomal replication initiation protein; Provisional

Probab=99.38  E-value=1.7e-11  Score=138.21  Aligned_cols=199  Identities=19%  Similarity=0.218  Sum_probs=126.7

Q ss_pred             CCccccccCHH---HHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc-----CCcEEEEcCCCchhh
Q 005987          146 RSLEELAVQRK---KVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL-----GARLYEWDTPTPTIW  217 (666)
Q Consensus       146 ~sl~eLvg~~k---~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel-----g~~viE~nasd~~~~  217 (666)
                      .+|+++++.+.   ....+..+++.+     +.. .+.|+|||++|+|||+|++++|+++     ++.++.+++.+.  .
T Consensus       285 ~TFDnFvvG~sN~~A~aaa~avae~~-----~~~-~NpL~LyG~sGsGKTHLL~AIa~~a~~~~~g~~V~Yitaeef--~  356 (617)
T PRK14086        285 YTFDTFVIGASNRFAHAAAVAVAEAP-----AKA-YNPLFIYGESGLGKTHLLHAIGHYARRLYPGTRVRYVSSEEF--T  356 (617)
T ss_pred             CCHhhhcCCCccHHHHHHHHHHHhCc-----ccc-CCcEEEECCCCCCHHHHHHHHHHHHHHhCCCCeEEEeeHHHH--H
Confidence            47888875332   333444444321     222 2469999999999999999999987     567777765431  1


Q ss_pred             hhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhH-HHHHHHHHHHHHhcCCCce
Q 005987          218 QEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTA-FERLRQCLLLLVRSTHIPT  296 (666)
Q Consensus       218 ~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~-~~~l~~~L~~l~~~~~~Pi  296 (666)
                      .+.......     .   .+..|.++   |.           ..-+|||||++.+.+... .+.+..++..+.+.. .++
T Consensus       357 ~el~~al~~-----~---~~~~f~~~---y~-----------~~DLLlIDDIq~l~gke~tqeeLF~l~N~l~e~g-k~I  413 (617)
T PRK14086        357 NEFINSIRD-----G---KGDSFRRR---YR-----------EMDILLVDDIQFLEDKESTQEEFFHTFNTLHNAN-KQI  413 (617)
T ss_pred             HHHHHHHHh-----c---cHHHHHHH---hh-----------cCCEEEEehhccccCCHHHHHHHHHHHHHHHhcC-CCE
Confidence            111111000     0   11223322   21           124899999998865432 233445555555544 344


Q ss_pred             EEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCcHHHHH
Q 005987          297 AVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASGGDIRQAI  376 (666)
Q Consensus       297 ViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~s~GDIR~AI  376 (666)
                       +|+++.....    .....+.|++.+..  ...+.+.+|+.+...++|++.+...++.++++++++|+....+|+|...
T Consensus       414 -IITSd~~P~e----L~~l~~rL~SRf~~--GLvv~I~~PD~EtR~aIL~kka~~r~l~l~~eVi~yLa~r~~rnvR~Le  486 (617)
T PRK14086        414 -VLSSDRPPKQ----LVTLEDRLRNRFEW--GLITDVQPPELETRIAILRKKAVQEQLNAPPEVLEFIASRISRNIRELE  486 (617)
T ss_pred             -EEecCCChHh----hhhccHHHHhhhhc--CceEEcCCCCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHhccCCHHHHH
Confidence             4556543211    11123456776654  7789999999999999999999999999999999999999999999866


Q ss_pred             HHHHHH
Q 005987          377 TSLQFS  382 (666)
Q Consensus       377 n~LQf~  382 (666)
                      ..|.-+
T Consensus       487 gaL~rL  492 (617)
T PRK14086        487 GALIRV  492 (617)
T ss_pred             HHHHHH
Confidence            655433

>TIGR01242 26Sp45 26S proteasome subunit P45 family

Probab=99.37  E-value=8.8e-12  Score=135.48  Aligned_cols=210  Identities=16%  Similarity=0.231  Sum_probs=122.6

Q ss_pred             ccccCCCCccccccCHHHHHHHHHHHHHhhcCC-----CCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCc
Q 005987          140 AEKYKPRSLEELAVQRKKVEEVRAWFEERLGDS-----KDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTP  214 (666)
Q Consensus       140 ~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~-----~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~  214 (666)
                      +++....+++++.|.++.+++++.++...+...     -|-.+++.+||+||||||||++|+++|++++..++.+..++ 
T Consensus       113 ~~~~p~~~~~di~Gl~~~~~~l~~~i~~~~~~~~~~~~~g~~~p~gvLL~GppGtGKT~lakaia~~l~~~~~~v~~~~-  191 (364)
T TIGR01242       113 VEERPNVSYEDIGGLEEQIREIREAVELPLKHPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAHETNATFIRVVGSE-  191 (364)
T ss_pred             eccCCCCCHHHhCChHHHHHHHHHHHHHHhcCHHHHHhcCCCCCceEEEECCCCCCHHHHHHHHHHhCCCCEEecchHH-
Confidence            345556788999999999999999987443321     12233478999999999999999999999998888776432 


Q ss_pred             hhhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchh------HHHHHHHHHHHH
Q 005987          215 TIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRT------AFERLRQCLLLL  288 (666)
Q Consensus       215 ~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~------~~~~l~~~L~~l  288 (666)
                       ....+.     |    .....+..++..+..            ..+.||+|||+|.+....      .-...+..+..+
T Consensus       192 -l~~~~~-----g----~~~~~i~~~f~~a~~------------~~p~il~iDEiD~l~~~~~~~~~~~~~~~~~~l~~l  249 (364)
T TIGR01242       192 -LVRKYI-----G----EGARLVREIFELAKE------------KAPSIIFIDEIDAIAAKRTDSGTSGDREVQRTLMQL  249 (364)
T ss_pred             -HHHHhh-----h----HHHHHHHHHHHHHHh------------cCCcEEEhhhhhhhccccccCCCCccHHHHHHHHHH
Confidence             111111     1    111223444444432            135799999999763210      001112222222


Q ss_pred             H---hc--CCCceEEEEecCCCCCCccchhhhhhHHHHHHhhc--CeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHH
Q 005987          289 V---RS--THIPTAVVLTECGKADSVDSTAQSFEELQSILVDA--GARKVALNPITNGSIKRTLSKICRQEQYSLSTEQI  361 (666)
Q Consensus       289 ~---~~--~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~--r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l  361 (666)
                      +   ..  ...++++|++. +..+.          +...+.++  ....|.|++|+.++..++++..+....+. ++..+
T Consensus       250 l~~ld~~~~~~~v~vI~tt-n~~~~----------ld~al~r~grfd~~i~v~~P~~~~r~~Il~~~~~~~~l~-~~~~~  317 (364)
T TIGR01242       250 LAELDGFDPRGNVKVIAAT-NRPDI----------LDPALLRPGRFDRIIEVPLPDFEGRLEILKIHTRKMKLA-EDVDL  317 (364)
T ss_pred             HHHhhCCCCCCCEEEEEec-CChhh----------CChhhcCcccCceEEEeCCcCHHHHHHHHHHHHhcCCCC-ccCCH
Confidence            2   21  12234444433 22211          22222211  14579999999999999998776543332 11235


Q ss_pred             HHHHHHcC----CcHHHHHHHHHHHhc
Q 005987          362 DLVAQASG----GDIRQAITSLQFSSL  384 (666)
Q Consensus       362 ~~Ia~~s~----GDIR~AIn~LQf~~~  384 (666)
                      ..|+..+.    +||+.++...-+.|.
T Consensus       318 ~~la~~t~g~sg~dl~~l~~~A~~~a~  344 (364)
T TIGR01242       318 EAIAKMTEGASGADLKAICTEAGMFAI  344 (364)
T ss_pred             HHHHHHcCCCCHHHHHHHHHHHHHHHH
Confidence            66666654    488877776655554

Many proteins may score above the trusted cutoff because an internal

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=99.36  E-value=7.7e-12  Score=149.45  Aligned_cols=213  Identities=17%  Similarity=0.192  Sum_probs=142.5

Q ss_pred             CCCccccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc----------CC
Q 005987          135 TQQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL----------GA  204 (666)
Q Consensus       135 ~~~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel----------g~  204 (666)
                      ....++++.+|..+++++|+++.++.+...|.+.      .  .+.+||+||||||||++++.||+.+          +.
T Consensus       159 ~~~~l~~~~~~~~~~~~igr~~ei~~~~~~l~r~------~--~~n~lL~G~pGvGKT~l~~~la~~i~~~~~p~~l~~~  230 (852)
T TIGR03346       159 YARDLTERAREGKLDPVIGRDEEIRRTIQVLSRR------T--KNNPVLIGEPGVGKTAIVEGLAQRIVNGDVPESLKNK  230 (852)
T ss_pred             HhhhHHHHhhCCCCCcCCCcHHHHHHHHHHHhcC------C--CCceEEEcCCCCCHHHHHHHHHHHHhccCCchhhcCC
Confidence            4567999999999999999999999998887652      1  2578899999999999999999986          45


Q ss_pred             cEEEEcCCCchhhhhhhhcccCCcccc-chhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcch---hHHHH
Q 005987          205 RLYEWDTPTPTIWQEYMHNCKTGLEYT-SKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGR---TAFER  280 (666)
Q Consensus       205 ~viE~nasd~~~~~e~l~~~~~g~~~~-s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~---~~~~~  280 (666)
                      .++.++...          ...|..|. .....+..++.++..+.           .+.||||||++.+.+.   ..-..
T Consensus       231 ~~~~l~~~~----------l~a~~~~~g~~e~~l~~~l~~~~~~~-----------~~~ILfIDEih~l~~~g~~~~~~d  289 (852)
T TIGR03346       231 RLLALDMGA----------LIAGAKYRGEFEERLKAVLNEVTKSE-----------GQIILFIDELHTLVGAGKAEGAMD  289 (852)
T ss_pred             eEEEeeHHH----------HhhcchhhhhHHHHHHHHHHHHHhcC-----------CCeEEEeccHHHhhcCCCCcchhH
Confidence            555554221          11222222 22335666666664332           3579999999987531   11112


Q ss_pred             HHHHHHHHHhcCCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHH----hCCCC
Q 005987          281 LRQCLLLLVRSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQ----EQYSL  356 (666)
Q Consensus       281 l~~~L~~l~~~~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~----e~i~v  356 (666)
                      ..+.|...+..+.  +.+|.++ +..    .+.+.+. +...+.+ |+..|.+..|+.++..++|+.+...    .++.+
T Consensus       290 ~~~~Lk~~l~~g~--i~~IgaT-t~~----e~r~~~~-~d~al~r-Rf~~i~v~~p~~~~~~~iL~~~~~~~e~~~~v~~  360 (852)
T TIGR03346       290 AGNMLKPALARGE--LHCIGAT-TLD----EYRKYIE-KDAALER-RFQPVFVDEPTVEDTISILRGLKERYEVHHGVRI  360 (852)
T ss_pred             HHHHhchhhhcCc--eEEEEeC-cHH----HHHHHhh-cCHHHHh-cCCEEEeCCCCHHHHHHHHHHHHHHhccccCCCC
Confidence            3455666665554  3333332 221    1111122 2344444 6888999999999999999877654    35778


Q ss_pred             CHHHHHHHHHHcCC---c---HHHHHHHHHHHhcC
Q 005987          357 STEQIDLVAQASGG---D---IRQAITSLQFSSLK  385 (666)
Q Consensus       357 ~~~~l~~Ia~~s~G---D---IR~AIn~LQf~~~~  385 (666)
                      .++++..++..|.+   |   ..+||..|.-+|..
T Consensus       361 ~d~~i~~~~~ls~~yi~~r~lPdkAidlld~a~a~  395 (852)
T TIGR03346       361 TDPAIVAAATLSHRYITDRFLPDKAIDLIDEAAAR  395 (852)
T ss_pred             CHHHHHHHHHhccccccccCCchHHHHHHHHHHHH
Confidence            99999999988764   3   57899999888753

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.

>CHL00095 clpC Clp protease ATP binding subunit

Probab=99.36  E-value=4.3e-12  Score=151.20  Aligned_cols=210  Identities=17%  Similarity=0.186  Sum_probs=143.1

Q ss_pred             CccccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc----------CCcE
Q 005987          137 QLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL----------GARL  206 (666)
Q Consensus       137 ~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel----------g~~v  206 (666)
                      ..++++-+...++.++|+++.++.+..+|..+.        ++.+||+||||||||++|+.||+.+          +..+
T Consensus       167 ~~l~~~a~~~~~~~~igr~~ei~~~~~~L~r~~--------~~n~lL~G~pGvGKTal~~~la~~i~~~~vp~~l~~~~i  238 (821)
T CHL00095        167 TNLTKEAIDGNLDPVIGREKEIERVIQILGRRT--------KNNPILIGEPGVGKTAIAEGLAQRIVNRDVPDILEDKLV  238 (821)
T ss_pred             HHHHHHHHcCCCCCCCCcHHHHHHHHHHHcccc--------cCCeEEECCCCCCHHHHHHHHHHHHHhCCCChhhcCCeE
Confidence            456777788899999999999999999997532        2578999999999999999999987          3667


Q ss_pred             EEEcCCCchhhhhhhhcccCCccccc-hhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhH---HHHHH
Q 005987          207 YEWDTPTPTIWQEYMHNCKTGLEYTS-KLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTA---FERLR  282 (666)
Q Consensus       207 iE~nasd~~~~~e~l~~~~~g~~~~s-~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~---~~~l~  282 (666)
                      ++++...          ...|..|.. ..+.++.+++.+...            .+.||+|||++.+.+...   -..+.
T Consensus       239 ~~l~~~~----------l~ag~~~~ge~e~rl~~i~~~~~~~------------~~~ILfiDEih~l~~~g~~~g~~~~a  296 (821)
T CHL00095        239 ITLDIGL----------LLAGTKYRGEFEERLKRIFDEIQEN------------NNIILVIDEVHTLIGAGAAEGAIDAA  296 (821)
T ss_pred             EEeeHHH----------HhccCCCccHHHHHHHHHHHHHHhc------------CCeEEEEecHHHHhcCCCCCCcccHH
Confidence            7766432          123444432 234566677766432            257999999997643210   01234


Q ss_pred             HHHHHHHhcCCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHH----hCCCCCH
Q 005987          283 QCLLLLVRSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQ----EQYSLST  358 (666)
Q Consensus       283 ~~L~~l~~~~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~----e~i~v~~  358 (666)
                      +.|...+..+..  .+|. .++..    .+.+.++ ....+.+ ++..|.+..++..+...+|+.+...    .++.+++
T Consensus       297 ~lLkp~l~rg~l--~~Ig-aTt~~----ey~~~ie-~D~aL~r-Rf~~I~v~ep~~~e~~aILr~l~~~~e~~~~v~i~d  367 (821)
T CHL00095        297 NILKPALARGEL--QCIG-ATTLD----EYRKHIE-KDPALER-RFQPVYVGEPSVEETIEILFGLRSRYEKHHNLSISD  367 (821)
T ss_pred             HHhHHHHhCCCc--EEEE-eCCHH----HHHHHHh-cCHHHHh-cceEEecCCCCHHHHHHHHHHHHHHHHHHcCCCCCH
Confidence            556666666653  2332 22211    1222222 2334444 6889999999999998888876543    3567899


Q ss_pred             HHHHHHHHHcCCc------HHHHHHHHHHHhcC
Q 005987          359 EQIDLVAQASGGD------IRQAITSLQFSSLK  385 (666)
Q Consensus       359 ~~l~~Ia~~s~GD------IR~AIn~LQf~~~~  385 (666)
                      +++..++..|.|-      .++||..|..+|..
T Consensus       368 eal~~i~~ls~~yi~~r~lPdkaidlld~a~a~  400 (821)
T CHL00095        368 KALEAAAKLSDQYIADRFLPDKAIDLLDEAGSR  400 (821)
T ss_pred             HHHHHHHHHhhccCccccCchHHHHHHHHHHHH
Confidence            9999999998763      56799999888763

>KOG0734 consensus AAA+-type ATPase containing the peptidase M41 domain [Posttranslational modification, protein turnover, chaperones]

Probab=99.36  E-value=1.2e-11  Score=133.10  Aligned_cols=208  Identities=16%  Similarity=0.266  Sum_probs=130.4

Q ss_pred             cccCCCCccccccCHHHHHHHH---HHHHHh--hcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCch
Q 005987          141 EKYKPRSLEELAVQRKKVEEVR---AWFEER--LGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPT  215 (666)
Q Consensus       141 eKY~P~sl~eLvg~~k~i~el~---~wL~~~--~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~  215 (666)
                      ++-.-.+|+|+.|-++..++|.   ++|++-  +..-.|++| +.+||+||||+|||.+||++|-|.+..++....|.. 
T Consensus       296 ~~~~nv~F~dVkG~DEAK~ELeEiVefLkdP~kftrLGGKLP-KGVLLvGPPGTGKTlLARAvAGEA~VPFF~~sGSEF-  373 (752)
T KOG0734|consen  296 EQMKNVTFEDVKGVDEAKQELEEIVEFLKDPTKFTRLGGKLP-KGVLLVGPPGTGKTLLARAVAGEAGVPFFYASGSEF-  373 (752)
T ss_pred             hhhcccccccccChHHHHHHHHHHHHHhcCcHHhhhccCcCC-CceEEeCCCCCchhHHHHHhhcccCCCeEeccccch-
Confidence            3444567999999776655554   555432  112237787 889999999999999999999999999988777652 


Q ss_pred             hhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchh---HHHHHHHHHHHHHhc-
Q 005987          216 IWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRT---AFERLRQCLLLLVRS-  291 (666)
Q Consensus       216 ~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~---~~~~l~~~L~~l~~~-  291 (666)
                        .|    ...|+.    ..++++++..++..            .|+||+|||+|.+.+..   ........|.+++-. 
T Consensus       374 --dE----m~VGvG----ArRVRdLF~aAk~~------------APcIIFIDEiDavG~kR~~~~~~y~kqTlNQLLvEm  431 (752)
T KOG0734|consen  374 --DE----MFVGVG----ARRVRDLFAAAKAR------------APCIIFIDEIDAVGGKRNPSDQHYAKQTLNQLLVEM  431 (752)
T ss_pred             --hh----hhhccc----HHHHHHHHHHHHhc------------CCeEEEEechhhhcccCCccHHHHHHHHHHHHHHHh
Confidence              11    123333    34667777777543            48999999999764321   111223344444322 


Q ss_pred             ---CCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcC--eeEEEeCCCCHHHHHHHHHHHHHHhCCCCCH-HHHHHHH
Q 005987          292 ---THIPTAVVLTECGKADSVDSTAQSFEELQSILVDAG--ARKVALNPITNGSIKRTLSKICRQEQYSLST-EQIDLVA  365 (666)
Q Consensus       292 ---~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r--~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~-~~l~~Ia  365 (666)
                         .+.--||++++++.++          .|...|-||+  -.+|..+.|+..-..++|...+.+-  ..++ -.+..||
T Consensus       432 DGF~qNeGiIvigATNfpe----------~LD~AL~RPGRFD~~v~Vp~PDv~GR~eIL~~yl~ki--~~~~~VD~~iiA  499 (752)
T KOG0734|consen  432 DGFKQNEGIIVIGATNFPE----------ALDKALTRPGRFDRHVTVPLPDVRGRTEILKLYLSKI--PLDEDVDPKIIA  499 (752)
T ss_pred             cCcCcCCceEEEeccCChh----------hhhHHhcCCCccceeEecCCCCcccHHHHHHHHHhcC--CcccCCCHhHhc
Confidence               2222345556665543          3455555553  3468888888888888888777552  2221 2234566


Q ss_pred             HH----cCCcHHHHHHHHHHHhc
Q 005987          366 QA----SGGDIRQAITSLQFSSL  384 (666)
Q Consensus       366 ~~----s~GDIR~AIn~LQf~~~  384 (666)
                      ..    ++.|+-+.+|..-..+.
T Consensus       500 RGT~GFsGAdLaNlVNqAAlkAa  522 (752)
T KOG0734|consen  500 RGTPGFSGADLANLVNQAALKAA  522 (752)
T ss_pred             cCCCCCchHHHHHHHHHHHHHHH
Confidence            65    45588888887655544

>PRK08058 DNA polymerase III subunit delta'; Validated

Probab=99.35  E-value=3.5e-11  Score=128.87  Aligned_cols=194  Identities=17%  Similarity=0.223  Sum_probs=120.2

Q ss_pred             Ccccccc-CHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcE-EEEcCCCchhhhhhhhc-
Q 005987          147 SLEELAV-QRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARL-YEWDTPTPTIWQEYMHN-  223 (666)
Q Consensus       147 sl~eLvg-~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~v-iE~nasd~~~~~e~l~~-  223 (666)
                      .++.|+| |+..++.++..+..      |+.+ +.+||+||+|+||+++|+.+|+.+.+.- ..-.+...+.....+.+ 
T Consensus         3 ~~~~i~~~q~~~~~~L~~~~~~------~~l~-ha~Lf~G~~G~gk~~~a~~la~~l~c~~~~~~~~cg~C~~c~~~~~~   75 (329)
T PRK08058          3 TWEQLTALQPVVVKMLQNSIAK------NRLS-HAYLFEGAKGTGKKATALWLAKSLFCLERNGVEPCGTCTNCKRIDSG   75 (329)
T ss_pred             cHHHHHhhHHHHHHHHHHHHHc------CCCC-ceEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCcCHHHHHHhcC
Confidence            3567888 99999999998876      7776 7899999999999999999999985431 00000000000000000 


Q ss_pred             ccCCc------cccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcCCCceE
Q 005987          224 CKTGL------EYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHIPTA  297 (666)
Q Consensus       224 ~~~g~------~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~~~PiV  297 (666)
                      .....      .-.-..++++++++.+...+     ..   ...+|+||||++.++..     ..++|++.++.....++
T Consensus        76 ~hpD~~~i~~~~~~i~id~ir~l~~~~~~~~-----~~---~~~kvviI~~a~~~~~~-----a~NaLLK~LEEPp~~~~  142 (329)
T PRK08058         76 NHPDVHLVAPDGQSIKKDQIRYLKEEFSKSG-----VE---SNKKVYIIEHADKMTAS-----AANSLLKFLEEPSGGTT  142 (329)
T ss_pred             CCCCEEEeccccccCCHHHHHHHHHHHhhCC-----cc---cCceEEEeehHhhhCHH-----HHHHHHHHhcCCCCCce
Confidence            00000      01123566777666654222     11   13579999999988643     33457777777554444


Q ss_pred             EEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCcHHHHHH
Q 005987          298 VVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASGGDIRQAIT  377 (666)
Q Consensus       298 iIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~s~GDIR~AIn  377 (666)
                      +|.....       ..+.++.|++     ||..|.|.+++..++.+.|.    .++  ++++....++..+ |+++.|+.
T Consensus       143 ~Il~t~~-------~~~ll~TIrS-----Rc~~i~~~~~~~~~~~~~L~----~~g--i~~~~~~~l~~~~-g~~~~A~~  203 (329)
T PRK08058        143 AILLTEN-------KHQILPTILS-----RCQVVEFRPLPPESLIQRLQ----EEG--ISESLATLLAGLT-NSVEEALA  203 (329)
T ss_pred             EEEEeCC-------hHhCcHHHHh-----hceeeeCCCCCHHHHHHHHH----HcC--CChHHHHHHHHHc-CCHHHHHH
Confidence            4433321       2344455554     69999999999999987775    345  5566666666664 78988876


Q ss_pred             HH
Q 005987          378 SL  379 (666)
Q Consensus       378 ~L  379 (666)
                      .+
T Consensus       204 l~  205 (329)
T PRK08058        204 LS  205 (329)
T ss_pred             Hh
Confidence            54

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=99.33  E-value=2.3e-11  Score=143.72  Aligned_cols=203  Identities=16%  Similarity=0.233  Sum_probs=125.7

Q ss_pred             CCCccccccCHHHHHHHHHHHHHhhcCC-----CCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCchhhhh
Q 005987          145 PRSLEELAVQRKKVEEVRAWFEERLGDS-----KDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTIWQE  219 (666)
Q Consensus       145 P~sl~eLvg~~k~i~el~~wL~~~~~~~-----~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~~~~e  219 (666)
                      ..+++++.|.+...++|++.+.-.+...     -|..+++.+|||||||||||++|+++|++++..++.+..++.  ...
T Consensus       449 ~~~~~di~g~~~~k~~l~~~v~~~~~~~~~~~~~g~~~~~giLL~GppGtGKT~lakalA~e~~~~fi~v~~~~l--~~~  526 (733)
T TIGR01243       449 NVRWSDIGGLEEVKQELREAVEWPLKHPEIFEKMGIRPPKGVLLFGPPGTGKTLLAKAVATESGANFIAVRGPEI--LSK  526 (733)
T ss_pred             ccchhhcccHHHHHHHHHHHHHhhhhCHHHHHhcCCCCCceEEEECCCCCCHHHHHHHHHHhcCCCEEEEehHHH--hhc
Confidence            4578999999999999988876433211     132334789999999999999999999999999999887641  111


Q ss_pred             hhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcch-------hHHHHHHHHHHHHHhc-
Q 005987          220 YMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGR-------TAFERLRQCLLLLVRS-  291 (666)
Q Consensus       220 ~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~-------~~~~~l~~~L~~l~~~-  291 (666)
                               .+......++.++..+...            .++||||||+|.+...       ....++...|+..+.. 
T Consensus       527 ---------~vGese~~i~~~f~~A~~~------------~p~iifiDEid~l~~~r~~~~~~~~~~~~~~~lL~~ldg~  585 (733)
T TIGR01243       527 ---------WVGESEKAIREIFRKARQA------------APAIIFFDEIDAIAPARGARFDTSVTDRIVNQLLTEMDGI  585 (733)
T ss_pred             ---------ccCcHHHHHHHHHHHHHhc------------CCEEEEEEChhhhhccCCCCCCccHHHHHHHHHHHHhhcc
Confidence                     1122234566677766543            3679999999976321       1123344434444432 


Q ss_pred             -CCCceEEEEecCCCCCCccchhhhhhHHHHHHhhc-C-eeEEEeCCCCHHHHHHHHHHHHHHhCCCCCH-HHHHHHHHH
Q 005987          292 -THIPTAVVLTECGKADSVDSTAQSFEELQSILVDA-G-ARKVALNPITNGSIKRTLSKICRQEQYSLST-EQIDLVAQA  367 (666)
Q Consensus       292 -~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~-r-~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~-~~l~~Ia~~  367 (666)
                       ....+++| +.++.++.          |.+.+.|+ | -..|.|++|+..+..++++.....  ..+++ ..++.||..
T Consensus       586 ~~~~~v~vI-~aTn~~~~----------ld~allRpgRfd~~i~v~~Pd~~~R~~i~~~~~~~--~~~~~~~~l~~la~~  652 (733)
T TIGR01243       586 QELSNVVVI-AATNRPDI----------LDPALLRPGRFDRLILVPPPDEEARKEIFKIHTRS--MPLAEDVDLEELAEM  652 (733)
T ss_pred             cCCCCEEEE-EeCCChhh----------CCHhhcCCCccceEEEeCCcCHHHHHHHHHHHhcC--CCCCccCCHHHHHHH
Confidence             12234444 33343322          22333321 2 357899999999999998866543  33332 346778876


Q ss_pred             c----CCcHHHHHHHHHHHh
Q 005987          368 S----GGDIRQAITSLQFSS  383 (666)
Q Consensus       368 s----~GDIR~AIn~LQf~~  383 (666)
                      +    +.||..+++...+.+
T Consensus       653 t~g~sgadi~~~~~~A~~~a  672 (733)
T TIGR01243       653 TEGYTGADIEAVCREAAMAA  672 (733)
T ss_pred             cCCCCHHHHHHHHHHHHHHH
Confidence            4    457776665444444

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.

>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=99.31  E-value=6.8e-11  Score=124.41  Aligned_cols=114  Identities=20%  Similarity=0.308  Sum_probs=75.6

Q ss_pred             ceEEEEeCCCCCcchhHHHHHHHHHHHHHhcCCCceEEEEecCCCCC--Cccc-hhhhhhHHHHHHhhcCeeEEEeCCCC
Q 005987          261 SAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHIPTAVVLTECGKAD--SVDS-TAQSFEELQSILVDAGARKVALNPIT  337 (666)
Q Consensus       261 ~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~~~PiViIit~~~~~~--s~d~-~~r~l~~L~s~L~r~r~~~I~F~p~s  337 (666)
                      |-||||||++.++-. .|.    .|...+++.-.|+|+++++.+...  ..|. ..+.++  ..+|.  ||..|+-.|++
T Consensus       279 pGVLFIDEvHmLDiE-cFs----fLnralEs~~sPiiIlATNRg~~~irGt~~~sphGiP--~DlLD--RllII~t~py~  349 (398)
T PF06068_consen  279 PGVLFIDEVHMLDIE-CFS----FLNRALESELSPIIILATNRGITKIRGTDIISPHGIP--LDLLD--RLLIIRTKPYS  349 (398)
T ss_dssp             E-EEEEESGGGSBHH-HHH----HHHHHHTSTT--EEEEEES-SEEE-BTTS-EEETT----HHHHT--TEEEEEE----
T ss_pred             cceEEecchhhccHH-HHH----HHHHHhcCCCCcEEEEecCceeeeccCccCcCCCCCC--cchHh--hcEEEECCCCC
Confidence            569999999988643 232    466777888889999999865321  1122 222232  45666  49999999999


Q ss_pred             HHHHHHHHHHHHHHhCCCCCHHHHHHHHHH-cCCcHHHHHHHHHHHh
Q 005987          338 NGSIKRTLSKICRQEQYSLSTEQIDLVAQA-SGGDIRQAITSLQFSS  383 (666)
Q Consensus       338 ~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~-s~GDIR~AIn~LQf~~  383 (666)
                      .++++++|...|+.|++.+++++++.|+.. ....+|.|++.|..+.
T Consensus       350 ~~ei~~Il~iR~~~E~v~i~~~al~~L~~ig~~~SLRYAiqLi~~a~  396 (398)
T PF06068_consen  350 EEEIKQILKIRAKEEDVEISEDALDLLTKIGVETSLRYAIQLITPAS  396 (398)
T ss_dssp             HHHHHHHHHHHHHHCT--B-HHHHHHHHHHHHHS-HHHHHHCHHHHH
T ss_pred             HHHHHHHHHhhhhhhcCcCCHHHHHHHHHHhhhccHHHHHHhhhhhh
Confidence            999999999999999999999999999976 4578999999886553

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.

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

Probab=99.31  E-value=3.1e-10  Score=113.98  Aligned_cols=205  Identities=18%  Similarity=0.230  Sum_probs=130.3

Q ss_pred             cccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcCCCchhh
Q 005987          141 EKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL---GARLYEWDTPTPTIW  217 (666)
Q Consensus       141 eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~nasd~~~~  217 (666)
                      ....|..+++|+|-+...+.|..-.+..+.   |.+. +++||+|++|||||++|+++..++   |+.++|+...+    
T Consensus        19 ~~~~~~~l~~L~Gie~Qk~~l~~Nt~~Fl~---G~pa-nnvLL~G~rGtGKSSlVkall~~y~~~GLRlIev~k~~----   90 (249)
T PF05673_consen   19 KHPDPIRLDDLIGIERQKEALIENTEQFLQ---GLPA-NNVLLWGARGTGKSSLVKALLNEYADQGLRLIEVSKED----   90 (249)
T ss_pred             CCCCCCCHHHhcCHHHHHHHHHHHHHHHHc---CCCC-cceEEecCCCCCHHHHHHHHHHHHhhcCceEEEECHHH----
Confidence            445678899999999988888877776664   5544 789999999999999999999987   88999987533    


Q ss_pred             hhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcCCCceE
Q 005987          218 QEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHIPTA  297 (666)
Q Consensus       218 ~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~~~PiV  297 (666)
                                      +..+..+++.++..           ..+.||++||+---.....+..+..+|..-++... .-|
T Consensus        91 ----------------L~~l~~l~~~l~~~-----------~~kFIlf~DDLsFe~~d~~yk~LKs~LeGgle~~P-~Nv  142 (249)
T PF05673_consen   91 ----------------LGDLPELLDLLRDR-----------PYKFILFCDDLSFEEGDTEYKALKSVLEGGLEARP-DNV  142 (249)
T ss_pred             ----------------hccHHHHHHHHhcC-----------CCCEEEEecCCCCCCCcHHHHHHHHHhcCccccCC-CcE
Confidence                            22344555555422           24679999998643333445555554444333222 234


Q ss_pred             EEEecCCCCCC-----ccc---------hhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHH
Q 005987          298 VVLTECGKADS-----VDS---------TAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDL  363 (666)
Q Consensus       298 iIit~~~~~~s-----~d~---------~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~  363 (666)
                      +|..+++....     .|.         ..-.++.--++-.| ....|.|.+++.++-.+++...+.+.++.++++.+..
T Consensus       143 liyATSNRRHLv~E~~~d~~~~~~~eih~~d~~eEklSLsDR-FGL~l~F~~~~q~~YL~IV~~~~~~~g~~~~~e~l~~  221 (249)
T PF05673_consen  143 LIYATSNRRHLVPESFSDREDIQDDEIHPSDTIEEKLSLSDR-FGLWLSFYPPDQEEYLAIVRHYAERYGLELDEEELRQ  221 (249)
T ss_pred             EEEEecchhhccchhhhhccCCCccccCcchHHHHHHhHHHh-CCcEEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHH
Confidence            44443332110     000         01111221233334 5678999999999999999999999999998644433


Q ss_pred             -----HHHHcCCcHHHHHHHHHHH
Q 005987          364 -----VAQASGGDIRQAITSLQFS  382 (666)
Q Consensus       364 -----Ia~~s~GDIR~AIn~LQf~  382 (666)
                           -....+..-|.|-.-...+
T Consensus       222 ~Al~wa~~rg~RSGRtA~QF~~~l  245 (249)
T PF05673_consen  222 EALQWALRRGGRSGRTARQFIDDL  245 (249)
T ss_pred             HHHHHHHHcCCCCHHHHHHHHHHH
Confidence                 3333334555555444433

>PRK10865 protein disaggregation chaperone; Provisional

Probab=99.31  E-value=1.5e-11  Score=146.54  Aligned_cols=214  Identities=17%  Similarity=0.184  Sum_probs=142.4

Q ss_pred             CCCccccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc----------CC
Q 005987          135 TQQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL----------GA  204 (666)
Q Consensus       135 ~~~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel----------g~  204 (666)
                      ...+.+++.+|..+++++|+++.++.+...|.+..        .+.+||+||||||||++|+.||+.+          ++
T Consensus       164 ~~~~l~~~~r~~~l~~vigr~~ei~~~i~iL~r~~--------~~n~lL~G~pGvGKT~l~~~la~~i~~~~vp~~l~~~  235 (857)
T PRK10865        164 YTIDLTERAEQGKLDPVIGRDEEIRRTIQVLQRRT--------KNNPVLIGEPGVGKTAIVEGLAQRIINGEVPEGLKGR  235 (857)
T ss_pred             HhhhHHHHHhcCCCCcCCCCHHHHHHHHHHHhcCC--------cCceEEECCCCCCHHHHHHHHHHHhhcCCCchhhCCC
Confidence            45678999999999999999999999988887521        1478999999999999999999998          56


Q ss_pred             cEEEEcCCCchhhhhhhhcccCCcccc-chhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchh---HHHH
Q 005987          205 RLYEWDTPTPTIWQEYMHNCKTGLEYT-SKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRT---AFER  280 (666)
Q Consensus       205 ~viE~nasd~~~~~e~l~~~~~g~~~~-s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~---~~~~  280 (666)
                      .++.++...          ...|..|. .....++.+++++....           .+.||||||++.+.+..   .-..
T Consensus       236 ~~~~l~l~~----------l~ag~~~~g~~e~~lk~~~~~~~~~~-----------~~~ILfIDEih~l~~~~~~~~~~d  294 (857)
T PRK10865        236 RVLALDMGA----------LVAGAKYRGEFEERLKGVLNDLAKQE-----------GNVILFIDELHTMVGAGKADGAMD  294 (857)
T ss_pred             EEEEEehhh----------hhhccchhhhhHHHHHHHHHHHHHcC-----------CCeEEEEecHHHhccCCCCccchh
Confidence            666655432          11233332 22335666666654322           35799999999875321   0112


Q ss_pred             HHHHHHHHHhcCCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHH----hCCCC
Q 005987          281 LRQCLLLLVRSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQ----EQYSL  356 (666)
Q Consensus       281 l~~~L~~l~~~~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~----e~i~v  356 (666)
                      ..+.|...+..+.  +. ++++++..+    +.+.++ +...+.| |+..|.+..|+.++...+|+.+...    .++.+
T Consensus       295 ~~~~lkp~l~~g~--l~-~IgaTt~~e----~r~~~~-~d~al~r-Rf~~i~v~eP~~~~~~~iL~~l~~~~e~~~~v~~  365 (857)
T PRK10865        295 AGNMLKPALARGE--LH-CVGATTLDE----YRQYIE-KDAALER-RFQKVFVAEPSVEDTIAILRGLKERYELHHHVQI  365 (857)
T ss_pred             HHHHhcchhhcCC--Ce-EEEcCCCHH----HHHHhh-hcHHHHh-hCCEEEeCCCCHHHHHHHHHHHhhhhccCCCCCc
Confidence            3455666666664  33 334433221    122222 3444444 5778999999999999999877654    35778


Q ss_pred             CHHHHHHHHHHcCCc------HHHHHHHHHHHhcCC
Q 005987          357 STEQIDLVAQASGGD------IRQAITSLQFSSLKQ  386 (666)
Q Consensus       357 ~~~~l~~Ia~~s~GD------IR~AIn~LQf~~~~~  386 (666)
                      +++++...+..+.+=      ..+|+..+..+|.+-
T Consensus       366 ~d~a~~~a~~ls~ry~~~~~~pdkAi~LiD~aaa~~  401 (857)
T PRK10865        366 TDPAIVAAATLSHRYIADRQLPDKAIDLIDEAASSI  401 (857)
T ss_pred             CHHHHHHHHHHhhccccCCCCChHHHHHHHHHhccc
Confidence            899988887776543      356777777777643

>KOG0731 consensus AAA+-type ATPase containing the peptidase M41 domain [Posttranslational modification, protein turnover, chaperones]

Probab=99.30  E-value=2.5e-11  Score=138.21  Aligned_cols=207  Identities=16%  Similarity=0.230  Sum_probs=133.9

Q ss_pred             CCCCccccccCHHHHHHHHHHHHHhhcCC-----CCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCchhhh
Q 005987          144 KPRSLEELAVQRKKVEEVRAWFEERLGDS-----KDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTIWQ  218 (666)
Q Consensus       144 ~P~sl~eLvg~~k~i~el~~wL~~~~~~~-----~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~~~~  218 (666)
                      .+-+|+|++|-++..++|.+++. .++++     .|...++.+||+||||||||.+|+++|.|.|..++.+++++...  
T Consensus       306 t~V~FkDVAG~deAK~El~E~V~-fLKNP~~Y~~lGAKiPkGvLL~GPPGTGKTLLAKAiAGEAgVPF~svSGSEFvE--  382 (774)
T KOG0731|consen  306 TGVKFKDVAGVDEAKEELMEFVK-FLKNPEQYQELGAKIPKGVLLVGPPGTGKTLLAKAIAGEAGVPFFSVSGSEFVE--  382 (774)
T ss_pred             CCCccccccCcHHHHHHHHHHHH-HhcCHHHHHHcCCcCcCceEEECCCCCcHHHHHHHHhcccCCceeeechHHHHH--
Confidence            34679999999988888887765 23221     24334489999999999999999999999999999999876221  


Q ss_pred             hhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhH---H-----HHHHHHHHHHHh
Q 005987          219 EYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTA---F-----ERLRQCLLLLVR  290 (666)
Q Consensus       219 e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~---~-----~~l~~~L~~l~~  290 (666)
                       .    ..|.    .....++++..++..            .|+||+|||+|.......   .     ++- ..|.+++-
T Consensus       383 -~----~~g~----~asrvr~lf~~ar~~------------aP~iifideida~~~~r~G~~~~~~~~e~e-~tlnQll~  440 (774)
T KOG0731|consen  383 -M----FVGV----GASRVRDLFPLARKN------------APSIIFIDEIDAVGRKRGGKGTGGGQDERE-QTLNQLLV  440 (774)
T ss_pred             -H----hccc----chHHHHHHHHHhhcc------------CCeEEEecccccccccccccccCCCChHHH-HHHHHHHH
Confidence             1    1111    133566666666543            478999999997643220   0     111 12333332


Q ss_pred             c----CCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcC--eeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHH
Q 005987          291 S----THIPTAVVLTECGKADSVDSTAQSFEELQSILVDAG--ARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLV  364 (666)
Q Consensus       291 ~----~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r--~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~I  364 (666)
                      .    ...--|++++.|+..+.          |...|.|++  -..|....|+......++.-.+..-....++..+..|
T Consensus       441 emDgf~~~~~vi~~a~tnr~d~----------ld~allrpGRfdr~i~i~~p~~~~r~~i~~~h~~~~~~~~e~~dl~~~  510 (774)
T KOG0731|consen  441 EMDGFETSKGVIVLAATNRPDI----------LDPALLRPGRFDRQIQIDLPDVKGRASILKVHLRKKKLDDEDVDLSKL  510 (774)
T ss_pred             HhcCCcCCCcEEEEeccCCccc----------cCHHhcCCCccccceeccCCchhhhHHHHHHHhhccCCCcchhhHHHH
Confidence            1    11122444555554443          333333332  3468999999999999999877766665566666668


Q ss_pred             HHHcC----CcHHHHHHHHHHHhcC
Q 005987          365 AQASG----GDIRQAITSLQFSSLK  385 (666)
Q Consensus       365 a~~s~----GDIR~AIn~LQf~~~~  385 (666)
                      |..+.    -||....|.....+..
T Consensus       511 a~~t~gf~gadl~n~~neaa~~a~r  535 (774)
T KOG0731|consen  511 ASLTPGFSGADLANLCNEAALLAAR  535 (774)
T ss_pred             HhcCCCCcHHHHHhhhhHHHHHHHH
Confidence            87754    4777777776666654

>PRK05707 DNA polymerase III subunit delta'; Validated

Probab=99.30  E-value=1.4e-10  Score=123.71  Aligned_cols=176  Identities=15%  Similarity=0.148  Sum_probs=108.2

Q ss_pred             CCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEE-EcCCCchhhhhhhhc--------cc-CCccccchhHHHHHHHHH
Q 005987          174 DKFSTNVLVITGQAGVGKTATVRQIASHLGARLYE-WDTPTPTIWQEYMHN--------CK-TGLEYTSKLDEFENFVER  243 (666)
Q Consensus       174 g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE-~nasd~~~~~e~l~~--------~~-~g~~~~s~~~~f~~fl~~  243 (666)
                      |+.+ +.+||+||+|+|||++|+.+|+.+.+.--. ..+...+.....+..        .. .+..-.-.+++++++++.
T Consensus        19 ~r~~-ha~Lf~G~~G~GK~~~A~~~A~~llC~~~~~~~~Cg~C~sC~~~~~g~HPD~~~i~~~~~~~~i~id~iR~l~~~   97 (328)
T PRK05707         19 GRHP-HAYLLHGPAGIGKRALAERLAAALLCEAPQGGGACGSCKGCQLLRAGSHPDNFVLEPEEADKTIKVDQVRELVSF   97 (328)
T ss_pred             CCcc-eeeeeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHhcCCCCCEEEEeccCCCCCCCHHHHHHHHHH
Confidence            6666 789999999999999999999999653110 001011100000000        00 010112346777777766


Q ss_pred             HHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcCCCceEEEEecCCCCCCccchhhhhhHHHHHH
Q 005987          244 IRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHIPTAVVLTECGKADSVDSTAQSFEELQSIL  323 (666)
Q Consensus       244 a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L  323 (666)
                      +...+.        ....+|+|||+++.++..     ..++|++.++.....++||+....       ..+.++.|++  
T Consensus        98 ~~~~~~--------~~~~kv~iI~~a~~m~~~-----aaNaLLK~LEEPp~~~~fiL~t~~-------~~~ll~TI~S--  155 (328)
T PRK05707         98 VVQTAQ--------LGGRKVVLIEPAEAMNRN-----AANALLKSLEEPSGDTVLLLISHQ-------PSRLLPTIKS--  155 (328)
T ss_pred             Hhhccc--------cCCCeEEEECChhhCCHH-----HHHHHHHHHhCCCCCeEEEEEECC-------hhhCcHHHHh--
Confidence            643221        123568999999998653     234566666765433344433321       2234444554  


Q ss_pred             hhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCcHHHHHHHH
Q 005987          324 VDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASGGDIRQAITSL  379 (666)
Q Consensus       324 ~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~s~GDIR~AIn~L  379 (666)
                         ||..+.|.+++.+++.+.|...+.    ..+++....++..++|.+..|+..+
T Consensus       156 ---Rc~~~~~~~~~~~~~~~~L~~~~~----~~~~~~~~~~l~la~Gsp~~A~~l~  204 (328)
T PRK05707        156 ---RCQQQACPLPSNEESLQWLQQALP----ESDERERIELLTLAGGSPLRALQLH  204 (328)
T ss_pred             ---hceeeeCCCcCHHHHHHHHHHhcc----cCChHHHHHHHHHcCCCHHHHHHHH
Confidence               699999999999999999875431    2456667788899999999887653

>TIGR00763 lon ATP-dependent protease La

Probab=99.29  E-value=4.3e-11  Score=141.80  Aligned_cols=187  Identities=14%  Similarity=0.171  Sum_probs=111.0

Q ss_pred             ccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCchhhhhhhhcccCCcc
Q 005987          150 ELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTIWQEYMHNCKTGLE  229 (666)
Q Consensus       150 eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~~~~e~l~~~~~g~~  229 (666)
                      ++.|+++.++.|.+|+..+...  +....++++|+||||||||++|+++|++++..++.++........+.....   ..
T Consensus       321 ~~~G~~~~k~~i~~~~~~~~~~--~~~~~~~lll~GppG~GKT~lAk~iA~~l~~~~~~i~~~~~~~~~~i~g~~---~~  395 (775)
T TIGR00763       321 DHYGLKKVKERILEYLAVQKLR--GKMKGPILCLVGPPGVGKTSLGKSIAKALNRKFVRFSLGGVRDEAEIRGHR---RT  395 (775)
T ss_pred             hcCChHHHHHHHHHHHHHHHhh--cCCCCceEEEECCCCCCHHHHHHHHHHHhcCCeEEEeCCCcccHHHHcCCC---Cc
Confidence            4778999999999998754332  222335899999999999999999999999999988765432222211110   00


Q ss_pred             c-cchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhc---C------------C
Q 005987          230 Y-TSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRS---T------------H  293 (666)
Q Consensus       230 ~-~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~---~------------~  293 (666)
                      | ......+.+.+..+..             ...||||||+|.+.... .+...++|+.+++.   .            .
T Consensus       396 ~~g~~~g~i~~~l~~~~~-------------~~~villDEidk~~~~~-~~~~~~aLl~~ld~~~~~~f~d~~~~~~~d~  461 (775)
T TIGR00763       396 YVGAMPGRIIQGLKKAKT-------------KNPLFLLDEIDKIGSSF-RGDPASALLEVLDPEQNNAFSDHYLDVPFDL  461 (775)
T ss_pred             eeCCCCchHHHHHHHhCc-------------CCCEEEEechhhcCCcc-CCCHHHHHHHhcCHHhcCccccccCCceecc
Confidence            1 1111222222332211             12389999999875321 00111223333321   0            0


Q ss_pred             CceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHH-----H-----hCCCCCHHHHHH
Q 005987          294 IPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICR-----Q-----EQYSLSTEQIDL  363 (666)
Q Consensus       294 ~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~-----~-----e~i~v~~~~l~~  363 (666)
                      ..++||++. +..          ..+...|.+ |+..|.|++++.++..+++++.+.     .     +++.++++++..
T Consensus       462 s~v~~I~Tt-N~~----------~~i~~~L~~-R~~vi~~~~~~~~e~~~I~~~~l~~~~~~~~~l~~~~~~~~~~~l~~  529 (775)
T TIGR00763       462 SKVIFIATA-NSI----------DTIPRPLLD-RMEVIELSGYTEEEKLEIAKKYLIPKALEDHGLKPDELKITDEALLL  529 (775)
T ss_pred             CCEEEEEec-CCc----------hhCCHHHhC-CeeEEecCCCCHHHHHHHHHHHHHHHHHHHcCCCcceEEECHHHHHH
Confidence            124444433 221          112222323 588999999999999988876542     1     245789999999


Q ss_pred             HHHH
Q 005987          364 VAQA  367 (666)
Q Consensus       364 Ia~~  367 (666)
                      |++.
T Consensus       530 i~~~  533 (775)
T TIGR00763       530 LIKY  533 (775)
T ss_pred             HHHh
Confidence            9975

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.

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

Probab=99.29  E-value=1.5e-10  Score=124.83  Aligned_cols=206  Identities=19%  Similarity=0.264  Sum_probs=135.6

Q ss_pred             cccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc---C--CcEEEEcCCC
Q 005987          139 WAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL---G--ARLYEWDTPT  213 (666)
Q Consensus       139 W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel---g--~~viE~nasd  213 (666)
                      .-.+|...+|-.=.++.........|-+.     +|. +.+.|+||||.|+|||+++++++++.   +  ..++.+.+.+
T Consensus        80 l~~~ytFdnFv~g~~N~~A~aa~~~va~~-----~g~-~~nplfi~G~~GlGKTHLl~Aign~~~~~~~~a~v~y~~se~  153 (408)
T COG0593          80 LNPKYTFDNFVVGPSNRLAYAAAKAVAEN-----PGG-AYNPLFIYGGVGLGKTHLLQAIGNEALANGPNARVVYLTSED  153 (408)
T ss_pred             CCCCCchhheeeCCchHHHHHHHHHHHhc-----cCC-cCCcEEEECCCCCCHHHHHHHHHHHHHhhCCCceEEeccHHH
Confidence            44556555542222355566666666554     233 34789999999999999999999987   2  3455544332


Q ss_pred             chhhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhH-HHHHHHHHHHHHhcC
Q 005987          214 PTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTA-FERLRQCLLLLVRST  292 (666)
Q Consensus       214 ~~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~-~~~l~~~L~~l~~~~  292 (666)
                        ...+.+.+..     ....+.|+++      | .           --+++|||++.+.+... .+.+-..+..+...+
T Consensus       154 --f~~~~v~a~~-----~~~~~~Fk~~------y-~-----------~dlllIDDiq~l~gk~~~qeefFh~FN~l~~~~  208 (408)
T COG0593         154 --FTNDFVKALR-----DNEMEKFKEK------Y-S-----------LDLLLIDDIQFLAGKERTQEEFFHTFNALLENG  208 (408)
T ss_pred             --HHHHHHHHHH-----hhhHHHHHHh------h-c-----------cCeeeechHhHhcCChhHHHHHHHHHHHHHhcC
Confidence              1111111110     1122233322      2 1           12899999998866532 233445566676666


Q ss_pred             CCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCcH
Q 005987          293 HIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASGGDI  372 (666)
Q Consensus       293 ~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~s~GDI  372 (666)
                      +  .|+++++..+..    ..-..++|++++..  +..+.+.||+.+....+|++.+...++.++++++..|+.....|+
T Consensus       209 k--qIvltsdr~P~~----l~~~~~rL~SR~~~--Gl~~~I~~Pd~e~r~aiL~kka~~~~~~i~~ev~~~la~~~~~nv  280 (408)
T COG0593         209 K--QIVLTSDRPPKE----LNGLEDRLRSRLEW--GLVVEIEPPDDETRLAILRKKAEDRGIEIPDEVLEFLAKRLDRNV  280 (408)
T ss_pred             C--EEEEEcCCCchh----hccccHHHHHHHhc--eeEEeeCCCCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccH
Confidence            6  566777654332    12233568888875  789999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHh
Q 005987          373 RQAITSLQFSS  383 (666)
Q Consensus       373 R~AIn~LQf~~  383 (666)
                      |.+...|..+.
T Consensus       281 ReLegaL~~l~  291 (408)
T COG0593         281 RELEGALNRLD  291 (408)
T ss_pred             HHHHHHHHHHH
Confidence            98776664443

>KOG0743 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=99.28  E-value=8.5e-11  Score=125.95  Aligned_cols=166  Identities=19%  Similarity=0.217  Sum_probs=108.6

Q ss_pred             cCCCCccccccCHHHHHHHHHHHHHhhcC-----CCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCchhh
Q 005987          143 YKPRSLEELAVQRKKVEEVRAWFEERLGD-----SKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTIW  217 (666)
Q Consensus       143 Y~P~sl~eLvg~~k~i~el~~wL~~~~~~-----~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~~~  217 (666)
                      =+|.+|+-|+-.+++.++|.+=|......     ..|++=.|..|||||||||||+++.|+|+.|+|.|+-++-+...  
T Consensus       195 ~HpstF~TlaMd~~~K~~I~~Dl~~F~k~k~~YkrvGkawKRGYLLYGPPGTGKSS~IaAmAn~L~ydIydLeLt~v~--  272 (457)
T KOG0743|consen  195 PHPSTFETLAMDPDLKERIIDDLDDFIKGKDFYKRVGKAWKRGYLLYGPPGTGKSSFIAAMANYLNYDIYDLELTEVK--  272 (457)
T ss_pred             CCCCCccccccChhHHHHHHHHHHHHHhcchHHHhcCcchhccceeeCCCCCCHHHHHHHHHhhcCCceEEeeecccc--
Confidence            46789999999888877777666544332     23666568999999999999999999999999999877644310  


Q ss_pred             hhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcc-----------------hhHHHH
Q 005987          218 QEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNG-----------------RTAFER  280 (666)
Q Consensus       218 ~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~-----------------~~~~~~  280 (666)
                                     .-.+++.+|....              .+.||||+|||-...                 .-.+.+
T Consensus       273 ---------------~n~dLr~LL~~t~--------------~kSIivIEDIDcs~~l~~~~~~~~~~~~~~~~~VTlSG  323 (457)
T KOG0743|consen  273 ---------------LDSDLRHLLLATP--------------NKSILLIEDIDCSFDLRERRKKKKENFEGDLSRVTLSG  323 (457)
T ss_pred             ---------------CcHHHHHHHHhCC--------------CCcEEEEeecccccccccccccccccccCCcceeehHH
Confidence                           1123555554321              245999999995311                 012344


Q ss_pred             HHHHHHHHHhcCCC-ceEEEEecCCCCCCccchhhhhhHHHHHHhhcC--eeEEEeCCCCHHHHHHHHHHHHHH
Q 005987          281 LRQCLLLLVRSTHI-PTAVVLTECGKADSVDSTAQSFEELQSILVDAG--ARKVALNPITNGSIKRTLSKICRQ  351 (666)
Q Consensus       281 l~~~L~~l~~~~~~-PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r--~~~I~F~p~s~~~i~kiL~~I~~~  351 (666)
                      +.+++..+-..+.. -|||++|+            ..+.|.+.|-|++  -.+|.+...+....+....+.+..
T Consensus       324 LLNfiDGlwSscg~ERIivFTTN------------h~EkLDPALlRpGRmDmhI~mgyCtf~~fK~La~nYL~~  385 (457)
T KOG0743|consen  324 LLNFLDGLWSSCGDERIIVFTTN------------HKEKLDPALLRPGRMDMHIYMGYCTFEAFKTLASNYLGI  385 (457)
T ss_pred             hhhhhccccccCCCceEEEEecC------------ChhhcCHhhcCCCcceeEEEcCCCCHHHHHHHHHHhcCC
Confidence            55555555444422 24444444            2334666666654  346899999999888887776654

>KOG0737 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=99.27  E-value=6.9e-11  Score=123.44  Aligned_cols=191  Identities=17%  Similarity=0.242  Sum_probs=117.0

Q ss_pred             CccccccCHHHHHHHHHHHHHhhcCC----CCC--CCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCchhhhhh
Q 005987          147 SLEELAVQRKKVEEVRAWFEERLGDS----KDK--FSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTIWQEY  220 (666)
Q Consensus       147 sl~eLvg~~k~i~el~~wL~~~~~~~----~g~--~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~~~~e~  220 (666)
                      +++|+-|-+..++++++.+.--+...    .|+  .+.+.+||+||||||||-+|+++|++.|..++.+.-+....  + 
T Consensus        90 ~f~DIggLe~v~~~L~e~VilPlr~pelF~~g~Ll~p~kGiLL~GPpG~GKTmlAKA~Akeaga~fInv~~s~lt~--K-  166 (386)
T KOG0737|consen   90 SFDDIGGLEEVKDALQELVILPLRRPELFAKGKLLRPPKGILLYGPPGTGKTMLAKAIAKEAGANFINVSVSNLTS--K-  166 (386)
T ss_pred             ehhhccchHHHHHHHHHHHhhcccchhhhcccccccCCccceecCCCCchHHHHHHHHHHHcCCCcceeeccccch--h-
Confidence            57888888888888887764221110    111  13478999999999999999999999999988776554211  1 


Q ss_pred             hhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcch------hHHHHHHHHHHHH---Hhc
Q 005987          221 MHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGR------TAFERLRQCLLLL---VRS  291 (666)
Q Consensus       221 l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~------~~~~~l~~~L~~l---~~~  291 (666)
                              .|....+-.+.++.-+.+.            .|.||+|||+|.+-+.      ++.....+.+..+   +.+
T Consensus       167 --------WfgE~eKlv~AvFslAsKl------------~P~iIFIDEvds~L~~R~s~dHEa~a~mK~eFM~~WDGl~s  226 (386)
T KOG0737|consen  167 --------WFGEAQKLVKAVFSLASKL------------QPSIIFIDEVDSFLGQRRSTDHEATAMMKNEFMALWDGLSS  226 (386)
T ss_pred             --------hHHHHHHHHHHHHhhhhhc------------CcceeehhhHHHHHhhcccchHHHHHHHHHHHHHHhccccC
Confidence                    1111111222222222221            4789999999964321      1111111111111   112


Q ss_pred             CCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCc
Q 005987          292 THIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASGGD  371 (666)
Q Consensus       292 ~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~s~GD  371 (666)
                      ...-.|++.++++.+..          |.+.+-|+-+..++.+-|+..+..++|+-+++.|.+. ++-.++.||..+.|=
T Consensus       227 ~~~~rVlVlgATNRP~D----------lDeAiiRR~p~rf~V~lP~~~qR~kILkviLk~e~~e-~~vD~~~iA~~t~Gy  295 (386)
T KOG0737|consen  227 KDSERVLVLGATNRPFD----------LDEAIIRRLPRRFHVGLPDAEQRRKILKVILKKEKLE-DDVDLDEIAQMTEGY  295 (386)
T ss_pred             CCCceEEEEeCCCCCcc----------HHHHHHHhCcceeeeCCCchhhHHHHHHHHhcccccC-cccCHHHHHHhcCCC
Confidence            22234777777765432          3333333358899999999999999999999999875 344467788776653

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=99.26  E-value=1.1e-10  Score=137.85  Aligned_cols=194  Identities=17%  Similarity=0.246  Sum_probs=121.7

Q ss_pred             CCCCccccccCHHHHHHHHHHHHHhhcC-----CCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCchhhh
Q 005987          144 KPRSLEELAVQRKKVEEVRAWFEERLGD-----SKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTIWQ  218 (666)
Q Consensus       144 ~P~sl~eLvg~~k~i~el~~wL~~~~~~-----~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~~~~  218 (666)
                      ...++++|.|.++.++.|++++...+..     .-|-.+++.+||+||||||||++++++|++++..++.++.++..   
T Consensus       173 ~~~~~~di~G~~~~~~~l~~~i~~~~~~~~~~~~~gi~~~~giLL~GppGtGKT~laraia~~~~~~~i~i~~~~i~---  249 (733)
T TIGR01243       173 PKVTYEDIGGLKEAKEKIREMVELPMKHPELFEHLGIEPPKGVLLYGPPGTGKTLLAKAVANEAGAYFISINGPEIM---  249 (733)
T ss_pred             CCCCHHHhcCHHHHHHHHHHHHHHHhhCHHHHHhcCCCCCceEEEECCCCCChHHHHHHHHHHhCCeEEEEecHHHh---
Confidence            4468999999999999999998743321     11333447899999999999999999999999999998875410   


Q ss_pred             hhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchh------HHHHHHHHHHHHHhcC
Q 005987          219 EYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRT------AFERLRQCLLLLVRST  292 (666)
Q Consensus       219 e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~------~~~~l~~~L~~l~~~~  292 (666)
                              +..+......+..+++.+...            .+.||+|||+|.+....      .-.++...|..+++.-
T Consensus       250 --------~~~~g~~~~~l~~lf~~a~~~------------~p~il~iDEid~l~~~r~~~~~~~~~~~~~~Ll~~ld~l  309 (733)
T TIGR01243       250 --------SKYYGESEERLREIFKEAEEN------------APSIIFIDEIDAIAPKREEVTGEVEKRVVAQLLTLMDGL  309 (733)
T ss_pred             --------cccccHHHHHHHHHHHHHHhc------------CCcEEEeehhhhhcccccCCcchHHHHHHHHHHHHhhcc
Confidence                    001122234566666665432            35699999998764221      1123344455555432


Q ss_pred             --CCceEEEEecCCCCCCccchhhhhhHHHHHHhhc--CeeEEEeCCCCHHHHHHHHHHHHHHhCCCC-CHHHHHHHHHH
Q 005987          293 --HIPTAVVLTECGKADSVDSTAQSFEELQSILVDA--GARKVALNPITNGSIKRTLSKICRQEQYSL-STEQIDLVAQA  367 (666)
Q Consensus       293 --~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~--r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v-~~~~l~~Ia~~  367 (666)
                        +..+++| +.++....          +...+.++  ....|.|..|+.++..++|+..+..  ..+ ++..++.|++.
T Consensus       310 ~~~~~vivI-~atn~~~~----------ld~al~r~gRfd~~i~i~~P~~~~R~~Il~~~~~~--~~l~~d~~l~~la~~  376 (733)
T TIGR01243       310 KGRGRVIVI-GATNRPDA----------LDPALRRPGRFDREIVIRVPDKRARKEILKVHTRN--MPLAEDVDLDKLAEV  376 (733)
T ss_pred             ccCCCEEEE-eecCChhh----------cCHHHhCchhccEEEEeCCcCHHHHHHHHHHHhcC--CCCccccCHHHHHHh
Confidence              2344444 33333221          22222221  2357899999999999999865543  333 24457888888


Q ss_pred             cCCcHH
Q 005987          368 SGGDIR  373 (666)
Q Consensus       368 s~GDIR  373 (666)
                      +.|-..
T Consensus       377 t~G~~g  382 (733)
T TIGR01243       377 THGFVG  382 (733)
T ss_pred             CCCCCH
Confidence            777443

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.

>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=99.25  E-value=8e-11  Score=108.03  Aligned_cols=100  Identities=22%  Similarity=0.328  Sum_probs=68.3

Q ss_pred             EEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCchhhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCC
Q 005987          181 LVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKS  260 (666)
Q Consensus       181 LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~  260 (666)
                      +||+||||||||++|+.+|+.++..+++++.+...           +.........+..++.++....           .
T Consensus         1 ill~G~~G~GKT~l~~~la~~l~~~~~~i~~~~~~-----------~~~~~~~~~~i~~~~~~~~~~~-----------~   58 (132)
T PF00004_consen    1 ILLHGPPGTGKTTLARALAQYLGFPFIEIDGSELI-----------SSYAGDSEQKIRDFFKKAKKSA-----------K   58 (132)
T ss_dssp             EEEESSTTSSHHHHHHHHHHHTTSEEEEEETTHHH-----------TSSTTHHHHHHHHHHHHHHHTS-----------T
T ss_pred             CEEECcCCCCeeHHHHHHHhhcccccccccccccc-----------cccccccccccccccccccccc-----------c
Confidence            68999999999999999999999999999987511           1122344556777777775432           2


Q ss_pred             ceEEEEeCCCCCcchh------HHHHHHHHHHHHHhcCCC---ceEEEEec
Q 005987          261 SAILLIDDLPVTNGRT------AFERLRQCLLLLVRSTHI---PTAVVLTE  302 (666)
Q Consensus       261 ~~IIlIDEid~l~~~~------~~~~l~~~L~~l~~~~~~---PiViIit~  302 (666)
                      +.||+|||+|.+....      .-..+.+.|...++....   ++++|++.
T Consensus        59 ~~vl~iDe~d~l~~~~~~~~~~~~~~~~~~L~~~l~~~~~~~~~~~vI~tt  109 (132)
T PF00004_consen   59 PCVLFIDEIDKLFPKSQPSSSSFEQRLLNQLLSLLDNPSSKNSRVIVIATT  109 (132)
T ss_dssp             SEEEEEETGGGTSHHCSTSSSHHHHHHHHHHHHHHHTTTTTSSSEEEEEEE
T ss_pred             ceeeeeccchhcccccccccccccccccceeeecccccccccccceeEEee
Confidence            5799999999875432      223344556666665443   35555444

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 ....

>COG0464 SpoVK ATPases of the AAA+ class [Posttranslational modification, protein turnover, chaperones]

Probab=99.24  E-value=1.6e-10  Score=130.81  Aligned_cols=191  Identities=15%  Similarity=0.191  Sum_probs=120.5

Q ss_pred             CCccccccCHHHHHHHHHHHHHhhcCCC-----CCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCchhhhhh
Q 005987          146 RSLEELAVQRKKVEEVRAWFEERLGDSK-----DKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTIWQEY  220 (666)
Q Consensus       146 ~sl~eLvg~~k~i~el~~wL~~~~~~~~-----g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~~~~e~  220 (666)
                      .++.++.|-+...+.++..+.--+....     +..+.+.+||+||||||||.+|+++|++++..++.+..++  .    
T Consensus       239 v~~~diggl~~~k~~l~e~v~~~~~~~e~~~~~~~~~~~giLl~GpPGtGKT~lAkava~~~~~~fi~v~~~~--l----  312 (494)
T COG0464         239 VTLDDIGGLEEAKEELKEAIETPLKRPELFRKLGLRPPKGVLLYGPPGTGKTLLAKAVALESRSRFISVKGSE--L----  312 (494)
T ss_pred             cceehhhcHHHHHHHHHHHHHhHhhChHHHHhcCCCCCCeeEEECCCCCCHHHHHHHHHhhCCCeEEEeeCHH--H----
Confidence            4667777765555555555442222211     3334478999999999999999999999999999998874  1    


Q ss_pred             hhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchh------HHHHHHHHHHHHHhc--C
Q 005987          221 MHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRT------AFERLRQCLLLLVRS--T  292 (666)
Q Consensus       221 l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~------~~~~l~~~L~~l~~~--~  292 (666)
                           .+..+......++..+..+.+.            .++||+|||+|.+....      ...++...++..+..  .
T Consensus       313 -----~sk~vGesek~ir~~F~~A~~~------------~p~iiFiDEiDs~~~~r~~~~~~~~~r~~~~lL~~~d~~e~  375 (494)
T COG0464         313 -----LSKWVGESEKNIRELFEKARKL------------APSIIFIDEIDSLASGRGPSEDGSGRRVVGQLLTELDGIEK  375 (494)
T ss_pred             -----hccccchHHHHHHHHHHHHHcC------------CCcEEEEEchhhhhccCCCCCchHHHHHHHHHHHHhcCCCc
Confidence                 2222344556677777777643            36899999999763211      112444334444321  1


Q ss_pred             CCceEEEEecCCCCCCccchhhhhhHHHHHHhh--cCeeEEEeCCCCHHHHHHHHHHHHHHhCCC-CCHHHHHHHHHHcC
Q 005987          293 HIPTAVVLTECGKADSVDSTAQSFEELQSILVD--AGARKVALNPITNGSIKRTLSKICRQEQYS-LSTEQIDLVAQASG  369 (666)
Q Consensus       293 ~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r--~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~-v~~~~l~~Ia~~s~  369 (666)
                      ... |+++..++.++..|          +.+.|  +.-..|.|.+|+..+..++++..+...... ..+-.++.|++.+.
T Consensus       376 ~~~-v~vi~aTN~p~~ld----------~a~lR~gRfd~~i~v~~pd~~~r~~i~~~~~~~~~~~~~~~~~~~~l~~~t~  444 (494)
T COG0464         376 AEG-VLVIAATNRPDDLD----------PALLRPGRFDRLIYVPLPDLEERLEIFKIHLRDKKPPLAEDVDLEELAEITE  444 (494)
T ss_pred             cCc-eEEEecCCCccccC----------HhhcccCccceEeecCCCCHHHHHHHHHHHhcccCCcchhhhhHHHHHHHhc
Confidence            223 44555555544322          22222  124579999999999999999888765543 44566777777554


Q ss_pred             C
Q 005987          370 G  370 (666)
Q Consensus       370 G  370 (666)
                      |
T Consensus       445 ~  445 (494)
T COG0464         445 G  445 (494)
T ss_pred             C
Confidence            4

>KOG0736 consensus Peroxisome assembly factor 2 containing the AAA+-type ATPase domain [Posttranslational modification, protein turnover, chaperones]

Probab=99.23  E-value=1.6e-10  Score=129.44  Aligned_cols=202  Identities=18%  Similarity=0.279  Sum_probs=121.6

Q ss_pred             CccccccCHHHHHHHHHHHHHhhcC----CCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCchhhhhhhh
Q 005987          147 SLEELAVQRKKVEEVRAWFEERLGD----SKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTIWQEYMH  222 (666)
Q Consensus       147 sl~eLvg~~k~i~el~~wL~~~~~~----~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~~~~e~l~  222 (666)
                      +++|+-|-++...+|.+-++--++-    +.|-.+...+|||||||||||.+|+++|-|+...++.+..|.       +.
T Consensus       670 ~WdDVGGLeevK~eIldTIqlPL~hpeLfssglrkRSGILLYGPPGTGKTLlAKAVATEcsL~FlSVKGPE-------LL  742 (953)
T KOG0736|consen  670 SWDDVGGLEEVKTEILDTIQLPLKHPELFSSGLRKRSGILLYGPPGTGKTLLAKAVATECSLNFLSVKGPE-------LL  742 (953)
T ss_pred             chhcccCHHHHHHHHHHHhcCcccChhhhhccccccceeEEECCCCCchHHHHHHHHhhceeeEEeecCHH-------HH
Confidence            5688999999999998887642221    112211246999999999999999999999999999888775       11


Q ss_pred             cccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcch--------hHHHHHHHHHH----HHHh
Q 005987          223 NCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGR--------TAFERLRQCLL----LLVR  290 (666)
Q Consensus       223 ~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~--------~~~~~l~~~L~----~l~~  290 (666)
                      |...    ....+..++++++|+..            .|+||++||+|.+...        .-..|+...|+    .+.+
T Consensus       743 NMYV----GqSE~NVR~VFerAR~A------------~PCVIFFDELDSlAP~RG~sGDSGGVMDRVVSQLLAELDgls~  806 (953)
T KOG0736|consen  743 NMYV----GQSEENVREVFERARSA------------APCVIFFDELDSLAPNRGRSGDSGGVMDRVVSQLLAELDGLSD  806 (953)
T ss_pred             HHHh----cchHHHHHHHHHHhhcc------------CCeEEEeccccccCccCCCCCCccccHHHHHHHHHHHhhcccC
Confidence            2222    33456788899998643            4899999999976321        12233332222    2222


Q ss_pred             cCCCceEEEEecCCCCCCccchhhhhhHHHHHHhhc-CeeE-EEeCCCCHHHH-HHHHHHHHHHhCCCCCHH-HHHHHHH
Q 005987          291 STHIPTAVVLTECGKADSVDSTAQSFEELQSILVDA-GARK-VALNPITNGSI-KRTLSKICRQEQYSLSTE-QIDLVAQ  366 (666)
Q Consensus       291 ~~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~-r~~~-I~F~p~s~~~i-~kiL~~I~~~e~i~v~~~-~l~~Ia~  366 (666)
                      . ..--|||+++++.++..|          ..|-|| |+.. +...+....+- .++|+.+.++  ++++++ -+..||+
T Consensus       807 ~-~s~~VFViGATNRPDLLD----------pALLRPGRFDKLvyvG~~~d~esk~~vL~AlTrk--FkLdedVdL~eiAk  873 (953)
T KOG0736|consen  807 S-SSQDVFVIGATNRPDLLD----------PALLRPGRFDKLVYVGPNEDAESKLRVLEALTRK--FKLDEDVDLVEIAK  873 (953)
T ss_pred             C-CCCceEEEecCCCccccC----------hhhcCCCccceeEEecCCccHHHHHHHHHHHHHH--ccCCCCcCHHHHHh
Confidence            1 222457778887766433          233333 3444 45555544333 3334433333  444433 3677887


Q ss_pred             H-----cCCcHHHHHHHHHHHhc
Q 005987          367 A-----SGGDIRQAITSLQFSSL  384 (666)
Q Consensus       367 ~-----s~GDIR~AIn~LQf~~~  384 (666)
                      .     ++-|+-+.+.+.-+.|.
T Consensus       874 ~cp~~~TGADlYsLCSdA~l~Ai  896 (953)
T KOG0736|consen  874 KCPPNMTGADLYSLCSDAMLAAI  896 (953)
T ss_pred             hCCcCCchhHHHHHHHHHHHHHH
Confidence            6     45666666655444443

>PRK10733 hflB ATP-dependent metalloprotease; Reviewed

Probab=99.23  E-value=2.1e-10  Score=133.05  Aligned_cols=214  Identities=15%  Similarity=0.224  Sum_probs=132.9

Q ss_pred             CccccccCCCCccccccCHHHHHHHHHHHHHhhc-----CCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcC
Q 005987          137 QLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLG-----DSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDT  211 (666)
Q Consensus       137 ~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~-----~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~na  211 (666)
                      ..|.......+++++.+.+...+++.+.+.-...     ...+..+ +.++|+||||||||++++++|++++..++.++.
T Consensus       140 ~~~~~~~~~~~~~di~g~~~~~~~l~~i~~~~~~~~~~~~~~~~~~-~gill~G~~G~GKt~~~~~~a~~~~~~f~~is~  218 (644)
T PRK10733        140 RMLTEDQIKTTFADVAGCDEAKEEVAELVEYLREPSRFQKLGGKIP-KGVLMVGPPGTGKTLLAKAIAGEAKVPFFTISG  218 (644)
T ss_pred             cccCchhhhCcHHHHcCHHHHHHHHHHHHHHhhCHHHHHhcCCCCC-CcEEEECCCCCCHHHHHHHHHHHcCCCEEEEeh
Confidence            4455556677899999988887777766542111     1112334 679999999999999999999999999998887


Q ss_pred             CCchhhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcch---------hHHHHHH
Q 005987          212 PTPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGR---------TAFERLR  282 (666)
Q Consensus       212 sd~~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~---------~~~~~l~  282 (666)
                      ++..   +    ...|.    ....++..+..+...            .|+||+|||+|.+..+         .......
T Consensus       219 ~~~~---~----~~~g~----~~~~~~~~f~~a~~~------------~P~IifIDEiD~l~~~r~~~~~g~~~~~~~~l  275 (644)
T PRK10733        219 SDFV---E----MFVGV----GASRVRDMFEQAKKA------------APCIIFIDEIDAVGRQRGAGLGGGHDEREQTL  275 (644)
T ss_pred             HHhH---H----hhhcc----cHHHHHHHHHHHHhc------------CCcEEEehhHhhhhhccCCCCCCCchHHHHHH
Confidence            6411   1    11111    223455556655332            3679999999976321         1112222


Q ss_pred             HHHHHHHhc--CCCceEEEEecCCCCCCccchhhhhhHHHHHHhhc-C-eeEEEeCCCCHHHHHHHHHHHHHHhCCCCCH
Q 005987          283 QCLLLLVRS--THIPTAVVLTECGKADSVDSTAQSFEELQSILVDA-G-ARKVALNPITNGSIKRTLSKICRQEQYSLST  358 (666)
Q Consensus       283 ~~L~~l~~~--~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~-r-~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~  358 (666)
                      +.|+..++.  ....+++| ..++.++          .|...+.|+ | -..|.|..|+..+..++|+..+....+.. +
T Consensus       276 n~lL~~mdg~~~~~~vivI-aaTN~p~----------~lD~Al~RpgRfdr~i~v~~Pd~~~R~~Il~~~~~~~~l~~-~  343 (644)
T PRK10733        276 NQMLVEMDGFEGNEGIIVI-AATNRPD----------VLDPALLRPGRFDRQVVVGLPDVRGREQILKVHMRRVPLAP-D  343 (644)
T ss_pred             HHHHHhhhcccCCCCeeEE-EecCChh----------hcCHHHhCCcccceEEEcCCCCHHHHHHHHHHHhhcCCCCC-c
Confidence            222222221  12234443 3333322          233333332 2 35799999999999999998876644321 2


Q ss_pred             HHHHHHHHHcCC----cHHHHHHHHHHHhcCC
Q 005987          359 EQIDLVAQASGG----DIRQAITSLQFSSLKQ  386 (666)
Q Consensus       359 ~~l~~Ia~~s~G----DIR~AIn~LQf~~~~~  386 (666)
                      ..+..|+..+.|    ||...++.....+...
T Consensus       344 ~d~~~la~~t~G~sgadl~~l~~eAa~~a~r~  375 (644)
T PRK10733        344 IDAAIIARGTPGFSGADLANLVNEAALFAARG  375 (644)
T ss_pred             CCHHHHHhhCCCCCHHHHHHHHHHHHHHHHHc
Confidence            335678888888    9999999887766543

>PRK07993 DNA polymerase III subunit delta'; Validated

Probab=99.23  E-value=3.2e-10  Score=121.28  Aligned_cols=189  Identities=16%  Similarity=0.161  Sum_probs=118.2

Q ss_pred             HHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEE-EcCCCchhhhhhh----hc----c-
Q 005987          155 RKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYE-WDTPTPTIWQEYM----HN----C-  224 (666)
Q Consensus       155 ~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE-~nasd~~~~~e~l----~~----~-  224 (666)
                      ...-+.+...+..      ++.+ +.+||+||+|+||+++|..+|+.+-+.--. -.+...+.....+    |.    . 
T Consensus         8 ~~~~~~l~~~~~~------~rl~-HA~Lf~G~~G~Gk~~lA~~~A~~LlC~~~~~~~~Cg~C~sC~~~~~g~HPD~~~i~   80 (334)
T PRK07993          8 RPDYEQLVGSYQA------GRGH-HALLIQALPGMGDDALIYALSRWLMCQQPQGHKSCGHCRGCQLMQAGTHPDYYTLT   80 (334)
T ss_pred             hHHHHHHHHHHHc------CCcc-eEEeeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHHcCCCCCEEEEe
Confidence            3445555555554      6777 799999999999999999999998542100 0000000000000    00    0 


Q ss_pred             cCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcCCCceEEEEecCC
Q 005987          225 KTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHIPTAVVLTECG  304 (666)
Q Consensus       225 ~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~~~PiViIit~~~  304 (666)
                      ..+....-.+++++++.+.+...+.        .+..+|+|||+++.++..     ..++|++.++....-++||....+
T Consensus        81 p~~~~~~I~idqiR~l~~~~~~~~~--------~g~~kV~iI~~ae~m~~~-----AaNaLLKtLEEPp~~t~fiL~t~~  147 (334)
T PRK07993         81 PEKGKSSLGVDAVREVTEKLYEHAR--------LGGAKVVWLPDAALLTDA-----AANALLKTLEEPPENTWFFLACRE  147 (334)
T ss_pred             cccccccCCHHHHHHHHHHHhhccc--------cCCceEEEEcchHhhCHH-----HHHHHHHHhcCCCCCeEEEEEECC
Confidence            0000012346677777766643321        124579999999988643     334577777776544444444322


Q ss_pred             CCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCcHHHHHHHHH
Q 005987          305 KADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASGGDIRQAITSLQ  380 (666)
Q Consensus       305 ~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~s~GDIR~AIn~LQ  380 (666)
                             ..+.++.++|     ||+.+.|.+++.+++...|..     ...++++.+..++..++|++..|+..++
T Consensus       148 -------~~~lLpTIrS-----RCq~~~~~~~~~~~~~~~L~~-----~~~~~~~~a~~~~~la~G~~~~Al~l~~  206 (334)
T PRK07993        148 -------PARLLATLRS-----RCRLHYLAPPPEQYALTWLSR-----EVTMSQDALLAALRLSAGAPGAALALLQ  206 (334)
T ss_pred             -------hhhChHHHHh-----ccccccCCCCCHHHHHHHHHH-----ccCCCHHHHHHHHHHcCCCHHHHHHHhc
Confidence                   2345555555     699999999999999988863     2246777788889999999999987653

>KOG0727 consensus 26S proteasome regulatory complex, ATPase RPT3 [Posttranslational modification, protein turnover, chaperones]

Probab=99.22  E-value=9e-11  Score=116.12  Aligned_cols=203  Identities=18%  Similarity=0.243  Sum_probs=119.1

Q ss_pred             CCccccccCHHHHHHHHHHHHHhhcC-----CCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCchhhhhh
Q 005987          146 RSLEELAVQRKKVEEVRAWFEERLGD-----SKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTIWQEY  220 (666)
Q Consensus       146 ~sl~eLvg~~k~i~el~~wL~~~~~~-----~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~~~~e~  220 (666)
                      -+..|+-|-+-..+++++.++--+..     .-|--|++.+|||||||||||.+++++|+.....++.++.+.  ..+++
T Consensus       152 vsy~diggld~qkqeireavelplt~~~ly~qigidpprgvllygppg~gktml~kava~~t~a~firvvgse--fvqky  229 (408)
T KOG0727|consen  152 VSYADIGGLDVQKQEIREAVELPLTHADLYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSE--FVQKY  229 (408)
T ss_pred             ccccccccchhhHHHHHHHHhccchHHHHHHHhCCCCCcceEEeCCCCCcHHHHHHHHhhccchheeeeccHH--HHHHH
Confidence            56788888777777777776522111     114445589999999999999999999999999999988765  33444


Q ss_pred             hhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcch------hHHHHHHHHHHHHHhc---
Q 005987          221 MHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGR------TAFERLRQCLLLLVRS---  291 (666)
Q Consensus       221 l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~------~~~~~l~~~L~~l~~~---  291 (666)
                      +...   .      ...++++.-++.            +.|.||+|||+|.+...      .+-+.++.+|..++..   
T Consensus       230 lgeg---p------rmvrdvfrlake------------napsiifideidaiatkrfdaqtgadrevqril~ellnqmdg  288 (408)
T KOG0727|consen  230 LGEG---P------RMVRDVFRLAKE------------NAPSIIFIDEIDAIATKRFDAQTGADREVQRILIELLNQMDG  288 (408)
T ss_pred             hccC---c------HHHHHHHHHHhc------------cCCcEEEeehhhhHhhhhccccccccHHHHHHHHHHHHhccC
Confidence            4321   1      133444433332            24679999999975321      1113345555555543   


Q ss_pred             ---CCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcC--eeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHH-
Q 005987          292 ---THIPTAVVLTECGKADSVDSTAQSFEELQSILVDAG--ARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVA-  365 (666)
Q Consensus       292 ---~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r--~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia-  365 (666)
                         +..--||++++..  +.          |...|-|++  -..|.|+-++..+-+-+...|+.+..+.-+-+ ++.++ 
T Consensus       289 fdq~~nvkvimatnra--dt----------ldpallrpgrldrkiefplpdrrqkrlvf~titskm~ls~~vd-le~~v~  355 (408)
T KOG0727|consen  289 FDQTTNVKVIMATNRA--DT----------LDPALLRPGRLDRKIEFPLPDRRQKRLVFSTITSKMNLSDEVD-LEDLVA  355 (408)
T ss_pred             cCcccceEEEEecCcc--cc----------cCHhhcCCccccccccCCCCchhhhhhhHHhhhhcccCCcccC-HHHHhc
Confidence               2223455666532  11          222222222  24799998888777777777877765432212 23332 


Q ss_pred             ---HHcCCcHHHHHHHHHHHhc
Q 005987          366 ---QASGGDIRQAITSLQFSSL  384 (666)
Q Consensus       366 ---~~s~GDIR~AIn~LQf~~~  384 (666)
                         ..|+.||-+...-.-+.+.
T Consensus       356 rpdkis~adi~aicqeagm~av  377 (408)
T KOG0727|consen  356 RPDKISGADINAICQEAGMLAV  377 (408)
T ss_pred             CccccchhhHHHHHHHHhHHHH
Confidence               2355666555444444443

>PRK06871 DNA polymerase III subunit delta'; Validated

Probab=99.22  E-value=7.7e-10  Score=117.39  Aligned_cols=187  Identities=13%  Similarity=0.098  Sum_probs=117.0

Q ss_pred             CHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEE-EcCCCchhhhhhhh----c-----
Q 005987          154 QRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYE-WDTPTPTIWQEYMH----N-----  223 (666)
Q Consensus       154 ~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE-~nasd~~~~~e~l~----~-----  223 (666)
                      +....+.+.+.+..      |+.+ +.+||+||+|+||+++|+.+|+.+.+.--. ..+...+.....+.    .     
T Consensus         7 ~~~~~~~l~~~~~~------~rl~-HA~Lf~G~~G~GK~~lA~~~A~~llC~~~~~~~~Cg~C~sC~~~~~g~HPD~~~i   79 (325)
T PRK06871          7 LQPTYQQITQAFQQ------GLGH-HALLFKADSGLGTEQLIRALAQWLMCQTPQGDQPCGQCHSCHLFQAGNHPDFHIL   79 (325)
T ss_pred             hHHHHHHHHHHHHc------CCcc-eeEEeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHhcCCCCCEEEE
Confidence            44455566666664      6766 789999999999999999999998653210 01111111001000    0     


Q ss_pred             -ccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcCCCceEEEEec
Q 005987          224 -CKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHIPTAVVLTE  302 (666)
Q Consensus       224 -~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~~~PiViIit~  302 (666)
                       ...|.  .-.+++++++.+.+...+.        .+..+|+|||+++.++..     ..++|++.++.....++||+..
T Consensus        80 ~p~~~~--~I~id~iR~l~~~~~~~~~--------~g~~KV~iI~~a~~m~~~-----AaNaLLKtLEEPp~~~~fiL~t  144 (325)
T PRK06871         80 EPIDNK--DIGVDQVREINEKVSQHAQ--------QGGNKVVYIQGAERLTEA-----AANALLKTLEEPRPNTYFLLQA  144 (325)
T ss_pred             ccccCC--CCCHHHHHHHHHHHhhccc--------cCCceEEEEechhhhCHH-----HHHHHHHHhcCCCCCeEEEEEE
Confidence             00111  1246677777766643321        124579999999998643     3345777777766555555544


Q ss_pred             CCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCcHHHHHHHH
Q 005987          303 CGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASGGDIRQAITSL  379 (666)
Q Consensus       303 ~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~s~GDIR~AIn~L  379 (666)
                      .+       ..+.++.+++     ||+.+.|+|++.+++...|....     ..++..+..++..++|.+-.|+..+
T Consensus       145 ~~-------~~~llpTI~S-----RC~~~~~~~~~~~~~~~~L~~~~-----~~~~~~~~~~~~l~~g~p~~A~~~~  204 (325)
T PRK06871        145 DL-------SAALLPTIYS-----RCQTWLIHPPEEQQALDWLQAQS-----SAEISEILTALRINYGRPLLALTFL  204 (325)
T ss_pred             CC-------hHhCchHHHh-----hceEEeCCCCCHHHHHHHHHHHh-----ccChHHHHHHHHHcCCCHHHHHHHh
Confidence            22       2344555554     69999999999999999998753     2344456677788999987776543

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

Probab=99.21  E-value=1.6e-10  Score=135.21  Aligned_cols=209  Identities=16%  Similarity=0.222  Sum_probs=135.7

Q ss_pred             CccccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc----------CCcE
Q 005987          137 QLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL----------GARL  206 (666)
Q Consensus       137 ~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel----------g~~v  206 (666)
                      ..++++-+--.++.++|+++.++++...|....        ++.+||+||||||||++|+.+|..+          +..+
T Consensus       174 ~~l~~~a~~g~~~~liGR~~ei~~~i~iL~r~~--------~~n~LLvGppGvGKT~lae~la~~i~~~~vP~~l~~~~~  245 (758)
T PRK11034        174 TNLNQLARVGGIDPLIGREKELERAIQVLCRRR--------KNNPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTI  245 (758)
T ss_pred             HhHHHHHHcCCCCcCcCCCHHHHHHHHHHhccC--------CCCeEEECCCCCCHHHHHHHHHHHHHhcCCCchhcCCeE
Confidence            345666677888999999999999999887621        1467899999999999999999875          2222


Q ss_pred             EEEcCCCchhhhhhhhcccCCcccc-chhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchh----HHHHH
Q 005987          207 YEWDTPTPTIWQEYMHNCKTGLEYT-SKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRT----AFERL  281 (666)
Q Consensus       207 iE~nasd~~~~~e~l~~~~~g~~~~-s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~----~~~~l  281 (666)
                      +..+.          .....|..|. .....++.++..+...            .+.||+|||++.+.+..    ....+
T Consensus       246 ~~l~~----------~~llaG~~~~Ge~e~rl~~l~~~l~~~------------~~~ILfIDEIh~L~g~g~~~~g~~d~  303 (758)
T PRK11034        246 YSLDI----------GSLLAGTKYRGDFEKRFKALLKQLEQD------------TNSILFIDEIHTIIGAGAASGGQVDA  303 (758)
T ss_pred             EeccH----------HHHhcccchhhhHHHHHHHHHHHHHhc------------CCCEEEeccHHHHhccCCCCCcHHHH
Confidence            22221          1111233222 2223455555555432            24599999999763211    11234


Q ss_pred             HHHHHHHHhcCCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHH----hCCCCC
Q 005987          282 RQCLLLLVRSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQ----EQYSLS  357 (666)
Q Consensus       282 ~~~L~~l~~~~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~----e~i~v~  357 (666)
                      .++|..++..++  +.+ ++.++..    .+.+.+. +.+.|.| |+..|.+.+|+.++..++|+.+...    .++.++
T Consensus       304 ~nlLkp~L~~g~--i~v-IgATt~~----E~~~~~~-~D~AL~r-RFq~I~v~ePs~~~~~~IL~~~~~~ye~~h~v~i~  374 (758)
T PRK11034        304 ANLIKPLLSSGK--IRV-IGSTTYQ----EFSNIFE-KDRALAR-RFQKIDITEPSIEETVQIINGLKPKYEAHHDVRYT  374 (758)
T ss_pred             HHHHHHHHhCCC--eEE-EecCChH----HHHHHhh-ccHHHHh-hCcEEEeCCCCHHHHHHHHHHHHHHhhhccCCCcC
Confidence            455777777664  333 3333321    1122222 3344444 6789999999999999999987653    468899


Q ss_pred             HHHHHHHHHHcCCcH------HHHHHHHHHHhc
Q 005987          358 TEQIDLVAQASGGDI------RQAITSLQFSSL  384 (666)
Q Consensus       358 ~~~l~~Ia~~s~GDI------R~AIn~LQf~~~  384 (666)
                      ++++..++..+..-|      .+||..|.-+|.
T Consensus       375 ~~al~~a~~ls~ryi~~r~lPdKaidlldea~a  407 (758)
T PRK11034        375 AKAVRAAVELAVKYINDRHLPDKAIDVIDEAGA  407 (758)
T ss_pred             HHHHHHHHHHhhccccCccChHHHHHHHHHHHH
Confidence            999999998876543      389999988775

>PRK08769 DNA polymerase III subunit delta'; Validated

Probab=99.21  E-value=2.4e-10  Score=121.07  Aligned_cols=185  Identities=15%  Similarity=0.171  Sum_probs=114.8

Q ss_pred             CHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCchhhhhhh----hc------
Q 005987          154 QRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTIWQEYM----HN------  223 (666)
Q Consensus       154 ~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~~~~e~l----~~------  223 (666)
                      +....+.+...+..      ++.+ +.+||+||+|+||+++|..+|+.+.+.-.  .....+.....+    |.      
T Consensus         9 ~~~~~~~l~~~~~~------~rl~-HA~Lf~Gp~G~GK~~lA~~lA~~LlC~~~--~~~~~c~~c~~~~~g~HPD~~~i~   79 (319)
T PRK08769          9 QQRAYDQTVAALDA------GRLG-HGLLICGPEGLGKRAVALALAEHVLASGP--DPAAAQRTRQLIAAGTHPDLQLVS   79 (319)
T ss_pred             HHHHHHHHHHHHHc------CCcc-eeEeeECCCCCCHHHHHHHHHHHHhCCCC--CCCCcchHHHHHhcCCCCCEEEEe
Confidence            55666777776665      7777 78999999999999999999999855310  000000000000    00      


Q ss_pred             --c-cCCcc--ccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcCCCc-eE
Q 005987          224 --C-KTGLE--YTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHIP-TA  297 (666)
Q Consensus       224 --~-~~g~~--~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~~~P-iV  297 (666)
                        . ..|..  ..-.+++++++.+.+...+.        .+..+|+|||+++.++..     ..++|++.++..... ++
T Consensus        80 ~~p~~~~~k~~~~I~idqIR~l~~~~~~~p~--------~g~~kV~iI~~ae~m~~~-----AaNaLLKtLEEPp~~~~f  146 (319)
T PRK08769         80 FIPNRTGDKLRTEIVIEQVREISQKLALTPQ--------YGIAQVVIVDPADAINRA-----ACNALLKTLEEPSPGRYL  146 (319)
T ss_pred             cCCCcccccccccccHHHHHHHHHHHhhCcc--------cCCcEEEEeccHhhhCHH-----HHHHHHHHhhCCCCCCeE
Confidence              0 01110  01235566666655532211        123579999999988643     234566666765433 34


Q ss_pred             EEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCcHHHHHH
Q 005987          298 VVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASGGDIRQAIT  377 (666)
Q Consensus       298 iIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~s~GDIR~AIn  377 (666)
                      |++++        ...+.++.|++     ||..|.|.+++.+++...|..    .+  +++.....++..++|.+..|+.
T Consensus       147 iL~~~--------~~~~lLpTIrS-----RCq~i~~~~~~~~~~~~~L~~----~~--~~~~~a~~~~~l~~G~p~~A~~  207 (319)
T PRK08769        147 WLISA--------QPARLPATIRS-----RCQRLEFKLPPAHEALAWLLA----QG--VSERAAQEALDAARGHPGLAAQ  207 (319)
T ss_pred             EEEEC--------ChhhCchHHHh-----hheEeeCCCcCHHHHHHHHHH----cC--CChHHHHHHHHHcCCCHHHHHH
Confidence            44444        12345556665     699999999999999988864    23  5666667788999999998876


Q ss_pred             HH
Q 005987          378 SL  379 (666)
Q Consensus       378 ~L  379 (666)
                      .+
T Consensus       208 ~~  209 (319)
T PRK08769        208 WL  209 (319)
T ss_pred             Hh
Confidence            54

>KOG2227 consensus Pre-initiation complex, subunit CDC6, AAA+ superfamily ATPase [Replication, recombination and repair; Cell cycle control, cell division, chromosome partitioning]

Probab=99.19  E-value=1.6e-10  Score=123.64  Aligned_cols=218  Identities=21%  Similarity=0.316  Sum_probs=136.7

Q ss_pred             CCccccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc-----CCcEEEEc
Q 005987          136 QQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL-----GARLYEWD  210 (666)
Q Consensus       136 ~~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel-----g~~viE~n  210 (666)
                      ++.....|+|.++   .|++.....|+.|+..++..   +-+ ..+.++|.||+|||.+...+-..+     ...++.+|
T Consensus       140 ~~~l~~t~~p~~l---~gRe~e~~~v~~F~~~hle~---~t~-gSlYVsG~PGtgkt~~l~rvl~~~~~~~~~~~~v~in  212 (529)
T KOG2227|consen  140 SESLLNTAPPGTL---KGRELEMDIVREFFSLHLEL---NTS-GSLYVSGQPGTGKTALLSRVLDSLSKSSKSPVTVYIN  212 (529)
T ss_pred             HHHHHhcCCCCCc---cchHHHHHHHHHHHHhhhhc---ccC-cceEeeCCCCcchHHHHHHHHHhhhhhcccceeEEEe
Confidence            4557778888776   99999999999999988763   222 589999999999999998776666     34557777


Q ss_pred             CCCc----hhhhhhhhcccCCccc-cchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHH
Q 005987          211 TPTP----TIWQEYMHNCKTGLEY-TSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCL  285 (666)
Q Consensus       211 asd~----~~~~e~l~~~~~g~~~-~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L  285 (666)
                      +..-    ..+.........+... ....+....|......           .+...||++||+|.+..+.     +.+|
T Consensus       213 c~sl~~~~aiF~kI~~~~~q~~~s~~~~~~~~~~~~~h~~q-----------~k~~~llVlDEmD~L~tr~-----~~vL  276 (529)
T KOG2227|consen  213 CTSLTEASAIFKKIFSSLLQDLVSPGTGMQHLEKFEKHTKQ-----------SKFMLLLVLDEMDHLITRS-----QTVL  276 (529)
T ss_pred             eccccchHHHHHHHHHHHHHHhcCCchhHHHHHHHHHHHhc-----------ccceEEEEechhhHHhhcc-----ccee
Confidence            7641    2232222221000000 0111111222222111           1246799999999875432     2234


Q ss_pred             HHHHhcCCCc--eEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCC-CCHHHHH
Q 005987          286 LLLVRSTHIP--TAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYS-LSTEQID  362 (666)
Q Consensus       286 ~~l~~~~~~P--iViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~-v~~~~l~  362 (666)
                      +.+.+-...|  .+++|+-.+   +.|...|.|..|...+. .....+.|.|++.++|.++|+..+..+... +-+.+++
T Consensus       277 y~lFewp~lp~sr~iLiGiAN---slDlTdR~LprL~~~~~-~~P~~l~F~PYTk~qI~~Il~~rl~~~~t~~~~~~Aie  352 (529)
T KOG2227|consen  277 YTLFEWPKLPNSRIILIGIAN---SLDLTDRFLPRLNLDLT-IKPKLLVFPPYTKDQIVEILQQRLSEESTSIFLNAAIE  352 (529)
T ss_pred             eeehhcccCCcceeeeeeehh---hhhHHHHHhhhhhhccC-CCCceeeecCCCHHHHHHHHHHHHhcccccccchHHHH
Confidence            4444333332  122222211   34566777777665322 235679999999999999999998877643 4456888


Q ss_pred             HHHHH---cCCcHHHHHHHHH
Q 005987          363 LVAQA---SGGDIRQAITSLQ  380 (666)
Q Consensus       363 ~Ia~~---s~GDIR~AIn~LQ  380 (666)
                      .+|..   ..||+|.|+...+
T Consensus       353 ~~ArKvaa~SGDlRkaLdv~R  373 (529)
T KOG2227|consen  353 LCARKVAAPSGDLRKALDVCR  373 (529)
T ss_pred             HHHHHhccCchhHHHHHHHHH
Confidence            88865   4699999998876

>COG1224 TIP49 DNA helicase TIP49, TBP-interacting protein [Transcription]

Probab=99.19  E-value=6.2e-10  Score=115.42  Aligned_cols=111  Identities=17%  Similarity=0.293  Sum_probs=83.2

Q ss_pred             ceEEEEeCCCCCcchhHHHHHHHHHHHHHhcCCCceEEEEecCCCCCC--ccch-hhhhhHHHHHHhhcCeeEEEeCCCC
Q 005987          261 SAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHIPTAVVLTECGKADS--VDST-AQSFEELQSILVDAGARKVALNPIT  337 (666)
Q Consensus       261 ~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~~~PiViIit~~~~~~s--~d~~-~r~l~~L~s~L~r~r~~~I~F~p~s  337 (666)
                      |-||||||++.++-. .|.    .|...+++.-.|+|++++|.+....  .|.. .+-++  ..+|.  |..+|.-.|++
T Consensus       292 pGVLFIDEvHmLDIE-~Fs----FlnrAlEse~aPIii~AtNRG~~kiRGTd~~sPhGIP--~DlLD--RllII~t~py~  362 (450)
T COG1224         292 PGVLFIDEVHMLDIE-CFS----FLNRALESELAPIIILATNRGMTKIRGTDIESPHGIP--LDLLD--RLLIISTRPYS  362 (450)
T ss_pred             cceEEEechhhhhHH-HHH----HHHHHhhcccCcEEEEEcCCceeeecccCCcCCCCCC--Hhhhh--heeEEecCCCC
Confidence            569999999987532 232    3556667777899999998754321  1111 12221  34555  48899999999


Q ss_pred             HHHHHHHHHHHHHHhCCCCCHHHHHHHHHH-cCCcHHHHHHHHH
Q 005987          338 NGSIKRTLSKICRQEQYSLSTEQIDLVAQA-SGGDIRQAITSLQ  380 (666)
Q Consensus       338 ~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~-s~GDIR~AIn~LQ  380 (666)
                      .++++.+|+..|..+++.+++++++.++.. ..-.+|.|++.|.
T Consensus       363 ~~EireIi~iRa~ee~i~l~~~Ale~L~~ig~etSLRYa~qLL~  406 (450)
T COG1224         363 REEIREIIRIRAKEEDIELSDDALEYLTDIGEETSLRYAVQLLT  406 (450)
T ss_pred             HHHHHHHHHHhhhhhccccCHHHHHHHHhhchhhhHHHHHHhcc
Confidence            999999999999999999999999999987 3467999998886

>KOG0728 consensus 26S proteasome regulatory complex, ATPase RPT6 [Posttranslational modification, protein turnover, chaperones]

Probab=99.19  E-value=1.4e-10  Score=114.64  Aligned_cols=183  Identities=17%  Similarity=0.255  Sum_probs=116.4

Q ss_pred             CCccccccCCCCccccccCHHHHHHHHHHHHHhhcC-----CCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEc
Q 005987          136 QQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGD-----SKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWD  210 (666)
Q Consensus       136 ~~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~-----~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~n  210 (666)
                      +.+.++|-.-.+.+=+-|-++.++++++.++--.+.     .-|-..++.+|||||||+|||.+|+++|.+..+.++.+.
T Consensus       134 sLMmVeKvPDStYeMiGgLd~QIkeIkEVIeLPvKHPELF~aLGIaQPKGvlLygppgtGktLlaraVahht~c~firvs  213 (404)
T KOG0728|consen  134 SLMMVEKVPDSTYEMIGGLDKQIKEIKEVIELPVKHPELFEALGIAQPKGVLLYGPPGTGKTLLARAVAHHTDCTFIRVS  213 (404)
T ss_pred             HHHhhhhCCccHHHHhccHHHHHHHHHHHHhccccCHHHHHhcCCCCCcceEEecCCCCchhHHHHHHHhhcceEEEEec
Confidence            456778877777766777889999999988732221     114444588999999999999999999999999999988


Q ss_pred             CCCchhhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcch------hHHHHHHHH
Q 005987          211 TPTPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGR------TAFERLRQC  284 (666)
Q Consensus       211 asd~~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~------~~~~~l~~~  284 (666)
                      .+.  ..++++...         ....++++-.++..            .|.||++||+|.+...      ..-..++..
T Consensus       214 gse--lvqk~igeg---------srmvrelfvmareh------------apsiifmdeidsigs~r~e~~~ggdsevqrt  270 (404)
T KOG0728|consen  214 GSE--LVQKYIGEG---------SRMVRELFVMAREH------------APSIIFMDEIDSIGSSRVESGSGGDSEVQRT  270 (404)
T ss_pred             hHH--HHHHHhhhh---------HHHHHHHHHHHHhc------------CCceEeeecccccccccccCCCCccHHHHHH
Confidence            764  233333221         11234444444433            3679999999975321      111234444


Q ss_pred             HHHHHh------cCCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcC--eeEEEeCCCCHHHHHHHHHHHHHHhC
Q 005987          285 LLLLVR------STHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAG--ARKVALNPITNGSIKRTLSKICRQEQ  353 (666)
Q Consensus       285 L~~l~~------~~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r--~~~I~F~p~s~~~i~kiL~~I~~~e~  353 (666)
                      ++.++.      .++.--||++++.            ++-|.+.|-|++  -..|.|+||+......+|+-...+.+
T Consensus       271 mlellnqldgfeatknikvimatnr------------idild~allrpgridrkiefp~p~e~ar~~ilkihsrkmn  335 (404)
T KOG0728|consen  271 MLELLNQLDGFEATKNIKVIMATNR------------IDILDPALLRPGRIDRKIEFPPPNEEARLDILKIHSRKMN  335 (404)
T ss_pred             HHHHHHhccccccccceEEEEeccc------------cccccHhhcCCCcccccccCCCCCHHHHHHHHHHhhhhhc
Confidence            444443      3444455666652            222333333332  34699999999999999887665543

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=99.16  E-value=9.5e-10  Score=130.93  Aligned_cols=212  Identities=15%  Similarity=0.159  Sum_probs=128.0

Q ss_pred             cccccCHHHHHHHHHHHHHhhcCCC-CCCCccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcCCCchhh---hhhh
Q 005987          149 EELAVQRKKVEEVRAWFEERLGDSK-DKFSTNVLVITGQAGVGKTATVRQIASHL---GARLYEWDTPTPTIW---QEYM  221 (666)
Q Consensus       149 ~eLvg~~k~i~el~~wL~~~~~~~~-g~~~~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~nasd~~~~---~e~l  221 (666)
                      ..|+||+..++.|..++.....+.. ..-|...+||+||||||||.+|++||+.+   .-.++.++.++....   ...+
T Consensus       566 ~~v~GQ~~Av~~v~~~i~~~~~gl~~~~~p~~~~lf~Gp~GvGKT~lA~~La~~l~~~~~~~~~~dmse~~~~~~~~~l~  645 (852)
T TIGR03345       566 ERVIGQDHALEAIAERIRTARAGLEDPRKPLGVFLLVGPSGVGKTETALALAELLYGGEQNLITINMSEFQEAHTVSRLK  645 (852)
T ss_pred             CeEcChHHHHHHHHHHHHHHhcCCCCCCCCceEEEEECCCCCCHHHHHHHHHHHHhCCCcceEEEeHHHhhhhhhhcccc
Confidence            4578999999999999986543211 11222469999999999999999999998   335677775532110   0111


Q ss_pred             hcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcC---------
Q 005987          222 HNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRST---------  292 (666)
Q Consensus       222 ~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~---------  292 (666)
                      ......+.|. ....+.+.+   ++            ++..||+|||++..+.     .+.+.|..+++.+         
T Consensus       646 g~~~gyvg~~-~~g~L~~~v---~~------------~p~svvllDEieka~~-----~v~~~Llq~ld~g~l~d~~Gr~  704 (852)
T TIGR03345       646 GSPPGYVGYG-EGGVLTEAV---RR------------KPYSVVLLDEVEKAHP-----DVLELFYQVFDKGVMEDGEGRE  704 (852)
T ss_pred             CCCCCccccc-ccchHHHHH---Hh------------CCCcEEEEechhhcCH-----HHHHHHHHHhhcceeecCCCcE
Confidence            1110011111 111222222   21            1345999999986643     2344566666554         


Q ss_pred             ---CCceEEEEecCCCCCC----ccc---------hhhhhhHH-----HHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHH
Q 005987          293 ---HIPTAVVLTECGKADS----VDS---------TAQSFEEL-----QSILVDAGARKVALNPITNGSIKRTLSKICRQ  351 (666)
Q Consensus       293 ---~~PiViIit~~~~~~s----~d~---------~~r~l~~L-----~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~  351 (666)
                         +..+||++++......    .+.         .......+     +++++  |+.+|.|+|++.+++.+++...+..
T Consensus       705 vd~~n~iiI~TSNlg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~PEfln--Ri~iI~F~pLs~e~l~~Iv~~~L~~  782 (852)
T TIGR03345       705 IDFKNTVILLTSNAGSDLIMALCADPETAPDPEALLEALRPELLKVFKPAFLG--RMTVIPYLPLDDDVLAAIVRLKLDR  782 (852)
T ss_pred             EeccccEEEEeCCCchHHHHHhccCcccCcchHHHHHHHHHHHHHhccHHHhc--ceeEEEeCCCCHHHHHHHHHHHHHH
Confidence               3356666666432110    000         00000111     24444  4789999999999999998876643


Q ss_pred             ------h--C--CCCCHHHHHHHHHHcCC---cHHHHHHHHHHHh
Q 005987          352 ------E--Q--YSLSTEQIDLVAQASGG---DIRQAITSLQFSS  383 (666)
Q Consensus       352 ------e--~--i~v~~~~l~~Ia~~s~G---DIR~AIn~LQf~~  383 (666)
                            +  +  +.+++++++.|++.+.+   +.|...+.||-.-
T Consensus       783 l~~rl~~~~gi~l~i~d~a~~~La~~g~~~~~GAR~L~r~Ie~~i  827 (852)
T TIGR03345       783 IARRLKENHGAELVYSEALVEHIVARCTEVESGARNIDAILNQTL  827 (852)
T ss_pred             HHHHHHHhcCceEEECHHHHHHHHHHcCCCCCChHHHHHHHHHHH
Confidence                  1  3  45799999999999877   7898888887643

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.

>KOG0739 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=99.16  E-value=3.6e-10  Score=114.42  Aligned_cols=191  Identities=14%  Similarity=0.186  Sum_probs=111.1

Q ss_pred             CccccccCHHHHHHHHHHHHHhhcC----CCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCchhhhhhhh
Q 005987          147 SLEELAVQRKKVEEVRAWFEERLGD----SKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTIWQEYMH  222 (666)
Q Consensus       147 sl~eLvg~~k~i~el~~wL~~~~~~----~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~~~~e~l~  222 (666)
                      .++|++|-+...+.|++.+---++-    ..++.|-+.+||+||||+||+.+|+++|-+.+-.++.+..+|  ...+.+.
T Consensus       131 kWsDVAGLE~AKeALKEAVILPIKFPqlFtGkR~PwrgiLLyGPPGTGKSYLAKAVATEAnSTFFSvSSSD--LvSKWmG  208 (439)
T KOG0739|consen  131 KWSDVAGLEGAKEALKEAVILPIKFPQLFTGKRKPWRGILLYGPPGTGKSYLAKAVATEANSTFFSVSSSD--LVSKWMG  208 (439)
T ss_pred             chhhhccchhHHHHHHhheeecccchhhhcCCCCcceeEEEeCCCCCcHHHHHHHHHhhcCCceEEeehHH--HHHHHhc
Confidence            4578899988888888765321110    113344578999999999999999999999998888888776  2233332


Q ss_pred             cccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcc------hhHHHHHHHHHHHHHhc-CC-C
Q 005987          223 NCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNG------RTAFERLRQCLLLLVRS-TH-I  294 (666)
Q Consensus       223 ~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~------~~~~~~l~~~L~~l~~~-~~-~  294 (666)
                      .         .....+++++.++.            ++|.||+|||+|.+.+      ..+.+++...++--++. +. .
T Consensus       209 E---------SEkLVknLFemARe------------~kPSIIFiDEiDslcg~r~enEseasRRIKTEfLVQMqGVG~d~  267 (439)
T KOG0739|consen  209 E---------SEKLVKNLFEMARE------------NKPSIIFIDEIDSLCGSRSENESEASRRIKTEFLVQMQGVGNDN  267 (439)
T ss_pred             c---------HHHHHHHHHHHHHh------------cCCcEEEeehhhhhccCCCCCchHHHHHHHHHHHHhhhccccCC
Confidence            2         22334555665543            2577999999997643      23445555333322222 11 1


Q ss_pred             ceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCC
Q 005987          295 PTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASGG  370 (666)
Q Consensus       295 PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~s~G  370 (666)
                      --|++++.++.+-          .|.+.++|+.-..|.++-|.........+-.+-.-...+++..+..|+..+.|
T Consensus       268 ~gvLVLgATNiPw----------~LDsAIRRRFekRIYIPLPe~~AR~~MF~lhlG~tp~~LT~~d~~eL~~kTeG  333 (439)
T KOG0739|consen  268 DGVLVLGATNIPW----------VLDSAIRRRFEKRIYIPLPEAHARARMFKLHLGDTPHVLTEQDFKELARKTEG  333 (439)
T ss_pred             CceEEEecCCCch----------hHHHHHHHHhhcceeccCCcHHHhhhhheeccCCCccccchhhHHHHHhhcCC
Confidence            2355566665442          24455555334456666555443333322222222234566666677666544

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

Probab=99.15  E-value=1.3e-09  Score=127.65  Aligned_cols=204  Identities=18%  Similarity=0.257  Sum_probs=121.5

Q ss_pred             ccccCHHHHHHHHHHHHHhhcCC--CCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCchh---hhhhhhcc
Q 005987          150 ELAVQRKKVEEVRAWFEERLGDS--KDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTI---WQEYMHNC  224 (666)
Q Consensus       150 eLvg~~k~i~el~~wL~~~~~~~--~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~~---~~e~l~~~  224 (666)
                      .++||++.++.|..++..+..+.  ++++ ...+||+||||||||++|++||+.++..++.++.+....   ....+...
T Consensus       459 ~ViGQ~~ai~~l~~~i~~~~~gl~~~~kp-~~~~Lf~GP~GvGKT~lAk~LA~~l~~~~i~id~se~~~~~~~~~LiG~~  537 (758)
T PRK11034        459 LVFGQDKAIEALTEAIKMSRAGLGHEHKP-VGSFLFAGPTGVGKTEVTVQLSKALGIELLRFDMSEYMERHTVSRLIGAP  537 (758)
T ss_pred             eEeCcHHHHHHHHHHHHHHhccccCCCCC-cceEEEECCCCCCHHHHHHHHHHHhCCCcEEeechhhcccccHHHHcCCC
Confidence            37899999999999998664321  1222 247999999999999999999999999999888765221   11111111


Q ss_pred             cCC-ccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcC-----------
Q 005987          225 KTG-LEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRST-----------  292 (666)
Q Consensus       225 ~~g-~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~-----------  292 (666)
                       .| ..+ .....+.+.+   ..            ++..||++||++.++.     .+++.|+.+++.+           
T Consensus       538 -~gyvg~-~~~g~L~~~v---~~------------~p~sVlllDEieka~~-----~v~~~LLq~ld~G~ltd~~g~~vd  595 (758)
T PRK11034        538 -PGYVGF-DQGGLLTDAV---IK------------HPHAVLLLDEIEKAHP-----DVFNLLLQVMDNGTLTDNNGRKAD  595 (758)
T ss_pred             -CCcccc-cccchHHHHH---Hh------------CCCcEEEeccHhhhhH-----HHHHHHHHHHhcCeeecCCCceec
Confidence             11 111 0111122211   11            1246999999998753     3445566666543           


Q ss_pred             -CCceEEEEecCCCCC----C-----ccchhhhhhHH-----HHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHH------
Q 005987          293 -HIPTAVVLTECGKAD----S-----VDSTAQSFEEL-----QSILVDAGARKVALNPITNGSIKRTLSKICRQ------  351 (666)
Q Consensus       293 -~~PiViIit~~~~~~----s-----~d~~~r~l~~L-----~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~------  351 (666)
                       +..+||++++.+...    .     .+.....+..+     ++++.| --.+|.|+|++.+++.+++...+..      
T Consensus       596 ~rn~iiI~TsN~g~~~~~~~~~g~~~~~~~~~~~~~~~~~f~pefl~R-id~ii~f~~L~~~~l~~I~~~~l~~~~~~l~  674 (758)
T PRK11034        596 FRNVVLVMTTNAGVRETERKSIGLIHQDNSTDAMEEIKKIFTPEFRNR-LDNIIWFDHLSTDVIHQVVDKFIVELQAQLD  674 (758)
T ss_pred             CCCcEEEEeCCcCHHHHhhcccCcccchhhHHHHHHHHHhcCHHHHcc-CCEEEEcCCCCHHHHHHHHHHHHHHHHHHHH
Confidence             223455555532110    0     00000011111     344444 2358999999999999998876643      


Q ss_pred             -hC--CCCCHHHHHHHHHHc------CCcHHHHHH
Q 005987          352 -EQ--YSLSTEQIDLVAQAS------GGDIRQAIT  377 (666)
Q Consensus       352 -e~--i~v~~~~l~~Ia~~s------~GDIR~AIn  377 (666)
                       .+  +.+++++++.|++..      ...+|++|.
T Consensus       675 ~~~i~l~~~~~~~~~l~~~~~~~~~GAR~l~r~i~  709 (758)
T PRK11034        675 QKGVSLEVSQEARDWLAEKGYDRAMGARPMARVIQ  709 (758)
T ss_pred             HCCCCceECHHHHHHHHHhCCCCCCCCchHHHHHH
Confidence             23  457899999999763      245666664

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

Probab=99.14  E-value=4.1e-09  Score=109.41  Aligned_cols=178  Identities=20%  Similarity=0.258  Sum_probs=97.6

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCC-cEE--EEcCCCchhhhhhhhc--ccCCccc--cchh---HHHHHHHHHHHhhc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGA-RLY--EWDTPTPTIWQEYMHN--CKTGLEY--TSKL---DEFENFVERIRRYG  248 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~-~vi--E~nasd~~~~~e~l~~--~~~g~~~--~s~~---~~f~~fl~~a~~~~  248 (666)
                      ..++|+||+|+||||+++.+++++.. .++  .+..+.. ...+.+..  ...|...  ....   ..+..++.....  
T Consensus        44 ~~~~l~G~~G~GKTtl~~~l~~~l~~~~~~~~~~~~~~~-~~~~~l~~i~~~lG~~~~~~~~~~~~~~l~~~l~~~~~--  120 (269)
T TIGR03015        44 GFILITGEVGAGKTTLIRNLLKRLDQERVVAAKLVNTRV-DAEDLLRMVAADFGLETEGRDKAALLRELEDFLIEQFA--  120 (269)
T ss_pred             CEEEEEcCCCCCHHHHHHHHHHhcCCCCeEEeeeeCCCC-CHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHHHHHHHh--
Confidence            47999999999999999999999853 222  2211111 11111110  0112221  1111   223333322211  


Q ss_pred             CCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcCCCceE-EEEecCCCCCCccchhhhhh--HHHHHHhh
Q 005987          249 STSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHIPTA-VVLTECGKADSVDSTAQSFE--ELQSILVD  325 (666)
Q Consensus       249 ~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~~~PiV-iIit~~~~~~s~d~~~r~l~--~L~s~L~r  325 (666)
                               .+.+.+|+|||++.+... ..+.+.. |..+.......+. ++++...       ....+.  .+..+.+|
T Consensus       121 ---------~~~~~vliiDe~~~l~~~-~~~~l~~-l~~~~~~~~~~~~vvl~g~~~-------~~~~l~~~~~~~l~~r  182 (269)
T TIGR03015       121 ---------AGKRALLVVDEAQNLTPE-LLEELRM-LSNFQTDNAKLLQIFLVGQPE-------FRETLQSPQLQQLRQR  182 (269)
T ss_pred             ---------CCCCeEEEEECcccCCHH-HHHHHHH-HhCcccCCCCeEEEEEcCCHH-------HHHHHcCchhHHHHhh
Confidence                     123569999999987532 2332221 2222111122222 3333211       011110  11222222


Q ss_pred             cCeeEEEeCCCCHHHHHHHHHHHHHHhC----CCCCHHHHHHHHHHcCCcHHHHHHHH
Q 005987          326 AGARKVALNPITNGSIKRTLSKICRQEQ----YSLSTEQIDLVAQASGGDIRQAITSL  379 (666)
Q Consensus       326 ~r~~~I~F~p~s~~~i~kiL~~I~~~e~----i~v~~~~l~~Ia~~s~GDIR~AIn~L  379 (666)
                       -+..+.+.+++.+++.+++...+...+    ..+++++++.|++.|+|+.|. ||.+
T Consensus       183 -~~~~~~l~~l~~~e~~~~l~~~l~~~g~~~~~~~~~~~~~~i~~~s~G~p~~-i~~l  238 (269)
T TIGR03015       183 -IIASCHLGPLDREETREYIEHRLERAGNRDAPVFSEGAFDAIHRFSRGIPRL-INIL  238 (269)
T ss_pred             -eeeeeeCCCCCHHHHHHHHHHHHHHcCCCCCCCcCHHHHHHHHHHcCCcccH-HHHH
Confidence             266889999999999999999887654    468999999999999999998 4443

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.

>CHL00206 ycf2 Ycf2; Provisional

Probab=99.13  E-value=2.9e-10  Score=138.39  Aligned_cols=189  Identities=11%  Similarity=0.090  Sum_probs=110.7

Q ss_pred             CCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCchhhh--hhhhcc-cCC----------------cc-------
Q 005987          176 FSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTIWQ--EYMHNC-KTG----------------LE-------  229 (666)
Q Consensus       176 ~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~~~~--e~l~~~-~~g----------------~~-------  229 (666)
                      .+++.+||+||||||||.+|++||.+.+..++.+..++-..-.  .++... ..|                ..       
T Consensus      1628 ~pPKGILLiGPPGTGKTlLAKALA~es~VPFIsISgs~fl~~~~~~~~~d~i~iges~~~~~~~~~~~~~~~e~~e~~n~ 1707 (2281)
T CHL00206       1628 SPSRGILVIGSIGTGRSYLVKYLATNSYVPFITVFLNKFLDNKPKGFLIDDIDIDDSDDIDDSDDIDRDLDTELLTMMNA 1707 (2281)
T ss_pred             CCCCceEEECCCCCCHHHHHHHHHHhcCCceEEEEHHHHhhcccccccccccccccccccccccccccccchhhhhhcch
Confidence            3458999999999999999999999999999998876521100  000000 000                00       


Q ss_pred             ----ccchhH--HHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcC----CCceEEE
Q 005987          230 ----YTSKLD--EFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRST----HIPTAVV  299 (666)
Q Consensus       230 ----~~s~~~--~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~----~~PiViI  299 (666)
                          ......  .++..++.|++.            .|+||+|||+|.+...+........|...+...    ...-|++
T Consensus      1708 ~~~~m~~~e~~~rIr~lFelARk~------------SPCIIFIDEIDaL~~~ds~~ltL~qLLneLDg~~~~~s~~~VIV 1775 (2281)
T CHL00206       1708 LTMDMMPKIDRFYITLQFELAKAM------------SPCIIWIPNIHDLNVNESNYLSLGLLVNSLSRDCERCSTRNILV 1775 (2281)
T ss_pred             hhhhhhhhhhHHHHHHHHHHHHHC------------CCeEEEEEchhhcCCCccceehHHHHHHHhccccccCCCCCEEE
Confidence                001111  245566666554            389999999998865422111122333333311    1123455


Q ss_pred             EecCCCCCCccchhhhhhHHHHHHhhc--CeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHH--HHHHHHHHc----CCc
Q 005987          300 LTECGKADSVDSTAQSFEELQSILVDA--GARKVALNPITNGSIKRTLSKICRQEQYSLSTE--QIDLVAQAS----GGD  371 (666)
Q Consensus       300 it~~~~~~s~d~~~r~l~~L~s~L~r~--r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~--~l~~Ia~~s----~GD  371 (666)
                      +++++.++..          .+.|.|+  .-..|.+..|+..+.++++...+...++.+.++  .++.+|..+    +.|
T Consensus      1776 IAATNRPD~L----------DPALLRPGRFDR~I~Ir~Pd~p~R~kiL~ILl~tkg~~L~~~~vdl~~LA~~T~GfSGAD 1845 (2281)
T CHL00206       1776 IASTHIPQKV----------DPALIAPNKLNTCIKIRRLLIPQQRKHFFTLSYTRGFHLEKKMFHTNGFGSITMGSNARD 1845 (2281)
T ss_pred             EEeCCCcccC----------CHhHcCCCCCCeEEEeCCCCchhHHHHHHHHHhhcCCCCCcccccHHHHHHhCCCCCHHH
Confidence            5666655433          3333332  245789998888777777765554455555433  367888875    558


Q ss_pred             HHHHHHHHHHHhcCC
Q 005987          372 IRQAITSLQFSSLKQ  386 (666)
Q Consensus       372 IR~AIn~LQf~~~~~  386 (666)
                      +...+|-.-..|...
T Consensus      1846 LanLvNEAaliAirq 1860 (2281)
T CHL00206       1846 LVALTNEALSISITQ 1860 (2281)
T ss_pred             HHHHHHHHHHHHHHc
Confidence            888877655555443

>KOG0735 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=99.13  E-value=1.2e-09  Score=121.42  Aligned_cols=204  Identities=16%  Similarity=0.252  Sum_probs=127.7

Q ss_pred             CccccccCHHHHHHHHHHHHHh------hcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCchhhhhh
Q 005987          147 SLEELAVQRKKVEEVRAWFEER------LGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTIWQEY  220 (666)
Q Consensus       147 sl~eLvg~~k~i~el~~wL~~~------~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~~~~e~  220 (666)
                      .++|+.|-....+-|.+.++--      +...+-+.+ ..+|||||||||||.+|.++|...+..++.+..|.  ...++
T Consensus       665 ~w~digg~~~~k~~l~~~i~~P~kyp~if~~~plr~~-~giLLyGppGcGKT~la~a~a~~~~~~fisvKGPE--lL~Ky  741 (952)
T KOG0735|consen  665 RWEDIGGLFEAKKVLEEVIEWPSKYPQIFANCPLRLR-TGILLYGPPGCGKTLLASAIASNSNLRFISVKGPE--LLSKY  741 (952)
T ss_pred             CceecccHHHHHHHHHHHHhccccchHHHhhCCcccc-cceEEECCCCCcHHHHHHHHHhhCCeeEEEecCHH--HHHHH
Confidence            3456666544444444444311      111223344 57999999999999999999999999999998875  33333


Q ss_pred             hhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchh------HHHHHHHHHHHHHhcCC-
Q 005987          221 MHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRT------AFERLRQCLLLLVRSTH-  293 (666)
Q Consensus       221 l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~------~~~~l~~~L~~l~~~~~-  293 (666)
                      +++         .....++++++++..            +|+|+++||+|.+..+.      -..++.+.|+.-++... 
T Consensus       742 IGa---------SEq~vR~lF~rA~~a------------~PCiLFFDEfdSiAPkRGhDsTGVTDRVVNQlLTelDG~Eg  800 (952)
T KOG0735|consen  742 IGA---------SEQNVRDLFERAQSA------------KPCILFFDEFDSIAPKRGHDSTGVTDRVVNQLLTELDGAEG  800 (952)
T ss_pred             hcc---------cHHHHHHHHHHhhcc------------CCeEEEeccccccCcccCCCCCCchHHHHHHHHHhhccccc
Confidence            332         234567788887533            58999999999874321      12344433333333221 


Q ss_pred             CceEEEEecCCCCCCccchhhhhhHHHHHHhhcC--eeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHH----
Q 005987          294 IPTAVVLTECGKADSVDSTAQSFEELQSILVDAG--ARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQA----  367 (666)
Q Consensus       294 ~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r--~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~----  367 (666)
                      .--|+|++.+..++..|          +.|-|++  -..|..+.|++.+...+|+.+...... -++..++.+|..    
T Consensus       801 l~GV~i~aaTsRpdliD----------pALLRpGRlD~~v~C~~P~~~eRl~il~~ls~s~~~-~~~vdl~~~a~~T~g~  869 (952)
T KOG0735|consen  801 LDGVYILAATSRPDLID----------PALLRPGRLDKLVYCPLPDEPERLEILQVLSNSLLK-DTDVDLECLAQKTDGF  869 (952)
T ss_pred             cceEEEEEecCCccccC----------HhhcCCCccceeeeCCCCCcHHHHHHHHHHhhccCC-ccccchHHHhhhcCCC
Confidence            23355555555544333          2232332  345788899999999998877654322 234557778876    


Q ss_pred             cCCcHHHHHHHHHHHhcC
Q 005987          368 SGGDIRQAITSLQFSSLK  385 (666)
Q Consensus       368 s~GDIR~AIn~LQf~~~~  385 (666)
                      ++.|+...+-+.|+++..
T Consensus       870 tgADlq~ll~~A~l~avh  887 (952)
T KOG0735|consen  870 TGADLQSLLYNAQLAAVH  887 (952)
T ss_pred             chhhHHHHHHHHHHHHHH
Confidence            456999999999998753

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

Probab=99.13  E-value=1.1e-09  Score=128.90  Aligned_cols=210  Identities=13%  Similarity=0.163  Sum_probs=123.6

Q ss_pred             CCccccccCCCCc----------cccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCc
Q 005987          136 QQLWAEKYKPRSL----------EELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGAR  205 (666)
Q Consensus       136 ~~~W~eKY~P~sl----------~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~  205 (666)
                      +.+| .+|.+.++          ++..|.++..++|.+|+......  +.....+++|+|||||||||+++.+|+.++..
T Consensus       300 ~~pw-~~~~~~~~~~~~~~~~l~~~~~g~~~vK~~i~~~l~~~~~~--~~~~g~~i~l~GppG~GKTtl~~~ia~~l~~~  376 (784)
T PRK10787        300 QVPW-NARSKVKKDLRQAQEILDTDHYGLERVKDRILEYLAVQSRV--NKIKGPILCLVGPPGVGKTSLGQSIAKATGRK  376 (784)
T ss_pred             hCCC-CCCCcccccHHHHHHHhhhhccCHHHHHHHHHHHHHHHHhc--ccCCCceEEEECCCCCCHHHHHHHHHHHhCCC
Confidence            5678 44565544          23778999999999998854322  22233589999999999999999999999999


Q ss_pred             EEEEcCCCchhhhhhhhcccCCccc-cchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHH
Q 005987          206 LYEWDTPTPTIWQEYMHNCKTGLEY-TSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQC  284 (666)
Q Consensus       206 viE~nasd~~~~~e~l~~~~~g~~~-~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~  284 (666)
                      ++.++....+...+.....   ..| ......+   +......+         . ...||||||+|.+..... +...++
T Consensus       377 ~~~i~~~~~~d~~~i~g~~---~~~~g~~~G~~---~~~l~~~~---------~-~~~villDEidk~~~~~~-g~~~~a  439 (784)
T PRK10787        377 YVRMALGGVRDEAEIRGHR---RTYIGSMPGKL---IQKMAKVG---------V-KNPLFLLDEIDKMSSDMR-GDPASA  439 (784)
T ss_pred             EEEEEcCCCCCHHHhccch---hccCCCCCcHH---HHHHHhcC---------C-CCCEEEEEChhhcccccC-CCHHHH
Confidence            8888755422211111000   000 0111111   11111111         1 124899999998754311 112334


Q ss_pred             HHHHHhcCC---------------CceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHH
Q 005987          285 LLLLVRSTH---------------IPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKIC  349 (666)
Q Consensus       285 L~~l~~~~~---------------~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~  349 (666)
                      |+.+++..+               ..+++|+|+ +..       . +  ..+++.  |+..|.|.+++.+++.++.++.+
T Consensus       440 Llevld~~~~~~~~d~~~~~~~dls~v~~i~Ta-N~~-------~-i--~~aLl~--R~~ii~~~~~t~eek~~Ia~~~L  506 (784)
T PRK10787        440 LLEVLDPEQNVAFSDHYLEVDYDLSDVMFVATS-NSM-------N-I--PAPLLD--RMEVIRLSGYTEDEKLNIAKRHL  506 (784)
T ss_pred             HHHHhccccEEEEecccccccccCCceEEEEcC-CCC-------C-C--CHHHhc--ceeeeecCCCCHHHHHHHHHHhh
Confidence            555554311               124555543 211       1 1  133333  58999999999999999987776


Q ss_pred             HH----------hCCCCCHHHHHHHHHHcC-----CcHHHHHHH
Q 005987          350 RQ----------EQYSLSTEQIDLVAQASG-----GDIRQAITS  378 (666)
Q Consensus       350 ~~----------e~i~v~~~~l~~Ia~~s~-----GDIR~AIn~  378 (666)
                      ..          ..+.+++++++.|++.+.     ..+++.|..
T Consensus       507 ~~k~~~~~~l~~~~l~i~~~ai~~ii~~yt~e~GaR~LeR~I~~  550 (784)
T PRK10787        507 LPKQIERNALKKGELTVDDSAIIGIIRYYTREAGVRSLEREISK  550 (784)
T ss_pred             hHHHHHHhCCCCCeEEECHHHHHHHHHhCCcccCCcHHHHHHHH
Confidence            31          125689999999997532     345555544

>KOG1514 consensus Origin recognition complex, subunit 1, and related proteins [Replication, recombination and repair]

Probab=99.12  E-value=1.8e-09  Score=120.50  Aligned_cols=213  Identities=19%  Similarity=0.292  Sum_probs=135.5

Q ss_pred             CCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc----------CCcEEEEcCCC
Q 005987          144 KPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL----------GARLYEWDTPT  213 (666)
Q Consensus       144 ~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel----------g~~viE~nasd  213 (666)
                      .|.++   .+++....+|..+++..+.. .+.  ...+.++|-||+|||.+|+.+-++|          .+.++|+|+.-
T Consensus       394 vp~sL---pcRe~E~~~I~~f~~~~i~~-~~~--g~~mYIsGvPGtGKT~tV~~Vm~~Lq~~s~~~e~p~f~yveINgm~  467 (767)
T KOG1514|consen  394 VPESL---PCRENEFSEIEDFLRSFISD-QGL--GSCMYISGVPGTGKTATVLEVMKELQTSSAQKELPKFDYVEINGLR  467 (767)
T ss_pred             ccccc---cchhHHHHHHHHHHHhhcCC-CCC--ceeEEEecCCCCCceehHHHHHHHHHHHHhhcCCCCccEEEEccee
Confidence            55554   78999999999999987764 122  2489999999999999999999977          47889999764


Q ss_pred             ch---hhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHh
Q 005987          214 PT---IWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVR  290 (666)
Q Consensus       214 ~~---~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~  290 (666)
                      -.   ...+.+.....|......     .-++-...+-.    ..+..+.++||||||+|.+-++     -+++|+.+.+
T Consensus       468 l~~~~~~Y~~I~~~lsg~~~~~~-----~al~~L~~~f~----~~k~~~~~~VvLiDElD~Lvtr-----~QdVlYn~fd  533 (767)
T KOG1514|consen  468 LASPREIYEKIWEALSGERVTWD-----AALEALNFRFT----VPKPKRSTTVVLIDELDILVTR-----SQDVLYNIFD  533 (767)
T ss_pred             ecCHHHHHHHHHHhcccCcccHH-----HHHHHHHHhhc----cCCCCCCCEEEEeccHHHHhcc-----cHHHHHHHhc
Confidence            22   222333333334332110     01111111111    1233456789999999987543     2345666554


Q ss_pred             cCC---Cc-eEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHH
Q 005987          291 STH---IP-TAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQ  366 (666)
Q Consensus       291 ~~~---~P-iViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~  366 (666)
                      =..   .. +||.++++     +|...+.+..  ..-+|.+...|.|+|++.+++.+++...+..- -.+..++++.++.
T Consensus       534 Wpt~~~sKLvvi~IaNT-----mdlPEr~l~n--rvsSRlg~tRi~F~pYth~qLq~Ii~~RL~~~-~~f~~~aielvar  605 (767)
T KOG1514|consen  534 WPTLKNSKLVVIAIANT-----MDLPERLLMN--RVSSRLGLTRICFQPYTHEQLQEIISARLKGL-DAFENKAIELVAR  605 (767)
T ss_pred             CCcCCCCceEEEEeccc-----ccCHHHHhcc--chhhhccceeeecCCCCHHHHHHHHHHhhcch-hhcchhHHHHHHH
Confidence            322   22 33334442     3344454431  12234578999999999999999988776544 3467778777775


Q ss_pred             H---cCCcHHHHHHHHHHHhc
Q 005987          367 A---SGGDIRQAITSLQFSSL  384 (666)
Q Consensus       367 ~---s~GDIR~AIn~LQf~~~  384 (666)
                      .   -.||.|+|+....-++.
T Consensus       606 kVAavSGDaRraldic~RA~E  626 (767)
T KOG1514|consen  606 KVAAVSGDARRALDICRRAAE  626 (767)
T ss_pred             HHHhccccHHHHHHHHHHHHH
Confidence            4   45999999998877764

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

Probab=99.11  E-value=2.4e-09  Score=126.37  Aligned_cols=206  Identities=15%  Similarity=0.260  Sum_probs=121.3

Q ss_pred             ccccCHHHHHHHHHHHHHhhcC--CCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCchh---hhhhhhcc
Q 005987          150 ELAVQRKKVEEVRAWFEERLGD--SKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTI---WQEYMHNC  224 (666)
Q Consensus       150 eLvg~~k~i~el~~wL~~~~~~--~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~~---~~e~l~~~  224 (666)
                      .++||+..++.|..++......  .++++ ...+||+||||||||++|++||+.++..++.++.+....   ....+...
T Consensus       455 ~v~GQ~~ai~~l~~~i~~~~~g~~~~~~p-~~~~lf~Gp~GvGKT~lA~~la~~l~~~~~~~d~se~~~~~~~~~lig~~  533 (731)
T TIGR02639       455 KIFGQDEAIDSLVSSIKRSRAGLGNPNKP-VGSFLFTGPTGVGKTELAKQLAEALGVHLERFDMSEYMEKHTVSRLIGAP  533 (731)
T ss_pred             ceeCcHHHHHHHHHHHHHHhcCCCCCCCC-ceeEEEECCCCccHHHHHHHHHHHhcCCeEEEeCchhhhcccHHHHhcCC
Confidence            4789999999999998854321  11222 246999999999999999999999999999888765221   01111111


Q ss_pred             cCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcC------------
Q 005987          225 KTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRST------------  292 (666)
Q Consensus       225 ~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~------------  292 (666)
                      ...+.+ .....+.   +.++.            ++..||+|||++.++.     .+++.|+.+++.+            
T Consensus       534 ~gyvg~-~~~~~l~---~~~~~------------~p~~VvllDEieka~~-----~~~~~Ll~~ld~g~~~d~~g~~vd~  592 (731)
T TIGR02639       534 PGYVGF-EQGGLLT---EAVRK------------HPHCVLLLDEIEKAHP-----DIYNILLQVMDYATLTDNNGRKADF  592 (731)
T ss_pred             CCCccc-chhhHHH---HHHHh------------CCCeEEEEechhhcCH-----HHHHHHHHhhccCeeecCCCcccCC
Confidence            111111 1111222   22221            1346999999998753     2444566666543            


Q ss_pred             CCceEEEEecCCCCC----Cccchhh-----hhhHH-----HHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHh------
Q 005987          293 HIPTAVVLTECGKAD----SVDSTAQ-----SFEEL-----QSILVDAGARKVALNPITNGSIKRTLSKICRQE------  352 (666)
Q Consensus       293 ~~PiViIit~~~~~~----s~d~~~r-----~l~~L-----~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e------  352 (666)
                      +..+||++++.+...    ..+....     ....+     ++++.| --.+|.|+|++.+++.+++.+.+...      
T Consensus       593 ~~~iii~Tsn~g~~~~~~~~~~f~~~~~~~~~~~~~~~~f~pef~~R-id~Vi~F~pLs~e~l~~Iv~~~L~~l~~~l~~  671 (731)
T TIGR02639       593 RNVILIMTSNAGASEMSKPPIGFGSENVESKSDKAIKKLFSPEFRNR-LDAIIHFNPLSEEVLEKIVQKFVDELSKQLNE  671 (731)
T ss_pred             CCCEEEECCCcchhhhhhccCCcchhhhHHHHHHHHHhhcChHHHhc-CCeEEEcCCCCHHHHHHHHHHHHHHHHHHHHh
Confidence            123444444432110    0000000     00111     233443 23689999999999999999887631      


Q ss_pred             ---CCCCCHHHHHHHHHHc------CCcHHHHHHH
Q 005987          353 ---QYSLSTEQIDLVAQAS------GGDIRQAITS  378 (666)
Q Consensus       353 ---~i~v~~~~l~~Ia~~s------~GDIR~AIn~  378 (666)
                         .+.+++++++.|++.+      ...+|++|..
T Consensus       672 ~~~~l~i~~~a~~~La~~~~~~~~GaR~l~r~i~~  706 (731)
T TIGR02639       672 KNIKLELTDDAKKYLAEKGYDEEFGARPLARVIQE  706 (731)
T ss_pred             CCCeEEeCHHHHHHHHHhCCCcccCchHHHHHHHH
Confidence               2568999999999863      2345555543

>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=99.10  E-value=1.1e-09  Score=105.25  Aligned_cols=153  Identities=14%  Similarity=0.180  Sum_probs=82.9

Q ss_pred             cCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCchhhhhhhh----c-----
Q 005987          153 VQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTIWQEYMH----N-----  223 (666)
Q Consensus       153 g~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~~~~e~l~----~-----  223 (666)
                      ||++.++.+...++.      ++.+ +.+||+||+|+||+++|+.+|+.+...-..-.....+.....+.    .     
T Consensus         1 gq~~~~~~L~~~~~~------~~l~-ha~L~~G~~g~gk~~~a~~~a~~ll~~~~~~~~c~~c~~c~~~~~~~~~d~~~~   73 (162)
T PF13177_consen    1 GQEEIIELLKNLIKS------GRLP-HALLFHGPSGSGKKTLALAFARALLCSNPNEDPCGECRSCRRIEEGNHPDFIII   73 (162)
T ss_dssp             S-HHHHHHHHHHHHC------TC---SEEEEECSTTSSHHHHHHHHHHHHC-TT-CTT--SSSHHHHHHHTT-CTTEEEE
T ss_pred             CcHHHHHHHHHHHHc------CCcc-eeEEEECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHhccCcceEEE
Confidence            688888888888876      6777 78999999999999999999999844322100000000000000    0     


Q ss_pred             ccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcCCCceEEEEecC
Q 005987          224 CKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHIPTAVVLTEC  303 (666)
Q Consensus       224 ~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~~~PiViIit~~  303 (666)
                      ...+....-..++++++.+.+....        .....+|++|||+|.+...     .+++|++.++....-++||+...
T Consensus        74 ~~~~~~~~i~i~~ir~i~~~~~~~~--------~~~~~KviiI~~ad~l~~~-----a~NaLLK~LEepp~~~~fiL~t~  140 (162)
T PF13177_consen   74 KPDKKKKSIKIDQIREIIEFLSLSP--------SEGKYKVIIIDEADKLTEE-----AQNALLKTLEEPPENTYFILITN  140 (162)
T ss_dssp             ETTTSSSSBSHHHHHHHHHHCTSS---------TTSSSEEEEEETGGGS-HH-----HHHHHHHHHHSTTTTEEEEEEES
T ss_pred             ecccccchhhHHHHHHHHHHHHHHH--------hcCCceEEEeehHhhhhHH-----HHHHHHHHhcCCCCCEEEEEEEC
Confidence            0001100223556666655442111        1124679999999988643     34567777777654344443332


Q ss_pred             CCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCC
Q 005987          304 GKADSVDSTAQSFEELQSILVDAGARKVALNPIT  337 (666)
Q Consensus       304 ~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s  337 (666)
                             ...+.++.+++     ||..|+|++++
T Consensus       141 -------~~~~il~TI~S-----Rc~~i~~~~ls  162 (162)
T PF13177_consen  141 -------NPSKILPTIRS-----RCQVIRFRPLS  162 (162)
T ss_dssp             --------GGGS-HHHHT-----TSEEEEE----
T ss_pred             -------ChHHChHHHHh-----hceEEecCCCC
Confidence                   12345555554     69999999874

...

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

Probab=99.06  E-value=5.6e-09  Score=114.50  Aligned_cols=63  Identities=16%  Similarity=0.173  Sum_probs=48.3

Q ss_pred             cccCHHHHHHHHHHHHHhhcCC--------CCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCC
Q 005987          151 LAVQRKKVEEVRAWFEERLGDS--------KDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPT  213 (666)
Q Consensus       151 Lvg~~k~i~el~~wL~~~~~~~--------~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd  213 (666)
                      ++||+.+++.|...+.+.....        ....+...+||+||||||||++|++||+.++..++.++++.
T Consensus        73 ViGq~~ak~~l~~av~~~~~r~~~~~~~~~~~~~~~~~iLl~Gp~GtGKT~lAr~lA~~l~~pf~~id~~~  143 (412)
T PRK05342         73 VIGQERAKKVLSVAVYNHYKRLRHGDKKDDDVELQKSNILLIGPTGSGKTLLAQTLARILDVPFAIADATT  143 (412)
T ss_pred             eeChHHHHHHHHHHHHHHHHhhhcccccccccccCCceEEEEcCCCCCHHHHHHHHHHHhCCCceecchhh
Confidence            7899999999877764332211        01123367999999999999999999999999998887754

>COG0465 HflB ATP-dependent Zn proteases [Posttranslational modification, protein turnover, chaperones]

Probab=99.05  E-value=1.8e-09  Score=121.13  Aligned_cols=201  Identities=15%  Similarity=0.232  Sum_probs=124.2

Q ss_pred             CCCccccccCHHHHHHHHHHHHHh-----hcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCchhhhh
Q 005987          145 PRSLEELAVQRKKVEEVRAWFEER-----LGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTIWQE  219 (666)
Q Consensus       145 P~sl~eLvg~~k~i~el~~wL~~~-----~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~~~~e  219 (666)
                      -.+|.|++|.++..+++.+.+.--     +..-.++.| +.+||.||||+|||.+|+++|-+.+.....+..|+...+  
T Consensus       146 ~v~F~DVAG~dEakeel~EiVdfLk~p~ky~~lGakiP-kGvlLvGpPGTGKTLLAkAvAgEA~VPFf~iSGS~FVem--  222 (596)
T COG0465         146 KVTFADVAGVDEAKEELSELVDFLKNPKKYQALGAKIP-KGVLLVGPPGTGKTLLAKAVAGEAGVPFFSISGSDFVEM--  222 (596)
T ss_pred             CcChhhhcCcHHHHHHHHHHHHHHhCchhhHhcccccc-cceeEecCCCCCcHHHHHHHhcccCCCceeccchhhhhh--
Confidence            358999999888877766655421     111124555 889999999999999999999999999999888763222  


Q ss_pred             hhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcch---------hHHHHHHHHHHHHHh
Q 005987          220 YMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGR---------TAFERLRQCLLLLVR  290 (666)
Q Consensus       220 ~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~---------~~~~~l~~~L~~l~~  290 (666)
                           ..|+..    ...++.++++++.            .|+||+|||+|.+...         +..+   +.|.+++-
T Consensus       223 -----fVGvGA----sRVRdLF~qAkk~------------aP~IIFIDEiDAvGr~Rg~g~GggnderE---QTLNQlLv  278 (596)
T COG0465         223 -----FVGVGA----SRVRDLFEQAKKN------------APCIIFIDEIDAVGRQRGAGLGGGNDERE---QTLNQLLV  278 (596)
T ss_pred             -----hcCCCc----HHHHHHHHHhhcc------------CCCeEEEehhhhcccccCCCCCCCchHHH---HHHHHHHh
Confidence                 233332    2556667777654            3689999999975321         1111   22333322


Q ss_pred             c-----CCCceEEEEecCCCCCCccchhhhhhHHHHHHhhc--CeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHH
Q 005987          291 S-----THIPTAVVLTECGKADSVDSTAQSFEELQSILVDA--GARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDL  363 (666)
Q Consensus       291 ~-----~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~--r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~  363 (666)
                      .     +..++| ++++++.++-          |.+.|.|+  +-..|....|+.....++|+-.+..-.+. ++--+..
T Consensus       279 EmDGF~~~~gvi-viaaTNRpdV----------lD~ALlRpgRFDRqI~V~~PDi~gRe~IlkvH~~~~~l~-~~Vdl~~  346 (596)
T COG0465         279 EMDGFGGNEGVI-VIAATNRPDV----------LDPALLRPGRFDRQILVELPDIKGREQILKVHAKNKPLA-EDVDLKK  346 (596)
T ss_pred             hhccCCCCCceE-EEecCCCccc----------chHhhcCCCCcceeeecCCcchhhHHHHHHHHhhcCCCC-CcCCHHH
Confidence            1     123454 4555554432          33333333  24578899999999999999555443333 1122334


Q ss_pred             HHHH----cCCcHHHHHHHHHHHhc
Q 005987          364 VAQA----SGGDIRQAITSLQFSSL  384 (666)
Q Consensus       364 Ia~~----s~GDIR~AIn~LQf~~~  384 (666)
                      ||..    ++.|+-..+|---..+.
T Consensus       347 iAr~tpGfsGAdL~nl~NEAal~aa  371 (596)
T COG0465         347 IARGTPGFSGADLANLLNEAALLAA  371 (596)
T ss_pred             HhhhCCCcccchHhhhHHHHHHHHH
Confidence            6666    55677777765444443

>KOG0652 consensus 26S proteasome regulatory complex, ATPase RPT5 [Posttranslational modification, protein turnover, chaperones]

Probab=99.05  E-value=2.8e-09  Score=106.15  Aligned_cols=190  Identities=16%  Similarity=0.258  Sum_probs=108.8

Q ss_pred             CCCccccccCHHHHHHHHHHHHH------hhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCchhhh
Q 005987          145 PRSLEELAVQRKKVEEVRAWFEE------RLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTIWQ  218 (666)
Q Consensus       145 P~sl~eLvg~~k~i~el~~wL~~------~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~~~~  218 (666)
                      -.+.+|+-|-++.++++.+.+--      .+..- |-.|++.+|+|||||+|||.+|++.|.+.+..++.+..|.  ..+
T Consensus       167 tE~YsDiGGldkQIqELvEAiVLpmth~ekF~~l-gi~pPKGvLmYGPPGTGKTlmARAcAaqT~aTFLKLAgPQ--LVQ  243 (424)
T KOG0652|consen  167 TEQYSDIGGLDKQIQELVEAIVLPMTHKEKFENL-GIRPPKGVLMYGPPGTGKTLMARACAAQTNATFLKLAGPQ--LVQ  243 (424)
T ss_pred             cccccccccHHHHHHHHHHHhccccccHHHHHhc-CCCCCCceEeeCCCCCcHHHHHHHHHHhccchHHHhcchH--HHh
Confidence            35788999999999999887641      12211 3334589999999999999999999999877666655543  111


Q ss_pred             hhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcch------hHHHHHHHHHHHHHhcC
Q 005987          219 EYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGR------TAFERLRQCLLLLVRST  292 (666)
Q Consensus       219 e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~------~~~~~l~~~L~~l~~~~  292 (666)
                      -++   ..|.      .-.++.+.-++            .+.|.||+|||+|.+...      ..-+.++..++.++..-
T Consensus       244 MfI---GdGA------kLVRDAFaLAK------------EkaP~IIFIDElDAIGtKRfDSek~GDREVQRTMLELLNQL  302 (424)
T KOG0652|consen  244 MFI---GDGA------KLVRDAFALAK------------EKAPTIIFIDELDAIGTKRFDSEKAGDREVQRTMLELLNQL  302 (424)
T ss_pred             hhh---cchH------HHHHHHHHHhh------------ccCCeEEEEechhhhccccccccccccHHHHHHHHHHHHhh
Confidence            111   1111      11222222221            245789999999976321      11123444555554431


Q ss_pred             ----CCceEEEEecCCCCCCccchhhhhhHHHHHHhhcC-eeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHH
Q 005987          293 ----HIPTAVVLTECGKADSVDSTAQSFEELQSILVDAG-ARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQA  367 (666)
Q Consensus       293 ----~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r-~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~  367 (666)
                          ..--|=++..++..+..|         ..+|++-| -..|.|+-|+.+...++|+-...+..+. ++--.+.++..
T Consensus       303 DGFss~~~vKviAATNRvDiLD---------PALlRSGRLDRKIEfP~Pne~aRarIlQIHsRKMnv~-~DvNfeELaRs  372 (424)
T KOG0652|consen  303 DGFSSDDRVKVIAATNRVDILD---------PALLRSGRLDRKIEFPHPNEEARARILQIHSRKMNVS-DDVNFEELARS  372 (424)
T ss_pred             cCCCCccceEEEeecccccccC---------HHHhhcccccccccCCCCChHHHHHHHHHhhhhcCCC-CCCCHHHHhhc
Confidence                111233344444333222         12222212 3479999999998888887666555432 22234566655


Q ss_pred             c
Q 005987          368 S  368 (666)
Q Consensus       368 s  368 (666)
                      +
T Consensus       373 T  373 (424)
T KOG0652|consen  373 T  373 (424)
T ss_pred             c
Confidence            4

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

Probab=99.04  E-value=2.5e-09  Score=123.02  Aligned_cols=211  Identities=18%  Similarity=0.241  Sum_probs=147.3

Q ss_pred             CCCccccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc----------CC
Q 005987          135 TQQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL----------GA  204 (666)
Q Consensus       135 ~~~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel----------g~  204 (666)
                      .....++.-+--.++.++|+++.++++.+.|.+..+        +.-+|.|+||+|||++|.-||..+          +.
T Consensus       156 y~~dlt~~Ar~gklDPvIGRd~EI~r~iqIL~RR~K--------NNPvLiGEpGVGKTAIvEGLA~rIv~g~VP~~L~~~  227 (786)
T COG0542         156 YTRDLTELAREGKLDPVIGRDEEIRRTIQILSRRTK--------NNPVLVGEPGVGKTAIVEGLAQRIVNGDVPESLKDK  227 (786)
T ss_pred             HhhhhHHHHhcCCCCCCcChHHHHHHHHHHHhccCC--------CCCeEecCCCCCHHHHHHHHHHHHhcCCCCHHHcCC
Confidence            345577777888899999999999999999886432        467899999999999999999987          33


Q ss_pred             cEEEEcCCCchhhhhhhhcccCCccccc-hhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHH----H
Q 005987          205 RLYEWDTPTPTIWQEYMHNCKTGLEYTS-KLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAF----E  279 (666)
Q Consensus       205 ~viE~nasd~~~~~e~l~~~~~g~~~~s-~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~----~  279 (666)
                      +++.++          +.....|..|.. ..+.++.+++.+.+.            .+.||||||++.+-+...-    -
T Consensus       228 ~i~sLD----------~g~LvAGakyRGeFEeRlk~vl~ev~~~------------~~vILFIDEiHtiVGAG~~~G~a~  285 (786)
T COG0542         228 RIYSLD----------LGSLVAGAKYRGEFEERLKAVLKEVEKS------------KNVILFIDEIHTIVGAGATEGGAM  285 (786)
T ss_pred             EEEEec----------HHHHhccccccCcHHHHHHHHHHHHhcC------------CCeEEEEechhhhcCCCccccccc
Confidence            344333          223345666643 344567777776532            2679999999986443221    1


Q ss_pred             HHHHHHHHHHhcCCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHH----hCCC
Q 005987          280 RLRQCLLLLVRSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQ----EQYS  355 (666)
Q Consensus       280 ~l~~~L~~l~~~~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~----e~i~  355 (666)
                      ...+.|...+..+..  -| ++.++    ++.+.+.+++ ...|.| |++.|..+.|+.++...+|+-+..+    .++.
T Consensus       286 DAaNiLKPaLARGeL--~~-IGATT----~~EYRk~iEK-D~AL~R-RFQ~V~V~EPs~e~ti~ILrGlk~~yE~hH~V~  356 (786)
T COG0542         286 DAANLLKPALARGEL--RC-IGATT----LDEYRKYIEK-DAALER-RFQKVLVDEPSVEDTIAILRGLKERYEAHHGVR  356 (786)
T ss_pred             chhhhhHHHHhcCCe--EE-EEecc----HHHHHHHhhh-chHHHh-cCceeeCCCCCHHHHHHHHHHHHHHHHHccCce
Confidence            234567777777753  22 33332    2345556665 566776 7999999999999999999988765    4788


Q ss_pred             CCHHHHHHHHHHcCCcH------HHHHHHHHHHhc
Q 005987          356 LSTEQIDLVAQASGGDI------RQAITSLQFSSL  384 (666)
Q Consensus       356 v~~~~l~~Ia~~s~GDI------R~AIn~LQf~~~  384 (666)
                      +++++|.+.+..|..-|      .+||..|.-+|.
T Consensus       357 i~D~Al~aAv~LS~RYI~dR~LPDKAIDLiDeA~a  391 (786)
T COG0542         357 ITDEALVAAVTLSDRYIPDRFLPDKAIDLLDEAGA  391 (786)
T ss_pred             ecHHHHHHHHHHHHhhcccCCCCchHHHHHHHHHH
Confidence            99999999998875433      345555554443

>KOG0729 consensus 26S proteasome regulatory complex, ATPase RPT1 [Posttranslational modification, protein turnover, chaperones]

Probab=99.04  E-value=7.5e-10  Score=110.42  Aligned_cols=215  Identities=17%  Similarity=0.242  Sum_probs=129.3

Q ss_pred             CCccccccCCCCccccccCHHHHHHHHHHHHHhhcCC-----CCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEc
Q 005987          136 QQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDS-----KDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWD  210 (666)
Q Consensus       136 ~~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~-----~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~n  210 (666)
                      ..+-+|.-.-.+..|+-|-++.++.+++.++--+...     -|--|++.+|+|||||+|||.+|+++|+..+.-++.+.
T Consensus       164 tmm~veekpdvty~dvggckeqieklrevve~pll~perfv~lgidppkgvllygppgtgktl~aravanrtdacfirvi  243 (435)
T KOG0729|consen  164 TMMQVEEKPDVTYSDVGGCKEQIEKLREVVELPLLHPERFVNLGIDPPKGVLLYGPPGTGKTLCARAVANRTDACFIRVI  243 (435)
T ss_pred             eEEEeecCCCcccccccchHHHHHHHHHHHhccccCHHHHhhcCCCCCCceEEeCCCCCchhHHHHHHhcccCceEEeeh
Confidence            3455665555789999999999999999887433211     14445589999999999999999999999998888877


Q ss_pred             CCCchhhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcch------hHHHHHHHH
Q 005987          211 TPTPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGR------TAFERLRQC  284 (666)
Q Consensus       211 asd~~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~------~~~~~l~~~  284 (666)
                      .|.  ..++++..         .....+++++.++            .++-+||++||+|.+.+.      ..-+.++..
T Consensus       244 gse--lvqkyvge---------garmvrelf~mar------------tkkaciiffdeidaiggarfddg~ggdnevqrt  300 (435)
T KOG0729|consen  244 GSE--LVQKYVGE---------GARMVRELFEMAR------------TKKACIIFFDEIDAIGGARFDDGAGGDNEVQRT  300 (435)
T ss_pred             hHH--HHHHHhhh---------hHHHHHHHHHHhc------------ccceEEEEeeccccccCccccCCCCCcHHHHHH
Confidence            664  23333322         1223455555553            134589999999976431      112445656


Q ss_pred             HHHHHhcC-----C-CceEEEEecCCCCCCccchhhhhhHHHHHHhhcC--eeEEEeCCCCHHHHHHHHHHHHHHhCCC-
Q 005987          285 LLLLVRST-----H-IPTAVVLTECGKADSVDSTAQSFEELQSILVDAG--ARKVALNPITNGSIKRTLSKICRQEQYS-  355 (666)
Q Consensus       285 L~~l~~~~-----~-~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r--~~~I~F~p~s~~~i~kiL~~I~~~e~i~-  355 (666)
                      ++.++..-     + .--|+++++.  ++.          |...|.|++  -..|.|.-|+-+-...+++-.++...+. 
T Consensus       301 mleli~qldgfdprgnikvlmatnr--pdt----------ldpallrpgrldrkvef~lpdlegrt~i~kihaksmsver  368 (435)
T KOG0729|consen  301 MLELINQLDGFDPRGNIKVLMATNR--PDT----------LDPALLRPGRLDRKVEFGLPDLEGRTHIFKIHAKSMSVER  368 (435)
T ss_pred             HHHHHHhccCCCCCCCeEEEeecCC--CCC----------cCHhhcCCcccccceeccCCcccccceeEEEecccccccc
Confidence            66666542     1 2234555542  222          222233322  2368888887766665555443332221 


Q ss_pred             -CCHHHHHHHHH-HcCCcHHHHHHHHHHHhcC
Q 005987          356 -LSTEQIDLVAQ-ASGGDIRQAITSLQFSSLK  385 (666)
Q Consensus       356 -v~~~~l~~Ia~-~s~GDIR~AIn~LQf~~~~  385 (666)
                       +--+.|..|+- .++.+||+...-.-+++..
T Consensus       369 dir~ellarlcpnstgaeirsvcteagmfair  400 (435)
T KOG0729|consen  369 DIRFELLARLCPNSTGAEIRSVCTEAGMFAIR  400 (435)
T ss_pred             chhHHHHHhhCCCCcchHHHHHHHHhhHHHHH
Confidence             11233333332 2456889887776666653

>KOG0730 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=99.03  E-value=4.7e-09  Score=116.75  Aligned_cols=195  Identities=18%  Similarity=0.254  Sum_probs=132.5

Q ss_pred             CCCCccccccCHHHHHHHHHHHHHhhcCC-----CCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCchhhh
Q 005987          144 KPRSLEELAVQRKKVEEVRAWFEERLGDS-----KDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTIWQ  218 (666)
Q Consensus       144 ~P~sl~eLvg~~k~i~el~~wL~~~~~~~-----~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~~~~  218 (666)
                      .|-+ .++.|-...+..++..+.-.+...     -|-.+++.+|+|||||||||-+++++|++.+..++.+|.+..  ..
T Consensus       180 ~~~~-~~~gg~~~~~~~i~e~v~~pl~~~~~~~s~g~~~prg~Ll~gppg~Gkt~l~~aVa~e~~a~~~~i~~pel--i~  256 (693)
T KOG0730|consen  180 PEVG-DDIGGLKRQLSVIRELVELPLRHPALFKSIGIKPPRGLLLYGPPGTGKTFLVRAVANEYGAFLFLINGPEL--IS  256 (693)
T ss_pred             cccc-cccchhHHHHHHHHHHHHhhhcchhhhhhcCCCCCCCccccCCCCCChHHHHHHHHHHhCceeEecccHHH--HH
Confidence            5555 677787887777777766433221     133445889999999999999999999999999999998751  11


Q ss_pred             hhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcch----hH-HHHHHHHHHHHHhcCC
Q 005987          219 EYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGR----TA-FERLRQCLLLLVRSTH  293 (666)
Q Consensus       219 e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~----~~-~~~l~~~L~~l~~~~~  293 (666)
                      .+         ...+...++..++++.++.           .|.+|+|||+|.+.++    .. -.++...|+.+++.-.
T Consensus       257 k~---------~gEte~~LR~~f~~a~k~~-----------~psii~IdEld~l~p~r~~~~~~e~Rv~sqlltL~dg~~  316 (693)
T KOG0730|consen  257 KF---------PGETESNLRKAFAEALKFQ-----------VPSIIFIDELDALCPKREGADDVESRVVSQLLTLLDGLK  316 (693)
T ss_pred             hc---------ccchHHHHHHHHHHHhccC-----------CCeeEeHHhHhhhCCcccccchHHHHHHHHHHHHHhhCc
Confidence            11         1234456777778776553           2679999999987542    11 2344444666655432


Q ss_pred             -CceEEEEecCCCCCCccchhhhhhHHHHHHhh-cCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCc
Q 005987          294 -IPTAVVLTECGKADSVDSTAQSFEELQSILVD-AGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASGGD  371 (666)
Q Consensus       294 -~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r-~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~s~GD  371 (666)
                       ..-+|++..++.+++.|.          .++| +.-..+.+.-|+.+....+|+.+++..+.. ++..+..|+..+.|-
T Consensus       317 ~~~~vivl~atnrp~sld~----------alRRgRfd~ev~IgiP~~~~RldIl~~l~k~~~~~-~~~~l~~iA~~thGy  385 (693)
T KOG0730|consen  317 PDAKVIVLAATNRPDSLDP----------ALRRGRFDREVEIGIPGSDGRLDILRVLTKKMNLL-SDVDLEDIAVSTHGY  385 (693)
T ss_pred             CcCcEEEEEecCCccccCh----------hhhcCCCcceeeecCCCchhHHHHHHHHHHhcCCc-chhhHHHHHHHccch
Confidence             234555555555554332          2331 124578999999999999999999887765 678888999887775


Q ss_pred             H
Q 005987          372 I  372 (666)
Q Consensus       372 I  372 (666)
                      +
T Consensus       386 v  386 (693)
T KOG0730|consen  386 V  386 (693)
T ss_pred             h
Confidence            4

>KOG0726 consensus 26S proteasome regulatory complex, ATPase RPT2 [Posttranslational modification, protein turnover, chaperones]

Probab=99.03  E-value=5.1e-10  Score=112.95  Aligned_cols=212  Identities=17%  Similarity=0.285  Sum_probs=128.2

Q ss_pred             CCccccccCCCCccccccCHHHHHHHHHHHHHhhcCC-----CCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEc
Q 005987          136 QQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDS-----KDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWD  210 (666)
Q Consensus       136 ~~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~-----~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~n  210 (666)
                      +.+=+||-.-.+++|+-|-+..++++++.++--+...     -|--|++.++|||+||+|||.+|+++|++....++.+-
T Consensus       172 ~vmK~eKaP~Ety~diGGle~QiQEiKEsvELPLthPE~YeemGikpPKGVIlyG~PGTGKTLLAKAVANqTSATFlRvv  251 (440)
T KOG0726|consen  172 SVMKVEKAPQETYADIGGLESQIQEIKESVELPLTHPEYYEEMGIKPPKGVILYGEPGTGKTLLAKAVANQTSATFLRVV  251 (440)
T ss_pred             eeeecccCchhhhcccccHHHHHHHHHHhhcCCCCCHHHHHHcCCCCCCeeEEeCCCCCchhHHHHHHhcccchhhhhhh
Confidence            4567788888999999999999999999876332211     13344589999999999999999999999877766655


Q ss_pred             CCCchhhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcch------hHHHHHHHH
Q 005987          211 TPTPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGR------TAFERLRQC  284 (666)
Q Consensus       211 asd~~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~------~~~~~l~~~  284 (666)
                      .++  ..++++..   |      ....++++.-+..+            .|.|+||||+|.+.+.      ..-+.++..
T Consensus       252 Gse--LiQkylGd---G------pklvRqlF~vA~e~------------apSIvFiDEIdAiGtKRyds~SggerEiQrt  308 (440)
T KOG0726|consen  252 GSE--LIQKYLGD---G------PKLVRELFRVAEEH------------APSIVFIDEIDAIGTKRYDSNSGGEREIQRT  308 (440)
T ss_pred             hHH--HHHHHhcc---c------hHHHHHHHHHHHhc------------CCceEEeehhhhhccccccCCCccHHHHHHH
Confidence            443  22333322   1      12344555555433            3679999999965321      122345555


Q ss_pred             HHHHHhc-----CCCc-eEEEEecCCCCCCccchhhhhhHHHHHHhhcCe--eEEEeCCCCHHHHHHHHHHHHHHhCCCC
Q 005987          285 LLLLVRS-----THIP-TAVVLTECGKADSVDSTAQSFEELQSILVDAGA--RKVALNPITNGSIKRTLSKICRQEQYSL  356 (666)
Q Consensus       285 L~~l~~~-----~~~P-iViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~--~~I~F~p~s~~~i~kiL~~I~~~e~i~v  356 (666)
                      ++.++..     ++.- -||++++            .++.|...|-|+++  ..|.|.-|+...-++++.-...+  ..+
T Consensus       309 mLELLNQldGFdsrgDvKvimATn------------rie~LDPaLiRPGrIDrKIef~~pDe~TkkkIf~IHTs~--Mtl  374 (440)
T KOG0726|consen  309 MLELLNQLDGFDSRGDVKVIMATN------------RIETLDPALIRPGRIDRKIEFPLPDEKTKKKIFQIHTSR--MTL  374 (440)
T ss_pred             HHHHHHhccCccccCCeEEEEecc------------cccccCHhhcCCCccccccccCCCchhhhceeEEEeecc--cch
Confidence            6665543     2222 3455554            23335555555543  36899988877766665432222  122


Q ss_pred             CHH-HHHHHH----HHcCCcHHHHHHHHHHHhc
Q 005987          357 STE-QIDLVA----QASGGDIRQAITSLQFSSL  384 (666)
Q Consensus       357 ~~~-~l~~Ia----~~s~GDIR~AIn~LQf~~~  384 (666)
                      .++ .++.++    +.|+.||.....-.-++|+
T Consensus       375 ~~dVnle~li~~kddlSGAdIkAictEaGllAl  407 (440)
T KOG0726|consen  375 AEDVNLEELIMTKDDLSGADIKAICTEAGLLAL  407 (440)
T ss_pred             hccccHHHHhhcccccccccHHHHHHHHhHHHH
Confidence            211 133333    3477777766555555554

>TIGR01650 PD_CobS cobaltochelatase, CobS subunit

Probab=99.03  E-value=3.7e-09  Score=111.37  Aligned_cols=207  Identities=13%  Similarity=0.121  Sum_probs=113.2

Q ss_pred             cCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCchhhhhhhh
Q 005987          143 YKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTIWQEYMH  222 (666)
Q Consensus       143 Y~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~~~~e~l~  222 (666)
                      |.|..-.+.+.++.....|..|+..      +    +.+||.||||||||++++.+|+.+++.++.++........+.+.
T Consensus        39 ~~p~~d~~y~f~~~~~~~vl~~l~~------~----~~ilL~G~pGtGKTtla~~lA~~l~~~~~rV~~~~~l~~~DliG  108 (327)
T TIGR01650        39 HVPDIDPAYLFDKATTKAICAGFAY------D----RRVMVQGYHGTGKSTHIEQIAARLNWPCVRVNLDSHVSRIDLVG  108 (327)
T ss_pred             CCCCCCCCccCCHHHHHHHHHHHhc------C----CcEEEEeCCCChHHHHHHHHHHHHCCCeEEEEecCCCChhhcCC
Confidence            4455555677888888888887753      1    47999999999999999999999999999998765332222222


Q ss_pred             cccCCccccchhHHHH-HHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHH---H-H-hcC----
Q 005987          223 NCKTGLEYTSKLDEFE-NFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLL---L-V-RST----  292 (666)
Q Consensus       223 ~~~~g~~~~s~~~~f~-~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~---l-~-~~~----  292 (666)
                      .....+.-......|+ ..+..+             ...+.++|+||++..... ....++.+|..   + + +.+    
T Consensus       109 ~~~~~l~~g~~~~~f~~GpL~~A-------------~~~g~illlDEin~a~p~-~~~~L~~lLE~~~~l~i~~~~~~i~  174 (327)
T TIGR01650       109 KDAIVLKDGKQITEFRDGILPWA-------------LQHNVALCFDEYDAGRPD-VMFVIQRVLEAGGKLTLLDQNRVIR  174 (327)
T ss_pred             CceeeccCCcceeEEecCcchhH-------------HhCCeEEEechhhccCHH-HHHHHHHHhccCCeEEECCCceEec
Confidence            1100000000000010 011111             123568999999976543 22333333321   0 0 111    


Q ss_pred             CCceEEEEecCCCCCCccc---hhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcC
Q 005987          293 HIPTAVVLTECGKADSVDS---TAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASG  369 (666)
Q Consensus       293 ~~PiViIit~~~~~~s~d~---~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~s~  369 (666)
                      ..|-+.++.+.|..++.|.   +.-....-.+.+.| .+.++.+..++.+.-.++|...+....-..+++.++.+++.. 
T Consensus       175 ~hp~FrviAT~Np~g~Gd~~G~y~Gt~~l~~A~lDR-F~i~~~~~Yp~~e~E~~Il~~~~~~~~~~~~~~i~~~mV~la-  252 (327)
T TIGR01650       175 AHPAFRLFATANTIGLGDTTGLYHGTQQINQAQMDR-WSIVTTLNYLEHDNEAAIVLAKAKGFDDTEGKDIINAMVRVA-  252 (327)
T ss_pred             CCCCeEEEEeeCCCCcCCCCcceeeeecCCHHHHhh-eeeEeeCCCCCHHHHHHHHHhhccCCCccchHHHHHHHHHHH-
Confidence            1244545555554433332   11111111344444 234678999999999999887643211112356777777765 


Q ss_pred             CcHHHH
Q 005987          370 GDIRQA  375 (666)
Q Consensus       370 GDIR~A  375 (666)
                      ..+|.+
T Consensus       253 ~~tR~~  258 (327)
T TIGR01650       253 DMTRNA  258 (327)
T ss_pred             HHHHhh
Confidence            555653

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.

>PRK06090 DNA polymerase III subunit delta'; Validated

Probab=99.03  E-value=1.5e-08  Score=107.42  Aligned_cols=186  Identities=10%  Similarity=0.120  Sum_probs=110.3

Q ss_pred             CHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCchhhhhhhhc-ccCCc----
Q 005987          154 QRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTIWQEYMHN-CKTGL----  228 (666)
Q Consensus       154 ~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~~~~e~l~~-~~~g~----  228 (666)
                      +....+.+...+..      ++.+ +.+||+||.|+||+++|+.+|+.+-+.-..-.+...+.....+.+ .....    
T Consensus         8 l~~~~~~l~~~~~~------~rl~-hA~L~~G~~G~Gk~~lA~~~a~~llC~~~~~~~Cg~C~sC~~~~~g~HPD~~~i~   80 (319)
T PRK06090          8 LVPVWQNWKAGLDA------GRIP-GALLLQSDEGLGVESLVELFSRALLCQNYQSEACGFCHSCELMQSGNHPDLHVIK   80 (319)
T ss_pred             HHHHHHHHHHHHHc------CCcc-eeEeeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHcCCCCCEEEEe
Confidence            34445556665554      6776 789999999999999999999998553211001001110110000 00000    


Q ss_pred             ----cccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcCCCceEEEEecCC
Q 005987          229 ----EYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHIPTAVVLTECG  304 (666)
Q Consensus       229 ----~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~~~PiViIit~~~  304 (666)
                          .-.-.+++++++.+.+....        ..+..+|+|||+++.++..     ..++|++.++....-++||....+
T Consensus        81 p~~~~~~I~vdqiR~l~~~~~~~~--------~~~~~kV~iI~~ae~m~~~-----AaNaLLKtLEEPp~~t~fiL~t~~  147 (319)
T PRK06090         81 PEKEGKSITVEQIRQCNRLAQESS--------QLNGYRLFVIEPADAMNES-----ASNALLKTLEEPAPNCLFLLVTHN  147 (319)
T ss_pred             cCcCCCcCCHHHHHHHHHHHhhCc--------ccCCceEEEecchhhhCHH-----HHHHHHHHhcCCCCCeEEEEEECC
Confidence                00123456665554442211        1123579999999988643     334567777776544444443321


Q ss_pred             CCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCcHHHHHHHH
Q 005987          305 KADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASGGDIRQAITSL  379 (666)
Q Consensus       305 ~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~s~GDIR~AIn~L  379 (666)
                             ..+.++.|++     ||..+.|.+++.+++...|..    +++.    ....++..++|.+..|+..+
T Consensus       148 -------~~~lLpTI~S-----RCq~~~~~~~~~~~~~~~L~~----~~~~----~~~~~l~l~~G~p~~A~~~~  202 (319)
T PRK06090        148 -------QKRLLPTIVS-----RCQQWVVTPPSTAQAMQWLKG----QGIT----VPAYALKLNMGSPLKTLAMM  202 (319)
T ss_pred             -------hhhChHHHHh-----cceeEeCCCCCHHHHHHHHHH----cCCc----hHHHHHHHcCCCHHHHHHHh
Confidence                   2345555554     699999999999999988864    3433    23466788999999887654

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

Probab=99.03  E-value=2.8e-09  Score=118.83  Aligned_cols=202  Identities=13%  Similarity=0.160  Sum_probs=118.1

Q ss_pred             cCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCchhhhhhhhcccCCccccc
Q 005987          153 VQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTIWQEYMHNCKTGLEYTS  232 (666)
Q Consensus       153 g~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~~~~e~l~~~~~g~~~~s  232 (666)
                      |-++..++|.++|.=.  .-+|...+++|.|+||||+|||++++.+|+.||-+++.+.-...+...+.-....  ..+..
T Consensus       415 gm~dVKeRILEfiAV~--kLrgs~qGkIlCf~GPPGVGKTSI~kSIA~ALnRkFfRfSvGG~tDvAeIkGHRR--TYVGA  490 (906)
T KOG2004|consen  415 GMEDVKERILEFIAVG--KLRGSVQGKILCFVGPPGVGKTSIAKSIARALNRKFFRFSVGGMTDVAEIKGHRR--TYVGA  490 (906)
T ss_pred             chHHHHHHHHHHHHHH--hhcccCCCcEEEEeCCCCCCcccHHHHHHHHhCCceEEEeccccccHHhhcccce--eeecc
Confidence            4567777888887532  2235666689999999999999999999999999988876433222222111100  11112


Q ss_pred             hhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcC----------CCc-----eE
Q 005987          233 KLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRST----------HIP-----TA  297 (666)
Q Consensus       233 ~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~----------~~P-----iV  297 (666)
                      ....+-+-+.++   +.          ...++||||+|.+... ..+.-..+|+.+++..          ..|     ++
T Consensus       491 MPGkiIq~LK~v---~t----------~NPliLiDEvDKlG~g-~qGDPasALLElLDPEQNanFlDHYLdVp~DLSkVL  556 (906)
T KOG2004|consen  491 MPGKIIQCLKKV---KT----------ENPLILIDEVDKLGSG-HQGDPASALLELLDPEQNANFLDHYLDVPVDLSKVL  556 (906)
T ss_pred             CChHHHHHHHhh---CC----------CCceEEeehhhhhCCC-CCCChHHHHHHhcChhhccchhhhccccccchhheE
Confidence            222333333332   21          1238999999976421 1111122343333221          112     56


Q ss_pred             EEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHH----------hCCCCCHHHHHHHHHH
Q 005987          298 VVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQ----------EQYSLSTEQIDLVAQA  367 (666)
Q Consensus       298 iIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~----------e~i~v~~~~l~~Ia~~  367 (666)
                      ||||+-.       .....++|+.     |...|.+.-+..++-.++.++.+..          +.++++++++..|++.
T Consensus       557 FicTAN~-------idtIP~pLlD-----RMEvIelsGYv~eEKv~IA~~yLip~a~~~~gl~~e~v~is~~al~~lI~~  624 (906)
T KOG2004|consen  557 FICTANV-------IDTIPPPLLD-----RMEVIELSGYVAEEKVKIAERYLIPQALKDCGLKPEQVKISDDALLALIER  624 (906)
T ss_pred             EEEeccc-------cccCChhhhh-----hhheeeccCccHHHHHHHHHHhhhhHHHHHcCCCHHhcCccHHHHHHHHHH
Confidence            6666521       1122233333     5889999999999888776665432          4577899998888866


Q ss_pred             cC--CcHHHHHHHHHHHhc
Q 005987          368 SG--GDIRQAITSLQFSSL  384 (666)
Q Consensus       368 s~--GDIR~AIn~LQf~~~  384 (666)
                      ..  --+|+.-.+++-+|.
T Consensus       625 YcrEaGVRnLqk~iekI~R  643 (906)
T KOG2004|consen  625 YCREAGVRNLQKQIEKICR  643 (906)
T ss_pred             HHHHHhHHHHHHHHHHHHH
Confidence            21  336766666666654

>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN

Probab=99.02  E-value=1.1e-08  Score=106.12  Aligned_cols=168  Identities=11%  Similarity=0.136  Sum_probs=89.8

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCchhhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCC------C
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTS------P  252 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~------~  252 (666)
                      +.+||+||||||||++|+.+|+.+|..++.+++.......+.+... .+....   ..+..|+....+.....      +
T Consensus        22 ~~vLL~G~~GtGKT~lA~~la~~lg~~~~~i~~~~~~~~~dllg~~-~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~g   97 (262)
T TIGR02640        22 YPVHLRGPAGTGKTTLAMHVARKRDRPVMLINGDAELTTSDLVGSY-AGYTRK---KVHDQFIHNVVKLEDIVRQNWVDN   97 (262)
T ss_pred             CeEEEEcCCCCCHHHHHHHHHHHhCCCEEEEeCCccCCHHHHhhhh-cccchh---hHHHHHHHHhhhhhcccceeecCc
Confidence            4699999999999999999999999999998876533222222211 110000   11112222111110000      0


Q ss_pred             CCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcCC----------------Cc-eEEEEecCCCCCCccchhhh
Q 005987          253 SIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTH----------------IP-TAVVLTECGKADSVDSTAQS  315 (666)
Q Consensus       253 s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~~----------------~P-iViIit~~~~~~s~d~~~r~  315 (666)
                      ........+.+|+|||++.+...     .+..|..+++...                .+ .||++++...     +.  .
T Consensus        98 ~l~~A~~~g~~lllDEi~r~~~~-----~q~~Ll~~Le~~~~~i~~~~~~~~~i~~~~~frvIaTsN~~~-----~~--g  165 (262)
T TIGR02640        98 RLTLAVREGFTLVYDEFTRSKPE-----TNNVLLSVFEEGVLELPGKRGTSRYVDVHPEFRVIFTSNPVE-----YA--G  165 (262)
T ss_pred             hHHHHHHcCCEEEEcchhhCCHH-----HHHHHHHHhcCCeEEccCCCCCCceEecCCCCEEEEeeCCcc-----cc--c
Confidence            00000012358999999987542     2333444443321                02 2333333211     00  0


Q ss_pred             hhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHc
Q 005987          316 FEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQAS  368 (666)
Q Consensus       316 l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~s  368 (666)
                      ...+...|.+ ||..+.+..|+.++..++|...+     .++++.++.|+...
T Consensus       166 ~~~l~~aL~~-R~~~i~i~~P~~~~e~~Il~~~~-----~~~~~~~~~iv~~~  212 (262)
T TIGR02640       166 VHETQDALLD-RLITIFMDYPDIDTETAILRAKT-----DVAEDSAATIVRLV  212 (262)
T ss_pred             eecccHHHHh-hcEEEECCCCCHHHHHHHHHHhh-----CCCHHHHHHHHHHH
Confidence            0112233333 58899999999999998888653     46777777777653

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).

>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=99.02  E-value=6e-09  Score=104.90  Aligned_cols=198  Identities=16%  Similarity=0.317  Sum_probs=101.6

Q ss_pred             cccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCC---cEEEEcCCCchhh---hhh----
Q 005987          151 LAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGA---RLYEWDTPTPTIW---QEY----  220 (666)
Q Consensus       151 Lvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~---~viE~nasd~~~~---~e~----  220 (666)
                      ++|+++.++.|.+++..      +.  .+.++|+||.|+|||++++.+.+.+.-   .++.+........   ...    
T Consensus         1 F~gR~~el~~l~~~l~~------~~--~~~~~l~G~rg~GKTsLl~~~~~~~~~~~~~~~y~~~~~~~~~~~~~~~~~~~   72 (234)
T PF01637_consen    1 FFGREKELEKLKELLES------GP--SQHILLYGPRGSGKTSLLKEFINELKEKGYKVVYIDFLEESNESSLRSFIEET   72 (234)
T ss_dssp             S-S-HHHHHHHHHCHHH----------SSEEEEEESTTSSHHHHHHHHHHHCT--EECCCHHCCTTBSHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHh------hc--CcEEEEEcCCcCCHHHHHHHHHHHhhhcCCcEEEEecccchhhhHHHHHHHHH
Confidence            36899999999999886      22  258999999999999999999998822   2222222221110   000    


Q ss_pred             ---------hhcccCCcc--------ccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCc-chhHHHHHH
Q 005987          221 ---------MHNCKTGLE--------YTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTN-GRTAFERLR  282 (666)
Q Consensus       221 ---------l~~~~~g~~--------~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~-~~~~~~~l~  282 (666)
                               +.....+..        .......+..+++.+.+.+           .+.||+|||++.+. .......+.
T Consensus        73 ~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~-----------~~~iiviDe~~~~~~~~~~~~~~~  141 (234)
T PF01637_consen   73 SLADELSEALGISIPSITLEKISKDLSEDSFSALERLLEKLKKKG-----------KKVIIVIDEFQYLAIASEEDKDFL  141 (234)
T ss_dssp             HHHCHCHHHHHHHCCTSTTEEEECTS-GG-G--HHHHHHHHHHCH-----------CCEEEEEETGGGGGBCTTTTHHHH
T ss_pred             HHHHHHHHHHhhhcccccchhhhhcchhhHHHHHHHHHHHHHhcC-----------CcEEEEEecHHHHhhcccchHHHH
Confidence                     111111100        0122344556666665432           23799999999876 211112233


Q ss_pred             HHHHHHHhc--CCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCC--CH
Q 005987          283 QCLLLLVRS--THIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSL--ST  358 (666)
Q Consensus       283 ~~L~~l~~~--~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v--~~  358 (666)
                      ..|..++..  ...++.+|++.+...    ........-.....  ++..+.+.|++.++..+.+....... ..+  ++
T Consensus       142 ~~l~~~~~~~~~~~~~~~v~~~S~~~----~~~~~~~~~~~~~~--~~~~~~l~~l~~~e~~~~~~~~~~~~-~~~~~~~  214 (234)
T PF01637_consen  142 KSLRSLLDSLLSQQNVSIVITGSSDS----LMEEFLDDKSPLFG--RFSHIELKPLSKEEAREFLKELFKEL-IKLPFSD  214 (234)
T ss_dssp             HHHHHHHHH----TTEEEEEEESSHH----HHHHTT-TTSTTTT-----EEEE----HHHHHHHHHHHHHCC-------H
T ss_pred             HHHHHHHhhccccCCceEEEECCchH----HHHHhhcccCcccc--ccceEEEeeCCHHHHHHHHHHHHHHh-hcccCCH
Confidence            334444443  122233333322100    00000000011122  35669999999999999999987665 555  99


Q ss_pred             HHHHHHHHHcCCcHHH
Q 005987          359 EQIDLVAQASGGDIRQ  374 (666)
Q Consensus       359 ~~l~~Ia~~s~GDIR~  374 (666)
                      +.++.|...++|-.+.
T Consensus       215 ~~~~~i~~~~gG~P~~  230 (234)
T PF01637_consen  215 EDIEEIYSLTGGNPRY  230 (234)
T ss_dssp             HHHHHHHHHHTT-HHH
T ss_pred             HHHHHHHHHhCCCHHH
Confidence            9999999999998874

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

>KOG0742 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=99.01  E-value=5.4e-09  Score=109.88  Aligned_cols=172  Identities=17%  Similarity=0.199  Sum_probs=102.7

Q ss_pred             CCC-ccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCchhhhhhhhc
Q 005987          145 PRS-LEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTIWQEYMHN  223 (666)
Q Consensus       145 P~s-l~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~~~~e~l~~  223 (666)
                      ++. +++++.|+..-..|......-......+.+.+.+|||||||+|||..|+-||+.-|.++--+...|..        
T Consensus       350 gk~pl~~ViL~psLe~Rie~lA~aTaNTK~h~apfRNilfyGPPGTGKTm~ArelAr~SGlDYA~mTGGDVA--------  421 (630)
T KOG0742|consen  350 GKDPLEGVILHPSLEKRIEDLAIATANTKKHQAPFRNILFYGPPGTGKTMFARELARHSGLDYAIMTGGDVA--------  421 (630)
T ss_pred             CCCCcCCeecCHHHHHHHHHHHHHhcccccccchhhheeeeCCCCCCchHHHHHHHhhcCCceehhcCCCcc--------
Confidence            444 88899999888888877654333223455668999999999999999999999999887766654411        


Q ss_pred             ccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCc-ch---hHHHHHHHHHHHHH----hcCCCc
Q 005987          224 CKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTN-GR---TAFERLRQCLLLLV----RSTHIP  295 (666)
Q Consensus       224 ~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~-~~---~~~~~l~~~L~~l~----~~~~~P  295 (666)
                       ..|   ...+..+.++++=+++           +++..+|||||+|-.- .+   --.+..+.+|..++    +.++- 
T Consensus       422 -PlG---~qaVTkiH~lFDWakk-----------S~rGLllFIDEADAFLceRnktymSEaqRsaLNAlLfRTGdqSrd-  485 (630)
T KOG0742|consen  422 -PLG---AQAVTKIHKLFDWAKK-----------SRRGLLLFIDEADAFLCERNKTYMSEAQRSALNALLFRTGDQSRD-  485 (630)
T ss_pred             -ccc---hHHHHHHHHHHHHHhh-----------cccceEEEehhhHHHHHHhchhhhcHHHHHHHHHHHHHhcccccc-
Confidence             011   1122344444444432           2456799999999421 00   00011122233222    22232 


Q ss_pred             eEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHH
Q 005987          296 TAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQ  351 (666)
Q Consensus       296 iViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~  351 (666)
                      +|+++ .++.+.          .+.+.+..+--.+|.|+-|..++..++|...+.+
T Consensus       486 ivLvl-AtNrpg----------dlDsAV~DRide~veFpLPGeEERfkll~lYlnk  530 (630)
T KOG0742|consen  486 IVLVL-ATNRPG----------DLDSAVNDRIDEVVEFPLPGEEERFKLLNLYLNK  530 (630)
T ss_pred             eEEEe-ccCCcc----------chhHHHHhhhhheeecCCCChHHHHHHHHHHHHH
Confidence            33332 223222          2333333323568999999999999998877654

>KOG0740 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=98.97  E-value=1.2e-08  Score=110.44  Aligned_cols=244  Identities=15%  Similarity=0.154  Sum_probs=145.9

Q ss_pred             cccCCCCccccccCHHHHHHHHHHHH------HhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCc
Q 005987          141 EKYKPRSLEELAVQRKKVEEVRAWFE------ERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTP  214 (666)
Q Consensus       141 eKY~P~sl~eLvg~~k~i~el~~wL~------~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~  214 (666)
                      +.-++-.++|++|-+...+.+...+.      ..+.  .-+.+.+.+||.||||+|||.+++++|-|.+..+..+.++.-
T Consensus       145 ~~~~~v~~~di~gl~~~k~~l~e~vi~p~lr~d~F~--glr~p~rglLLfGPpgtGKtmL~~aiAsE~~atff~iSassL  222 (428)
T KOG0740|consen  145 DTLRNVGWDDIAGLEDAKQSLKEAVILPLLRPDLFL--GLREPVRGLLLFGPPGTGKTMLAKAIATESGATFFNISASSL  222 (428)
T ss_pred             ccCCcccccCCcchhhHHHHhhhhhhhcccchHhhh--ccccccchhheecCCCCchHHHHHHHHhhhcceEeeccHHHh
Confidence            55566778888886555555544432      1111  123345789999999999999999999999999998887651


Q ss_pred             hhhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcch------hHHHHHH-HHHHH
Q 005987          215 TIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGR------TAFERLR-QCLLL  287 (666)
Q Consensus       215 ~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~------~~~~~l~-~~L~~  287 (666)
                        ..++     .|    .....++.++.-++.            ..|.||+|||+|.+...      ..-.+++ +.|..
T Consensus       223 --tsK~-----~G----e~eK~vralf~vAr~------------~qPsvifidEidslls~Rs~~e~e~srr~ktefLiq  279 (428)
T KOG0740|consen  223 --TSKY-----VG----ESEKLVRALFKVARS------------LQPSVIFIDEIDSLLSKRSDNEHESSRRLKTEFLLQ  279 (428)
T ss_pred             --hhhc-----cC----hHHHHHHHHHHHHHh------------cCCeEEEechhHHHHhhcCCcccccchhhhhHHHhh
Confidence              1111     11    112233333333332            24679999999975321      1112232 22332


Q ss_pred             HHh--cCCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHH
Q 005987          288 LVR--STHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVA  365 (666)
Q Consensus       288 l~~--~~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia  365 (666)
                      ..-  ....+.|+++++++.+...          ...+.|+....+.++.|+.+....++...+...+..+.+..+..|+
T Consensus       280 ~~~~~s~~~drvlvigaTN~P~e~----------Dea~~Rrf~kr~yiplPd~etr~~~~~~ll~~~~~~l~~~d~~~l~  349 (428)
T KOG0740|consen  280 FDGKNSAPDDRVLVIGATNRPWEL----------DEAARRRFVKRLYIPLPDYETRSLLWKQLLKEQPNGLSDLDISLLA  349 (428)
T ss_pred             hccccCCCCCeEEEEecCCCchHH----------HHHHHHHhhceeeecCCCHHHHHHHHHHHHHhCCCCccHHHHHHHH
Confidence            221  1223577888887755432          2223232355678999999999999999998887788889999999


Q ss_pred             HH----cCCcHHHHHHHHHHHhcCCCCcccccccCCCCCCCccccCCCCCcccccCCccccchHHHHhHHhhCC
Q 005987          366 QA----SGGDIRQAITSLQFSSLKQDPMLNLSLSISKPNFPEEKADGHGGFSIQFGRDETLSLFHALGKFLHNK  435 (666)
Q Consensus       366 ~~----s~GDIR~AIn~LQf~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~~~~~RD~~l~lFhalGkil~~K  435 (666)
                      +.    ++|||.+...-.   ++++......        .     .....+....-|..++.-|....+.++++
T Consensus       350 ~~Tegysgsdi~~l~kea---~~~p~r~~~~--------~-----~~~~~~~~~~~r~i~~~df~~a~~~i~~~  407 (428)
T KOG0740|consen  350 KVTEGYSGSDITALCKEA---AMGPLRELGG--------T-----TDLEFIDADKIRPITYPDFKNAFKNIKPS  407 (428)
T ss_pred             HHhcCcccccHHHHHHHh---hcCchhhccc--------c-----hhhhhcchhccCCCCcchHHHHHHhhccc
Confidence            87    556777655443   2222111110        0     00011122345777777888888777765

>CHL00095 clpC Clp protease ATP binding subunit

Probab=98.97  E-value=2.6e-08  Score=118.99  Aligned_cols=205  Identities=15%  Similarity=0.230  Sum_probs=119.7

Q ss_pred             cccccCHHHHHHHHHHHHHhhcC--CCCCCCccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcCCCchh---hhhh
Q 005987          149 EELAVQRKKVEEVRAWFEERLGD--SKDKFSTNVLVITGQAGVGKTATVRQIASHL---GARLYEWDTPTPTI---WQEY  220 (666)
Q Consensus       149 ~eLvg~~k~i~el~~wL~~~~~~--~~g~~~~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~nasd~~~---~~e~  220 (666)
                      +.|+||+..++.|...+......  .++++ ...+||+||+|||||++|++||+.+   +..++.++.+....   ....
T Consensus       509 ~~v~GQ~~ai~~l~~~i~~~~~gl~~~~~p-~~~~lf~Gp~GvGKt~lA~~LA~~l~~~~~~~~~~d~s~~~~~~~~~~l  587 (821)
T CHL00095        509 KRIIGQDEAVVAVSKAIRRARVGLKNPNRP-IASFLFSGPTGVGKTELTKALASYFFGSEDAMIRLDMSEYMEKHTVSKL  587 (821)
T ss_pred             CcCcChHHHHHHHHHHHHHHhhcccCCCCC-ceEEEEECCCCCcHHHHHHHHHHHhcCCccceEEEEchhccccccHHHh
Confidence            45789999999999998754331  11222 2468999999999999999999998   34567776654211   0111


Q ss_pred             hhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcC--------
Q 005987          221 MHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRST--------  292 (666)
Q Consensus       221 l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~--------  292 (666)
                      +......+.|. ....+.   +.++.            ++..||||||++.++.     .+++.|+.+++.+        
T Consensus       588 ~g~~~gyvg~~-~~~~l~---~~~~~------------~p~~VvllDeieka~~-----~v~~~Llq~le~g~~~d~~g~  646 (821)
T CHL00095        588 IGSPPGYVGYN-EGGQLT---EAVRK------------KPYTVVLFDEIEKAHP-----DIFNLLLQILDDGRLTDSKGR  646 (821)
T ss_pred             cCCCCcccCcC-ccchHH---HHHHh------------CCCeEEEECChhhCCH-----HHHHHHHHHhccCceecCCCc
Confidence            11110011111 111222   22221            1346999999997753     2445566666653        


Q ss_pred             ----CCceEEEEecCCCC------CCc----------c-chhh---h-hhHH-----HHHHhhcCe-eEEEeCCCCHHHH
Q 005987          293 ----HIPTAVVLTECGKA------DSV----------D-STAQ---S-FEEL-----QSILVDAGA-RKVALNPITNGSI  341 (666)
Q Consensus       293 ----~~PiViIit~~~~~------~s~----------d-~~~r---~-l~~L-----~s~L~r~r~-~~I~F~p~s~~~i  341 (666)
                          +..+||++++.+..      ...          + .+..   . ...+     +++++|  + .+|.|+|++.+++
T Consensus       647 ~v~~~~~i~I~Tsn~g~~~i~~~~~~~gf~~~~~~~~~~~~~~~~~~~~~~~~~~f~peflnR--id~ii~F~pL~~~~l  724 (821)
T CHL00095        647 TIDFKNTLIIMTSNLGSKVIETNSGGLGFELSENQLSEKQYKRLSNLVNEELKQFFRPEFLNR--LDEIIVFRQLTKNDV  724 (821)
T ss_pred             EEecCceEEEEeCCcchHHHHhhccccCCcccccccccccHHHHHHHHHHHHHHhcCHHHhcc--CCeEEEeCCCCHHHH
Confidence                22355555554321      000          0 0000   0 0011     244544  5 7899999999999


Q ss_pred             HHHHHHHHHH-------h--CCCCCHHHHHHHHHHc------CCcHHHHHH
Q 005987          342 KRTLSKICRQ-------E--QYSLSTEQIDLVAQAS------GGDIRQAIT  377 (666)
Q Consensus       342 ~kiL~~I~~~-------e--~i~v~~~~l~~Ia~~s------~GDIR~AIn  377 (666)
                      .+++.+.+..       .  .+.+++++++.|++.+      ...+|++|.
T Consensus       725 ~~Iv~~~l~~l~~rl~~~~i~l~~~~~~~~~La~~~~~~~~GAR~l~r~i~  775 (821)
T CHL00095        725 WEIAEIMLKNLFKRLNEQGIQLEVTERIKTLLIEEGYNPLYGARPLRRAIM  775 (821)
T ss_pred             HHHHHHHHHHHHHHHHHCCcEEEECHHHHHHHHHhcCCCCCChhhHHHHHH
Confidence            9998887764       1  2568999999999873      235666664

>KOG0744 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=98.96  E-value=8.5e-09  Score=105.80  Aligned_cols=172  Identities=19%  Similarity=0.307  Sum_probs=95.3

Q ss_pred             cccccCHHHHHHHHHHHHHhhcCCCCC------CCccEEEEECCCCchHHHHHHHHHHHcC---------CcEEEEcCCC
Q 005987          149 EELAVQRKKVEEVRAWFEERLGDSKDK------FSTNVLVITGQAGVGKTATVRQIASHLG---------ARLYEWDTPT  213 (666)
Q Consensus       149 ~eLvg~~k~i~el~~wL~~~~~~~~g~------~~~k~LLL~GPpG~GKTtla~~LAkelg---------~~viE~nasd  213 (666)
                      +.|+......++|..+....+.-...+      .-.+.+||+||||+|||++.++||+.+.         ..++|+|+-.
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            345555556666666655433211000      1137899999999999999999999983         3567887643


Q ss_pred             chhhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcc-----------hhHHHHHH
Q 005987          214 PTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNG-----------RTAFERLR  282 (666)
Q Consensus       214 ~~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~-----------~~~~~~l~  282 (666)
                        .+.+.+...  |.-+.   ..|+++-+-+..           .+.-++++|||+..+..           .++.+ +.
T Consensus       222 --LFSKWFsES--gKlV~---kmF~kI~ELv~d-----------~~~lVfvLIDEVESLa~aR~s~~S~~EpsDaIR-vV  282 (423)
T KOG0744|consen  222 --LFSKWFSES--GKLVA---KMFQKIQELVED-----------RGNLVFVLIDEVESLAAARTSASSRNEPSDAIR-VV  282 (423)
T ss_pred             --HHHHHHhhh--hhHHH---HHHHHHHHHHhC-----------CCcEEEEEeHHHHHHHHHHHhhhcCCCCchHHH-HH
Confidence              444444321  22111   123332222221           12347899999986421           22333 33


Q ss_pred             HHHHHHHh-cCCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHH
Q 005987          283 QCLLLLVR-STHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKIC  349 (666)
Q Consensus       283 ~~L~~l~~-~~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~  349 (666)
                      ++++.-++ -.++|-|+|.++.+..+          .|.-.+..+---+....||+...+.++|+.-.
T Consensus       283 NalLTQlDrlK~~~NvliL~TSNl~~----------siD~AfVDRADi~~yVG~Pt~~ai~~Ilksci  340 (423)
T KOG0744|consen  283 NALLTQLDRLKRYPNVLILATSNLTD----------SIDVAFVDRADIVFYVGPPTAEAIYEILKSCI  340 (423)
T ss_pred             HHHHHHHHHhccCCCEEEEeccchHH----------HHHHHhhhHhhheeecCCccHHHHHHHHHHHH
Confidence            44444333 34568777777655332          22222222112345678999998888887544

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

Probab=98.95  E-value=8.3e-09  Score=115.85  Aligned_cols=203  Identities=14%  Similarity=0.151  Sum_probs=115.8

Q ss_pred             cCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCchhhhhhhhcccCCccccc
Q 005987          153 VQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTIWQEYMHNCKTGLEYTS  232 (666)
Q Consensus       153 g~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~~~~e~l~~~~~g~~~~s  232 (666)
                      |-++..++|.++|.-....  ++..+.+|+|.||||+|||++++.+|+.+|-+++.+.-...+.-.|.-+.-.  ....+
T Consensus       327 GLekVKeRIlEyLAV~~l~--~~~kGpILcLVGPPGVGKTSLgkSIA~al~RkfvR~sLGGvrDEAEIRGHRR--TYIGa  402 (782)
T COG0466         327 GLEKVKERILEYLAVQKLT--KKLKGPILCLVGPPGVGKTSLGKSIAKALGRKFVRISLGGVRDEAEIRGHRR--TYIGA  402 (782)
T ss_pred             CchhHHHHHHHHHHHHHHh--ccCCCcEEEEECCCCCCchhHHHHHHHHhCCCEEEEecCccccHHHhccccc--ccccc
Confidence            5577788888887632211  3333469999999999999999999999999999887543332222211100  11122


Q ss_pred             hhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcch---hHHHHHHHHHHHHHhcC------C-----CceEE
Q 005987          233 KLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGR---TAFERLRQCLLLLVRST------H-----IPTAV  298 (666)
Q Consensus       233 ~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~---~~~~~l~~~L~~l~~~~------~-----~PiVi  298 (666)
                      ....+   ++.+++.+.          ...+++|||+|.+...   +....+.++|..--...      .     .-++|
T Consensus       403 mPGrI---iQ~mkka~~----------~NPv~LLDEIDKm~ss~rGDPaSALLEVLDPEQN~~F~DhYLev~yDLS~VmF  469 (782)
T COG0466         403 MPGKI---IQGMKKAGV----------KNPVFLLDEIDKMGSSFRGDPASALLEVLDPEQNNTFSDHYLEVPYDLSKVMF  469 (782)
T ss_pred             CChHH---HHHHHHhCC----------cCCeEEeechhhccCCCCCChHHHHHhhcCHhhcCchhhccccCccchhheEE
Confidence            22233   333333321          2239999999987432   11122333332110000      0     12566


Q ss_pred             EEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHH-----HHhC-----CCCCHHHHHHHHHHc
Q 005987          299 VLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKIC-----RQEQ-----YSLSTEQIDLVAQAS  368 (666)
Q Consensus       299 Iit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~-----~~e~-----i~v~~~~l~~Ia~~s  368 (666)
                      |+|+-+.        ..+  ..++|.  |..+|++..++..+-..+.++.+     ...|     +.+++++|..|++.-
T Consensus       470 iaTANsl--------~tI--P~PLlD--RMEiI~lsgYt~~EKl~IAk~~LiPk~~~~~gL~~~el~i~d~ai~~iI~~Y  537 (782)
T COG0466         470 IATANSL--------DTI--PAPLLD--RMEVIRLSGYTEDEKLEIAKRHLIPKQLKEHGLKKGELTITDEAIKDIIRYY  537 (782)
T ss_pred             EeecCcc--------ccC--ChHHhc--ceeeeeecCCChHHHHHHHHHhcchHHHHHcCCCccceeecHHHHHHHHHHH
Confidence            6665211        111  123333  59999999999998777766543     2333     568899999998762


Q ss_pred             C--CcHHHHHHHHHHHhc
Q 005987          369 G--GDIRQAITSLQFSSL  384 (666)
Q Consensus       369 ~--GDIR~AIn~LQf~~~  384 (666)
                      -  --+|..=..|.-+|.
T Consensus       538 TREAGVR~LeR~i~ki~R  555 (782)
T COG0466         538 TREAGVRNLEREIAKICR  555 (782)
T ss_pred             hHhhhhhHHHHHHHHHHH
Confidence            2  235665555655554

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

Probab=98.95  E-value=9.9e-08  Score=94.61  Aligned_cols=208  Identities=20%  Similarity=0.248  Sum_probs=135.3

Q ss_pred             ccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcCCCchh
Q 005987          140 AEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL---GARLYEWDTPTPTI  216 (666)
Q Consensus       140 ~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~nasd~~~  216 (666)
                      +..|-|-.+.+|+|-+...+.+.+--+....   |.+. +++||+|..|+|||++++++-.++   |..++|++..+   
T Consensus        51 v~~~~~i~L~~l~Gvd~qk~~L~~NT~~F~~---G~pA-NnVLLwGaRGtGKSSLVKA~~~e~~~~glrLVEV~k~d---  123 (287)
T COG2607          51 VPDPDPIDLADLVGVDRQKEALVRNTEQFAE---GLPA-NNVLLWGARGTGKSSLVKALLNEYADEGLRLVEVDKED---  123 (287)
T ss_pred             CCCCCCcCHHHHhCchHHHHHHHHHHHHHHc---CCcc-cceEEecCCCCChHHHHHHHHHHHHhcCCeEEEEcHHH---
Confidence            4456678899999988877777665554443   4444 899999999999999999999988   78899988544   


Q ss_pred             hhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcCCCce
Q 005987          217 WQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHIPT  296 (666)
Q Consensus       217 ~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~~~Pi  296 (666)
                                       +..+-.+++.++..+           .+.||+.||+---.+..++..+..+|..-++.... -
T Consensus       124 -----------------l~~Lp~l~~~Lr~~~-----------~kFIlFcDDLSFe~gd~~yK~LKs~LeG~ve~rP~-N  174 (287)
T COG2607         124 -----------------LATLPDLVELLRARP-----------EKFILFCDDLSFEEGDDAYKALKSALEGGVEGRPA-N  174 (287)
T ss_pred             -----------------HhhHHHHHHHHhcCC-----------ceEEEEecCCCCCCCchHHHHHHHHhcCCcccCCC-e
Confidence                             234555666665433           46899999987555555555554444433322221 3


Q ss_pred             EEEEecCCCCCCc-----cc--------hhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHH
Q 005987          297 AVVLTECGKADSV-----DS--------TAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDL  363 (666)
Q Consensus       297 ViIit~~~~~~s~-----d~--------~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~  363 (666)
                      |++..+++.....     |.        .....+. +-.|+.+....+.|.|.+.++..+++...++..++.++++.++.
T Consensus       175 Vl~YATSNRRHLl~e~~~dn~~~~~eih~~eaveE-KlSlSDRFGLwL~F~~~~Q~~YL~~V~~~a~~~~l~~~~e~l~~  253 (287)
T COG2607         175 VLFYATSNRRHLLPEDMKDNEGSTGEIHPSEAVEE-KLSLSDRFGLWLSFYPCDQDEYLKIVDHYAKHFGLDISDEELHA  253 (287)
T ss_pred             EEEEEecCCcccccHhhhhCCCcccccChhHHHHH-hhchhhhcceeecccCCCHHHHHHHHHHHHHHcCCCCCHHHHHH
Confidence            3343333322111     10        0111111 11233335678999999999999999999999999998766655


Q ss_pred             HH-----HHcCCcHHHHHHHHHHHhc
Q 005987          364 VA-----QASGGDIRQAITSLQFSSL  384 (666)
Q Consensus       364 Ia-----~~s~GDIR~AIn~LQf~~~  384 (666)
                      =|     ...+..=|.|-.-.+.++.
T Consensus       254 eAl~WAt~rg~RSGR~A~QF~~~~~g  279 (287)
T COG2607         254 EALQWATTRGGRSGRVAWQFIRDLAG  279 (287)
T ss_pred             HHHHHHHhcCCCccHhHHHHHHHHHh
Confidence            44     2344566777766666664

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

Probab=98.94  E-value=1.7e-08  Score=116.25  Aligned_cols=196  Identities=18%  Similarity=0.265  Sum_probs=120.8

Q ss_pred             ccccCHHHHHHHHHHHHHhhcC--CCCCCCccEEEEECCCCchHHHHHHHHHHHcC---CcEEEEcCCCchh---hhhhh
Q 005987          150 ELAVQRKKVEEVRAWFEERLGD--SKDKFSTNVLVITGQAGVGKTATVRQIASHLG---ARLYEWDTPTPTI---WQEYM  221 (666)
Q Consensus       150 eLvg~~k~i~el~~wL~~~~~~--~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg---~~viE~nasd~~~---~~e~l  221 (666)
                      .++||+.++..|.+.++....+  .+.++ ...+||.||+|||||.+|++||..|.   -.++.++.|....   ....+
T Consensus       492 rViGQd~AV~avs~aIrraRaGL~dp~rP-igsFlF~GPTGVGKTELAkaLA~~Lfg~e~aliR~DMSEy~EkHsVSrLI  570 (786)
T COG0542         492 RVIGQDEAVEAVSDAIRRARAGLGDPNRP-IGSFLFLGPTGVGKTELAKALAEALFGDEQALIRIDMSEYMEKHSVSRLI  570 (786)
T ss_pred             ceeChHHHHHHHHHHHHHHhcCCCCCCCC-ceEEEeeCCCcccHHHHHHHHHHHhcCCCccceeechHHHHHHHHHHHHh
Confidence            4789999999999999876543  22333 35899999999999999999999996   5677777665221   11122


Q ss_pred             hcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcC---------
Q 005987          222 HNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRST---------  292 (666)
Q Consensus       222 ~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~---------  292 (666)
                      ..+...+.|.. ...+.   +.++            .++..|||+||+...+     ..+.+.|++.++.+         
T Consensus       571 GaPPGYVGyee-GG~LT---EaVR------------r~PySViLlDEIEKAH-----pdV~nilLQVlDdGrLTD~~Gr~  629 (786)
T COG0542         571 GAPPGYVGYEE-GGQLT---EAVR------------RKPYSVILLDEIEKAH-----PDVFNLLLQVLDDGRLTDGQGRT  629 (786)
T ss_pred             CCCCCCceecc-ccchh---Hhhh------------cCCCeEEEechhhhcC-----HHHHHHHHHHhcCCeeecCCCCE
Confidence            22222222321 11111   1111            1345799999998654     34556677777654         


Q ss_pred             ---CCceEEEEecCCCCCCc-----c----c---hhhhhhHH-----HHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHH-
Q 005987          293 ---HIPTAVVLTECGKADSV-----D----S---TAQSFEEL-----QSILVDAGARKVALNPITNGSIKRTLSKICRQ-  351 (666)
Q Consensus       293 ---~~PiViIit~~~~~~s~-----d----~---~~r~l~~L-----~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~-  351 (666)
                         +.-+||+++|.+.....     +    .   ....+..+     +++|+| --.+|.|++++.+.+.+++...+.. 
T Consensus       630 VdFrNtiIImTSN~Gs~~i~~~~~~~~~~~~~~~~~~v~~~l~~~F~PEFLNR-id~II~F~~L~~~~l~~Iv~~~L~~l  708 (786)
T COG0542         630 VDFRNTIIIMTSNAGSEEILRDADGDDFADKEALKEAVMEELKKHFRPEFLNR-IDEIIPFNPLSKEVLERIVDLQLNRL  708 (786)
T ss_pred             EecceeEEEEecccchHHHHhhccccccchhhhHHHHHHHHHHhhCCHHHHhh-cccEEeccCCCHHHHHHHHHHHHHHH
Confidence               22466666665432100     0    0   00111112     244544 2348999999999999887766543 


Q ss_pred             ------hC--CCCCHHHHHHHHHHc
Q 005987          352 ------EQ--YSLSTEQIDLVAQAS  368 (666)
Q Consensus       352 ------e~--i~v~~~~l~~Ia~~s  368 (666)
                            .+  +.+++++.+.|++.+
T Consensus       709 ~~~L~~~~i~l~~s~~a~~~l~~~g  733 (786)
T COG0542         709 AKRLAERGITLELSDEAKDFLAEKG  733 (786)
T ss_pred             HHHHHhCCceEEECHHHHHHHHHhc
Confidence                  23  457899999999884

>PRK06964 DNA polymerase III subunit delta'; Validated

Probab=98.92  E-value=3.4e-08  Score=105.59  Aligned_cols=172  Identities=13%  Similarity=0.160  Sum_probs=101.5

Q ss_pred             CCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEE--EcCCCchhhhhhhhc--------c--c----------------
Q 005987          174 DKFSTNVLVITGQAGVGKTATVRQIASHLGARLYE--WDTPTPTIWQEYMHN--------C--K----------------  225 (666)
Q Consensus       174 g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE--~nasd~~~~~e~l~~--------~--~----------------  225 (666)
                      ++.+ +.+||+||+|+||+++|+.+|+.+.+.--.  -.+...+.....+..        .  .                
T Consensus        18 ~rl~-ha~Lf~Gp~G~GK~~lA~~~A~~LlC~~~~~~~~~Cg~C~~C~~~~~~~HPD~~~i~p~~~~~~~~~~~~~~~~~   96 (342)
T PRK06964         18 ARLP-HALLLHGQAGIGKLDFAQHLAQGLLCETPQPDGEPCGTCAACNWFAQGNHPDYRIVRPEALAAEAPGAADEAKEA   96 (342)
T ss_pred             CCcc-eEEEEECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCCHHHHHHHcCCCCCEEEEecccccccccccccccccc
Confidence            5666 789999999999999999999999664210  001011100000000        0  0                


Q ss_pred             ----CCcc-----ccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcCCCce
Q 005987          226 ----TGLE-----YTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHIPT  296 (666)
Q Consensus       226 ----~g~~-----~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~~~Pi  296 (666)
                          .|..     -.-.+++++++.+.+...+        .....+|+|||+++.++..     ..++|++.++.....+
T Consensus        97 ~~~~~~~k~~~~~~~I~idqiR~l~~~~~~~~--------~~~~~kV~iI~~ae~m~~~-----AaNaLLKtLEEPp~~t  163 (342)
T PRK06964         97 DADEGGKKTKAPSKEIKIEQVRALLDFCGVGT--------HRGGARVVVLYPAEALNVA-----AANALLKTLEEPPPGT  163 (342)
T ss_pred             hhhcccccccccccccCHHHHHHHHHHhccCC--------ccCCceEEEEechhhcCHH-----HHHHHHHHhcCCCcCc
Confidence                0100     0123456666665443111        1123579999999998654     2345666667665444


Q ss_pred             EEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCcHHHHH
Q 005987          297 AVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASGGDIRQAI  376 (666)
Q Consensus       297 ViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~s~GDIR~AI  376 (666)
                      +||.....       ..+.++.|++     ||+.|.|.+++.+++...|...    +  +++  .+.++..++|.+..|+
T Consensus       164 ~fiL~t~~-------~~~LLpTI~S-----Rcq~i~~~~~~~~~~~~~L~~~----~--~~~--~~~~l~~~~Gsp~~Al  223 (342)
T PRK06964        164 VFLLVSAR-------IDRLLPTILS-----RCRQFPMTVPAPEAAAAWLAAQ----G--VAD--ADALLAEAGGAPLAAL  223 (342)
T ss_pred             EEEEEECC-------hhhCcHHHHh-----cCEEEEecCCCHHHHHHHHHHc----C--CCh--HHHHHHHcCCCHHHHH
Confidence            44443322       2334444444     6999999999999999998753    3  333  2345677899999887


Q ss_pred             HHH
Q 005987          377 TSL  379 (666)
Q Consensus       377 n~L  379 (666)
                      ..+
T Consensus       224 ~~~  226 (342)
T PRK06964        224 ALA  226 (342)
T ss_pred             HHH
Confidence            654

>PRK10865 protein disaggregation chaperone; Provisional

Probab=98.91  E-value=4.1e-08  Score=117.44  Aligned_cols=207  Identities=15%  Similarity=0.224  Sum_probs=117.2

Q ss_pred             ccccccCHHHHHHHHHHHHHhhcC--CCCCCCccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcCCCchhh---hh
Q 005987          148 LEELAVQRKKVEEVRAWFEERLGD--SKDKFSTNVLVITGQAGVGKTATVRQIASHL---GARLYEWDTPTPTIW---QE  219 (666)
Q Consensus       148 l~eLvg~~k~i~el~~wL~~~~~~--~~g~~~~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~nasd~~~~---~e  219 (666)
                      ...|+||+..++.|...+......  .++++. ..+||+||+|||||++|++||+.+   +..++.++.+.....   ..
T Consensus       567 ~~~viGQ~~ai~~l~~~i~~~~~gl~~~~~p~-~~~Lf~Gp~G~GKT~lA~aLa~~l~~~~~~~i~id~se~~~~~~~~~  645 (857)
T PRK10865        567 HHRVIGQNEAVEAVSNAIRRSRAGLSDPNRPI-GSFLFLGPTGVGKTELCKALANFMFDSDDAMVRIDMSEFMEKHSVSR  645 (857)
T ss_pred             CCeEeCCHHHHHHHHHHHHHHHhcccCCCCCC-ceEEEECCCCCCHHHHHHHHHHHhhcCCCcEEEEEhHHhhhhhhHHH
Confidence            346889999999999999865421  112221 479999999999999999999987   345677766542110   01


Q ss_pred             hhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcC-------
Q 005987          220 YMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRST-------  292 (666)
Q Consensus       220 ~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~-------  292 (666)
                      .+.. ..|  |.... . ..++..+.+.           ++..||+|||++.++..     .++.|..+++.+       
T Consensus       646 LiG~-~pg--y~g~~-~-~g~l~~~v~~-----------~p~~vLllDEieka~~~-----v~~~Ll~ile~g~l~d~~g  704 (857)
T PRK10865        646 LVGA-PPG--YVGYE-E-GGYLTEAVRR-----------RPYSVILLDEVEKAHPD-----VFNILLQVLDDGRLTDGQG  704 (857)
T ss_pred             HhCC-CCc--ccccc-h-hHHHHHHHHh-----------CCCCeEEEeehhhCCHH-----HHHHHHHHHhhCceecCCc
Confidence            1111 111  11000 0 0112221111           12359999999977532     334455555443       


Q ss_pred             -----CCceEEEEecCCCCCCc-----cchhhhhh--------HH-HHHHhhcCe-eEEEeCCCCHHHHHHHHHHHHHHh
Q 005987          293 -----HIPTAVVLTECGKADSV-----DSTAQSFE--------EL-QSILVDAGA-RKVALNPITNGSIKRTLSKICRQE  352 (666)
Q Consensus       293 -----~~PiViIit~~~~~~s~-----d~~~r~l~--------~L-~s~L~r~r~-~~I~F~p~s~~~i~kiL~~I~~~e  352 (666)
                           +..+||++++.+.....     ....+.-.        .+ ++++.|  + .+|.|+|++.+.+.+++...+...
T Consensus       705 r~vd~rn~iiI~TSN~g~~~~~~~~~~~~~~~~~~~~~~~~~~~f~PELlnR--ld~iivF~PL~~edl~~Iv~~~L~~l  782 (857)
T PRK10865        705 RTVDFRNTVVIMTSNLGSDLIQERFGELDYAHMKELVLGVVSHNFRPEFINR--IDEVVVFHPLGEQHIASIAQIQLQRL  782 (857)
T ss_pred             eEEeecccEEEEeCCcchHHHHHhccccchHHHHHHHHHHHcccccHHHHHh--CCeeEecCCCCHHHHHHHHHHHHHHH
Confidence                 22345555554321100     00000000        01 234443  5 789999999999999888776541


Q ss_pred             -------C--CCCCHHHHHHHHHHcC----C--cHHHHHHH
Q 005987          353 -------Q--YSLSTEQIDLVAQASG----G--DIRQAITS  378 (666)
Q Consensus       353 -------~--i~v~~~~l~~Ia~~s~----G--DIR~AIn~  378 (666)
                             +  +.+++++++.|+...-    |  .+|++|..
T Consensus       783 ~~rl~~~gi~l~is~~al~~L~~~gy~~~~GARpL~r~I~~  823 (857)
T PRK10865        783 YKRLEERGYEIHISDEALKLLSENGYDPVYGARPLKRAIQQ  823 (857)
T ss_pred             HHHHHhCCCcCcCCHHHHHHHHHcCCCccCChHHHHHHHHH
Confidence                   3  4579999999998632    3  55665543

>KOG0651 consensus 26S proteasome regulatory complex, ATPase RPT4 [Posttranslational modification, protein turnover, chaperones]

Probab=98.90  E-value=7.8e-09  Score=105.60  Aligned_cols=105  Identities=20%  Similarity=0.339  Sum_probs=72.3

Q ss_pred             CccccccCHHHHHHHHHHHHHhhcC-----CCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCchhhhhhh
Q 005987          147 SLEELAVQRKKVEEVRAWFEERLGD-----SKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTIWQEYM  221 (666)
Q Consensus       147 sl~eLvg~~k~i~el~~wL~~~~~~-----~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~~~~e~l  221 (666)
                      +++.+-|-...++++++-++-.+.+     .-|-.++++++||||||+|||.+++++|..+|++.+-+.++.  ...++ 
T Consensus       130 s~~~~ggl~~qirelre~ielpl~np~lf~rvgIk~Pkg~ll~GppGtGKTlla~~Vaa~mg~nfl~v~ss~--lv~ky-  206 (388)
T KOG0651|consen  130 SFENVGGLFYQIRELREVIELPLTNPELFLRVGIKPPKGLLLYGPPGTGKTLLARAVAATMGVNFLKVVSSA--LVDKY-  206 (388)
T ss_pred             CHHHhCChHHHHHHHHhheEeeccCchhccccCCCCCceeEEeCCCCCchhHHHHHHHHhcCCceEEeeHhh--hhhhh-
Confidence            7888888888999988887643332     113334589999999999999999999999999999887764  11111 


Q ss_pred             hcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcc
Q 005987          222 HNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNG  274 (666)
Q Consensus       222 ~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~  274 (666)
                          .|    .....+++....++..            .++||++||+|-..+
T Consensus       207 ----iG----EsaRlIRemf~yA~~~------------~pciifmdeiDAigG  239 (388)
T KOG0651|consen  207 ----IG----ESARLIRDMFRYAREV------------IPCIIFMDEIDAIGG  239 (388)
T ss_pred             ----cc----cHHHHHHHHHHHHhhh------------CceEEeehhhhhhcc
Confidence                11    1222334433333322            368999999996543

>KOG1942 consensus DNA helicase, TBP-interacting protein [Replication, recombination and repair]

Probab=98.90  E-value=5.6e-08  Score=98.45  Aligned_cols=111  Identities=18%  Similarity=0.287  Sum_probs=81.7

Q ss_pred             ceEEEEeCCCCCcchhHHHHHHHHHHHHHhcCCCceEEEEecCCCC---CCccch-hhhhhHHHHHHhhcCeeEEEeCCC
Q 005987          261 SAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHIPTAVVLTECGKA---DSVDST-AQSFEELQSILVDAGARKVALNPI  336 (666)
Q Consensus       261 ~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~~~PiViIit~~~~~---~s~d~~-~r~l~~L~s~L~r~r~~~I~F~p~  336 (666)
                      |-++||||+++++-. .|.    .|...+++.-.|+|+++++.+.-   ...|.. .+-++  ..+|.  |..+|+-.++
T Consensus       297 PGVLFIDEVhMLDiE-cFT----yL~kalES~iaPivifAsNrG~~~irGt~d~~sPhGip--~dllD--Rl~Iirt~~y  367 (456)
T KOG1942|consen  297 PGVLFIDEVHMLDIE-CFT----YLHKALESPIAPIVIFASNRGMCTIRGTEDILSPHGIP--PDLLD--RLLIIRTLPY  367 (456)
T ss_pred             CcceEeeehhhhhhH-HHH----HHHHHhcCCCCceEEEecCCcceeecCCcCCCCCCCCC--HHHhh--heeEEeeccC
Confidence            669999999987532 233    35566677778999999886532   111211 11121  34444  4789999999


Q ss_pred             CHHHHHHHHHHHHHHhCCCCCHHHHHHHHHH-cCCcHHHHHHHHH
Q 005987          337 TNGSIKRTLSKICRQEQYSLSTEQIDLVAQA-SGGDIRQAITSLQ  380 (666)
Q Consensus       337 s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~-s~GDIR~AIn~LQ  380 (666)
                      +++++++++++.++.|++.+++++++.++.. +.-.+|.|+..|-
T Consensus       368 ~~~e~r~Ii~~Ra~~E~l~~~e~a~~~l~~~gt~tsLRy~vqLl~  412 (456)
T KOG1942|consen  368 DEEEIRQIIKIRAQVEGLQVEEEALDLLAEIGTSTSLRYAVQLLT  412 (456)
T ss_pred             CHHHHHHHHHHHHhhhcceecHHHHHHHHhhccchhHHHHHHhcC
Confidence            9999999999999999999999999999986 4577999988775

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=98.89  E-value=7.3e-08  Score=115.60  Aligned_cols=212  Identities=17%  Similarity=0.206  Sum_probs=124.5

Q ss_pred             cccccCHHHHHHHHHHHHHhhcC--CCCCCCccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcCCCchh---hhhh
Q 005987          149 EELAVQRKKVEEVRAWFEERLGD--SKDKFSTNVLVITGQAGVGKTATVRQIASHL---GARLYEWDTPTPTI---WQEY  220 (666)
Q Consensus       149 ~eLvg~~k~i~el~~wL~~~~~~--~~g~~~~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~nasd~~~---~~e~  220 (666)
                      ..|+||+..++.|...+......  .+.++ ...+||+||+|||||++|++||+.+   +..++.++.+....   ....
T Consensus       565 ~~v~GQ~~av~~v~~~i~~~~~gl~~~~~p-~~~~Lf~Gp~GvGKt~lA~~La~~l~~~~~~~i~~d~s~~~~~~~~~~l  643 (852)
T TIGR03346       565 ERVVGQDEAVEAVSDAIRRSRAGLSDPNRP-IGSFLFLGPTGVGKTELAKALAEFLFDDEDAMVRIDMSEYMEKHSVARL  643 (852)
T ss_pred             cccCCChHHHHHHHHHHHHHhccCCCCCCC-CeEEEEEcCCCCCHHHHHHHHHHHhcCCCCcEEEEechhhcccchHHHh
Confidence            45899999999999999865431  11222 2579999999999999999999988   45677777664211   1111


Q ss_pred             hhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcC--------
Q 005987          221 MHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRST--------  292 (666)
Q Consensus       221 l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~--------  292 (666)
                      ++.......|.. ...+   .+.++..            +..|||+||++.++..     +++.|+.+++.+        
T Consensus       644 ~g~~~g~~g~~~-~g~l---~~~v~~~------------p~~vlllDeieka~~~-----v~~~Ll~~l~~g~l~d~~g~  702 (852)
T TIGR03346       644 IGAPPGYVGYEE-GGQL---TEAVRRK------------PYSVVLFDEVEKAHPD-----VFNVLLQVLDDGRLTDGQGR  702 (852)
T ss_pred             cCCCCCccCccc-ccHH---HHHHHcC------------CCcEEEEeccccCCHH-----HHHHHHHHHhcCceecCCCe
Confidence            111110011111 1112   1222211            2359999999977532     344455555543        


Q ss_pred             ----CCceEEEEecCCCCCCcc------c--hh-hhhhHH-----HHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHH---
Q 005987          293 ----HIPTAVVLTECGKADSVD------S--TA-QSFEEL-----QSILVDAGARKVALNPITNGSIKRTLSKICRQ---  351 (666)
Q Consensus       293 ----~~PiViIit~~~~~~s~d------~--~~-r~l~~L-----~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~---  351 (666)
                          +..+||++++.+.....+      +  .. ..+..+     .+++.| --.+|.|+|++.+.+.+++...+..   
T Consensus       703 ~vd~rn~iiI~TSn~g~~~~~~~~~~~~~~~~~~~~~~~~~~~F~pel~~R-id~IivF~PL~~e~l~~I~~l~L~~l~~  781 (852)
T TIGR03346       703 TVDFRNTVIIMTSNLGSQFIQELAGGDDYEEMREAVMEVLRAHFRPEFLNR-IDEIVVFHPLGREQIARIVEIQLGRLRK  781 (852)
T ss_pred             EEecCCcEEEEeCCcchHhHhhhcccccHHHHHHHHHHHHHhhcCHHHhcC-cCeEEecCCcCHHHHHHHHHHHHHHHHH
Confidence                234566666653321000      0  00 000111     233333 2368999999999999998877652   


Q ss_pred             ----h--CCCCCHHHHHHHHHHc---CCcHHHHHHHHHHHh
Q 005987          352 ----E--QYSLSTEQIDLVAQAS---GGDIRQAITSLQFSS  383 (666)
Q Consensus       352 ----e--~i~v~~~~l~~Ia~~s---~GDIR~AIn~LQf~~  383 (666)
                          .  .+.+++++++.|++..   .+.+|..-+.++-..
T Consensus       782 ~l~~~~~~l~i~~~a~~~L~~~~~~~~~gaR~L~~~i~~~i  822 (852)
T TIGR03346       782 RLAERKITLELSDAALDFLAEAGYDPVYGARPLKRAIQREI  822 (852)
T ss_pred             HHHHCCCeecCCHHHHHHHHHhCCCCCCCchhHHHHHHHHH
Confidence                1  2568999999999873   366776666665543

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.

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

Probab=98.83  E-value=4e-08  Score=107.38  Aligned_cols=114  Identities=18%  Similarity=0.390  Sum_probs=73.2

Q ss_pred             ccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCc-------EEEEcCCCchhhhhh
Q 005987          148 LEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGAR-------LYEWDTPTPTIWQEY  220 (666)
Q Consensus       148 l~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~-------viE~nasd~~~~~e~  220 (666)
                      ++++++.+..++.+...|..          .+.++|+||||||||++|+.+|+.+...       .+++..  ...+.+.
T Consensus       174 l~d~~i~e~~le~l~~~L~~----------~~~iil~GppGtGKT~lA~~la~~l~~~~~~~~v~~VtFHp--sySYeDF  241 (459)
T PRK11331        174 LNDLFIPETTIETILKRLTI----------KKNIILQGPPGVGKTFVARRLAYLLTGEKAPQRVNMVQFHQ--SYSYEDF  241 (459)
T ss_pred             hhcccCCHHHHHHHHHHHhc----------CCCEEEECCCCCCHHHHHHHHHHHhcCCcccceeeEEeecc--cccHHHH
Confidence            67788888898888887764          1579999999999999999999998532       222221  1222333


Q ss_pred             hhc-ccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHH
Q 005987          221 MHN-CKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQ  283 (666)
Q Consensus       221 l~~-~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~  283 (666)
                      +.. ...+..|.....-|.+++.++....          ..+.+|||||+++.+....|+.+..
T Consensus       242 I~G~rP~~vgy~~~~G~f~~~~~~A~~~p----------~~~~vliIDEINRani~kiFGel~~  295 (459)
T PRK11331        242 IQGYRPNGVGFRRKDGIFYNFCQQAKEQP----------EKKYVFIIDEINRANLSKVFGEVMM  295 (459)
T ss_pred             hcccCCCCCCeEecCchHHHHHHHHHhcc----------cCCcEEEEehhhccCHHHhhhhhhh
Confidence            211 1122333333345777777775432          2467999999998765555555543

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

Probab=98.83  E-value=1.5e-07  Score=102.87  Aligned_cols=63  Identities=19%  Similarity=0.205  Sum_probs=47.1

Q ss_pred             cccCHHHHHHHHHHHHHhhcCC-----CCC-----CCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCC
Q 005987          151 LAVQRKKVEEVRAWFEERLGDS-----KDK-----FSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPT  213 (666)
Q Consensus       151 Lvg~~k~i~el~~wL~~~~~~~-----~g~-----~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd  213 (666)
                      ++||+++++.+...+.++....     ...     .....+||+||||||||++|++||+.++..+..++++.
T Consensus        79 ViGQe~A~~~l~~av~~h~~~~~~~~~~~~~~~~~~~~~~iLL~GP~GsGKT~lAraLA~~l~~pf~~~da~~  151 (413)
T TIGR00382        79 VIGQEQAKKVLSVAVYNHYKRLNFEKNKKSDNGVELSKSNILLIGPTGSGKTLLAQTLARILNVPFAIADATT  151 (413)
T ss_pred             ecCHHHHHHHHHHHHHHHHhhhccccccccccccccCCceEEEECCCCcCHHHHHHHHHHhcCCCeEEechhh
Confidence            5899999999987775333211     000     12357999999999999999999999998888777653

A member of the ATP-dependent proteases, ClpX has ATP-dependent chaperone activity and is required for specific ATP-dependent proteolytic activities expressed by ClpPX. The gene is also found to be involved in stress tolerance in Bacillus subtilis and is essential for the efficient acquisition of genes specifying type IA and IB restriction.

>TIGR00390 hslU ATP-dependent protease HslVU, ATPase subunit

Probab=98.82  E-value=5.6e-08  Score=105.11  Aligned_cols=63  Identities=22%  Similarity=0.337  Sum_probs=48.9

Q ss_pred             cccCHHHHHHHHHHHHHh-hcCC-----CCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCC
Q 005987          151 LAVQRKKVEEVRAWFEER-LGDS-----KDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPT  213 (666)
Q Consensus       151 Lvg~~k~i~el~~wL~~~-~~~~-----~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd  213 (666)
                      ++||++.++.+...+... ....     ....+++.+||+||||||||+++++||+.++..++.++++.
T Consensus        14 IiGQ~eAkk~lsvAl~n~~~r~~~~~~~~~e~~p~~ILLiGppG~GKT~lAraLA~~l~~~fi~vdat~   82 (441)
T TIGR00390        14 IIGQDNAKKSVAIALRNRYRRSQLNEELKDEVTPKNILMIGPTGVGKTEIARRLAKLANAPFIKVEATK   82 (441)
T ss_pred             ccCHHHHHHHHHHHHHhhhhhhccccccccccCCceEEEECCCCCCHHHHHHHHHHHhCCeEEEeecce
Confidence            689999999998777642 2110     11223478999999999999999999999999998888653

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.

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

Probab=98.81  E-value=5.3e-08  Score=105.35  Aligned_cols=63  Identities=21%  Similarity=0.317  Sum_probs=49.6

Q ss_pred             cccCHHHHHHHHHHHHHhh-cC----C-CCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCC
Q 005987          151 LAVQRKKVEEVRAWFEERL-GD----S-KDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPT  213 (666)
Q Consensus       151 Lvg~~k~i~el~~wL~~~~-~~----~-~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd  213 (666)
                      ++||++.++.|..++.... ..    . .....++.+||+||||||||++|+.||+.++..++.++++.
T Consensus        17 IiGQe~AkkalavAl~~~~~r~~l~~~~~~e~~~~~ILliGp~G~GKT~LAr~LAk~l~~~fi~vD~t~   85 (443)
T PRK05201         17 IIGQDDAKRAVAIALRNRWRRMQLPEELRDEVTPKNILMIGPTGVGKTEIARRLAKLANAPFIKVEATK   85 (443)
T ss_pred             cCCHHHHHHHHHHHHHHHHHHhcCCcccccccCCceEEEECCCCCCHHHHHHHHHHHhCChheeecchh
Confidence            7899999999999996532 11    0 01112368999999999999999999999999999888753

>PRK05917 DNA polymerase III subunit delta'; Validated

Probab=98.80  E-value=2.7e-07  Score=96.12  Aligned_cols=164  Identities=13%  Similarity=0.133  Sum_probs=100.2

Q ss_pred             HHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCch-hhhhhhhcc-----cCCccccc
Q 005987          159 EEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPT-IWQEYMHNC-----KTGLEYTS  232 (666)
Q Consensus       159 ~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~-~~~e~l~~~-----~~g~~~~s  232 (666)
                      +.+...++.      ++.+ +.+||+||+|+||+++|..+|+.+-+.-    .+..+ .+....|..     ..|..-.-
T Consensus         7 ~~L~~~i~~------~rl~-HAyLf~G~~G~Gk~~lA~~~A~~llC~~----~~~~c~~~~~~~HPD~~~i~p~~~~~~I   75 (290)
T PRK05917          7 EALIQRVRD------QKVP-SAIILHGQDLSNLSARAYELASLILKET----SPEAAYKISQKIHPDIHEFSPQGKGRLH   75 (290)
T ss_pred             HHHHHHHHc------CCcC-eeEeeECCCCCcHHHHHHHHHHHHhCCC----CccHHHHHhcCCCCCEEEEecCCCCCcC
Confidence            455555554      6777 7999999999999999999999985531    11111 000000000     01110012


Q ss_pred             hhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcCCCceEEEEecCCCCCCccch
Q 005987          233 KLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHIPTAVVLTECGKADSVDST  312 (666)
Q Consensus       233 ~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~~~PiViIit~~~~~~s~d~~  312 (666)
                      .+++++++.+.+...+        .....+|++||+++.+...     ..++|++.++.....+++|....+       .
T Consensus        76 ~idqiR~l~~~~~~~p--------~e~~~kv~ii~~ad~mt~~-----AaNaLLK~LEEPp~~~~fiL~~~~-------~  135 (290)
T PRK05917         76 SIETPRAIKKQIWIHP--------YESPYKIYIIHEADRMTLD-----AISAFLKVLEDPPQHGVIILTSAK-------P  135 (290)
T ss_pred             cHHHHHHHHHHHhhCc--------cCCCceEEEEechhhcCHH-----HHHHHHHHhhcCCCCeEEEEEeCC-------h
Confidence            4667777666654322        1124579999999988643     334567777776544444443322       2


Q ss_pred             hhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCcHH
Q 005987          313 AQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASGGDIR  373 (666)
Q Consensus       313 ~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~s~GDIR  373 (666)
                      .+.++.+++     ||+.+.|+++               +...++++.+..++..++|+++
T Consensus       136 ~~ll~TI~S-----Rcq~~~~~~~---------------~~~~i~~~~~~~l~~~~~g~~~  176 (290)
T PRK05917        136 QRLPPTIRS-----RSLSIHIPME---------------EKTLVSKEDIAYLIGYAQGKES  176 (290)
T ss_pred             hhCcHHHHh-----cceEEEccch---------------hccCCCHHHHHHHHHHhCCChh
Confidence            334445554     6999999986               2224788889999999999986

>PRK08699 DNA polymerase III subunit delta'; Validated

Probab=98.77  E-value=7.5e-08  Score=102.74  Aligned_cols=147  Identities=16%  Similarity=0.203  Sum_probs=83.5

Q ss_pred             CCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEE--cCCCchhhhhhh----hc------c-----cCCcc-ccchhH
Q 005987          174 DKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEW--DTPTPTIWQEYM----HN------C-----KTGLE-YTSKLD  235 (666)
Q Consensus       174 g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~--nasd~~~~~e~l----~~------~-----~~g~~-~~s~~~  235 (666)
                      ++.+ +.+||+||+|+|||++|+.+|+.+.+.--.-  .+...+.....+    +.      .     ..|.. -.-.++
T Consensus        18 ~r~~-hA~Lf~G~~G~GK~~la~~~a~~llC~~~~~~~~~Cg~C~~C~~~~~~~HpD~~~~~p~~~~~~~g~~~~~I~id   96 (325)
T PRK08699         18 ERRP-NAWLFAGKKGIGKTAFARFAAQALLCETPAPGHKPCGECMSCHLFGQGSHPDFYEITPLSDEPENGRKLLQIKID   96 (325)
T ss_pred             CCcc-eEEEeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCcCHHHHHHhcCCCCCEEEEecccccccccccCCCcCHH
Confidence            5666 7899999999999999999999986531000  000101000000    00      0     00100 012467


Q ss_pred             HHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcCC-CceEEEEecCCCCCCccchhh
Q 005987          236 EFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTH-IPTAVVLTECGKADSVDSTAQ  314 (666)
Q Consensus       236 ~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~~-~PiViIit~~~~~~s~d~~~r  314 (666)
                      +++++++.+...+.        ....+|+|||+++.++... .+.    |+..++... .-++|+++..        ...
T Consensus        97 ~iR~l~~~~~~~p~--------~~~~kV~iiEp~~~Ld~~a-~na----LLk~LEep~~~~~~Ilvth~--------~~~  155 (325)
T PRK08699         97 AVREIIDNVYLTSV--------RGGLRVILIHPAESMNLQA-ANS----LLKVLEEPPPQVVFLLVSHA--------ADK  155 (325)
T ss_pred             HHHHHHHHHhhCcc--------cCCceEEEEechhhCCHHH-HHH----HHHHHHhCcCCCEEEEEeCC--------hHh
Confidence            77877776643221        1235799999999987542 233    444444432 2234444431        122


Q ss_pred             hhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHH
Q 005987          315 SFEELQSILVDAGARKVALNPITNGSIKRTLSK  347 (666)
Q Consensus       315 ~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~  347 (666)
                      .++.+++     ||..+.|.+++.+++...|..
T Consensus       156 ll~ti~S-----Rc~~~~~~~~~~~~~~~~L~~  183 (325)
T PRK08699        156 VLPTIKS-----RCRKMVLPAPSHEEALAYLRE  183 (325)
T ss_pred             ChHHHHH-----HhhhhcCCCCCHHHHHHHHHh
Confidence            3333333     699999999999999988864

>KOG0732 consensus AAA+-type ATPase containing the bromodomain [Posttranslational modification, protein turnover, chaperones]

Probab=98.76  E-value=1.2e-07  Score=111.48  Aligned_cols=200  Identities=14%  Similarity=0.132  Sum_probs=126.4

Q ss_pred             CCccccccCHHHHHHHHHHHHHhhcCCC-----CCCCccEEEEECCCCchHHHHHHHHHHHcC--CcEEEEcCCCchhhh
Q 005987          146 RSLEELAVQRKKVEEVRAWFEERLGDSK-----DKFSTNVLVITGQAGVGKTATVRQIASHLG--ARLYEWDTPTPTIWQ  218 (666)
Q Consensus       146 ~sl~eLvg~~k~i~el~~wL~~~~~~~~-----g~~~~k~LLL~GPpG~GKTtla~~LAkelg--~~viE~nasd~~~~~  218 (666)
                      ..|+++.|-+..+.++++.+..-+.+..     +-.|++.+|++||||+|||..|+++|..+.  .+-+-.-.-.     
T Consensus       262 v~fd~vggl~~~i~~LKEmVl~PLlyPE~f~~~~itpPrgvL~~GppGTGkTl~araLa~~~s~~~~kisffmrk-----  336 (1080)
T KOG0732|consen  262 VGFDSVGGLENYINQLKEMVLLPLLYPEFFDNFNITPPRGVLFHGPPGTGKTLMARALAAACSRGNRKISFFMRK-----  336 (1080)
T ss_pred             cCccccccHHHHHHHHHHHHHhHhhhhhHhhhcccCCCcceeecCCCCCchhHHHHhhhhhhcccccccchhhhc-----
Confidence            4678899999999998887654433221     233458899999999999999999999982  2111110000     


Q ss_pred             hhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchh------HHHHHHHHHHHHHhcC
Q 005987          219 EYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRT------AFERLRQCLLLLVRST  292 (666)
Q Consensus       219 e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~------~~~~l~~~L~~l~~~~  292 (666)
                         ++.-.+..+.....+++-..+.+++.            .|.||++||||++..-.      ....+...|+.++..-
T Consensus       337 ---gaD~lskwvgEaERqlrllFeeA~k~------------qPSIIffdeIdGlapvrSskqEqih~SIvSTLLaLmdGl  401 (1080)
T KOG0732|consen  337 ---GADCLSKWVGEAERQLRLLFEEAQKT------------QPSIIFFDEIDGLAPVRSSKQEQIHASIVSTLLALMDGL  401 (1080)
T ss_pred             ---CchhhccccCcHHHHHHHHHHHHhcc------------CceEEeccccccccccccchHHHhhhhHHHHHHHhccCC
Confidence               00011222333445666666777543            36799999999874311      1112334455555432


Q ss_pred             -CCceEEEEecCCCCCCccchhhhhhHHHHHHhhcC--eeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcC
Q 005987          293 -HIPTAVVLTECGKADSVDSTAQSFEELQSILVDAG--ARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASG  369 (666)
Q Consensus       293 -~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r--~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~s~  369 (666)
                       .++-|++|++++..+.          +...|+|++  -..+.|.-++.+...++|...-.+..-.++...+..||+.+.
T Consensus       402 dsRgqVvvigATnRpda----------~dpaLRRPgrfdref~f~lp~~~ar~~Il~Ihtrkw~~~i~~~l~~~la~~t~  471 (1080)
T KOG0732|consen  402 DSRGQVVVIGATNRPDA----------IDPALRRPGRFDREFYFPLPDVDARAKILDIHTRKWEPPISRELLLWLAEETS  471 (1080)
T ss_pred             CCCCceEEEcccCCccc----------cchhhcCCcccceeEeeeCCchHHHHHHHHHhccCCCCCCCHHHHHHHHHhcc
Confidence             2344566677665443          333444432  346899999999999998877666667788999999999987


Q ss_pred             CcHHHH
Q 005987          370 GDIRQA  375 (666)
Q Consensus       370 GDIR~A  375 (666)
                      |-...-
T Consensus       472 gy~gaD  477 (1080)
T KOG0732|consen  472 GYGGAD  477 (1080)
T ss_pred             ccchHH
Confidence            766654

>PRK07132 DNA polymerase III subunit delta'; Validated

Probab=98.71  E-value=1.7e-06  Score=91.17  Aligned_cols=177  Identities=14%  Similarity=0.100  Sum_probs=106.8

Q ss_pred             HHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcE----EEEcCCCchhhhhhhhcccCCccccch
Q 005987          158 VEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARL----YEWDTPTPTIWQEYMHNCKTGLEYTSK  233 (666)
Q Consensus       158 i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~v----iE~nasd~~~~~e~l~~~~~g~~~~s~  233 (666)
                      ++.+++-++.      ++.+ +.+||+|+.|.||+++++.+|+.+.+.-    -.-+.++...+   + + ..|.  .-.
T Consensus         5 ~~~l~~~i~~------~~l~-haYLf~G~eg~gk~~~a~~~a~~l~c~~~~~~~~~~~p~n~~~---~-d-~~g~--~i~   70 (299)
T PRK07132          5 IKFLDNSATQ------NKIS-HSFLLKSNYNEDIDEKILYFLNKFNNLQITNLNEQELPANIIL---F-D-IFDK--DLS   70 (299)
T ss_pred             HHHHHHHHHh------CCCC-eEEEEeCCCCCCHHHHHHHHHHHHcCcCCCCCCCCCCCcceEE---e-c-cCCC--cCC
Confidence            4445555543      5666 7899999999999999999999984421    00011110000   0 0 0011  123


Q ss_pred             hHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcCCCceEEEEecCCCCCCccchh
Q 005987          234 LDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHIPTAVVLTECGKADSVDSTA  313 (666)
Q Consensus       234 ~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~~~PiViIit~~~~~~s~d~~~  313 (666)
                      .+++++.++.+...+      . ..+.++|+|||+++.+...     ..++|+.+++....-+++|....+       ..
T Consensus        71 vd~Ir~l~~~~~~~~------~-~~~~~KvvII~~~e~m~~~-----a~NaLLK~LEEPp~~t~~il~~~~-------~~  131 (299)
T PRK07132         71 KSEFLSAINKLYFSS------F-VQSQKKILIIKNIEKTSNS-----LLNALLKTIEEPPKDTYFLLTTKN-------IN  131 (299)
T ss_pred             HHHHHHHHHHhccCC------c-ccCCceEEEEecccccCHH-----HHHHHHHHhhCCCCCeEEEEEeCC-------hH
Confidence            456666665543211      0 1124679999999987532     334567777776544444443321       12


Q ss_pred             hhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCcHHHHHHHH
Q 005987          314 QSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASGGDIRQAITSL  379 (666)
Q Consensus       314 r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~s~GDIR~AIn~L  379 (666)
                      +.++.+++     ||+.+.|.|++..++.+.|...    +  ++++....++..++| +..|+..+
T Consensus       132 kll~TI~S-----Rc~~~~f~~l~~~~l~~~l~~~----~--~~~~~a~~~a~~~~~-~~~a~~~~  185 (299)
T PRK07132        132 KVLPTIVS-----RCQVFNVKEPDQQKILAKLLSK----N--KEKEYNWFYAYIFSN-FEQAEKYI  185 (299)
T ss_pred             hChHHHHh-----CeEEEECCCCCHHHHHHHHHHc----C--CChhHHHHHHHHcCC-HHHHHHHH
Confidence            34444443     6999999999999999888742    2  677777777777764 88887763

>KOG0735 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=98.70  E-value=3.8e-07  Score=102.04  Aligned_cols=160  Identities=20%  Similarity=0.281  Sum_probs=99.4

Q ss_pred             CccEEEEECCCCchHHHHHHHHHHHcC----CcEEEEcCCCchhhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCC
Q 005987          177 STNVLVITGQAGVGKTATVRQIASHLG----ARLYEWDTPTPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSP  252 (666)
Q Consensus       177 ~~k~LLL~GPpG~GKTtla~~LAkelg----~~viE~nasd~~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~  252 (666)
                      .+..+||+||+|||||.+++++++++.    +.+..+.++.           ..    .+..+.++.++..+-..+.   
T Consensus       430 ~~~~Ill~G~~GsGKT~L~kal~~~~~k~~~~hv~~v~Cs~-----------l~----~~~~e~iQk~l~~vfse~~---  491 (952)
T KOG0735|consen  430 RHGNILLNGPKGSGKTNLVKALFDYYSKDLIAHVEIVSCST-----------LD----GSSLEKIQKFLNNVFSEAL---  491 (952)
T ss_pred             ccccEEEeCCCCCCHhHHHHHHHHHhccccceEEEEEechh-----------cc----chhHHHHHHHHHHHHHHHH---
Confidence            346899999999999999999999984    2333344443           11    2235566666655422210   


Q ss_pred             CCCCCCCCceEEEEeCCCCCcc-------hh--HHHHHHHHHHH----HHhcCCCceEEEEecCCCCCCccchhhhhhHH
Q 005987          253 SIPGESKSSAILLIDDLPVTNG-------RT--AFERLRQCLLL----LVRSTHIPTAVVLTECGKADSVDSTAQSFEEL  319 (666)
Q Consensus       253 s~~~~~~~~~IIlIDEid~l~~-------~~--~~~~l~~~L~~----l~~~~~~PiViIit~~~~~~s~d~~~r~l~~L  319 (666)
                           ...|.||++|++|.+.+       +.  ..+++...|..    +.+..+ -+.+|.+..           .+..|
T Consensus       492 -----~~~PSiIvLDdld~l~~~s~~e~~q~~~~~~rla~flnqvi~~y~~~~~-~ia~Iat~q-----------e~qtl  554 (952)
T KOG0735|consen  492 -----WYAPSIIVLDDLDCLASASSNENGQDGVVSERLAAFLNQVIKIYLKRNR-KIAVIATGQ-----------ELQTL  554 (952)
T ss_pred             -----hhCCcEEEEcchhhhhccCcccCCcchHHHHHHHHHHHHHHHHHHccCc-EEEEEEech-----------hhhhc
Confidence                 11367999999997643       11  12233333333    223332 244554431           12223


Q ss_pred             HHHHhhcC--eeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCc
Q 005987          320 QSILVDAG--ARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASGGD  371 (666)
Q Consensus       320 ~s~L~r~r--~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~s~GD  371 (666)
                      ...|..++  -.++++.+|+.++..++|..++.+....+..+.|+.++..+.|-
T Consensus       555 ~~~L~s~~~Fq~~~~L~ap~~~~R~~IL~~~~s~~~~~~~~~dLd~ls~~TEGy  608 (952)
T KOG0735|consen  555 NPLLVSPLLFQIVIALPAPAVTRRKEILTTIFSKNLSDITMDDLDFLSVKTEGY  608 (952)
T ss_pred             ChhhcCccceEEEEecCCcchhHHHHHHHHHHHhhhhhhhhHHHHHHHHhcCCc
Confidence            33333322  34679999999999999999999887777788888899888883

>PRK07952 DNA replication protein DnaC; Validated

Probab=98.69  E-value=3.3e-07  Score=93.79  Aligned_cols=67  Identities=19%  Similarity=0.297  Sum_probs=48.6

Q ss_pred             ccccCCCCccccccC----HHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcCC
Q 005987          140 AEKYKPRSLEELAVQ----RKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL---GARLYEWDTP  212 (666)
Q Consensus       140 ~eKY~P~sl~eLvg~----~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~nas  212 (666)
                      .+.|++.+|+.+...    ...+..+..+++...    ..  ...++|+||||||||+++.++|+++   |..++.+..+
T Consensus        63 ~~~~~~~tFdnf~~~~~~q~~al~~a~~~~~~~~----~~--~~~~~l~G~~GtGKThLa~aia~~l~~~g~~v~~it~~  136 (244)
T PRK07952         63 RPLHQNCSFENYRVECEGQMNALSKARQYVEEFD----GN--IASFIFSGKPGTGKNHLAAAICNELLLRGKSVLIITVA  136 (244)
T ss_pred             CccccCCccccccCCCchHHHHHHHHHHHHHhhc----cC--CceEEEECCCCCCHHHHHHHHHHHHHhcCCeEEEEEHH
Confidence            467788889888643    335566666665432    11  1479999999999999999999998   6777766543

>TIGR01817 nifA Nif-specific regulatory protein

Probab=98.69  E-value=6.4e-07  Score=102.47  Aligned_cols=215  Identities=13%  Similarity=0.180  Sum_probs=123.6

Q ss_pred             cccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcCCCchhh
Q 005987          141 EKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL---GARLYEWDTPTPTIW  217 (666)
Q Consensus       141 eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~nasd~~~~  217 (666)
                      .+++..+++.|+|+...++++.+-++....   ..   ..+||+|++||||+++|+++....   +..++.+|+..... 
T Consensus       188 ~~~~~~~~~~liG~s~~~~~~~~~~~~~a~---~~---~pvli~Ge~GtGK~~lA~~ih~~s~r~~~pfv~i~c~~~~~-  260 (534)
T TIGR01817       188 ARRRSGKEDGIIGKSPAMRQVVDQARVVAR---SN---STVLLRGESGTGKELIAKAIHYLSPRAKRPFVKVNCAALSE-  260 (534)
T ss_pred             cccccCccCceEECCHHHHHHHHHHHHHhC---cC---CCEEEECCCCccHHHHHHHHHHhCCCCCCCeEEeecCCCCH-
Confidence            345567889999999999999998886542   11   469999999999999999999875   46788898864210 


Q ss_pred             hhhhhcccCCccccchhHHHHHHHHHHH-hhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcCCC--
Q 005987          218 QEYMHNCKTGLEYTSKLDEFENFVERIR-RYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHI--  294 (666)
Q Consensus       218 ~e~l~~~~~g~~~~s~~~~f~~fl~~a~-~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~~~--  294 (666)
                       +.+.....|..-.    .|   ..... +.+.+      ....+.+|+|||++.+...     ++..|..+++.+..  
T Consensus       261 -~~~~~~lfg~~~~----~~---~~~~~~~~g~~------~~a~~GtL~ldei~~L~~~-----~Q~~Ll~~l~~~~~~~  321 (534)
T TIGR01817       261 -TLLESELFGHEKG----AF---TGAIAQRKGRF------ELADGGTLFLDEIGEISPA-----FQAKLLRVLQEGEFER  321 (534)
T ss_pred             -HHHHHHHcCCCCC----cc---CCCCcCCCCcc------cccCCCeEEEechhhCCHH-----HHHHHHHHHhcCcEEE
Confidence             0000000010000    00   00000 00000      0012347999999988643     23334445544321  


Q ss_pred             ----------ceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCC--HHHHHHHHHHHHHH----hC--CCC
Q 005987          295 ----------PTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPIT--NGSIKRTLSKICRQ----EQ--YSL  356 (666)
Q Consensus       295 ----------PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s--~~~i~kiL~~I~~~----e~--i~v  356 (666)
                                ..+|++++......  .....+  ...++.+.....|.++|+.  .++|..++...+.+    .+  +.+
T Consensus       322 ~~~~~~~~~~~riI~~s~~~l~~~--~~~~~f--~~~L~~rl~~~~i~lPpLreR~eDi~~L~~~~l~~~~~~~~~~~~~  397 (534)
T TIGR01817       322 VGGNRTLKVDVRLVAATNRDLEEA--VAKGEF--RADLYYRINVVPIFLPPLRERREDIPLLAEAFLEKFNRENGRPLTI  397 (534)
T ss_pred             CCCCceEeecEEEEEeCCCCHHHH--HHcCCC--CHHHHHHhcCCeeeCCCcccccccHHHHHHHHHHHHHHHcCCCCCC
Confidence                      12333332111000  000011  0223333345678898887  45665555554432    22  568


Q ss_pred             CHHHHHHHHHHc-CCcHHHHHHHHHHHhcC
Q 005987          357 STEQIDLVAQAS-GGDIRQAITSLQFSSLK  385 (666)
Q Consensus       357 ~~~~l~~Ia~~s-~GDIR~AIn~LQf~~~~  385 (666)
                      ++++++.|.... .|++|..-|.++.++..
T Consensus       398 s~~a~~~L~~~~WPGNvrEL~~v~~~a~~~  427 (534)
T TIGR01817       398 TPSAIRVLMSCKWPGNVRELENCLERTATL  427 (534)
T ss_pred             CHHHHHHHHhCCCCChHHHHHHHHHHHHHh
Confidence            999999999885 79999999999988753

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.

>KOG2680 consensus DNA helicase TIP49, TBP-interacting protein [Transcription]

Probab=98.68  E-value=8.2e-08  Score=97.61  Aligned_cols=115  Identities=20%  Similarity=0.348  Sum_probs=83.8

Q ss_pred             ceEEEEeCCCCCcchhHHHHHHHHHHHHHhcCCCceEEEEecCCCCCC--ccc-hhhhhhHHHHHHhhcCeeEEEeCCCC
Q 005987          261 SAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHIPTAVVLTECGKADS--VDS-TAQSFEELQSILVDAGARKVALNPIT  337 (666)
Q Consensus       261 ~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~~~PiViIit~~~~~~s--~d~-~~r~l~~L~s~L~r~r~~~I~F~p~s  337 (666)
                      |-||||||+++++-. .|.    .|...++..-.|++++.++......  .++ ..+-++  ..+|.  |..+|.-.|++
T Consensus       289 pGVLFIDEvHMLDIE-cFs----FlNrAlE~d~~PiiimaTNrgit~iRGTn~~SphGiP--~D~lD--R~lII~t~py~  359 (454)
T KOG2680|consen  289 PGVLFIDEVHMLDIE-CFS----FLNRALENDMAPIIIMATNRGITRIRGTNYRSPHGIP--IDLLD--RMLIISTQPYT  359 (454)
T ss_pred             cceEEEeeehhhhhH-HHH----HHHHHhhhccCcEEEEEcCCceEEeecCCCCCCCCCc--HHHhh--hhheeecccCc
Confidence            669999999987532 222    3556667777899999988653211  111 112221  23444  37899999999


Q ss_pred             HHHHHHHHHHHHHHhCCCCCHHHHHHHHHH-cCCcHHHHHHHHHHHhc
Q 005987          338 NGSIKRTLSKICRQEQYSLSTEQIDLVAQA-SGGDIRQAITSLQFSSL  384 (666)
Q Consensus       338 ~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~-s~GDIR~AIn~LQf~~~  384 (666)
                      .++++++|+..|..|.+.+++++++.|... ..-.+|.||+.+-.++.
T Consensus       360 ~~d~~~IL~iRc~EEdv~m~~~A~d~Lt~i~~~tsLRYai~Lit~a~~  407 (454)
T KOG2680|consen  360 EEDIKKILRIRCQEEDVEMNPDALDLLTKIGEATSLRYAIHLITAASL  407 (454)
T ss_pred             HHHHHHHHHhhhhhhccccCHHHHHHHHHhhhhhhHHHHHHHHHHHHH
Confidence            999999999999999999999999999876 44679999998865543

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

Probab=98.67  E-value=3.2e-07  Score=84.55  Aligned_cols=53  Identities=30%  Similarity=0.435  Sum_probs=40.7

Q ss_pred             cCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcCCC
Q 005987          153 VQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL---GARLYEWDTPT  213 (666)
Q Consensus       153 g~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~nasd  213 (666)
                      +++..+..+..++...        ..+.++|+||||||||++++.+++.+   +..++.++...
T Consensus         2 ~~~~~~~~i~~~~~~~--------~~~~v~i~G~~G~GKT~l~~~i~~~~~~~~~~v~~~~~~~   57 (151)
T cd00009           2 GQEEAIEALREALELP--------PPKNLLLYGPPGTGKTTLARAIANELFRPGAPFLYLNASD   57 (151)
T ss_pred             chHHHHHHHHHHHhCC--------CCCeEEEECCCCCCHHHHHHHHHHHhhcCCCCeEEEehhh
Confidence            4556666666666531        12589999999999999999999998   78888777654

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.

>PRK07276 DNA polymerase III subunit delta'; Validated

Probab=98.64  E-value=1.5e-06  Score=90.87  Aligned_cols=185  Identities=13%  Similarity=0.136  Sum_probs=106.3

Q ss_pred             cCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEE-EcCCCchhhhhhhhc-ccCCc--
Q 005987          153 VQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYE-WDTPTPTIWQEYMHN-CKTGL--  228 (666)
Q Consensus       153 g~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE-~nasd~~~~~e~l~~-~~~g~--  228 (666)
                      .|+..++.++..+..      ++.+ +.+||+||  +||+++|+.+|+.+-+.-.. ..+...+.....+.+ ....+  
T Consensus         6 ~q~~~~~~L~~~~~~------~rl~-hAyLf~G~--~G~~~~A~~~A~~llC~~~~~~~~Cg~C~~C~~i~~~~HPD~~~   76 (290)
T PRK07276          6 KQPKVFQRFQTILEQ------DRLN-HAYLFSGD--FASFEMALFLAQSLFCEQKEGVLPCGHCRSCRLIEQGEFSDVTV   76 (290)
T ss_pred             HHHHHHHHHHHHHHc------CCcc-eeeeeeCC--ccHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHhcCCCCCeee
Confidence            467777888887776      6776 78999996  68999999999998543110 000000111111100 00000  


Q ss_pred             ----cccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcCCCceEEEEecCC
Q 005987          229 ----EYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHIPTAVVLTECG  304 (666)
Q Consensus       229 ----~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~~~PiViIit~~~  304 (666)
                          .-.-.+++++++...+...+        ..+..+|+|||++|.+...     ..++|++.++.....+++|....+
T Consensus        77 i~p~~~~I~idqIR~l~~~~~~~p--------~~~~~kV~II~~ad~m~~~-----AaNaLLKtLEEPp~~t~~iL~t~~  143 (290)
T PRK07276         77 IEPQGQVIKTDTIRELVKNFSQSG--------YEGKQQVFIIKDADKMHVN-----AANSLLKVIEEPQSEIYIFLLTND  143 (290)
T ss_pred             ecCCCCcCCHHHHHHHHHHHhhCc--------ccCCcEEEEeehhhhcCHH-----HHHHHHHHhcCCCCCeEEEEEECC
Confidence                00123566666666553221        1124579999999998643     334577777776544444443322


Q ss_pred             CCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCcHHHHHHHH
Q 005987          305 KADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASGGDIRQAITSL  379 (666)
Q Consensus       305 ~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~s~GDIR~AIn~L  379 (666)
                             ..+.++.|++     ||+.|+|.+ +.+.+.++|.    .+|+  +.+....++..+ |.+..|+..+
T Consensus       144 -------~~~lLpTI~S-----Rcq~i~f~~-~~~~~~~~L~----~~g~--~~~~a~~la~~~-~s~~~A~~l~  198 (290)
T PRK07276        144 -------ENKVLPTIKS-----RTQIFHFPK-NEAYLIQLLE----QKGL--LKTQAELLAKLA-QSTSEAEKLA  198 (290)
T ss_pred             -------hhhCchHHHH-----cceeeeCCC-cHHHHHHHHH----HcCC--ChHHHHHHHHHC-CCHHHHHHHh
Confidence                   2345555555     699999976 6666665554    5554  444444455544 6788887665

>PRK12377 putative replication protein; Provisional

Probab=98.62  E-value=6.1e-07  Score=92.04  Aligned_cols=64  Identities=20%  Similarity=0.323  Sum_probs=44.2

Q ss_pred             cCCCCccccc----cCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcCC
Q 005987          143 YKPRSLEELA----VQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL---GARLYEWDTP  212 (666)
Q Consensus       143 Y~P~sl~eLv----g~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~nas  212 (666)
                      |.-.+|+.+.    ++...+..+..+++.+..   +   ...++|+||||||||+++.++|+++   |..++.++.+
T Consensus        68 ~~~~tFdnf~~~~~~~~~a~~~a~~~a~~~~~---~---~~~l~l~G~~GtGKThLa~AIa~~l~~~g~~v~~i~~~  138 (248)
T PRK12377         68 HRKCSFANYQVQNDGQRYALSQAKSIADELMT---G---CTNFVFSGKPGTGKNHLAAAIGNRLLAKGRSVIVVTVP  138 (248)
T ss_pred             cccCCcCCcccCChhHHHHHHHHHHHHHHHHh---c---CCeEEEECCCCCCHHHHHHHHHHHHHHcCCCeEEEEHH
Confidence            3334555554    344456666666666542   1   1479999999999999999999998   6677666654

>PRK05818 DNA polymerase III subunit delta'; Validated

Probab=98.60  E-value=1.6e-06  Score=88.63  Aligned_cols=170  Identities=11%  Similarity=0.080  Sum_probs=99.3

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCchhhhhhhh-cccCCccc------cchhHHHHHHHHHHHhhcCCC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTIWQEYMH-NCKTGLEY------TSKLDEFENFVERIRRYGSTS  251 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~~~~e~l~-~~~~g~~~------~s~~~~f~~fl~~a~~~~~l~  251 (666)
                      +.+||+||.|+||..+|..+|+.+-+.--. .+...+.....+. .......+      .-..++++++.+.+. +.+  
T Consensus         8 HA~Lf~G~~G~G~~~lA~~~A~~llC~~~~-~~Cg~C~sC~~i~~~~HPDl~~i~p~~~~I~id~ir~l~~~l~-~~s--   83 (261)
T PRK05818          8 HPLLLIERKGSFLKPFLYEYLTSIVCTKAN-GFCKTCESCLKILNGKYNDFYLIFDQKNPIKKEDALSIINKLN-RPS--   83 (261)
T ss_pred             cceeeeCCCCCcHHHHHHHHHHHHcCCCCC-CCCCCCHHHHHHhcCCCCCEEEecCCcccCCHHHHHHHHHHHc-cCc--
Confidence            789999999999999999999998543111 0011111111110 00011110      123456666655543 110  


Q ss_pred             CCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcCCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEE
Q 005987          252 PSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKV  331 (666)
Q Consensus       252 ~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I  331 (666)
                        .  ..+..+|++|++++.+...     ..++|+++++....-+++|....+       ..+.++.+++     ||+.+
T Consensus        84 --~--e~~~~KV~II~~ae~m~~~-----AaNaLLK~LEEPp~~t~fiLit~~-------~~~lLpTI~S-----RCq~~  142 (261)
T PRK05818         84 --V--ESNGKKIYIIYGIEKLNKQ-----SANSLLKLIEEPPKNTYGIFTTRN-------ENNILNTILS-----RCVQY  142 (261)
T ss_pred             --h--hcCCCEEEEeccHhhhCHH-----HHHHHHHhhcCCCCCeEEEEEECC-------hHhCchHhhh-----heeee
Confidence              0  1123579999999988643     334577777776554555544322       2344555554     69999


Q ss_pred             EeCCC----------CHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCcHHHHHHHHHHH
Q 005987          332 ALNPI----------TNGSIKRTLSKICRQEQYSLSTEQIDLVAQASGGDIRQAITSLQFS  382 (666)
Q Consensus       332 ~F~p~----------s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~s~GDIR~AIn~LQf~  382 (666)
                      .|.++          .+.++.+.|...     ..+++    .++..++|++..|+..++.+
T Consensus       143 ~~~~~~~~~~~~~~~~~~~i~~~L~~~-----~~~d~----~i~~~a~g~~~~a~~l~~~l  194 (261)
T PRK05818        143 VVLSKEKKVPFKVESNDRYFQYILLSF-----YSVDE----QLQAYNNGSFSKLKNIIETL  194 (261)
T ss_pred             ecCChhhhcccccccChHHHHHHHHHc-----cCccH----HHHHHcCCCHHHHHHHHHHH
Confidence            99988          444445444321     22443    67778899999999999965

>KOG0736 consensus Peroxisome assembly factor 2 containing the AAA+-type ATPase domain [Posttranslational modification, protein turnover, chaperones]

Probab=98.58  E-value=8.1e-07  Score=100.40  Aligned_cols=185  Identities=21%  Similarity=0.248  Sum_probs=111.0

Q ss_pred             cCHHHHHHHHHHHHHhhcCCC-CCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCchhhhhhhhcccCCcccc
Q 005987          153 VQRKKVEEVRAWFEERLGDSK-DKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTIWQEYMHNCKTGLEYT  231 (666)
Q Consensus       153 g~~k~i~el~~wL~~~~~~~~-g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~~~~e~l~~~~~g~~~~  231 (666)
                      ..+.++.++...+......+. +..-...+||+|+|||||||+++++|+++|..++|+.+..      ...+.     ..
T Consensus       405 ~~~~~~~~l~~vl~p~~~~s~~~~~~~~~vLLhG~~g~GK~t~V~~vas~lg~h~~evdc~e------l~~~s-----~~  473 (953)
T KOG0736|consen  405 GLEAKVLELVAVLSPQKQPSGALLTLNPSVLLHGPPGSGKTTVVRAVASELGLHLLEVDCYE------LVAES-----AS  473 (953)
T ss_pred             cchHHHHHHHHHhCcccCcchhccccceEEEEeCCCCCChHHHHHHHHHHhCCceEeccHHH------Hhhcc-----cc
Confidence            456666666666654332210 0011247999999999999999999999999999998643      11111     11


Q ss_pred             chhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCc----chhHHHHHHHHHHHHHh----c-CCCceEEEEec
Q 005987          232 SKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTN----GRTAFERLRQCLLLLVR----S-THIPTAVVLTE  302 (666)
Q Consensus       232 s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~----~~~~~~~l~~~L~~l~~----~-~~~PiViIit~  302 (666)
                      .....+..+..+++++.            +.||++-.+|-+.    +..+ .++...++.++.    . ...+++++++.
T Consensus       474 ~~etkl~~~f~~a~~~~------------pavifl~~~dvl~id~dgged-~rl~~~i~~~ls~e~~~~~~~~~ivv~t~  540 (953)
T KOG0736|consen  474 HTETKLQAIFSRARRCS------------PAVLFLRNLDVLGIDQDGGED-ARLLKVIRHLLSNEDFKFSCPPVIVVATT  540 (953)
T ss_pred             hhHHHHHHHHHHHhhcC------------ceEEEEeccceeeecCCCchh-HHHHHHHHHHHhcccccCCCCceEEEEec
Confidence            22345667788887663            6799999888542    2222 234445555544    1 22234444443


Q ss_pred             CCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCcHH
Q 005987          303 CGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASGGDIR  373 (666)
Q Consensus       303 ~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~s~GDIR  373 (666)
                       +...      ..-..+++.    ....|.+..++.++...+|+-....+.+. .+..++.++..+.|=.+
T Consensus       541 -~s~~------~lp~~i~~~----f~~ei~~~~lse~qRl~iLq~y~~~~~~n-~~v~~k~~a~~t~gfs~  599 (953)
T KOG0736|consen  541 -SSIE------DLPADIQSL----FLHEIEVPALSEEQRLEILQWYLNHLPLN-QDVNLKQLARKTSGFSF  599 (953)
T ss_pred             -cccc------cCCHHHHHh----hhhhccCCCCCHHHHHHHHHHHHhccccc-hHHHHHHHHHhcCCCCH
Confidence             2211      111123332    35689999999999999999877655432 23445666666665444

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=98.57  E-value=6.6e-07  Score=81.51  Aligned_cols=86  Identities=19%  Similarity=0.207  Sum_probs=51.8

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCc---EEEEcCCCchhh--hhh-hhcccCCccccchhHHHHHHHHHHHhhcCCCC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGAR---LYEWDTPTPTIW--QEY-MHNCKTGLEYTSKLDEFENFVERIRRYGSTSP  252 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~---viE~nasd~~~~--~e~-l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~  252 (666)
                      +.++|+|||||||||+++.+|+.+...   ++.++.......  ... ................+...+..+...     
T Consensus         3 ~~~~l~G~~G~GKTtl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----   77 (148)
T smart00382        3 EVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKASGSGELRLRLALALARKL-----   77 (148)
T ss_pred             CEEEEECCCCCcHHHHHHHHHhccCCCCCCEEEECCEEccccCHHHHHhhhhhccCCCCCHHHHHHHHHHHHHhc-----
Confidence            589999999999999999999999765   777665432110  000 000001111122333455555555422     


Q ss_pred             CCCCCCCCceEEEEeCCCCCcchh
Q 005987          253 SIPGESKSSAILLIDDLPVTNGRT  276 (666)
Q Consensus       253 s~~~~~~~~~IIlIDEid~l~~~~  276 (666)
                             .+.+|+|||++.+....
T Consensus        78 -------~~~viiiDei~~~~~~~   94 (148)
T smart00382       78 -------KPDVLILDEITSLLDAE   94 (148)
T ss_pred             -------CCCEEEEECCcccCCHH
Confidence                   13699999999876543

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.

>PRK08116 hypothetical protein; Validated

Probab=98.51  E-value=9.1e-07  Score=92.07  Aligned_cols=68  Identities=22%  Similarity=0.280  Sum_probs=44.8

Q ss_pred             cCCCCcccccc---CHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcCCC
Q 005987          143 YKPRSLEELAV---QRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL---GARLYEWDTPT  213 (666)
Q Consensus       143 Y~P~sl~eLvg---~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~nasd  213 (666)
                      |+-.+|+.+..   +...+..++.+++.+...   ......++|+||+|+|||+++.++|+++   +..++.++.++
T Consensus        79 ~~~~tFdnf~~~~~~~~a~~~a~~y~~~~~~~---~~~~~gl~l~G~~GtGKThLa~aia~~l~~~~~~v~~~~~~~  152 (268)
T PRK08116         79 FRNSTFENFLFDKGSEKAYKIARKYVKKFEEM---KKENVGLLLWGSVGTGKTYLAACIANELIEKGVPVIFVNFPQ  152 (268)
T ss_pred             HHhcchhcccCChHHHHHHHHHHHHHHHHHhh---ccCCceEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEEHHH
Confidence            33444554432   334556666666665321   1112469999999999999999999987   67777776543

>PRK08939 primosomal protein DnaI; Reviewed

Probab=98.49  E-value=7.8e-07  Score=94.21  Aligned_cols=67  Identities=21%  Similarity=0.252  Sum_probs=46.6

Q ss_pred             ccCCCCccccccC----HHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcCC
Q 005987          142 KYKPRSLEELAVQ----RKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL---GARLYEWDTP  212 (666)
Q Consensus       142 KY~P~sl~eLvg~----~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~nas  212 (666)
                      .|...+|+++...    .........|+.....   +.. .+.++|+||+|||||+++.++|+++   |+.+..+..+
T Consensus       120 ~~~~atf~~~~~~~~~~~~~~~~~~~fi~~~~~---~~~-~~gl~L~G~~G~GKThLa~Aia~~l~~~g~~v~~~~~~  193 (306)
T PRK08939        120 DLLQASLADIDLDDRDRLDALMAALDFLEAYPP---GEK-VKGLYLYGDFGVGKSYLLAAIANELAKKGVSSTLLHFP  193 (306)
T ss_pred             hHhcCcHHHhcCCChHHHHHHHHHHHHHHHhhc---cCC-CCeEEEECCCCCCHHHHHHHHHHHHHHcCCCEEEEEHH
Confidence            3445666666543    3445556667765432   212 2689999999999999999999998   7777776654

>PF05621 TniB: Bacterial TniB protein; InterPro: IPR008868 This family consists of several bacterial TniB NTP-binding proteins

Probab=98.49  E-value=1.6e-05  Score=82.85  Aligned_cols=184  Identities=17%  Similarity=0.211  Sum_probs=102.1

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcC---------CcEEEEcCCCc----hhhhhhhhcccCCccccchhHHHH-HHHHHH
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLG---------ARLYEWDTPTP----TIWQEYMHNCKTGLEYTSKLDEFE-NFVERI  244 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg---------~~viE~nasd~----~~~~e~l~~~~~g~~~~s~~~~f~-~fl~~a  244 (666)
                      +.+||+|++|.|||++++.+++...         +.|+.+.+|..    +.|...+................. ..+.-.
T Consensus        62 p~lLivG~snnGKT~Ii~rF~~~hp~~~d~~~~~~PVv~vq~P~~p~~~~~Y~~IL~~lgaP~~~~~~~~~~~~~~~~ll  141 (302)
T PF05621_consen   62 PNLLIVGDSNNGKTMIIERFRRLHPPQSDEDAERIPVVYVQMPPEPDERRFYSAILEALGAPYRPRDRVAKLEQQVLRLL  141 (302)
T ss_pred             CceEEecCCCCcHHHHHHHHHHHCCCCCCCCCccccEEEEecCCCCChHHHHHHHHHHhCcccCCCCCHHHHHHHHHHHH
Confidence            4799999999999999999998762         34555554431    222222222211111122222222 122222


Q ss_pred             HhhcCCCCCCCCCCCCceEEEEeCCCCC-cch-hHHHHHHHHHHHHHhcCCCceEEEEecCCCCCCccchhhhhhHHHHH
Q 005987          245 RRYGSTSPSIPGESKSSAILLIDDLPVT-NGR-TAFERLRQCLLLLVRSTHIPTAVVLTECGKADSVDSTAQSFEELQSI  322 (666)
Q Consensus       245 ~~~~~l~~s~~~~~~~~~IIlIDEid~l-~~~-~~~~~l~~~L~~l~~~~~~PiViIit~~~~~~s~d~~~r~l~~L~s~  322 (666)
                      +..            ..++|+|||++++ .+. ...+.+.++|..+.+..+.|+|++-+..        ....+.. ..-
T Consensus       142 r~~------------~vrmLIIDE~H~lLaGs~~~qr~~Ln~LK~L~NeL~ipiV~vGt~~--------A~~al~~-D~Q  200 (302)
T PF05621_consen  142 RRL------------GVRMLIIDEFHNLLAGSYRKQREFLNALKFLGNELQIPIVGVGTRE--------AYRALRT-DPQ  200 (302)
T ss_pred             HHc------------CCcEEEeechHHHhcccHHHHHHHHHHHHHHhhccCCCeEEeccHH--------HHHHhcc-CHH
Confidence            222            2469999999985 332 2334566778888888888988653321        0111111 122


Q ss_pred             HhhcCeeEEEeCCCCHH-HHHHHHHHHHHHhC----CCC-CHHHHHHHHHHcCCcHHHHHHHHHHHhc
Q 005987          323 LVDAGARKVALNPITNG-SIKRTLSKICRQEQ----YSL-STEQIDLVAQASGGDIRQAITSLQFSSL  384 (666)
Q Consensus       323 L~r~r~~~I~F~p~s~~-~i~kiL~~I~~~e~----i~v-~~~~l~~Ia~~s~GDIR~AIn~LQf~~~  384 (666)
                      +.+ |+..+.+++-..+ +..+.|...-..-.    -.+ +++....|...|+|-|-...+.|..+|.
T Consensus       201 La~-RF~~~~Lp~W~~d~ef~~LL~s~e~~LPLr~~S~l~~~~la~~i~~~s~G~iG~l~~ll~~aA~  267 (302)
T PF05621_consen  201 LAS-RFEPFELPRWELDEEFRRLLASFERALPLRKPSNLASPELARRIHERSEGLIGELSRLLNAAAI  267 (302)
T ss_pred             HHh-ccCCccCCCCCCCcHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHcCCchHHHHHHHHHHHH
Confidence            222 4666666655433 33444433322211    112 4677789999999988888877777664

TniB is a probable ATP-binding protein [] which is involved in Tn5053 mercury resistance transposition [].

>PRK13407 bchI magnesium chelatase subunit I; Provisional

Probab=98.47  E-value=5e-06  Score=88.92  Aligned_cols=51  Identities=22%  Similarity=0.314  Sum_probs=41.7

Q ss_pred             CCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc
Q 005987          144 KPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       144 ~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      .|..|++++|++..++.+.-.+-..     |   ..++||+||||+||||+|+++|+-+
T Consensus         3 ~~~~f~~i~Gq~~~~~~l~~~~~~~-----~---~~~vLl~G~pG~gKT~lar~la~ll   53 (334)
T PRK13407          3 KPFPFSAIVGQEEMKQAMVLTAIDP-----G---IGGVLVFGDRGTGKSTAVRALAALL   53 (334)
T ss_pred             CCCCHHHhCCHHHHHHHHHHHHhcc-----C---CCcEEEEcCCCCCHHHHHHHHHHHC
Confidence            5888999999999988776543210     2   1479999999999999999999998

>TIGR02974 phageshock_pspF psp operon transcriptional activator PspF

Probab=98.46  E-value=5.7e-06  Score=88.72  Aligned_cols=205  Identities=14%  Similarity=0.193  Sum_probs=112.5

Q ss_pred             cccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcCCCch--hhhhhhhccc
Q 005987          151 LAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL---GARLYEWDTPTPT--IWQEYMHNCK  225 (666)
Q Consensus       151 Lvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~nasd~~--~~~e~l~~~~  225 (666)
                      |+|+...++++..-++....   ..   ..+||+|++||||+++|+++-..-   +..++.+|+....  .+...+....
T Consensus         1 liG~S~~m~~~~~~~~~~a~---~~---~pVLI~GE~GtGK~~lAr~iH~~s~r~~~pfv~vnc~~~~~~~l~~~lfG~~   74 (329)
T TIGR02974         1 LIGESNAFLEVLEQVSRLAP---LD---RPVLIIGERGTGKELIAARLHYLSKRWQGPLVKLNCAALSENLLDSELFGHE   74 (329)
T ss_pred             CCcCCHHHHHHHHHHHHHhC---CC---CCEEEECCCCChHHHHHHHHHHhcCccCCCeEEEeCCCCChHHHHHHHhccc
Confidence            46777777888877776532   11   469999999999999999987654   4578888886421  0000000000


Q ss_pred             CCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcCC-----------C
Q 005987          226 TGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTH-----------I  294 (666)
Q Consensus       226 ~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~~-----------~  294 (666)
                      .|. ++.....-..+++.               .....|+|||++.+...     ++..|..+++...           .
T Consensus        75 ~g~-~~ga~~~~~G~~~~---------------a~gGtL~Ldei~~L~~~-----~Q~~Ll~~l~~~~~~~~g~~~~~~~  133 (329)
T TIGR02974        75 AGA-FTGAQKRHQGRFER---------------ADGGTLFLDELATASLL-----VQEKLLRVIEYGEFERVGGSQTLQV  133 (329)
T ss_pred             ccc-ccCcccccCCchhh---------------CCCCEEEeCChHhCCHH-----HHHHHHHHHHcCcEEecCCCceecc
Confidence            000 00000000000000               12347999999988643     2333444444432           1


Q ss_pred             c-eEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCC--HHHHHHHHHHH----HHHhC----CCCCHHHHHH
Q 005987          295 P-TAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPIT--NGSIKRTLSKI----CRQEQ----YSLSTEQIDL  363 (666)
Q Consensus       295 P-iViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s--~~~i~kiL~~I----~~~e~----i~v~~~~l~~  363 (666)
                      . .||++++.......  ....+  -..++.+.....|.++|+.  .++|..++...    +.+.+    ..+++++++.
T Consensus       134 ~~RiI~at~~~l~~~~--~~g~f--r~dL~~rl~~~~i~lPpLReR~eDI~~L~~~fl~~~~~~~~~~~~~~ls~~a~~~  209 (329)
T TIGR02974       134 DVRLVCATNADLPALA--AEGRF--RADLLDRLAFDVITLPPLRERQEDIMLLAEHFAIRMARELGLPLFPGFTPQAREQ  209 (329)
T ss_pred             ceEEEEechhhHHHHh--hcCch--HHHHHHHhcchhcCCCchhhhhhhHHHHHHHHHHHHHHHhCCCCCCCcCHHHHHH
Confidence            1 23333321110000  00011  1233333335678888887  45665554443    33333    3589999999


Q ss_pred             HHHHc-CCcHHHHHHHHHHHhcCC
Q 005987          364 VAQAS-GGDIRQAITSLQFSSLKQ  386 (666)
Q Consensus       364 Ia~~s-~GDIR~AIn~LQf~~~~~  386 (666)
                      |.... .|++|..-|.++-++...
T Consensus       210 L~~y~WPGNvrEL~n~i~~~~~~~  233 (329)
T TIGR02974       210 LLEYHWPGNVRELKNVVERSVYRH  233 (329)
T ss_pred             HHhCCCCchHHHHHHHHHHHHHhC
Confidence            99886 799999999998887643

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

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

Probab=98.44  E-value=3.8e-07  Score=83.71  Aligned_cols=107  Identities=21%  Similarity=0.299  Sum_probs=58.7

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc--------CCcEEEEcCCCchhhh----hhhhcccCCccc-cchhHHHHHHHHHHH
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL--------GARLYEWDTPTPTIWQ----EYMHNCKTGLEY-TSKLDEFENFVERIR  245 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel--------g~~viE~nasd~~~~~----e~l~~~~~g~~~-~s~~~~f~~fl~~a~  245 (666)
                      +.++|+||||+|||++++.+++++        ...++.++.+......    ..+......... ......+..+...+.
T Consensus         5 ~~~~i~G~~G~GKT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~l~~~~~~~l~   84 (131)
T PF13401_consen    5 RILVISGPPGSGKTTLIKRLARQLNAEAEIKNHPDVIYVNCPSSRTPRDFAQEILEALGLPLKSRQTSDELRSLLIDALD   84 (131)
T ss_dssp             --EEEEE-TTSSHHHHHHHHHHHHHHHHHHCCCEEEEEEEHHHHSSHHHHHHHHHHHHT-SSSSTS-HHHHHHHHHHHHH
T ss_pred             cccEEEcCCCCCHHHHHHHHHHHhHHhhhccCCCcEEEEEeCCCCCHHHHHHHHHHHhCccccccCCHHHHHHHHHHHHH
Confidence            689999999999999999999998        6778877765433221    111111111111 112222333344443


Q ss_pred             hhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcCCCceEEEEe
Q 005987          246 RYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHIPTAVVLT  301 (666)
Q Consensus       246 ~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~~~PiViIit  301 (666)
                      ...            ..+|+|||+|.+. .   ..+.+.|..+.+....++|++.+
T Consensus        85 ~~~------------~~~lviDe~~~l~-~---~~~l~~l~~l~~~~~~~vvl~G~  124 (131)
T PF13401_consen   85 RRR------------VVLLVIDEADHLF-S---DEFLEFLRSLLNESNIKVVLVGT  124 (131)
T ss_dssp             HCT------------EEEEEEETTHHHH-T---HHHHHHHHHHTCSCBEEEEEEES
T ss_pred             hcC------------CeEEEEeChHhcC-C---HHHHHHHHHHHhCCCCeEEEEEC
Confidence            322            2599999999863 1   23444455666655555554433

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

Probab=98.44  E-value=3.3e-06  Score=90.61  Aligned_cols=53  Identities=21%  Similarity=0.280  Sum_probs=44.5

Q ss_pred             cccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCC
Q 005987          151 LAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPT  213 (666)
Q Consensus       151 Lvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd  213 (666)
                      +++.+..+..+..++..      |    +++||-||||||||++|+.+|+.++..++.++...
T Consensus        26 ~~g~~~~~~~~l~a~~~------~----~~vll~G~PG~gKT~la~~lA~~l~~~~~~i~~t~   78 (329)
T COG0714          26 VVGDEEVIELALLALLA------G----GHVLLEGPPGVGKTLLARALARALGLPFVRIQCTP   78 (329)
T ss_pred             eeccHHHHHHHHHHHHc------C----CCEEEECCCCccHHHHHHHHHHHhCCCeEEEecCC
Confidence            56777777777666654      2    57999999999999999999999999999998765

>PRK06835 DNA replication protein DnaC; Validated

Probab=98.43  E-value=4.1e-06  Score=89.51  Aligned_cols=52  Identities=25%  Similarity=0.329  Sum_probs=38.8

Q ss_pred             HHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcCCC
Q 005987          156 KKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL---GARLYEWDTPT  213 (666)
Q Consensus       156 k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~nasd  213 (666)
                      ..++..+.|++.+..   ..   +.|+|+||+|+|||+++.++|+++   |+.|+.+++++
T Consensus       167 ~~~~~~~~f~~~f~~---~~---~~Lll~G~~GtGKThLa~aIa~~l~~~g~~V~y~t~~~  221 (329)
T PRK06835        167 KILEKCKNFIENFDK---NN---ENLLFYGNTGTGKTFLSNCIAKELLDRGKSVIYRTADE  221 (329)
T ss_pred             HHHHHHHHHHHHHhc---cC---CcEEEECCCCCcHHHHHHHHHHHHHHCCCeEEEEEHHH
Confidence            344445566665432   11   579999999999999999999997   78888877654

>PHA02244 ATPase-like protein

Probab=98.43  E-value=1.1e-05  Score=86.46  Aligned_cols=32  Identities=31%  Similarity=0.468  Sum_probs=29.9

Q ss_pred             EEEEECCCCchHHHHHHHHHHHcCCcEEEEcC
Q 005987          180 VLVITGQAGVGKTATVRQIASHLGARLYEWDT  211 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkelg~~viE~na  211 (666)
                      .+||+||||||||++|+++|+.++..++.++.
T Consensus       121 PVLL~GppGtGKTtLA~aLA~~lg~pfv~In~  152 (383)
T PHA02244        121 PVFLKGGAGSGKNHIAEQIAEALDLDFYFMNA  152 (383)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHhCCCEEEEec
Confidence            59999999999999999999999999998874

>PF13173 AAA_14: AAA domain

Probab=98.42  E-value=2.1e-06  Score=79.12  Aligned_cols=123  Identities=17%  Similarity=0.268  Sum_probs=68.8

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcC--CcEEEEcCCCchhhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLG--ARLYEWDTPTPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPG  256 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg--~~viE~nasd~~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~  256 (666)
                      ++++|+||.||||||+++.+++++.  -+++.++..+.......             ...+.+.+.+.  ..        
T Consensus         3 ~~~~l~G~R~vGKTtll~~~~~~~~~~~~~~yi~~~~~~~~~~~-------------~~~~~~~~~~~--~~--------   59 (128)
T PF13173_consen    3 KIIILTGPRGVGKTTLLKQLAKDLLPPENILYINFDDPRDRRLA-------------DPDLLEYFLEL--IK--------   59 (128)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHhcccccceeeccCCHHHHHHh-------------hhhhHHHHHHh--hc--------
Confidence            6899999999999999999999986  67777776553221000             00011222111  10        


Q ss_pred             CCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcCCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCC
Q 005987          257 ESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPI  336 (666)
Q Consensus       257 ~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~  336 (666)
                        ....+|+|||++.+..      +...+..+.+....-.|+ ++.+...       .......+.+.. |...+++.|+
T Consensus        60 --~~~~~i~iDEiq~~~~------~~~~lk~l~d~~~~~~ii-~tgS~~~-------~l~~~~~~~l~g-r~~~~~l~Pl  122 (128)
T PF13173_consen   60 --PGKKYIFIDEIQYLPD------WEDALKFLVDNGPNIKII-LTGSSSS-------LLSKDIAESLAG-RVIEIELYPL  122 (128)
T ss_pred             --cCCcEEEEehhhhhcc------HHHHHHHHHHhccCceEE-EEccchH-------HHhhcccccCCC-eEEEEEECCC
Confidence              1246899999998742      333455555555221233 3332111       011122233333 5778899999


Q ss_pred             CHHHH
Q 005987          337 TNGSI  341 (666)
Q Consensus       337 s~~~i  341 (666)
                      +-.+.
T Consensus       123 sf~E~  127 (128)
T PF13173_consen  123 SFREF  127 (128)
T ss_pred             CHHHh
Confidence            87664

>PRK13531 regulatory ATPase RavA; Provisional

Probab=98.41  E-value=5.9e-06  Score=91.36  Aligned_cols=43  Identities=12%  Similarity=0.153  Sum_probs=35.7

Q ss_pred             cccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcC
Q 005987          151 LAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLG  203 (666)
Q Consensus       151 Lvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg  203 (666)
                      ++|+++.++.+...+..      +    .++||.||||||||++|++|++.++
T Consensus        22 i~gre~vI~lll~aala------g----~hVLL~GpPGTGKT~LAraLa~~~~   64 (498)
T PRK13531         22 LYERSHAIRLCLLAALS------G----ESVFLLGPPGIAKSLIARRLKFAFQ   64 (498)
T ss_pred             ccCcHHHHHHHHHHHcc------C----CCEEEECCCChhHHHHHHHHHHHhc
Confidence            57888888887776654      2    4799999999999999999999874

>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional

Probab=98.39  E-value=9.9e-06  Score=94.76  Aligned_cols=209  Identities=12%  Similarity=0.175  Sum_probs=119.6

Q ss_pred             CCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcCCCchhhhhhh
Q 005987          145 PRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL---GARLYEWDTPTPTIWQEYM  221 (666)
Q Consensus       145 P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~nasd~~~~~e~l  221 (666)
                      +.++++|+|....++++...++....   ..   ..+||+|++||||+++|+++.+..   +..++.+|+.....  +.+
T Consensus       321 ~~~~~~l~g~s~~~~~~~~~~~~~a~---~~---~pvli~Ge~GtGK~~~A~~ih~~s~r~~~pfv~vnc~~~~~--~~~  392 (638)
T PRK11388        321 SHTFDHMPQDSPQMRRLIHFGRQAAK---SS---FPVLLCGEEGVGKALLAQAIHNESERAAGPYIAVNCQLYPD--EAL  392 (638)
T ss_pred             cccccceEECCHHHHHHHHHHHHHhC---cC---CCEEEECCCCcCHHHHHHHHHHhCCccCCCeEEEECCCCCh--HHH
Confidence            34789999999999999888887543   11   359999999999999999998875   35788888764210  000


Q ss_pred             hcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcCCC-------
Q 005987          222 HNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHI-------  294 (666)
Q Consensus       222 ~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~~~-------  294 (666)
                      .....|...            .....+ ..+.+.  ...+..|+|||++.+...     ++..|..+++....       
T Consensus       393 ~~elfg~~~------------~~~~~~-~~g~~~--~a~~GtL~ldei~~l~~~-----~Q~~Ll~~l~~~~~~~~~~~~  452 (638)
T PRK11388        393 AEEFLGSDR------------TDSENG-RLSKFE--LAHGGTLFLEKVEYLSPE-----LQSALLQVLKTGVITRLDSRR  452 (638)
T ss_pred             HHHhcCCCC------------cCccCC-CCCcee--ECCCCEEEEcChhhCCHH-----HHHHHHHHHhcCcEEeCCCCc
Confidence            000001000            000000 000000  012347999999988643     22334444443321       


Q ss_pred             --c--e-EEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHH--HHHHHHHHHHHH----h--CCCCCHHHH
Q 005987          295 --P--T-AVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNG--SIKRTLSKICRQ----E--QYSLSTEQI  361 (666)
Q Consensus       295 --P--i-ViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~--~i~kiL~~I~~~----e--~i~v~~~~l  361 (666)
                        |  + ||.+++.......  ....+.  +.++.+.....|.++|+...  ++..++...+.+    .  .+.++++++
T Consensus       453 ~~~~~~riI~~t~~~l~~~~--~~~~f~--~dL~~~l~~~~i~lPpLreR~~Di~~L~~~~l~~~~~~~~~~~~~s~~a~  528 (638)
T PRK11388        453 LIPVDVRVIATTTADLAMLV--EQNRFS--RQLYYALHAFEITIPPLRMRREDIPALVNNKLRSLEKRFSTRLKIDDDAL  528 (638)
T ss_pred             eEEeeEEEEEeccCCHHHHH--hcCCCh--HHHhhhhceeEEeCCChhhhhhHHHHHHHHHHHHHHHHhCCCCCcCHHHH
Confidence              1  2 3333322110000  001111  22333334677888888764  455555544432    2  256899999


Q ss_pred             HHHHHHc-CCcHHHHHHHHHHHhcC
Q 005987          362 DLVAQAS-GGDIRQAITSLQFSSLK  385 (666)
Q Consensus       362 ~~Ia~~s-~GDIR~AIn~LQf~~~~  385 (666)
                      +.|.... .|++|..-|.|+.++..
T Consensus       529 ~~L~~y~WPGNvreL~~~l~~~~~~  553 (638)
T PRK11388        529 ARLVSYRWPGNDFELRSVIENLALS  553 (638)
T ss_pred             HHHHcCCCCChHHHHHHHHHHHHHh
Confidence            9999987 79999999999987753

>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=98.37  E-value=3.7e-06  Score=88.03  Aligned_cols=182  Identities=16%  Similarity=0.289  Sum_probs=91.2

Q ss_pred             CHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHH--c--CCcEEEE-cCCCc----hhhhhhhhcc
Q 005987          154 QRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASH--L--GARLYEW-DTPTP----TIWQEYMHNC  224 (666)
Q Consensus       154 ~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAke--l--g~~viE~-nasd~----~~~~e~l~~~  224 (666)
                      +++.+++|.++|....      ...+++.|+|++|+|||++|..+++.  .  .+..+-| +....    ......+...
T Consensus         1 re~~~~~l~~~L~~~~------~~~~~v~I~G~~G~GKT~LA~~~~~~~~~~~~f~~v~wv~~~~~~~~~~~~~~i~~~l   74 (287)
T PF00931_consen    1 REKEIEKLKDWLLDNS------NEVRVVAIVGMGGIGKTTLARQVARDLRIKNRFDGVIWVSLSKNPSLEQLLEQILRQL   74 (287)
T ss_dssp             -HHHHHHHHHHHHTTT------TSSEEEEEEESTTSSHHHHHHHHHCHHHHCCCCTEEEEEEEES-SCCHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHhhCCC------CCeEEEEEEcCCcCCcceeeeecccccccccccccccccccccccccccccccccccc
Confidence            4678899999998622      22379999999999999999999988  3  3444433 22111    1111111111


Q ss_pred             cCC---ccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcCCCceEEEEe
Q 005987          225 KTG---LEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHIPTAVVLT  301 (666)
Q Consensus       225 ~~g---~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~~~PiViIit  301 (666)
                      ...   .............+.+.   -         .+++.+||+|+++...   .+..+..    .+.......-+|+|
T Consensus        75 ~~~~~~~~~~~~~~~~~~~l~~~---L---------~~~~~LlVlDdv~~~~---~~~~l~~----~~~~~~~~~kilvT  135 (287)
T PF00931_consen   75 GEPDSSISDPKDIEELQDQLREL---L---------KDKRCLLVLDDVWDEE---DLEELRE----PLPSFSSGSKILVT  135 (287)
T ss_dssp             TCC-STSSCCSSHHHHHHHHHHH---H---------CCTSEEEEEEEE-SHH---HH-----------HCHHSS-EEEEE
T ss_pred             cccccccccccccccccccchhh---h---------ccccceeeeeeecccc---ccccccc----cccccccccccccc
Confidence            111   00011111222222111   0         1237899999998642   2222222    11111111223444


Q ss_pred             cCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhC---CCCCHHHHHHHHHHcCCcHH
Q 005987          302 ECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQ---YSLSTEQIDLVAQASGGDIR  373 (666)
Q Consensus       302 ~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~---i~v~~~~l~~Ia~~s~GDIR  373 (666)
                      ....        ....    .... ....+.+.+++.++..+.+.+.+....   ....++..+.|++.|+|-.=
T Consensus       136 TR~~--------~v~~----~~~~-~~~~~~l~~L~~~ea~~L~~~~~~~~~~~~~~~~~~~~~~i~~~c~glPL  197 (287)
T PF00931_consen  136 TRDR--------SVAG----SLGG-TDKVIELEPLSEEEALELFKKRAGRKESESPEDLEDLAKEIVEKCGGLPL  197 (287)
T ss_dssp             ESCG--------GGGT----THHS-CEEEEECSS--HHHHHHHHHHHHTSHS----TTSCTHHHHHHHHTTT-HH
T ss_pred             cccc--------cccc----cccc-cccccccccccccccccccccccccccccccccccccccccccccccccc
Confidence            4221        0111    1111 167899999999999999998876544   12224567899999977443

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.

>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=98.35  E-value=5.4e-07  Score=83.95  Aligned_cols=41  Identities=24%  Similarity=0.441  Sum_probs=33.7

Q ss_pred             EEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCchhhhhh
Q 005987          180 VLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTIWQEY  220 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~~~~e~  220 (666)
                      .+||+||||||||++|+.+|+.++..++.++.+......+.
T Consensus         1 ~vlL~G~~G~GKt~l~~~la~~~~~~~~~i~~~~~~~~~dl   41 (139)
T PF07728_consen    1 PVLLVGPPGTGKTTLARELAALLGRPVIRINCSSDTTEEDL   41 (139)
T ss_dssp             EEEEEESSSSSHHHHHHHHHHHHTCEEEEEE-TTTSTHHHH
T ss_pred             CEEEECCCCCCHHHHHHHHHHHhhcceEEEEeccccccccc
Confidence            48999999999999999999999999998887764443333

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.

>TIGR02329 propionate_PrpR propionate catabolism operon regulatory protein PrpR

Probab=98.32  E-value=2e-05  Score=89.37  Aligned_cols=210  Identities=17%  Similarity=0.244  Sum_probs=117.7

Q ss_pred             CCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcCCCch--hhhh
Q 005987          145 PRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL---GARLYEWDTPTPT--IWQE  219 (666)
Q Consensus       145 P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~nasd~~--~~~e  219 (666)
                      ..++++|+|....++++..-++....   .  . ..+||+|++||||+.+|+++-+.-   +..++.+|+....  .+..
T Consensus       208 ~~~f~~iiG~S~~m~~~~~~i~~~A~---~--~-~pVLI~GE~GTGKe~lA~~IH~~S~r~~~pfv~inC~~l~e~lles  281 (526)
T TIGR02329       208 RYRLDDLLGASAPMEQVRALVRLYAR---S--D-ATVLILGESGTGKELVAQAIHQLSGRRDFPFVAINCGAIAESLLEA  281 (526)
T ss_pred             ccchhheeeCCHHHHHHHHHHHHHhC---C--C-CcEEEECCCCcCHHHHHHHHHHhcCcCCCCEEEeccccCChhHHHH
Confidence            35688999999999999998876432   1  1 469999999999999999998753   5678888886421  0100


Q ss_pred             hhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcCCC-----
Q 005987          220 YMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHI-----  294 (666)
Q Consensus       220 ~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~~~-----  294 (666)
                      .+.....|.-.......-..+++.               .....|+|||++.+...     ++..|..+++....     
T Consensus       282 eLFG~~~gaftga~~~~~~Gl~e~---------------A~gGTLfLdeI~~Lp~~-----~Q~~Ll~~L~~~~~~r~g~  341 (526)
T TIGR02329       282 ELFGYEEGAFTGARRGGRTGLIEA---------------AHRGTLFLDEIGEMPLP-----LQTRLLRVLEEREVVRVGG  341 (526)
T ss_pred             HhcCCcccccccccccccccchhh---------------cCCceEEecChHhCCHH-----HHHHHHHHHhcCcEEecCC
Confidence            000000000000000000000111               11347999999988643     23334444444321     


Q ss_pred             --c-----eEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCH--HHHHHH----HHHHHHHhCCCCCHHHH
Q 005987          295 --P-----TAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITN--GSIKRT----LSKICRQEQYSLSTEQI  361 (666)
Q Consensus       295 --P-----iViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~--~~i~ki----L~~I~~~e~i~v~~~~l  361 (666)
                        |     .|+++++.......  ....+  ...++.+..+..|.++|+..  +++..+    |.+.+...++.++++++
T Consensus       342 ~~~~~~dvRiIaat~~~l~~~v--~~g~f--r~dL~~rL~~~~I~lPPLReR~eDI~~L~~~fl~~~~~~~~~~~~~~a~  417 (526)
T TIGR02329       342 TEPVPVDVRVVAATHCALTTAV--QQGRF--RRDLFYRLSILRIALPPLRERPGDILPLAAEYLVQAAAALRLPDSEAAA  417 (526)
T ss_pred             CceeeecceEEeccCCCHHHHh--hhcch--hHHHHHhcCCcEEeCCCchhchhHHHHHHHHHHHHHHHHcCCCCCHHHH
Confidence              1     23333332211000  00011  12333343467889999865  344444    44444444567899988


Q ss_pred             HH-------HHHH-cCCcHHHHHHHHHHHhc
Q 005987          362 DL-------VAQA-SGGDIRQAITSLQFSSL  384 (666)
Q Consensus       362 ~~-------Ia~~-s~GDIR~AIn~LQf~~~  384 (666)
                      ..       |... -.|++|..-|.++-++.
T Consensus       418 ~~~~~~~~~L~~y~WPGNvrEL~nvier~~i  448 (526)
T TIGR02329       418 QVLAGVADPLQRYPWPGNVRELRNLVERLAL  448 (526)
T ss_pred             HHhHHHHHHHHhCCCCchHHHHHHHHHHHHH
Confidence            77       5544 45999999999998875

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.

>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=98.32  E-value=2.2e-06  Score=83.07  Aligned_cols=35  Identities=29%  Similarity=0.428  Sum_probs=31.1

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCC----cEEEEcCCC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGA----RLYEWDTPT  213 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~----~viE~nasd  213 (666)
                      ..+||+||+|||||.+|++||+.+..    .++.++++.
T Consensus         4 ~~~ll~GpsGvGKT~la~~la~~l~~~~~~~~~~~d~s~   42 (171)
T PF07724_consen    4 SNFLLAGPSGVGKTELAKALAELLFVGSERPLIRIDMSE   42 (171)
T ss_dssp             EEEEEESSTTSSHHHHHHHHHHHHT-SSCCEEEEEEGGG
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHhccCCccchHHHhhhc
Confidence            57999999999999999999999996    888888765

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 ....

>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional

Probab=98.29  E-value=2.4e-05  Score=89.11  Aligned_cols=211  Identities=13%  Similarity=0.201  Sum_probs=117.9

Q ss_pred             CCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcCCCchh--hh
Q 005987          144 KPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL---GARLYEWDTPTPTI--WQ  218 (666)
Q Consensus       144 ~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~nasd~~~--~~  218 (666)
                      ...+|++++|....++++...++....   .  . ..+||+|++||||+++|+++-...   +..++.+|+.....  +.
T Consensus       199 ~~~~f~~~ig~s~~~~~~~~~~~~~A~---~--~-~pvlI~GE~GtGK~~lA~aiH~~s~r~~~pfv~inca~~~~~~~e  272 (520)
T PRK10820        199 DDSAFSQIVAVSPKMRQVVEQARKLAM---L--D-APLLITGDTGTGKDLLAYACHLRSPRGKKPFLALNCASIPDDVVE  272 (520)
T ss_pred             ccccccceeECCHHHHHHHHHHHHHhC---C--C-CCEEEECCCCccHHHHHHHHHHhCCCCCCCeEEeccccCCHHHHH
Confidence            456899999999999999888876432   1  1 469999999999999999986543   34678888764210  00


Q ss_pred             hhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcCC-----
Q 005987          219 EYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTH-----  293 (666)
Q Consensus       219 e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~~-----  293 (666)
                      ..+.....|. +......-..+++.               .....|+|||++.+...     ++..|..+++.+.     
T Consensus       273 ~elFG~~~~~-~~~~~~~~~g~~e~---------------a~~GtL~LdeI~~L~~~-----~Q~~Ll~~l~~~~~~~~g  331 (520)
T PRK10820        273 SELFGHAPGA-YPNALEGKKGFFEQ---------------ANGGSVLLDEIGEMSPR-----MQAKLLRFLNDGTFRRVG  331 (520)
T ss_pred             HHhcCCCCCC-cCCcccCCCChhhh---------------cCCCEEEEeChhhCCHH-----HHHHHHHHHhcCCcccCC
Confidence            0000000000 00000000000111               11247899999988643     2223444444432     


Q ss_pred             ------CceEEEEecCCCCCCccch-hhhhhHHHHHHhhcCeeEEEeCCCCHH--HHHHH----HHHHHHHhC---CCCC
Q 005987          294 ------IPTAVVLTECGKADSVDST-AQSFEELQSILVDAGARKVALNPITNG--SIKRT----LSKICRQEQ---YSLS  357 (666)
Q Consensus       294 ------~PiViIit~~~~~~s~d~~-~r~l~~L~s~L~r~r~~~I~F~p~s~~--~i~ki----L~~I~~~e~---i~v~  357 (666)
                            ..+-+|++......  +.. ...+.  ..+..+..+..|.++|+...  ++..+    |.+.+.+.+   ..++
T Consensus       332 ~~~~~~~~vRiI~st~~~l~--~l~~~g~f~--~dL~~rL~~~~i~lPpLreR~~Di~~L~~~fl~~~~~~~g~~~~~ls  407 (520)
T PRK10820        332 EDHEVHVDVRVICATQKNLV--ELVQKGEFR--EDLYYRLNVLTLNLPPLRDRPQDIMPLTELFVARFADEQGVPRPKLA  407 (520)
T ss_pred             CCcceeeeeEEEEecCCCHH--HHHHcCCcc--HHHHhhcCeeEEeCCCcccChhHHHHHHHHHHHHHHHHcCCCCCCcC
Confidence                  11223333221100  000 00010  12333334678889888663  34433    444455444   3689


Q ss_pred             HHHHHHHHHH-cCCcHHHHHHHHHHHhcC
Q 005987          358 TEQIDLVAQA-SGGDIRQAITSLQFSSLK  385 (666)
Q Consensus       358 ~~~l~~Ia~~-s~GDIR~AIn~LQf~~~~  385 (666)
                      +++++.|... -.|++|..-|.|+-++..
T Consensus       408 ~~a~~~L~~y~WPGNvreL~nvl~~a~~~  436 (520)
T PRK10820        408 ADLNTVLTRYGWPGNVRQLKNAIYRALTQ  436 (520)
T ss_pred             HHHHHHHhcCCCCCHHHHHHHHHHHHHHh
Confidence            9999999887 679999999999877653

>PRK08181 transposase; Validated

Probab=98.29  E-value=1.9e-06  Score=89.50  Aligned_cols=34  Identities=29%  Similarity=0.319  Sum_probs=28.9

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcCC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL---GARLYEWDTP  212 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel---g~~viE~nas  212 (666)
                      ..++|+||||||||+++.++|+++   |+.++.++.+
T Consensus       107 ~nlll~Gp~GtGKTHLa~Aia~~a~~~g~~v~f~~~~  143 (269)
T PRK08181        107 ANLLLFGPPGGGKSHLAAAIGLALIENGWRVLFTRTT  143 (269)
T ss_pred             ceEEEEecCCCcHHHHHHHHHHHHHHcCCceeeeeHH
Confidence            479999999999999999999865   7777776654

>PRK15424 propionate catabolism operon regulatory protein PrpR; Provisional

Probab=98.26  E-value=3.9e-05  Score=87.07  Aligned_cols=209  Identities=16%  Similarity=0.219  Sum_probs=115.1

Q ss_pred             CCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHH-----------cCCcEEEEcCCCc
Q 005987          146 RSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASH-----------LGARLYEWDTPTP  214 (666)
Q Consensus       146 ~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAke-----------lg~~viE~nasd~  214 (666)
                      .++++|+|+...+++++.-++....   .  . ..+||+|++||||+.+|+++-+.           -+..++.+|+...
T Consensus       216 ~~f~~iiG~S~~m~~~~~~i~~~A~---s--~-~pVLI~GE~GTGKe~~A~~IH~~~~~~~~~~S~r~~~pfv~inCaal  289 (538)
T PRK15424        216 YVLGDLLGQSPQMEQVRQTILLYAR---S--S-AAVLIQGETGTGKELAAQAIHREYFARHDARQGKKSHPFVAVNCGAI  289 (538)
T ss_pred             cchhheeeCCHHHHHHHHHHHHHhC---C--C-CcEEEECCCCCCHHHHHHHHHHhhcccccccCccCCCCeEEeecccC
Confidence            3688999999999999998876432   1  1 46999999999999999999876           3567888887642


Q ss_pred             h--hhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcC
Q 005987          215 T--IWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRST  292 (666)
Q Consensus       215 ~--~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~  292 (666)
                      .  .+...+.....|.-.......-..+++.               .....|+|||++.+...     ++..|..+++..
T Consensus       290 ~e~lleseLFG~~~gaftga~~~~~~Gl~e~---------------A~gGTLfLdeI~~Lp~~-----~Q~kLl~~L~e~  349 (538)
T PRK15424        290 AESLLEAELFGYEEGAFTGSRRGGRAGLFEI---------------AHGGTLFLDEIGEMPLP-----LQTRLLRVLEEK  349 (538)
T ss_pred             ChhhHHHHhcCCccccccCccccccCCchhc---------------cCCCEEEEcChHhCCHH-----HHHHHHhhhhcC
Confidence            1  0100000000000000000000000010               11347999999988643     233344444443


Q ss_pred             C-------Cc-----eEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCH--HHHHHHHHHHHH----HhCC
Q 005987          293 H-------IP-----TAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITN--GSIKRTLSKICR----QEQY  354 (666)
Q Consensus       293 ~-------~P-----iViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~--~~i~kiL~~I~~----~e~i  354 (666)
                      .       .|     .||++++.......  ....+.  ..++.+..+..|.++|+..  +++..++...+.    ..+.
T Consensus       350 ~~~r~G~~~~~~~dvRiIaat~~~L~~~v--~~g~Fr--~dL~yrL~~~~I~lPPLReR~eDI~~L~~~fl~~~~~~~~~  425 (538)
T PRK15424        350 EVTRVGGHQPVPVDVRVISATHCDLEEDV--RQGRFR--RDLFYRLSILRLQLPPLRERVADILPLAESFLKQSLAALSA  425 (538)
T ss_pred             eEEecCCCceeccceEEEEecCCCHHHHH--hcccch--HHHHHHhcCCeecCCChhhchhHHHHHHHHHHHHHHHHcCC
Confidence            2       11     23333432210000  000011  1233344567888888865  455555554443    3566


Q ss_pred             CCCHHHHH-------HHHHH-cCCcHHHHHHHHHHHhc
Q 005987          355 SLSTEQID-------LVAQA-SGGDIRQAITSLQFSSL  384 (666)
Q Consensus       355 ~v~~~~l~-------~Ia~~-s~GDIR~AIn~LQf~~~  384 (666)
                      .++++++.       .|... -.|++|..-|.++-++.
T Consensus       426 ~~~~~a~~~~~~a~~~L~~y~WPGNvREL~nvier~~i  463 (538)
T PRK15424        426 PFSAALRQGLQQCETLLLHYDWPGNVRELRNLMERLAL  463 (538)
T ss_pred             CCCHHHHHhhHHHHHHHHhCCCCchHHHHHHHHHHHHH
Confidence            67887763       33322 45999999999998775

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

Probab=98.25  E-value=1.4e-05  Score=82.51  Aligned_cols=95  Identities=24%  Similarity=0.372  Sum_probs=58.0

Q ss_pred             CccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCchhhhhhhhcccCCccccchhHHHHHHHHHH---HhhcCCCCC
Q 005987          177 STNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTIWQEYMHNCKTGLEYTSKLDEFENFVERI---RRYGSTSPS  253 (666)
Q Consensus       177 ~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a---~~~~~l~~s  253 (666)
                      .+..+||.||+|||||.+|+.||+.++..+.--.+..-           +...|.  .++.+.++.++   ..|..    
T Consensus        96 ~KSNILLiGPTGsGKTlLAqTLAk~LnVPFaiADATtL-----------TEAGYV--GEDVENillkLlqaadydV----  158 (408)
T COG1219          96 SKSNILLIGPTGSGKTLLAQTLAKILNVPFAIADATTL-----------TEAGYV--GEDVENILLKLLQAADYDV----  158 (408)
T ss_pred             eeccEEEECCCCCcHHHHHHHHHHHhCCCeeeccccch-----------hhcccc--chhHHHHHHHHHHHcccCH----
Confidence            34579999999999999999999999988766555431           111111  12333333332   22221    


Q ss_pred             CCCCCCCceEEEEeCCCCCcch--------h-HHHHHHHHHHHHHhc
Q 005987          254 IPGESKSSAILLIDDLPVTNGR--------T-AFERLRQCLLLLVRS  291 (666)
Q Consensus       254 ~~~~~~~~~IIlIDEid~l~~~--------~-~~~~l~~~L~~l~~~  291 (666)
                         ..-.+-||.|||+|.+...        + .-++++++|+.+++.
T Consensus       159 ---~rAerGIIyIDEIDKIarkSeN~SITRDVSGEGVQQALLKiiEG  202 (408)
T COG1219         159 ---ERAERGIIYIDEIDKIARKSENPSITRDVSGEGVQQALLKIIEG  202 (408)
T ss_pred             ---HHHhCCeEEEechhhhhccCCCCCcccccCchHHHHHHHHHHcC
Confidence               0112459999999965311        1 124677888888865

>PRK14700 recombination factor protein RarA; Provisional

Probab=98.23  E-value=3.7e-06  Score=87.12  Aligned_cols=80  Identities=10%  Similarity=0.180  Sum_probs=63.4

Q ss_pred             eEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHh------CCCCCHHHHHHHHHHcC
Q 005987          296 TAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQE------QYSLSTEQIDLVAQASG  369 (666)
Q Consensus       296 iViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e------~i~v~~~~l~~Ia~~s~  369 (666)
                      .|++++.++.+++       +.-..++++  ||.++.|++++.+++.++|++.+..+      .+.+++++++.|+..|+
T Consensus         8 ~i~LIGATTENP~-------f~vn~ALlS--R~~v~~l~~L~~~di~~il~ral~~~~~~~~~~~~i~~~al~~ia~~a~   78 (300)
T PRK14700          8 KIILIGATTENPT-------YYLNDALVS--RLFILRLKRLSLVATQKLIEKALSQDEVLAKHKFKIDDGLYNAMHNYNE   78 (300)
T ss_pred             cEEEEeecCCCcc-------ceecHhhhh--hhheeeecCCCHHHHHHHHHHHHHhhhccCCcCCCcCHHHHHHHHHhcC
Confidence            4556666655542       322344444  59999999999999999999999753      36799999999999999


Q ss_pred             CcHHHHHHHHHHHhc
Q 005987          370 GDIRQAITSLQFSSL  384 (666)
Q Consensus       370 GDIR~AIn~LQf~~~  384 (666)
                      ||.|.|+|.|+.++.
T Consensus        79 GDaR~aLN~LE~a~~   93 (300)
T PRK14700         79 GDCRKILNLLERMFL   93 (300)
T ss_pred             CHHHHHHHHHHHHHh
Confidence            999999999999763

>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=98.20  E-value=3.8e-06  Score=76.53  Aligned_cols=33  Identities=27%  Similarity=0.458  Sum_probs=23.5

Q ss_pred             EEEEECCCCchHHHHHHHHHHHcCCcEEEEcCC
Q 005987          180 VLVITGQAGVGKTATVRQIASHLGARLYEWDTP  212 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkelg~~viE~nas  212 (666)
                      ++||.|+||+|||++|+++|+.+|..+..+...
T Consensus         1 HvLleg~PG~GKT~la~~lA~~~~~~f~RIq~t   33 (131)
T PF07726_consen    1 HVLLEGVPGVGKTTLAKALARSLGLSFKRIQFT   33 (131)
T ss_dssp             -EEEES---HHHHHHHHHHHHHTT--EEEEE--
T ss_pred             CEeeECCCccHHHHHHHHHHHHcCCceeEEEec
Confidence            489999999999999999999999998877543

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.

>PRK15429 formate hydrogenlyase transcriptional activator FhlA; Provisional

Probab=98.19  E-value=5.6e-05  Score=89.15  Aligned_cols=208  Identities=15%  Similarity=0.213  Sum_probs=116.9

Q ss_pred             CCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcCCCch--hhhhh
Q 005987          146 RSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL---GARLYEWDTPTPT--IWQEY  220 (666)
Q Consensus       146 ~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~nasd~~--~~~e~  220 (666)
                      ..+++++|+...++.+.+-++.+..   ..   ..+||+|++|||||++|+++....   +..++.+++....  .+...
T Consensus       373 ~~~~~liG~S~~~~~~~~~~~~~a~---~~---~pVLI~GE~GTGK~~lA~~ih~~s~r~~~~~v~i~c~~~~~~~~~~~  446 (686)
T PRK15429        373 SEFGEIIGRSEAMYSVLKQVEMVAQ---SD---STVLILGETGTGKELIARAIHNLSGRNNRRMVKMNCAAMPAGLLESD  446 (686)
T ss_pred             ccccceeecCHHHHHHHHHHHHHhC---CC---CCEEEECCCCcCHHHHHHHHHHhcCCCCCCeEEEecccCChhHhhhh
Confidence            4678999999999999888886532   11   369999999999999999998764   5688888876421  11111


Q ss_pred             hhcccCCccccch-hHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcCC------
Q 005987          221 MHNCKTGLEYTSK-LDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTH------  293 (666)
Q Consensus       221 l~~~~~g~~~~s~-~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~~------  293 (666)
                      +.....|. +... .... ..++.+               .+.+|+|||++.+...     ++..|..+++.+.      
T Consensus       447 lfg~~~~~-~~g~~~~~~-g~le~a---------------~~GtL~Ldei~~L~~~-----~Q~~L~~~l~~~~~~~~g~  504 (686)
T PRK15429        447 LFGHERGA-FTGASAQRI-GRFELA---------------DKSSLFLDEVGDMPLE-----LQPKLLRVLQEQEFERLGS  504 (686)
T ss_pred             hcCccccc-ccccccchh-hHHHhc---------------CCCeEEEechhhCCHH-----HHHHHHHHHHhCCEEeCCC
Confidence            11000010 0000 0000 011111               1237999999988643     2323444444321      


Q ss_pred             -----Cc-eEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCH--HHHHHH----HHHHHHHhCC---CCCH
Q 005987          294 -----IP-TAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITN--GSIKRT----LSKICRQEQY---SLST  358 (666)
Q Consensus       294 -----~P-iViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~--~~i~ki----L~~I~~~e~i---~v~~  358 (666)
                           .. .||.+++......  .....+.  ..+..+.....|.++|+..  ++|..+    |.+++.+.+.   .+++
T Consensus       505 ~~~~~~~~RiI~~t~~~l~~~--~~~~~f~--~~L~~~l~~~~i~lPpLreR~~Di~~L~~~~l~~~~~~~~~~~~~~s~  580 (686)
T PRK15429        505 NKIIQTDVRLIAATNRDLKKM--VADREFR--SDLYYRLNVFPIHLPPLRERPEDIPLLVKAFTFKIARRMGRNIDSIPA  580 (686)
T ss_pred             CCcccceEEEEEeCCCCHHHH--HHcCccc--HHHHhccCeeEEeCCChhhhHhHHHHHHHHHHHHHHHHcCCCCCCcCH
Confidence                 11 2333332111000  0000110  1233333466788888865  344433    3444443332   4789


Q ss_pred             HHHHHHHHH-cCCcHHHHHHHHHHHhcC
Q 005987          359 EQIDLVAQA-SGGDIRQAITSLQFSSLK  385 (666)
Q Consensus       359 ~~l~~Ia~~-s~GDIR~AIn~LQf~~~~  385 (666)
                      ++++.|... -.|++|..-|.++-++..
T Consensus       581 ~al~~L~~y~WPGNvrEL~~~i~~a~~~  608 (686)
T PRK15429        581 ETLRTLSNMEWPGNVRELENVIERAVLL  608 (686)
T ss_pred             HHHHHHHhCCCCCcHHHHHHHHHHHHHh
Confidence            999999876 359999999999988764

>PRK11608 pspF phage shock protein operon transcriptional activator; Provisional

Probab=98.18  E-value=4.1e-05  Score=82.13  Aligned_cols=208  Identities=14%  Similarity=0.193  Sum_probs=115.2

Q ss_pred             ccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcCCCchh--hhhhhh
Q 005987          148 LEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL---GARLYEWDTPTPTI--WQEYMH  222 (666)
Q Consensus       148 l~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~nasd~~~--~~e~l~  222 (666)
                      +++|+|....++++.+-++....   ..   ..+||+|++||||+++|+++-..-   +..++.+++.....  +...+.
T Consensus         5 ~~~liG~S~~~~~~~~~i~~~a~---~~---~pVlI~GE~GtGK~~lA~~iH~~s~r~~~pfv~v~c~~~~~~~~~~~lf   78 (326)
T PRK11608          5 KDNLLGEANSFLEVLEQVSRLAP---LD---KPVLIIGERGTGKELIASRLHYLSSRWQGPFISLNCAALNENLLDSELF   78 (326)
T ss_pred             cCccEECCHHHHHHHHHHHHHhC---CC---CCEEEECCCCCcHHHHHHHHHHhCCccCCCeEEEeCCCCCHHHHHHHHc
Confidence            56789999999999998887643   12   369999999999999999987654   35688888765210  000000


Q ss_pred             cccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcCCC--------
Q 005987          223 NCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHI--------  294 (666)
Q Consensus       223 ~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~~~--------  294 (666)
                      ....|. +......-...++.               .....|+|||++.+...     .+..|..+++.+..        
T Consensus        79 g~~~~~-~~g~~~~~~g~l~~---------------a~gGtL~l~~i~~L~~~-----~Q~~L~~~l~~~~~~~~g~~~~  137 (326)
T PRK11608         79 GHEAGA-FTGAQKRHPGRFER---------------ADGGTLFLDELATAPML-----VQEKLLRVIEYGELERVGGSQP  137 (326)
T ss_pred             cccccc-cCCcccccCCchhc---------------cCCCeEEeCChhhCCHH-----HHHHHHHHHhcCcEEeCCCCce
Confidence            000000 00000000000110               11237899999988643     23334444544321        


Q ss_pred             ---ceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCH--HHHHHHHHH----HHHHhC----CCCCHHHH
Q 005987          295 ---PTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITN--GSIKRTLSK----ICRQEQ----YSLSTEQI  361 (666)
Q Consensus       295 ---PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~--~~i~kiL~~----I~~~e~----i~v~~~~l  361 (666)
                         .+-+|++......... ....+  ...++.+..+..|.++|+..  ++|..++..    .+...+    ..++++++
T Consensus       138 ~~~~~RiI~~s~~~l~~l~-~~g~f--~~dL~~~l~~~~i~lPpLReR~eDI~~L~~~fl~~~~~~~~~~~~~~~s~~al  214 (326)
T PRK11608        138 LQVNVRLVCATNADLPAMV-AEGKF--RADLLDRLAFDVVQLPPLRERQSDIMLMAEHFAIQMCRELGLPLFPGFTERAR  214 (326)
T ss_pred             eeccEEEEEeCchhHHHHH-HcCCc--hHHHHHhcCCCEEECCChhhhhhhHHHHHHHHHHHHHHHhCCCCCCCCCHHHH
Confidence               1233333211100000 00011  12333333466788988865  344444433    344433    35899999


Q ss_pred             HHHHHHc-CCcHHHHHHHHHHHhcC
Q 005987          362 DLVAQAS-GGDIRQAITSLQFSSLK  385 (666)
Q Consensus       362 ~~Ia~~s-~GDIR~AIn~LQf~~~~  385 (666)
                      ..|.... .|++|..-|.++-++..
T Consensus       215 ~~L~~y~WPGNvrEL~~vl~~a~~~  239 (326)
T PRK11608        215 ETLLNYRWPGNIRELKNVVERSVYR  239 (326)
T ss_pred             HHHHhCCCCcHHHHHHHHHHHHHHh
Confidence            9998874 59999999999988763

>smart00763 AAA_PrkA PrkA AAA domain

Probab=98.17  E-value=2.9e-06  Score=90.65  Aligned_cols=61  Identities=16%  Similarity=0.251  Sum_probs=50.3

Q ss_pred             ccCCCCcc-ccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCC
Q 005987          142 KYKPRSLE-ELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGA  204 (666)
Q Consensus       142 KY~P~sl~-eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~  204 (666)
                      .++-.-|+ +++|+++.+.++..|++.+....  ....++++|+||||+||||+|++||+.++-
T Consensus        43 ~~~y~~F~~~~~G~~~~i~~lv~~l~~~a~g~--~~~r~il~L~GPPGsGKStla~~La~~l~~  104 (361)
T smart00763       43 IKRYRFFDHDFFGMEEAIERFVNYFKSAAQGL--EERKQILYLLGPVGGGKSSLVECLKRGLEE  104 (361)
T ss_pred             eeeccccchhccCcHHHHHHHHHHHHHHHhcC--CCCCcEEEEECCCCCCHHHHHHHHHHHHhh
Confidence            35555677 89999999999999999877532  223479999999999999999999999953

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

>COG1618 Predicted nucleotide kinase [Nucleotide transport and metabolism]

Probab=98.14  E-value=4.3e-05  Score=71.90  Aligned_cols=33  Identities=45%  Similarity=0.663  Sum_probs=26.1

Q ss_pred             EEEEECCCCchHHHHHHHHHHHc---CCcEEEEcCC
Q 005987          180 VLVITGQAGVGKTATVRQIASHL---GARLYEWDTP  212 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkel---g~~viE~nas  212 (666)
                      -+.++||||+||||++..+|..+   |+.+.-+-++
T Consensus         7 ki~ITG~PGvGKtTl~~ki~e~L~~~g~kvgGf~t~   42 (179)
T COG1618           7 KIFITGRPGVGKTTLVLKIAEKLREKGYKVGGFITP   42 (179)
T ss_pred             EEEEeCCCCccHHHHHHHHHHHHHhcCceeeeEEee
Confidence            48999999999999999999877   4555444433

>PF05729 NACHT: NACHT domain

Probab=98.14  E-value=3.9e-05  Score=72.81  Aligned_cols=78  Identities=22%  Similarity=0.320  Sum_probs=45.7

Q ss_pred             CceEEEEeCCCCCcchhH---HHHHHHHHHHHHhc--C-CCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEe
Q 005987          260 SSAILLIDDLPVTNGRTA---FERLRQCLLLLVRS--T-HIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVAL  333 (666)
Q Consensus       260 ~~~IIlIDEid~l~~~~~---~~~l~~~L~~l~~~--~-~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F  333 (666)
                      .+.+||||-+|.+.....   ...+.+.|..++..  . ...+++.+.. .          ....+...+..  ...+.+
T Consensus        81 ~~~llilDglDE~~~~~~~~~~~~~~~~l~~l~~~~~~~~~~liit~r~-~----------~~~~~~~~~~~--~~~~~l  147 (166)
T PF05729_consen   81 KRVLLILDGLDELEEQDQSQERQRLLDLLSQLLPQALPPGVKLIITSRP-R----------AFPDLRRRLKQ--AQILEL  147 (166)
T ss_pred             CceEEEEechHhcccchhhhHHHHHHHHHHHHhhhccCCCCeEEEEEcC-C----------hHHHHHHhcCC--CcEEEE
Confidence            467999999998754321   22344456556655  2 2233333222 1          12224444432  357899


Q ss_pred             CCCCHHHHHHHHHHHHH
Q 005987          334 NPITNGSIKRTLSKICR  350 (666)
Q Consensus       334 ~p~s~~~i~kiL~~I~~  350 (666)
                      .+.+..++.+++++...
T Consensus       148 ~~~~~~~~~~~~~~~f~  164 (166)
T PF05729_consen  148 EPFSEEDIKQYLRKYFS  164 (166)
T ss_pred             CCCCHHHHHHHHHHHhh
Confidence            99999999999987653

>PRK06921 hypothetical protein; Provisional

Probab=98.13  E-value=1.5e-05  Score=82.89  Aligned_cols=33  Identities=30%  Similarity=0.471  Sum_probs=28.3

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc----CCcEEEEcC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL----GARLYEWDT  211 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel----g~~viE~na  211 (666)
                      +.++|+||||+|||+++.++|+++    |..++.+..
T Consensus       118 ~~l~l~G~~G~GKThLa~aia~~l~~~~g~~v~y~~~  154 (266)
T PRK06921        118 NSIALLGQPGSGKTHLLTAAANELMRKKGVPVLYFPF  154 (266)
T ss_pred             CeEEEECCCCCcHHHHHHHHHHHHhhhcCceEEEEEH
Confidence            579999999999999999999986    566666664

>PRK05022 anaerobic nitric oxide reductase transcription regulator; Provisional

Probab=98.13  E-value=0.00012  Score=83.26  Aligned_cols=209  Identities=14%  Similarity=0.153  Sum_probs=117.1

Q ss_pred             CccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcCCCchh--hhhhh
Q 005987          147 SLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL---GARLYEWDTPTPTI--WQEYM  221 (666)
Q Consensus       147 sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~nasd~~~--~~e~l  221 (666)
                      ...+++|+...++++.+-++....   .  . ..+||+|++||||+++|+++....   +..++.+|+.....  ....+
T Consensus       185 ~~~~iig~s~~~~~~~~~i~~~a~---~--~-~pVlI~Ge~GtGK~~~A~~ih~~s~r~~~p~v~v~c~~~~~~~~e~~l  258 (509)
T PRK05022        185 KEGEMIGQSPAMQQLKKEIEVVAA---S--D-LNVLILGETGVGKELVARAIHAASPRADKPLVYLNCAALPESLAESEL  258 (509)
T ss_pred             cCCceeecCHHHHHHHHHHHHHhC---C--C-CcEEEECCCCccHHHHHHHHHHhCCcCCCCeEEEEcccCChHHHHHHh
Confidence            567889999999999999987532   1  1 469999999999999999998874   46788888765211  00000


Q ss_pred             hcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcCCC-------
Q 005987          222 HNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHI-------  294 (666)
Q Consensus       222 ~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~~~-------  294 (666)
                      .....|. +......-...++.               ..+..|+|||++.+...     ++..|..+++.+..       
T Consensus       259 fG~~~g~-~~ga~~~~~g~~~~---------------a~gGtL~ldeI~~L~~~-----~Q~~Ll~~l~~~~~~~~g~~~  317 (509)
T PRK05022        259 FGHVKGA-FTGAISNRSGKFEL---------------ADGGTLFLDEIGELPLA-----LQAKLLRVLQYGEIQRVGSDR  317 (509)
T ss_pred             cCccccc-cCCCcccCCcchhh---------------cCCCEEEecChhhCCHH-----HHHHHHHHHhcCCEeeCCCCc
Confidence            0000000 00000000000011               11237899999988643     22234444444321       


Q ss_pred             -----ceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCH--HHHHHHHH----HHHHHh---CCCCCHHH
Q 005987          295 -----PTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITN--GSIKRTLS----KICRQE---QYSLSTEQ  360 (666)
Q Consensus       295 -----PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~--~~i~kiL~----~I~~~e---~i~v~~~~  360 (666)
                           ..||++++......  .....+  ...++.+.....|.++|+..  ++|..+..    +.+.+.   .+.+++++
T Consensus       318 ~~~~~~RiI~~t~~~l~~~--~~~~~f--~~dL~~rl~~~~i~lPpLreR~eDI~~L~~~fl~~~~~~~~~~~~~~s~~a  393 (509)
T PRK05022        318 SLRVDVRVIAATNRDLREE--VRAGRF--RADLYHRLSVFPLSVPPLRERGDDVLLLAGYFLEQNRARLGLRSLRLSPAA  393 (509)
T ss_pred             ceecceEEEEecCCCHHHH--HHcCCc--cHHHHhcccccEeeCCCchhchhhHHHHHHHHHHHHHHHcCCCCCCCCHHH
Confidence                 13343443211000  000001  01222333355688888865  34444433    333332   25689999


Q ss_pred             HHHHHHHc-CCcHHHHHHHHHHHhcCC
Q 005987          361 IDLVAQAS-GGDIRQAITSLQFSSLKQ  386 (666)
Q Consensus       361 l~~Ia~~s-~GDIR~AIn~LQf~~~~~  386 (666)
                      ++.|.... .|++|..-|.++-++...
T Consensus       394 ~~~L~~y~WPGNvrEL~~~i~ra~~~~  420 (509)
T PRK05022        394 QAALLAYDWPGNVRELEHVISRAALLA  420 (509)
T ss_pred             HHHHHhCCCCCcHHHHHHHHHHHHHhc
Confidence            99999874 599999999999887643

>PRK06526 transposase; Provisional

Probab=98.12  E-value=3.2e-06  Score=87.19  Aligned_cols=32  Identities=25%  Similarity=0.309  Sum_probs=26.4

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc---CCcEEEEc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL---GARLYEWD  210 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel---g~~viE~n  210 (666)
                      ..++|+||||||||+++.+|+.++   |+.++...
T Consensus        99 ~nlll~Gp~GtGKThLa~al~~~a~~~g~~v~f~t  133 (254)
T PRK06526         99 ENVVFLGPPGTGKTHLAIGLGIRACQAGHRVLFAT  133 (254)
T ss_pred             ceEEEEeCCCCchHHHHHHHHHHHHHCCCchhhhh
Confidence            479999999999999999999886   66655443

>KOG0741 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=98.11  E-value=0.00013  Score=79.98  Aligned_cols=174  Identities=17%  Similarity=0.252  Sum_probs=102.0

Q ss_pred             CCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCchhhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCC
Q 005987          175 KFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSI  254 (666)
Q Consensus       175 ~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~  254 (666)
                      +.+...+||+||||+|||++|-.+|..-++.++.+..|+.          -.|.....+...+...++.+.+.       
T Consensus       535 ~s~lvSvLl~Gp~~sGKTaLAA~iA~~S~FPFvKiiSpe~----------miG~sEsaKc~~i~k~F~DAYkS-------  597 (744)
T KOG0741|consen  535 RSPLVSVLLEGPPGSGKTALAAKIALSSDFPFVKIISPED----------MIGLSESAKCAHIKKIFEDAYKS-------  597 (744)
T ss_pred             cCcceEEEEecCCCCChHHHHHHHHhhcCCCeEEEeChHH----------ccCccHHHHHHHHHHHHHHhhcC-------
Confidence            3444689999999999999999999999999999887752          23444344455566666666322       


Q ss_pred             CCCCCCceEEEEeCCCCCc-----chhHHHHHHHHHHHHHhcCCC--ceEEEEecCCCCCCccchhhhhhHHHHHHhhcC
Q 005987          255 PGESKSSAILLIDDLPVTN-----GRTAFERLRQCLLLLVRSTHI--PTAVVLTECGKADSVDSTAQSFEELQSILVDAG  327 (666)
Q Consensus       255 ~~~~~~~~IIlIDEid~l~-----~~~~~~~l~~~L~~l~~~~~~--PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r  327 (666)
                           +-.||+|||+..+-     +...-+-+.++|.-+++....  --.+|++++...    ...+.+.    ++. +.
T Consensus       598 -----~lsiivvDdiErLiD~vpIGPRfSN~vlQaL~VllK~~ppkg~kLli~~TTS~~----~vL~~m~----i~~-~F  663 (744)
T KOG0741|consen  598 -----PLSIIVVDDIERLLDYVPIGPRFSNLVLQALLVLLKKQPPKGRKLLIFGTTSRR----EVLQEMG----ILD-CF  663 (744)
T ss_pred             -----cceEEEEcchhhhhcccccCchhhHHHHHHHHHHhccCCCCCceEEEEecccHH----HHHHHcC----HHH-hh
Confidence                 23599999987642     111223344556666654321  123333332210    0111111    111 12


Q ss_pred             eeEEEeCCCCH-HHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCC-----cHHHHHHHHHHHhc
Q 005987          328 ARKVALNPITN-GSIKRTLSKICRQEQYSLSTEQIDLVAQASGG-----DIRQAITSLQFSSL  384 (666)
Q Consensus       328 ~~~I~F~p~s~-~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~s~G-----DIR~AIn~LQf~~~  384 (666)
                      ...|+.+.++. +++.++|...    + .++++.+..+++.-.+     -|.+.+..++++..
T Consensus       664 ~~~i~Vpnl~~~~~~~~vl~~~----n-~fsd~~~~~~~~~~~~~~~~vgIKklL~lie~a~q  721 (744)
T KOG0741|consen  664 SSTIHVPNLTTGEQLLEVLEEL----N-IFSDDEVRAIAEQLLSKKVNVGIKKLLMLIEMARQ  721 (744)
T ss_pred             hheeecCccCchHHHHHHHHHc----c-CCCcchhHHHHHHHhccccchhHHHHHHHHHHHhc
Confidence            34677777766 6666666532    2 2456666666655333     37777777777654

>COG3267 ExeA Type II secretory pathway, component ExeA (predicted ATPase) [Intracellular trafficking and secretion]

Probab=98.10  E-value=0.00036  Score=70.56  Aligned_cols=204  Identities=21%  Similarity=0.262  Sum_probs=116.0

Q ss_pred             ccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcC-Cc--EEEEcCCCch--hhhhhhhcccC
Q 005987          152 AVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLG-AR--LYEWDTPTPT--IWQEYMHNCKT  226 (666)
Q Consensus       152 vg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg-~~--viE~nasd~~--~~~e~l~~~~~  226 (666)
                      .-|++.+..+...+..      +.   .++.++|+-|+|||.+.|+++..++ -.  ++.+.++...  ...+.+.....
T Consensus        34 a~h~e~l~~l~~~i~d------~q---g~~~vtGevGsGKTv~~Ral~~s~~~d~~~~v~i~~~~~s~~~~~~ai~~~l~  104 (269)
T COG3267          34 ADHNEALLMLHAAIAD------GQ---GILAVTGEVGSGKTVLRRALLASLNEDQVAVVVIDKPTLSDATLLEAIVADLE  104 (269)
T ss_pred             hhhhHHHHHHHHHHhc------CC---ceEEEEecCCCchhHHHHHHHHhcCCCceEEEEecCcchhHHHHHHHHHHHhc
Confidence            3455566665554443      22   4899999999999999997777663 22  2334443311  11111111111


Q ss_pred             Cc---cccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcCCCce-EEEEec
Q 005987          227 GL---EYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHIPT-AVVLTE  302 (666)
Q Consensus       227 g~---~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~~~Pi-ViIit~  302 (666)
                      +.   ..........+.+....+.+          +++.++++||++.+... ..+.++- |.++......|. |++++-
T Consensus       105 ~~p~~~~~~~~e~~~~~L~al~~~g----------~r~v~l~vdEah~L~~~-~le~Lrl-l~nl~~~~~~~l~ivL~Gq  172 (269)
T COG3267         105 SQPKVNVNAVLEQIDRELAALVKKG----------KRPVVLMVDEAHDLNDS-ALEALRL-LTNLEEDSSKLLSIVLIGQ  172 (269)
T ss_pred             cCccchhHHHHHHHHHHHHHHHHhC----------CCCeEEeehhHhhhChh-HHHHHHH-HHhhcccccCceeeeecCC
Confidence            10   01112333334444333222          35689999999977653 2333332 333333444453 333443


Q ss_pred             CCCCCCccchhhhhhHHHHHHhhcCeeE-EEeCCCCHHHHHHHHHHHHHHhCCC---CCHHHHHHHHHHcCCcHHHHHHH
Q 005987          303 CGKADSVDSTAQSFEELQSILVDAGARK-VALNPITNGSIKRTLSKICRQEQYS---LSTEQIDLVAQASGGDIRQAITS  378 (666)
Q Consensus       303 ~~~~~s~d~~~r~l~~L~s~L~r~r~~~-I~F~p~s~~~i~kiL~~I~~~e~i~---v~~~~l~~Ia~~s~GDIR~AIn~  378 (666)
                      ....    ... ....++++-.  ||.. |...|++.++...+|+..++..+..   ++++++..|...+.| +-.+||+
T Consensus       173 p~L~----~~l-r~~~l~e~~~--R~~ir~~l~P~~~~~t~~yl~~~Le~a~~~~~l~~~~a~~~i~~~sqg-~P~lin~  244 (269)
T COG3267         173 PKLR----PRL-RLPVLRELEQ--RIDIRIELPPLTEAETGLYLRHRLEGAGLPEPLFSDDALLLIHEASQG-IPRLINN  244 (269)
T ss_pred             cccc----hhh-chHHHHhhhh--eEEEEEecCCcChHHHHHHHHHHHhccCCCcccCChhHHHHHHHHhcc-chHHHHH
Confidence            2111    111 2223444433  4666 9999999999999999988776532   678999999999999 6678888


Q ss_pred             HHHHhc
Q 005987          379 LQFSSL  384 (666)
Q Consensus       379 LQf~~~  384 (666)
                      +--.|+
T Consensus       245 ~~~~Al  250 (269)
T COG3267         245 LATLAL  250 (269)
T ss_pred             HHHHHH
Confidence            755544

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

Probab=98.09  E-value=2.9e-06  Score=82.91  Aligned_cols=35  Identities=26%  Similarity=0.343  Sum_probs=28.2

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcCCC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL---GARLYEWDTPT  213 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel---g~~viE~nasd  213 (666)
                      ..++|+||||+|||++|.++|+++   |+.+..++.++
T Consensus        48 ~~l~l~G~~G~GKThLa~ai~~~~~~~g~~v~f~~~~~   85 (178)
T PF01695_consen   48 ENLILYGPPGTGKTHLAVAIANEAIRKGYSVLFITASD   85 (178)
T ss_dssp             -EEEEEESTTSSHHHHHHHHHHHHHHTT--EEEEEHHH
T ss_pred             eEEEEEhhHhHHHHHHHHHHHHHhccCCcceeEeecCc
Confidence            579999999999999999999987   88888777543

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.

>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=98.07  E-value=3.7e-06  Score=81.33  Aligned_cols=70  Identities=13%  Similarity=0.201  Sum_probs=36.4

Q ss_pred             ceEEEEeCCCCCcchhHHHHHHHHHHHHHhcCCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHH
Q 005987          261 SAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGS  340 (666)
Q Consensus       261 ~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~  340 (666)
                      ..+|+|||+-.+--..  ..+.+++..+++ +..|+|.++-...          ..+-++.+..+..+..+...+-+.+.
T Consensus        96 ~~liviDEIG~mEl~~--~~F~~~v~~~l~-s~~~vi~vv~~~~----------~~~~l~~i~~~~~~~i~~vt~~NRd~  162 (168)
T PF03266_consen   96 SDLIVIDEIGKMELKS--PGFREAVEKLLD-SNKPVIGVVHKRS----------DNPFLEEIKRRPDVKIFEVTEENRDA  162 (168)
T ss_dssp             CHEEEE---STTCCC---CHHHHHHHHHHC-TTSEEEEE--SS------------SCCHHHHHTTTTSEEEE--TTTCCC
T ss_pred             CCEEEEeccchhhhcC--HHHHHHHHHHHc-CCCcEEEEEecCC----------CcHHHHHHHhCCCcEEEEeChhHHhh
Confidence            4599999998763321  345666777777 5556665554321          11124444455568888888877666


Q ss_pred             HHH
Q 005987          341 IKR  343 (666)
Q Consensus       341 i~k  343 (666)
                      +..
T Consensus       163 l~~  165 (168)
T PF03266_consen  163 LPE  165 (168)
T ss_dssp             HHH
T ss_pred             Hhh
Confidence            543

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.

>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=98.04  E-value=2.6e-05  Score=81.35  Aligned_cols=170  Identities=14%  Similarity=0.215  Sum_probs=83.3

Q ss_pred             ccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCc---EEEEcCCCchhhhhhhhcc
Q 005987          148 LEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGAR---LYEWDTPTPTIWQEYMHNC  224 (666)
Q Consensus       148 l~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~---viE~nasd~~~~~e~l~~~  224 (666)
                      +.+++++-........+++.++..   +   +.+||+||+|||||++++.+-+.+.-.   +..++.+..+         
T Consensus         9 ~~~~~VpT~dt~r~~~ll~~l~~~---~---~pvLl~G~~GtGKT~li~~~l~~l~~~~~~~~~~~~s~~T---------   73 (272)
T PF12775_consen    9 FNEILVPTVDTVRYSYLLDLLLSN---G---RPVLLVGPSGTGKTSLIQNFLSSLDSDKYLVITINFSAQT---------   73 (272)
T ss_dssp             ----T---HHHHHHHHHHHHHHHC---T---EEEEEESSTTSSHHHHHHHHHHCSTTCCEEEEEEES-TTH---------
T ss_pred             cceEEeCcHHHHHHHHHHHHHHHc---C---CcEEEECCCCCchhHHHHhhhccCCccccceeEeeccCCC---------
Confidence            556777666666677777776652   2   579999999999999998877766422   3334433211         


Q ss_pred             cCCccccchhHHHHHHHHHHHhhcCCCCCCCC-CCCCceEEEEeCCCCCcchh-HHHHHHHHHHHHHhcCCC--------
Q 005987          225 KTGLEYTSKLDEFENFVERIRRYGSTSPSIPG-ESKSSAILLIDDLPVTNGRT-AFERLRQCLLLLVRSTHI--------  294 (666)
Q Consensus       225 ~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~-~~~~~~IIlIDEid~l~~~~-~~~~l~~~L~~l~~~~~~--------  294 (666)
                              ....++.+++..  ...-.....| ..+++.|++|||+..-.... .-....+.|+++++.+..        
T Consensus        74 --------ts~~~q~~ie~~--l~k~~~~~~gP~~~k~lv~fiDDlN~p~~d~ygtq~~iElLRQ~i~~~g~yd~~~~~~  143 (272)
T PF12775_consen   74 --------TSNQLQKIIESK--LEKRRGRVYGPPGGKKLVLFIDDLNMPQPDKYGTQPPIELLRQLIDYGGFYDRKKLEW  143 (272)
T ss_dssp             --------HHHHHHHCCCTT--ECECTTEEEEEESSSEEEEEEETTT-S---TTS--HHHHHHHHHHHCSEEECTTTTEE
T ss_pred             --------CHHHHHHHHhhc--EEcCCCCCCCCCCCcEEEEEecccCCCCCCCCCCcCHHHHHHHHHHhcCcccCCCcEE
Confidence                    111222222211  0000000000 12356799999997532110 012244667777765310        


Q ss_pred             ----ceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHH
Q 005987          295 ----PTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQ  351 (666)
Q Consensus       295 ----PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~  351 (666)
                          -+.++++ .+...  .   +.  .+..++.| .+.++.+.+|+.+.+..+...++..
T Consensus       144 ~~i~~i~~vaa-~~p~~--G---r~--~is~R~~r-~f~i~~~~~p~~~sl~~If~~il~~  195 (272)
T PF12775_consen  144 KSIEDIQFVAA-MNPTG--G---RN--PISPRFLR-HFNILNIPYPSDESLNTIFSSILQS  195 (272)
T ss_dssp             EEECSEEEEEE-ESSTT--T-------SHHHHHHT-TEEEEE----TCCHHHHHHHHHHHH
T ss_pred             EEEeeeEEEEe-cCCCC--C---CC--CCChHHhh-heEEEEecCCChHHHHHHHHHHHhh
Confidence                2333333 22211  1   11  23444444 4889999999999999998888764

>CHL00081 chlI Mg-protoporyphyrin IX chelatase

Probab=98.04  E-value=9.6e-05  Score=79.37  Aligned_cols=51  Identities=22%  Similarity=0.339  Sum_probs=39.8

Q ss_pred             CCC-CccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc
Q 005987          144 KPR-SLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       144 ~P~-sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      +|. .|.+++||++....+...+.+      .+.  ..+||.||+|+||||+++.+++-+
T Consensus        11 ~~~~pf~~ivGq~~~k~al~~~~~~------p~~--~~vli~G~~GtGKs~~ar~~~~~l   62 (350)
T CHL00081         11 RPVFPFTAIVGQEEMKLALILNVID------PKI--GGVMIMGDRGTGKSTTIRALVDLL   62 (350)
T ss_pred             CCCCCHHHHhChHHHHHHHHHhccC------CCC--CeEEEEcCCCCCHHHHHHHHHHHH
Confidence            444 789999999877776554443      222  468999999999999999998876

>PRK13695 putative NTPase; Provisional

Probab=98.03  E-value=0.00016  Score=70.20  Aligned_cols=76  Identities=16%  Similarity=0.231  Sum_probs=45.9

Q ss_pred             CceEEEEeCCCCCcchhHHHHHHHHHHHHHhcCCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHH
Q 005987          260 SSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNG  339 (666)
Q Consensus       260 ~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~  339 (666)
                      .+.+|+|||+..+....  ..+.+.+..+++. ..|+|+++.....       .   ..+..+..++.+..+.+.+-+.+
T Consensus        96 ~~~~lllDE~~~~e~~~--~~~~~~l~~~~~~-~~~~i~v~h~~~~-------~---~~~~~i~~~~~~~i~~~~~~~r~  162 (174)
T PRK13695         96 EADVIIIDEIGKMELKS--PKFVKAVEEVLDS-EKPVIATLHRRSV-------H---PFVQEIKSRPGGRVYELTPENRD  162 (174)
T ss_pred             CCCEEEEECCCcchhhh--HHHHHHHHHHHhC-CCeEEEEECchhh-------H---HHHHHHhccCCcEEEEEcchhhh
Confidence            35689999975443221  3345667777744 4577666654211       1   12344555667888999888888


Q ss_pred             HHHHHHHHH
Q 005987          340 SIKRTLSKI  348 (666)
Q Consensus       340 ~i~kiL~~I  348 (666)
                      +|...+...
T Consensus       163 ~~~~~~~~~  171 (174)
T PRK13695        163 SLPFEILNR  171 (174)
T ss_pred             hHHHHHHHH
Confidence            777665543

>TIGR02030 BchI-ChlI magnesium chelatase ATPase subunit I

Probab=98.03  E-value=0.00021  Score=76.75  Aligned_cols=47  Identities=21%  Similarity=0.306  Sum_probs=36.7

Q ss_pred             ccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc
Q 005987          148 LEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       148 l~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      |..++||++.+..+.-.+-+      ...  ..++|.||||+||||++++++.-+
T Consensus         3 f~~ivgq~~~~~al~~~~~~------~~~--g~vli~G~~G~gKttl~r~~~~~~   49 (337)
T TIGR02030         3 FTAIVGQDEMKLALLLNVID------PKI--GGVMVMGDRGTGKSTAVRALAALL   49 (337)
T ss_pred             ccccccHHHHHHHHHHHhcC------CCC--CeEEEEcCCCCCHHHHHHHHHHhh
Confidence            56789999888776444332      111  469999999999999999999887

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.

>PRK04132 replication factor C small subunit; Provisional

Probab=97.99  E-value=3.4e-06  Score=99.37  Aligned_cols=51  Identities=29%  Similarity=0.660  Sum_probs=45.3

Q ss_pred             CCccccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHH
Q 005987          136 QQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTAT  194 (666)
Q Consensus       136 ~~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtl  194 (666)
                      ..+|++||||++|+|++||+..++.++.+++.      ++.+  +++|+||||+||+.+
T Consensus         6 ~~~~~~k~RP~~f~dIiGqe~i~~~Lk~~i~~------~~i~--h~l~~g~~g~~~cl~   56 (846)
T PRK04132          6 EKPWVEKYRPQRLDDIVGQEHIVKRLKHYVKT------GSMP--HLLFAGPPGVGKCLT   56 (846)
T ss_pred             cccHHHhhCCCCHHHhcCcHHHHHHHHHHHHc------CCCC--eEEEECCCCCCcccc
Confidence            46899999999999999999999999999986      5665  577999999999754

>PHA02774 E1; Provisional

Probab=97.98  E-value=7e-05  Score=84.10  Aligned_cols=37  Identities=22%  Similarity=0.275  Sum_probs=30.6

Q ss_pred             CCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEE-Ec
Q 005987          174 DKFSTNVLVITGQAGVGKTATVRQIASHLGARLYE-WD  210 (666)
Q Consensus       174 g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE-~n  210 (666)
                      +.+..+.++|+||||+|||.++-+|++.++..++- +|
T Consensus       430 ~~PKknciv~~GPP~TGKS~fa~sL~~~L~G~vi~fvN  467 (613)
T PHA02774        430 GIPKKNCLVIYGPPDTGKSMFCMSLIKFLKGKVISFVN  467 (613)
T ss_pred             cCCcccEEEEECCCCCCHHHHHHHHHHHhCCCEEEEEE
Confidence            34434689999999999999999999999877765 44

>TIGR02442 Cob-chelat-sub cobaltochelatase subunit

Probab=97.95  E-value=0.00037  Score=81.34  Aligned_cols=47  Identities=17%  Similarity=0.232  Sum_probs=37.5

Q ss_pred             ccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc
Q 005987          148 LEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       148 l~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      |.+|+||+..+..+.-.+.+      +..  ..+||.||+|||||++|++|++.+
T Consensus         3 f~~ivGq~~~~~al~~~av~------~~~--g~vli~G~~GtgKs~lar~l~~~l   49 (633)
T TIGR02442         3 FTAIVGQEDLKLALLLNAVD------PRI--GGVLIRGEKGTAKSTAARGLAALL   49 (633)
T ss_pred             cchhcChHHHHHHHHHHhhC------CCC--CeEEEEcCCCCcHHHHHHHHHHhC
Confidence            56899999888776554443      222  369999999999999999999987

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.

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

Probab=97.95  E-value=9.1e-05  Score=76.52  Aligned_cols=54  Identities=28%  Similarity=0.441  Sum_probs=40.0

Q ss_pred             cCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcCCC
Q 005987          153 VQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL---GARLYEWDTPT  213 (666)
Q Consensus       153 g~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~nasd  213 (666)
                      ++.+.+..+....+ |+.      ....++|+||||+|||++|-++|+++   |..|+.++.++
T Consensus        87 ~~~~~l~~~~~~~~-~~~------~~~nl~l~G~~G~GKThLa~Ai~~~l~~~g~sv~f~~~~e  143 (254)
T COG1484          87 IDKKALEDLASLVE-FFE------RGENLVLLGPPGVGKTHLAIAIGNELLKAGISVLFITAPD  143 (254)
T ss_pred             hhHHHHHHHHHHHH-Hhc------cCCcEEEECCCCCcHHHHHHHHHHHHHHcCCeEEEEEHHH
Confidence            34555666655544 332      12579999999999999999999998   77888877664

>KOG1051 consensus Chaperone HSP104 and related ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones]

Probab=97.94  E-value=0.00017  Score=84.87  Aligned_cols=122  Identities=16%  Similarity=0.235  Sum_probs=71.9

Q ss_pred             ccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcCCCchhhhhhhhcccC
Q 005987          150 ELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL---GARLYEWDTPTPTIWQEYMHNCKT  226 (666)
Q Consensus       150 eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~nasd~~~~~e~l~~~~~  226 (666)
                      .++||+.++..|...+..........-+.-.++|.||.|+|||-+|++||..+   .-.++.++.+......+.+.. ..
T Consensus       563 ~V~gQ~eAv~aIa~AI~~sr~gl~~~~~~awflflGpdgvGKt~lAkaLA~~~Fgse~~~IriDmse~~evskligs-p~  641 (898)
T KOG1051|consen  563 RVIGQDEAVAAIAAAIRRSRAGLKDPNPDAWFLFLGPDGVGKTELAKALAEYVFGSEENFIRLDMSEFQEVSKLIGS-PP  641 (898)
T ss_pred             hccchHHHHHHHHHHHHhhhcccCCCCCCeEEEEECCCchhHHHHHHHHHHHHcCCccceEEechhhhhhhhhccCC-Cc
Confidence            37899999999999998765432221133579999999999999999999998   224455554431111111111 11


Q ss_pred             CccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcC
Q 005987          227 GLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRST  292 (666)
Q Consensus       227 g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~  292 (666)
                      |..-....+.   +-+.+++            ++..|||+|||+..+.     .++..|.++++.+
T Consensus       642 gyvG~e~gg~---Lteavrr------------rP~sVVLfdeIEkAh~-----~v~n~llq~lD~G  687 (898)
T KOG1051|consen  642 GYVGKEEGGQ---LTEAVKR------------RPYSVVLFEEIEKAHP-----DVLNILLQLLDRG  687 (898)
T ss_pred             ccccchhHHH---HHHHHhc------------CCceEEEEechhhcCH-----HHHHHHHHHHhcC
Confidence            1110111222   2233322            2457999999996542     3445566666654

>PRK09183 transposase/IS protein; Provisional

Probab=97.94  E-value=3.7e-05  Score=79.67  Aligned_cols=34  Identities=24%  Similarity=0.337  Sum_probs=28.2

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcCC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL---GARLYEWDTP  212 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel---g~~viE~nas  212 (666)
                      ..++|+||||||||+++.+++.++   |+.+..++.+
T Consensus       103 ~~v~l~Gp~GtGKThLa~al~~~a~~~G~~v~~~~~~  139 (259)
T PRK09183        103 ENIVLLGPSGVGKTHLAIALGYEAVRAGIKVRFTTAA  139 (259)
T ss_pred             CeEEEEeCCCCCHHHHHHHHHHHHHHcCCeEEEEeHH
Confidence            479999999999999999997764   7777776643

>COG2204 AtoC Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]

Probab=97.93  E-value=0.00044  Score=76.41  Aligned_cols=203  Identities=14%  Similarity=0.213  Sum_probs=116.9

Q ss_pred             CCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcCCCchhhhhhhh
Q 005987          146 RSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL---GARLYEWDTPTPTIWQEYMH  222 (666)
Q Consensus       146 ~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~nasd~~~~~e~l~  222 (666)
                      ....+|+|+...+++|+.-+...-.   ..   -.+||+|++||||-.+|++|-+.-   +..++.+|+.....  +.+.
T Consensus       138 ~~~~~liG~S~am~~l~~~i~kvA~---s~---a~VLI~GESGtGKElvAr~IH~~S~R~~~PFVavNcaAip~--~l~E  209 (464)
T COG2204         138 SLGGELVGESPAMQQLRRLIAKVAP---SD---ASVLITGESGTGKELVARAIHQASPRAKGPFIAVNCAAIPE--NLLE  209 (464)
T ss_pred             cccCCceecCHHHHHHHHHHHHHhC---CC---CCEEEECCCCCcHHHHHHHHHhhCcccCCCceeeecccCCH--HHHH
Confidence            3567899999999999999986432   11   369999999999999999997764   56788888764210  0000


Q ss_pred             cccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCC---------CCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcCC
Q 005987          223 NCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGES---------KSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTH  293 (666)
Q Consensus       223 ~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~---------~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~~  293 (666)
                      ...                     |+.-.+.++|..         -..-.|++|||-.+.-.     ++.-|+..++...
T Consensus       210 SEL---------------------FGhekGAFTGA~~~r~G~fE~A~GGTLfLDEI~~mpl~-----~Q~kLLRvLqe~~  263 (464)
T COG2204         210 SEL---------------------FGHEKGAFTGAITRRIGRFEQANGGTLFLDEIGEMPLE-----LQVKLLRVLQERE  263 (464)
T ss_pred             HHh---------------------hcccccCcCCcccccCcceeEcCCceEEeeccccCCHH-----HHHHHHHHHHcCe
Confidence            000                     111111111110         12347999999877532     2222344444332


Q ss_pred             C-------c---eEEEEecCCCCCCccc--hhhhhhHHHHHHhhcCeeEEEeCCCCH--H----HHHHHHHHHHHHhC--
Q 005987          294 I-------P---TAVVLTECGKADSVDS--TAQSFEELQSILVDAGARKVALNPITN--G----SIKRTLSKICRQEQ--  353 (666)
Q Consensus       294 ~-------P---iViIit~~~~~~s~d~--~~r~l~~L~s~L~r~r~~~I~F~p~s~--~----~i~kiL~~I~~~e~--  353 (666)
                      +       |   -|=|++.++.+- ...  ..+.-++|-   .|.....|+++|+-.  +    ....+|++.|...+  
T Consensus       264 ~~rvG~~~~i~vdvRiIaaT~~dL-~~~v~~G~FReDLy---yRLnV~~i~iPpLRER~EDIp~L~~hfl~~~~~~~~~~  339 (464)
T COG2204         264 FERVGGNKPIKVDVRIIAATNRDL-EEEVAAGRFREDLY---YRLNVVPLRLPPLRERKEDIPLLAEHFLKRFAAELGRP  339 (464)
T ss_pred             eEecCCCcccceeeEEEeecCcCH-HHHHHcCCcHHHHH---hhhccceecCCcccccchhHHHHHHHHHHHHHHHcCCC
Confidence            1       1   122333332210 000  011112222   222345566666643  2    23445566666554  


Q ss_pred             -CCCCHHHHHHHHHHc-CCcHHHHHHHHHHHhcCC
Q 005987          354 -YSLSTEQIDLVAQAS-GGDIRQAITSLQFSSLKQ  386 (666)
Q Consensus       354 -i~v~~~~l~~Ia~~s-~GDIR~AIn~LQf~~~~~  386 (666)
                       ..++++++..|.... .|++|...|.++-++...
T Consensus       340 ~~~~s~~a~~~L~~y~WPGNVREL~N~ver~~il~  374 (464)
T COG2204         340 PKGFSPEALAALLAYDWPGNVRELENVVERAVILS  374 (464)
T ss_pred             CCCCCHHHHHHHHhCCCChHHHHHHHHHHHHHhcC
Confidence             458899999998774 599999999999988754

>COG1221 PspF Transcriptional regulators containing an AAA-type ATPase domain and a DNA-binding domain [Transcription / Signal transduction mechanisms]

Probab=97.92  E-value=0.00025  Score=76.96  Aligned_cols=205  Identities=17%  Similarity=0.207  Sum_probs=113.5

Q ss_pred             CCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc----CCcEEEEcCCCchh-hh--
Q 005987          146 RSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL----GARLYEWDTPTPTI-WQ--  218 (666)
Q Consensus       146 ~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel----g~~viE~nasd~~~-~~--  218 (666)
                      ..+.+|+|.....+++++-++.. .     +....+||.|++|+||+.+|+.+...-    +..++.+||..... ..  
T Consensus        75 ~~~~~LIG~~~~~~~~~eqik~~-a-----p~~~~vLi~GetGtGKel~A~~iH~~s~r~~~~PFI~~NCa~~~en~~~~  148 (403)
T COG1221          75 EALDDLIGESPSLQELREQIKAY-A-----PSGLPVLIIGETGTGKELFARLIHALSARRAEAPFIAFNCAAYSENLQEA  148 (403)
T ss_pred             hhhhhhhccCHHHHHHHHHHHhh-C-----CCCCcEEEecCCCccHHHHHHHHHHhhhcccCCCEEEEEHHHhCcCHHHH
Confidence            35788999999988888888762 1     112579999999999999999887432    45678888765210 00  


Q ss_pred             hhhh---cccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcCCC-
Q 005987          219 EYMH---NCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHI-  294 (666)
Q Consensus       219 e~l~---~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~~~-  294 (666)
                      +.++   ...+|..+. ..    .+++.               -....+++||+..+...     .+..|..+++.+.+ 
T Consensus       149 eLFG~~kGaftGa~~~-k~----Glfe~---------------A~GGtLfLDEI~~LP~~-----~Q~kLl~~le~g~~~  203 (403)
T COG1221         149 ELFGHEKGAFTGAQGG-KA----GLFEQ---------------ANGGTLFLDEIHRLPPE-----GQEKLLRVLEEGEYR  203 (403)
T ss_pred             HHhccccceeecccCC-cC----chhee---------------cCCCEEehhhhhhCCHh-----HHHHHHHHHHcCceE
Confidence            0000   000110000 00    00111               12348999999987643     23335555554311 


Q ss_pred             ---------ceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHH--HH----HHHHHHHHHHhCCCC---
Q 005987          295 ---------PTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNG--SI----KRTLSKICRQEQYSL---  356 (666)
Q Consensus       295 ---------PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~--~i----~kiL~~I~~~e~i~v---  356 (666)
                               .-|-++++++..    .....+.. ..+..|.-...|+++|+...  ++    .-.|...|.+.+..+   
T Consensus       204 rvG~~~~~~~dVRli~AT~~~----l~~~~~~g-~dl~~rl~~~~I~LPpLrER~~Di~~L~e~Fl~~~~~~l~~~~~~~  278 (403)
T COG1221         204 RVGGSQPRPVDVRLICATTED----LEEAVLAG-ADLTRRLNILTITLPPLRERKEDILLLAEHFLKSEARRLGLPLSVD  278 (403)
T ss_pred             ecCCCCCcCCCceeeeccccC----HHHHHHhh-cchhhhhcCceecCCChhhchhhHHHHHHHHHHHHHHHcCCCCCCC
Confidence                     112223332221    11111110 13333334667888888654  22    233444555555443   


Q ss_pred             CHHHHHHHHHH-cCCcHHHHHHHHHHHhcCC
Q 005987          357 STEQIDLVAQA-SGGDIRQAITSLQFSSLKQ  386 (666)
Q Consensus       357 ~~~~l~~Ia~~-s~GDIR~AIn~LQf~~~~~  386 (666)
                      +++++..+... ..|+||..-|.++++|...
T Consensus       279 ~~~a~~~L~~y~~pGNirELkN~Ve~~~~~~  309 (403)
T COG1221         279 SPEALRALLAYDWPGNIRELKNLVERAVAQA  309 (403)
T ss_pred             CHHHHHHHHhCCCCCcHHHHHHHHHHHHHHh
Confidence            34666666654 6799999999999999754

>PLN03210 Resistant to P

Probab=97.90  E-value=0.00037  Score=86.98  Aligned_cols=53  Identities=19%  Similarity=0.338  Sum_probs=42.9

Q ss_pred             CCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcC
Q 005987          145 PRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLG  203 (666)
Q Consensus       145 P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg  203 (666)
                      +..+++++|.+..++++..+|.-.      ....+++-|+||+|+||||+|+++++.+.
T Consensus       180 ~~~~~~~vG~~~~l~~l~~lL~l~------~~~~~vvgI~G~gGiGKTTLA~~l~~~l~  232 (1153)
T PLN03210        180 SNDFEDFVGIEDHIAKMSSLLHLE------SEEVRMVGIWGSSGIGKTTIARALFSRLS  232 (1153)
T ss_pred             CcccccccchHHHHHHHHHHHccc------cCceEEEEEEcCCCCchHHHHHHHHHHHh
Confidence            346778999999999999988531      11236899999999999999999988873

syringae 6; Provisional

>PF00910 RNA_helicase: RNA helicase; InterPro: IPR000605 Helicases have been classified in 5 superfamilies (SF1-SF5)

Probab=97.90  E-value=4.1e-05  Score=68.28  Aligned_cols=23  Identities=30%  Similarity=0.567  Sum_probs=21.1

Q ss_pred             EEEECCCCchHHHHHHHHHHHcC
Q 005987          181 LVITGQAGVGKTATVRQIASHLG  203 (666)
Q Consensus       181 LLL~GPpG~GKTtla~~LAkelg  203 (666)
                      +.|+||||+|||++++.||+.+.
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            47999999999999999999884

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

>PRK04841 transcriptional regulator MalT; Provisional

Probab=97.88  E-value=0.00039  Score=84.61  Aligned_cols=191  Identities=15%  Similarity=0.212  Sum_probs=106.2

Q ss_pred             CCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEE--cCCC--c-hhhh
Q 005987          144 KPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEW--DTPT--P-TIWQ  218 (666)
Q Consensus       144 ~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~--nasd--~-~~~~  218 (666)
                      .|..-..++.++...+.+...          . ..+.++|+||+|.||||++..++...+ .+.=+  ...|  + +.|.
T Consensus         9 ~p~~~~~~~~R~rl~~~l~~~----------~-~~~~~~v~apaG~GKTtl~~~~~~~~~-~~~w~~l~~~d~~~~~f~~   76 (903)
T PRK04841          9 RPVRLHNTVVRERLLAKLSGA----------N-NYRLVLVTSPAGYGKTTLISQWAAGKN-NLGWYSLDESDNQPERFAS   76 (903)
T ss_pred             CCCCccccCcchHHHHHHhcc----------c-CCCeEEEECCCCCCHHHHHHHHHHhCC-CeEEEecCcccCCHHHHHH
Confidence            466677888888777666421          1 126899999999999999999988776 43322  2222  1 1222


Q ss_pred             hhhhcc---cCCc-----------cccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHH
Q 005987          219 EYMHNC---KTGL-----------EYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQC  284 (666)
Q Consensus       219 e~l~~~---~~g~-----------~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~  284 (666)
                      ..+...   ..+.           ........+..++..+..           ...+.+|+|||++.+....    +.+.
T Consensus        77 ~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~-----------~~~~~~lvlDD~h~~~~~~----~~~~  141 (903)
T PRK04841         77 YLIAALQQATNGHCSKSEALAQKRQYASLSSLFAQLFIELAD-----------WHQPLYLVIDDYHLITNPE----IHEA  141 (903)
T ss_pred             HHHHHHHHhcCcccchhhhhhccCCcCCHHHHHHHHHHHHhc-----------CCCCEEEEEeCcCcCCChH----HHHH
Confidence            211111   0010           000001122233333221           1357899999999875432    2334


Q ss_pred             HHHHHhcCC-CceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeC--CCCHHHHHHHHHHHHHHhCCCCCHHHH
Q 005987          285 LLLLVRSTH-IPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALN--PITNGSIKRTLSKICRQEQYSLSTEQI  361 (666)
Q Consensus       285 L~~l~~~~~-~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~--p~s~~~i~kiL~~I~~~e~i~v~~~~l  361 (666)
                      |..+++... ...++| +....+..      .+..++   .+..+..|...  +++.+++...+...   .+..++++.+
T Consensus       142 l~~l~~~~~~~~~lv~-~sR~~~~~------~~~~l~---~~~~~~~l~~~~l~f~~~e~~~ll~~~---~~~~~~~~~~  208 (903)
T PRK04841        142 MRFFLRHQPENLTLVV-LSRNLPPL------GIANLR---VRDQLLEIGSQQLAFDHQEAQQFFDQR---LSSPIEAAES  208 (903)
T ss_pred             HHHHHHhCCCCeEEEE-EeCCCCCC------chHhHH---hcCcceecCHHhCCCCHHHHHHHHHhc---cCCCCCHHHH
Confidence            555555543 234444 33322110      011111   11123444444  88999999888754   3567899999


Q ss_pred             HHHHHHcCCcHHH
Q 005987          362 DLVAQASGGDIRQ  374 (666)
Q Consensus       362 ~~Ia~~s~GDIR~  374 (666)
                      ..|.+.|+|.+-.
T Consensus       209 ~~l~~~t~Gwp~~  221 (903)
T PRK04841        209 SRLCDDVEGWATA  221 (903)
T ss_pred             HHHHHHhCChHHH
Confidence            9999999998754

>PHA00729 NTP-binding motif containing protein

Probab=97.84  E-value=9.6e-05  Score=74.36  Aligned_cols=30  Identities=30%  Similarity=0.330  Sum_probs=25.6

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEEE
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLYE  208 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~viE  208 (666)
                      ..++|+||||+||||+|.+||++++..+..
T Consensus        18 ~nIlItG~pGvGKT~LA~aLa~~l~~~l~~   47 (226)
T PHA00729         18 VSAVIFGKQGSGKTTYALKVARDVFWKLNN   47 (226)
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHhhccc
Confidence            379999999999999999999998744433

>KOG0741 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=97.84  E-value=7.2e-05  Score=81.79  Aligned_cols=182  Identities=16%  Similarity=0.260  Sum_probs=89.2

Q ss_pred             ccEEEEECCCCchHHHHHHHHHHHcCCcE-EEEcCCCchhhhhhhhcccCCccccchhHHHHHHHHHHH-hhcCCCCCCC
Q 005987          178 TNVLVITGQAGVGKTATVRQIASHLGARL-YEWDTPTPTIWQEYMHNCKTGLEYTSKLDEFENFVERIR-RYGSTSPSIP  255 (666)
Q Consensus       178 ~k~LLL~GPpG~GKTtla~~LAkelg~~v-iE~nasd~~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~-~~~~l~~s~~  255 (666)
                      -+.+|||||||||||.+||.+.+-|+.+- --+|.|.  ++.+++..         ..+.++..+..+. .+...     
T Consensus       256 VKGiLLyGPPGTGKTLiARqIGkMLNArePKIVNGPe--IL~KYVGe---------SE~NvR~LFaDAEeE~r~~-----  319 (744)
T KOG0741|consen  256 VKGILLYGPPGTGKTLIARQIGKMLNAREPKIVNGPE--ILNKYVGE---------SEENVRKLFADAEEEQRRL-----  319 (744)
T ss_pred             eeeEEEECCCCCChhHHHHHHHHHhcCCCCcccCcHH--HHHHhhcc---------cHHHHHHHHHhHHHHHHhh-----
Confidence            36799999999999999999999996531 1234443  33333322         2233444443332 12211     


Q ss_pred             CCCCCceEEEEeCCCCCcchh----HHHHHH-HHHHHHHhc----CCCceEEEEecCCCCCCccchhhhhhHHHHHHhhc
Q 005987          256 GESKSSAILLIDDLPVTNGRT----AFERLR-QCLLLLVRS----THIPTAVVLTECGKADSVDSTAQSFEELQSILVDA  326 (666)
Q Consensus       256 ~~~~~~~IIlIDEid~l~~~~----~~~~l~-~~L~~l~~~----~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~  326 (666)
                      |....-.|||+||+|.+..+.    .-.+++ .+..+++..    .+.--|++++-++..          +-+.+.|-||
T Consensus       320 g~~SgLHIIIFDEiDAICKqRGS~~g~TGVhD~VVNQLLsKmDGVeqLNNILVIGMTNR~----------DlIDEALLRP  389 (744)
T KOG0741|consen  320 GANSGLHIIIFDEIDAICKQRGSMAGSTGVHDTVVNQLLSKMDGVEQLNNILVIGMTNRK----------DLIDEALLRP  389 (744)
T ss_pred             CccCCceEEEehhhHHHHHhcCCCCCCCCccHHHHHHHHHhcccHHhhhcEEEEeccCch----------hhHHHHhcCC
Confidence            111124699999999542110    000111 112222221    111234555554432          2356666666


Q ss_pred             CeeE--EEeCCCCHHHHHHHHHHHHHH--hCCCCC-HHHHHHHHHH----cCCcHHHHHHHHHHHhcC
Q 005987          327 GARK--VALNPITNGSIKRTLSKICRQ--EQYSLS-TEQIDLVAQA----SGGDIRQAITSLQFSSLK  385 (666)
Q Consensus       327 r~~~--I~F~p~s~~~i~kiL~~I~~~--e~i~v~-~~~l~~Ia~~----s~GDIR~AIn~LQf~~~~  385 (666)
                      +-..  +.+.-|+..-..++|+-...+  +.-.++ +-.++.||..    |+..|--.+...|-.|+.
T Consensus       390 GRlEVqmEIsLPDE~gRlQIl~IHT~rMre~~~l~~dVdl~elA~lTKNfSGAEleglVksA~S~A~n  457 (744)
T KOG0741|consen  390 GRLEVQMEISLPDEKGRLQILKIHTKRMRENNKLSADVDLKELAALTKNFSGAELEGLVKSAQSFAMN  457 (744)
T ss_pred             CceEEEEEEeCCCccCceEEEEhhhhhhhhcCCCCCCcCHHHHHHHhcCCchhHHHHHHHHHHHHHHH
Confidence            5544  455566666555555433322  111222 2235555544    444555555555655554

>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=97.82  E-value=0.00058  Score=74.23  Aligned_cols=206  Identities=14%  Similarity=0.245  Sum_probs=108.0

Q ss_pred             HHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHH--HHHHHHcCCcEEEEcCCCc------------------
Q 005987          155 RKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATV--RQIASHLGARLYEWDTPTP------------------  214 (666)
Q Consensus       155 ~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla--~~LAkelg~~viE~nasd~------------------  214 (666)
                      .+++++|+.||...       +. ..++++||.|+||+.++  ++|...-+  ++.++|-..                  
T Consensus         2 ~e~~~~L~~wL~e~-------~~-TFIvV~GPrGSGK~elV~d~~L~~r~~--vL~IDC~~i~~ar~D~~~I~~lA~qvG   71 (431)
T PF10443_consen    2 KEAIEQLKSWLNEN-------PN-TFIVVQGPRGSGKRELVMDHVLKDRKN--VLVIDCDQIVKARGDAAFIKNLASQVG   71 (431)
T ss_pred             chHHHHHHHHHhcC-------CC-eEEEEECCCCCCccHHHHHHHHhCCCC--EEEEEChHhhhccChHHHHHHHHHhcC
Confidence            46788999999862       12 58999999999999999  55544322  344433210                  


Q ss_pred             -----------hhhhhhhhcccCCccc---cchhHHHHHHHHHHH---------hhcCC---CCCCC-----CCCCCceE
Q 005987          215 -----------TIWQEYMHNCKTGLEY---TSKLDEFENFVERIR---------RYGST---SPSIP-----GESKSSAI  263 (666)
Q Consensus       215 -----------~~~~e~l~~~~~g~~~---~s~~~~f~~fl~~a~---------~~~~l---~~s~~-----~~~~~~~I  263 (666)
                                 ..+.+.......|...   .+...+++++++...         .+..-   .....     .....+.|
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                       0111111112223221   233445555554321         11000   00000     00112348


Q ss_pred             EEEeCCCCCcchhHH--HHHHHHHHHHHhcCCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHH
Q 005987          264 LLIDDLPVTNGRTAF--ERLRQCLLLLVRSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSI  341 (666)
Q Consensus       264 IlIDEid~l~~~~~~--~~l~~~L~~l~~~~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i  341 (666)
                      |+||.+..-.....+  ..+.+---.++...--.+||++++....          ..|...|-+.-+..|.+...+++.-
T Consensus       152 VVIdnF~~k~~~~~~iy~~laeWAa~Lv~~nIAHVIFlT~dv~~~----------k~LskaLPn~vf~tI~L~Das~~~A  221 (431)
T PF10443_consen  152 VVIDNFLHKAEENDFIYDKLAEWAASLVQNNIAHVIFLTDDVSYS----------KPLSKALPNRVFKTISLSDASPESA  221 (431)
T ss_pred             EEEcchhccCcccchHHHHHHHHHHHHHhcCccEEEEECCCCchh----------hhHHHhCCCCceeEEeecCCCHHHH
Confidence            999998654322111  2222111122333333566666554322          1233333333467899999999999


Q ss_pred             HHHHHHHHHHhC-C-------------------CCCHHHHHHHHHHcCCcHHHHHHHHHHHhc
Q 005987          342 KRTLSKICRQEQ-Y-------------------SLSTEQIDLVAQASGGDIRQAITSLQFSSL  384 (666)
Q Consensus       342 ~kiL~~I~~~e~-i-------------------~v~~~~l~~Ia~~s~GDIR~AIn~LQf~~~  384 (666)
                      ++++...+..+. .                   ......++.++..-||=+.    .||+++.
T Consensus       222 k~yV~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~eld~~i~~LGGRlt----DLe~lvr  280 (431)
T PF10443_consen  222 KQYVLSQLDEDTEDSSDSKESNEQNKNDKSAENEKDLAELDECIEPLGGRLT----DLEFLVR  280 (431)
T ss_pred             HHHHHHHhcccccccccccccccccccccccccccchHHHHHHHHHcCCcHH----HHHHHHH
Confidence            988888776531 1                   1345677888888888665    6777764

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 [].

>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=97.80  E-value=2e-05  Score=71.27  Aligned_cols=31  Identities=32%  Similarity=0.652  Sum_probs=28.5

Q ss_pred             EEEEECCCCchHHHHHHHHHHHcCCcEEEEc
Q 005987          180 VLVITGQAGVGKTATVRQIASHLGARLYEWD  210 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkelg~~viE~n  210 (666)
                      .++|+||||+||||+++.||+.+|+.++...
T Consensus         1 vI~I~G~~gsGKST~a~~La~~~~~~~i~~d   31 (121)
T PF13207_consen    1 VIIISGPPGSGKSTLAKELAERLGFPVISMD   31 (121)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHTCEEEEEH
T ss_pred             CEEEECCCCCCHHHHHHHHHHHHCCeEEEec
Confidence            4789999999999999999999999988765

...

>TIGR02915 PEP_resp_reg putative PEP-CTERM system response regulator

Probab=97.79  E-value=0.00041  Score=77.55  Aligned_cols=207  Identities=13%  Similarity=0.217  Sum_probs=111.0

Q ss_pred             CccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcCCCchhhhhhhhc
Q 005987          147 SLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL---GARLYEWDTPTPTIWQEYMHN  223 (666)
Q Consensus       147 sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~nasd~~~~~e~l~~  223 (666)
                      .+.++++....++.+...++....   ..   ..++|+|++|+||+++|+.+....   +..++.+++....  .+.+..
T Consensus       137 ~~~~lig~s~~~~~l~~~i~~~a~---~~---~~vli~Ge~GtGK~~lA~~ih~~s~~~~~~~v~v~c~~~~--~~~~~~  208 (445)
T TIGR02915       137 ALRGLITSSPGMQKICRTIEKIAP---SD---ITVLLLGESGTGKEVLARALHQLSDRKDKRFVAINCAAIP--ENLLES  208 (445)
T ss_pred             cccceeecCHHHHHHHHHHHHHhC---CC---CCEEEECCCCcCHHHHHHHHHHhCCcCCCCeEEEECCCCC--hHHHHH
Confidence            455788888888888887775321   11   358899999999999999998765   3567788876421  011100


Q ss_pred             ccCCccccchhHHHHHHHHHHHhhcCCCCCCCC--CCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcCCC-------
Q 005987          224 CKTGLEYTSKLDEFENFVERIRRYGSTSPSIPG--ESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHI-------  294 (666)
Q Consensus       224 ~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~--~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~~~-------  294 (666)
                      ...|....              .+........|  ....+..|+|||++.+...     .+..|..+++....       
T Consensus       209 ~lfg~~~~--------------~~~~~~~~~~g~~~~a~~gtl~l~~i~~l~~~-----~q~~l~~~l~~~~~~~~~~~~  269 (445)
T TIGR02915       209 ELFGYEKG--------------AFTGAVKQTLGKIEYAHGGTLFLDEIGDLPLN-----LQAKLLRFLQERVIERLGGRE  269 (445)
T ss_pred             HhcCCCCC--------------CcCCCccCCCCceeECCCCEEEEechhhCCHH-----HHHHHHHHHhhCeEEeCCCCc
Confidence            00010000              00000000000  0012347999999988643     22234444443210       


Q ss_pred             ----c-eEEEEecCCCCCCccch-hhhhhHHHHHHhhcCeeEEEeCCCCHH--HHHH----HHHHHHHHhC---CCCCHH
Q 005987          295 ----P-TAVVLTECGKADSVDST-AQSFEELQSILVDAGARKVALNPITNG--SIKR----TLSKICRQEQ---YSLSTE  359 (666)
Q Consensus       295 ----P-iViIit~~~~~~s~d~~-~r~l~~L~s~L~r~r~~~I~F~p~s~~--~i~k----iL~~I~~~e~---i~v~~~  359 (666)
                          . .||++++....   ... ...+.  ..+..+.....|.++|+...  ++..    +|.+.+...+   ..++++
T Consensus       270 ~~~~~~rii~~~~~~l~---~~~~~~~~~--~~L~~~l~~~~i~lPpLr~R~~Di~~l~~~~l~~~~~~~~~~~~~~~~~  344 (445)
T TIGR02915       270 EIPVDVRIVCATNQDLK---RMIAEGTFR--EDLFYRIAEISITIPPLRSRDGDAVLLANAFLERFARELKRKTKGFTDD  344 (445)
T ss_pred             eeeeceEEEEecCCCHH---HHHHcCCcc--HHHHHHhccceecCCCchhchhhHHHHHHHHHHHHHHHhCCCCCCCCHH
Confidence                1 23333321100   000 00110  11223334567888887553  3333    3344343333   458999


Q ss_pred             HHHHHHHHc-CCcHHHHHHHHHHHhcC
Q 005987          360 QIDLVAQAS-GGDIRQAITSLQFSSLK  385 (666)
Q Consensus       360 ~l~~Ia~~s-~GDIR~AIn~LQf~~~~  385 (666)
                      +++.|.... .|++|..-|.++-++..
T Consensus       345 a~~~L~~~~wpgNvreL~~~i~~a~~~  371 (445)
T TIGR02915       345 ALRALEAHAWPGNVRELENKVKRAVIM  371 (445)
T ss_pred             HHHHHHhCCCCChHHHHHHHHHHHHHh
Confidence            999998875 79999999999988763

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).

>cd01120 RecA-like_NTPases RecA-like NTPases

Probab=97.79  E-value=0.00016  Score=68.19  Aligned_cols=33  Identities=27%  Similarity=0.486  Sum_probs=27.0

Q ss_pred             EEEEECCCCchHHHHHHHHHHHc---CCcEEEEcCC
Q 005987          180 VLVITGQAGVGKTATVRQIASHL---GARLYEWDTP  212 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkel---g~~viE~nas  212 (666)
                      +++|+||||+|||+++..++..+   +..++.+...
T Consensus         1 ~~~i~G~~G~GKT~l~~~i~~~~~~~~~~v~~~~~e   36 (165)
T cd01120           1 LILVFGPTGSGKTTLALQLALNIATKGGKVVYVDIE   36 (165)
T ss_pred             CeeEeCCCCCCHHHHHHHHHHHHHhcCCEEEEEECC
Confidence            37899999999999999999887   5666666544

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=97.77  E-value=0.00091  Score=73.04  Aligned_cols=171  Identities=15%  Similarity=0.230  Sum_probs=83.6

Q ss_pred             HHHHHHHHHHHHhhcCCC---CCCCccEEEEECCCCchHHHHHHHHHHHc-------CCcEEEEcCCCchh---hhhhhh
Q 005987          156 KKVEEVRAWFEERLGDSK---DKFSTNVLVITGQAGVGKTATVRQIASHL-------GARLYEWDTPTPTI---WQEYMH  222 (666)
Q Consensus       156 k~i~el~~wL~~~~~~~~---g~~~~k~LLL~GPpG~GKTtla~~LAkel-------g~~viE~nasd~~~---~~e~l~  222 (666)
                      ...+.+..++...+....   ....+++++|.||+|+||||++..||..+       |..|.-+.+-..+.   ++-..+
T Consensus       149 ~v~~~l~~~l~~~i~~~~~~~~~~~~~vi~lvGptGvGKTTT~aKLA~~~~~~~~~~g~~V~lit~Dt~R~aa~eQL~~~  228 (388)
T PRK12723        149 KVRDSVIIYIAKTIKCSGSIIDNLKKRVFILVGPTGVGKTTTIAKLAAIYGINSDDKSLNIKIITIDNYRIGAKKQIQTY  228 (388)
T ss_pred             HHHHHHHHHHHHHhhccCccccCCCCeEEEEECCCCCCHHHHHHHHHHHHHhhhccCCCeEEEEeccCccHHHHHHHHHH
Confidence            344455555555443211   11223689999999999999999999865       34454444433221   111111


Q ss_pred             cccCCccc--cchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcCCCc--eEE
Q 005987          223 NCKTGLEY--TSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHIP--TAV  298 (666)
Q Consensus       223 ~~~~g~~~--~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~~~P--iVi  298 (666)
                      ....|+.+  ......+...+.+..              ..-+||||.+......  ...+.+ +..++.....|  +++
T Consensus       229 a~~lgvpv~~~~~~~~l~~~L~~~~--------------~~DlVLIDTaGr~~~~--~~~l~e-l~~~l~~~~~~~e~~L  291 (388)
T PRK12723        229 GDIMGIPVKAIESFKDLKEEITQSK--------------DFDLVLVDTIGKSPKD--FMKLAE-MKELLNACGRDAEFHL  291 (388)
T ss_pred             hhcCCcceEeeCcHHHHHHHHHHhC--------------CCCEEEEcCCCCCccC--HHHHHH-HHHHHHhcCCCCeEEE
Confidence            11123221  122233433333332              1348999999876432  112222 44444433323  445


Q ss_pred             EEecCCCCCCccchhhhhhHHHHHHhh---cCeeEEEeCCCCHHHHHHHHHHHHHHhC
Q 005987          299 VLTECGKADSVDSTAQSFEELQSILVD---AGARKVALNPITNGSIKRTLSKICRQEQ  353 (666)
Q Consensus       299 Iit~~~~~~s~d~~~r~l~~L~s~L~r---~r~~~I~F~p~s~~~i~kiL~~I~~~e~  353 (666)
                      +++.+...       .   .+..++.+   .+...+-|..++.+.---.+-.++...+
T Consensus       292 Vlsat~~~-------~---~~~~~~~~~~~~~~~~~I~TKlDet~~~G~~l~~~~~~~  339 (388)
T PRK12723        292 AVSSTTKT-------S---DVKEIFHQFSPFSYKTVIFTKLDETTCVGNLISLIYEMR  339 (388)
T ss_pred             EEcCCCCH-------H---HHHHHHHHhcCCCCCEEEEEeccCCCcchHHHHHHHHHC
Confidence            55543211       1   12222222   2355677777777665555555555443

>PRK05574 holA DNA polymerase III subunit delta; Reviewed

Probab=97.75  E-value=0.0025  Score=68.51  Aligned_cols=116  Identities=13%  Similarity=0.164  Sum_probs=76.8

Q ss_pred             ceEEEEeCCCCCcchhHHHHHHHHHHHHHhcCCCc-eEEEEecCCCCCCccchhhhhhH-HHHHHhhcCeeEEEeCCCCH
Q 005987          261 SAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHIP-TAVVLTECGKADSVDSTAQSFEE-LQSILVDAGARKVALNPITN  338 (666)
Q Consensus       261 ~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~~~P-iViIit~~~~~~s~d~~~r~l~~-L~s~L~r~r~~~I~F~p~s~  338 (666)
                      +++++|++++.+.... .......+..++.....+ +++++....    .+.... +.. .+. +.. .+..+.|.+++.
T Consensus        77 ~klvii~~~~~l~~~~-~~~~l~~l~~~l~~~~~~~~~li~~~~~----~~~~~k-~~k~~k~-~~~-~~~~~~~~~~~~  148 (340)
T PRK05574         77 RKLVELRLPEFLTGAK-GEKALKRLEAYLNPLPHPDLLLIVRLPK----LDKAKK-KSAWFKA-LKK-KAVVVEAQPPKE  148 (340)
T ss_pred             CeEEEEECCCCCCchh-HHHHHHHHHHhccCCCCCcEEEEEECCc----CCHHHH-hhHHHHH-HHh-CceEEEcCCCCH
Confidence            5699999998775432 112222233333112222 333433211    111111 101 122 222 478999999999


Q ss_pred             HHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCcHHHHHHHHHHHhc
Q 005987          339 GSIKRTLSKICRQEQYSLSTEQIDLVAQASGGDIRQAITSLQFSSL  384 (666)
Q Consensus       339 ~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~s~GDIR~AIn~LQf~~~  384 (666)
                      .++...+...+...|+.+++++++.|++.++||++.+.+-|+-++.
T Consensus       149 ~~~~~~i~~~~~~~g~~i~~~a~~~L~~~~~~d~~~l~~El~KL~l  194 (340)
T PRK05574        149 AELPQWIQQRLKQQGLQIDAAALQLLAERVEGNLLALAQELEKLAL  194 (340)
T ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHHHHhCchHHHHHHHHHHHHh
Confidence            9999999999999999999999999999999999999998887765

>PRK10923 glnG nitrogen regulation protein NR(I); Provisional

Probab=97.75  E-value=0.0013  Score=74.21  Aligned_cols=209  Identities=15%  Similarity=0.220  Sum_probs=112.4

Q ss_pred             CccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcCCCchhhhhhhhc
Q 005987          147 SLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL---GARLYEWDTPTPTIWQEYMHN  223 (666)
Q Consensus       147 sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~nasd~~~~~e~l~~  223 (666)
                      .+.+++|......++...+.....   ..   ..++|+|++|||||++|+++....   +..++.+++.....  +.+..
T Consensus       136 ~~~~lig~s~~~~~l~~~~~~~~~---~~---~~vli~Ge~GtGK~~lA~~ih~~s~~~~~~~i~i~c~~~~~--~~~~~  207 (469)
T PRK10923        136 PTTDIIGEAPAMQDVFRIIGRLSR---SS---ISVLINGESGTGKELVAHALHRHSPRAKAPFIALNMAAIPK--DLIES  207 (469)
T ss_pred             ccccceecCHHHHHHHHHHHHHhc---cC---CeEEEEeCCCCcHHHHHHHHHhcCCCCCCCeEeeeCCCCCH--HHHHH
Confidence            356789998888888887765332   11   469999999999999999998875   45678888765210  00000


Q ss_pred             ccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcCCC-------c-
Q 005987          224 CKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHI-------P-  295 (666)
Q Consensus       224 ~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~~~-------P-  295 (666)
                      ...|....    .|... .. .+.+.    .. . ..+..|+|||++.+...     .+..|..+++.+..       | 
T Consensus       208 ~lfg~~~g----~~~~~-~~-~~~g~----~~-~-a~~Gtl~l~~i~~l~~~-----~q~~L~~~l~~~~~~~~~~~~~~  270 (469)
T PRK10923        208 ELFGHEKG----AFTGA-NT-IRQGR----FE-Q-ADGGTLFLDEIGDMPLD-----VQTRLLRVLADGQFYRVGGYAPV  270 (469)
T ss_pred             HhcCCCCC----CCCCC-Cc-CCCCC----ee-E-CCCCEEEEeccccCCHH-----HHHHHHHHHhcCcEEeCCCCCeE
Confidence            00010000    00000 00 00000    00 0 11236899999988643     22234444444321       1 


Q ss_pred             ----eEEEEecCCCCCCccc-hhhhhhHHHHHHhhcCeeEEEeCCCCH--HHHHHHHHH----HHHHhC---CCCCHHHH
Q 005987          296 ----TAVVLTECGKADSVDS-TAQSFEELQSILVDAGARKVALNPITN--GSIKRTLSK----ICRQEQ---YSLSTEQI  361 (666)
Q Consensus       296 ----iViIit~~~~~~s~d~-~~r~l~~L~s~L~r~r~~~I~F~p~s~--~~i~kiL~~----I~~~e~---i~v~~~~l  361 (666)
                          .||++++....   +. ....+  ...++.+..+..|.++|+..  +++..++..    .+...+   ..++++++
T Consensus       271 ~~~~rii~~~~~~l~---~~~~~~~~--~~~L~~~l~~~~i~~PpLreR~~Di~~l~~~~l~~~~~~~~~~~~~~~~~a~  345 (469)
T PRK10923        271 KVDVRIIAATHQNLE---QRVQEGKF--REDLFHRLNVIRVHLPPLRERREDIPRLARHFLQVAARELGVEAKLLHPETE  345 (469)
T ss_pred             EeeEEEEEeCCCCHH---HHHHcCCc--hHHHHHHhcceeecCCCcccchhhHHHHHHHHHHHHHHHcCCCCCCcCHHHH
Confidence                23333321100   00 00011  12233333456788888755  344433333    333333   24789999


Q ss_pred             HHHHHHc-CCcHHHHHHHHHHHhcC
Q 005987          362 DLVAQAS-GGDIRQAITSLQFSSLK  385 (666)
Q Consensus       362 ~~Ia~~s-~GDIR~AIn~LQf~~~~  385 (666)
                      ..|.... .|++|..-|.++-++..
T Consensus       346 ~~L~~~~wpgNv~eL~~~i~~~~~~  370 (469)
T PRK10923        346 AALTRLAWPGNVRQLENTCRWLTVM  370 (469)
T ss_pred             HHHHhCCCCChHHHHHHHHHHHHHh
Confidence            9998774 59999999999888764

>PRK15115 response regulator GlrR; Provisional

Probab=97.74  E-value=0.0016  Score=72.87  Aligned_cols=202  Identities=12%  Similarity=0.184  Sum_probs=106.1

Q ss_pred             ccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcCCCchhhhhhhhcccC
Q 005987          150 ELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL---GARLYEWDTPTPTIWQEYMHNCKT  226 (666)
Q Consensus       150 eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~nasd~~~~~e~l~~~~~  226 (666)
                      ++++....+..+..-+.....   ..   ..++|+|++|+|||++|+.+.+..   +..++.+++.....  +.+.....
T Consensus       135 ~lig~s~~~~~~~~~~~~~a~---~~---~~vli~Ge~GtGk~~lA~~ih~~s~r~~~~f~~i~c~~~~~--~~~~~~lf  206 (444)
T PRK15115        135 AIVTRSPLMLRLLEQARMVAQ---SD---VSVLINGQSGTGKEILAQAIHNASPRASKPFIAINCGALPE--QLLESELF  206 (444)
T ss_pred             cccccCHHHHHHHHHHHhhcc---CC---CeEEEEcCCcchHHHHHHHHHHhcCCCCCCeEEEeCCCCCH--HHHHHHhc
Confidence            466766666655554443221   11   369999999999999999998875   46788888764110  00000000


Q ss_pred             CccccchhHHHHHHHHHHHhhcCCCC---CCCC--CCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcCCC-------
Q 005987          227 GLEYTSKLDEFENFVERIRRYGSTSP---SIPG--ESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHI-------  294 (666)
Q Consensus       227 g~~~~s~~~~f~~fl~~a~~~~~l~~---s~~~--~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~~~-------  294 (666)
                      |..                 .+...+   ...|  .......|+|||++.+...     .+..|..+++.+..       
T Consensus       207 g~~-----------------~~~~~~~~~~~~g~~~~a~~gtl~l~~i~~l~~~-----~q~~L~~~l~~~~~~~~g~~~  264 (444)
T PRK15115        207 GHA-----------------RGAFTGAVSNREGLFQAAEGGTLFLDEIGDMPAP-----LQVKLLRVLQERKVRPLGSNR  264 (444)
T ss_pred             CCC-----------------cCCCCCCccCCCCcEEECCCCEEEEEccccCCHH-----HHHHHHHHHhhCCEEeCCCCc
Confidence            000                 000000   0000  0012348999999988643     23334444444321       


Q ss_pred             ----ceEEEEecCCCCCCccch-hhhhhHHHHHHhhcCeeEEEeCCCCH--HHHHHHHHHHH----HHhC---CCCCHHH
Q 005987          295 ----PTAVVLTECGKADSVDST-AQSFEELQSILVDAGARKVALNPITN--GSIKRTLSKIC----RQEQ---YSLSTEQ  360 (666)
Q Consensus       295 ----PiViIit~~~~~~s~d~~-~r~l~~L~s~L~r~r~~~I~F~p~s~--~~i~kiL~~I~----~~e~---i~v~~~~  360 (666)
                          .+-+|++. +.+ ..... ...+  ...++.+.....|.++|+..  +++..++...+    ...+   ..+++++
T Consensus       265 ~~~~~~rii~~~-~~~-l~~~~~~~~f--~~~l~~~l~~~~i~lPpLr~R~eDi~~l~~~~l~~~~~~~~~~~~~~~~~a  340 (444)
T PRK15115        265 DIDIDVRIISAT-HRD-LPKAMARGEF--REDLYYRLNVVSLKIPALAERTEDIPLLANHLLRQAAERHKPFVRAFSTDA  340 (444)
T ss_pred             eeeeeEEEEEeC-CCC-HHHHHHcCCc--cHHHHHhhceeeecCCChHhccccHHHHHHHHHHHHHHHhCCCCCCcCHHH
Confidence                12233332 111 00000 0011  01122222355677777754  34444433333    3223   2489999


Q ss_pred             HHHHHHHc-CCcHHHHHHHHHHHhcC
Q 005987          361 IDLVAQAS-GGDIRQAITSLQFSSLK  385 (666)
Q Consensus       361 l~~Ia~~s-~GDIR~AIn~LQf~~~~  385 (666)
                      ++.|.... .|++|...|.++-++..
T Consensus       341 ~~~L~~~~WpgNvreL~~~i~~~~~~  366 (444)
T PRK15115        341 MKRLMTASWPGNVRQLVNVIEQCVAL  366 (444)
T ss_pred             HHHHHhCCCCChHHHHHHHHHHHHHh
Confidence            99999997 89999999999987753

>COG5271 MDN1 AAA ATPase containing von Willebrand factor type A (vWA) domain [General function prediction only]

Probab=97.73  E-value=0.00023  Score=85.89  Aligned_cols=159  Identities=19%  Similarity=0.260  Sum_probs=96.5

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCchhhhhhhhcccCCccccchhHHH----HHHHHHHHhhcCCCCCC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTIWQEYMHNCKTGLEYTSKLDEF----ENFVERIRRYGSTSPSI  254 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~~~~e~l~~~~~g~~~~s~~~~f----~~fl~~a~~~~~l~~s~  254 (666)
                      +.+||-|.||+|||+++.+||++.|-+++.+|-++++...+.++....+-.-    .+|    ..|+...+         
T Consensus      1544 kpilLEGsPGVGKTSlItaLAr~tG~kliRINLSeQTdL~DLfGsd~Pve~~----Gef~w~dapfL~amr--------- 1610 (4600)
T COG5271        1544 KPILLEGSPGVGKTSLITALARKTGKKLIRINLSEQTDLCDLFGSDLPVEEG----GEFRWMDAPFLHAMR--------- 1610 (4600)
T ss_pred             CceeecCCCCccHHHHHHHHHHHhcCceEEeeccccchHHHHhCCCCCcccC----ceeEecccHHHHHhh---------
Confidence            5799999999999999999999999999999999988777766554332210    111    12343332         


Q ss_pred             CCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHh----c-----CCCceEEEEecCCCCCCccchhhhhhHHHHHHhh
Q 005987          255 PGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVR----S-----THIPTAVVLTECGKADSVDSTAQSFEELQSILVD  325 (666)
Q Consensus       255 ~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~----~-----~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r  325 (666)
                           .+.-+|+||+. +..+..++++..||..--+    .     .-.|-+.+.++.++..... -.+.+  .++.+.|
T Consensus      1611 -----~G~WVlLDEiN-LaSQSVlEGLNacLDhR~eayIPEld~~f~~HpnfrVFAaqNPq~qgg-GRKgL--PkSF~nR 1681 (4600)
T COG5271        1611 -----DGGWVLLDEIN-LASQSVLEGLNACLDHRREAYIPELDKTFDVHPNFRVFAAQNPQDQGG-GRKGL--PKSFLNR 1681 (4600)
T ss_pred             -----cCCEEEeehhh-hhHHHHHHHHHHHHhhccccccccccceeeccCCeeeeeecCchhcCC-CcccC--CHHHhhh
Confidence                 22368999996 4445556666655532111    0     0114444444443322111 11222  2677765


Q ss_pred             cCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHH
Q 005987          326 AGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVA  365 (666)
Q Consensus       326 ~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia  365 (666)
                        +.+|.+..++.++|..++....    -.+.++.+-.|+
T Consensus      1682 --FsvV~~d~lt~dDi~~Ia~~~y----p~v~~d~~~kii 1715 (4600)
T COG5271        1682 --FSVVKMDGLTTDDITHIANKMY----PQVNEDWRLKII 1715 (4600)
T ss_pred             --hheEEecccccchHHHHHHhhC----CccChHHHHHHH
Confidence              7889999999998887666442    234444444443

>PRK00771 signal recognition particle protein Srp54; Provisional

Probab=97.71  E-value=0.0024  Score=70.90  Aligned_cols=59  Identities=20%  Similarity=0.325  Sum_probs=39.0

Q ss_pred             HHHHHHHHHHHHHhhcCCCC----CCCccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcCCC
Q 005987          155 RKKVEEVRAWFEERLGDSKD----KFSTNVLVITGQAGVGKTATVRQIASHL---GARLYEWDTPT  213 (666)
Q Consensus       155 ~k~i~el~~wL~~~~~~~~g----~~~~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~nasd  213 (666)
                      +..++.|.+.|...+.....    ..++..++|+||+|+||||++..||..+   |+.+.-+.+..
T Consensus        68 ~~~~~~v~~~L~~~l~~~~~~~~~~~~p~vI~lvG~~GsGKTTtaakLA~~L~~~g~kV~lV~~D~  133 (437)
T PRK00771         68 EHVIKIVYEELVKLLGEETEPLVLPLKPQTIMLVGLQGSGKTTTAAKLARYFKKKGLKVGLVAADT  133 (437)
T ss_pred             HHHHHHHHHHHHHHhCCCccccccCCCCeEEEEECCCCCcHHHHHHHHHHHHHHcCCeEEEecCCC
Confidence            34455555555544432110    0124789999999999999999999877   67776666543

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

Probab=97.69  E-value=8.2e-05  Score=67.72  Aligned_cols=53  Identities=32%  Similarity=0.341  Sum_probs=41.4

Q ss_pred             cccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc
Q 005987          149 EELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       149 ~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      ..|.||.-+++.|.+.|+.++.....+-| -+|-|+||||||||.+++.||+.+
T Consensus        25 ~~l~GQhla~~~v~~ai~~~l~~~~p~Kp-LVlSfHG~tGtGKn~v~~liA~~l   77 (127)
T PF06309_consen   25 RNLFGQHLAVEVVVNAIKGHLANPNPRKP-LVLSFHGWTGTGKNFVSRLIAEHL   77 (127)
T ss_pred             HHccCcHHHHHHHHHHHHHHHcCCCCCCC-EEEEeecCCCCcHHHHHHHHHHHH
Confidence            35789999999999888887764322222 245589999999999999999997

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

>KOG2170 consensus ATPase of the AAA+ superfamily [General function prediction only]

Probab=97.66  E-value=0.002  Score=66.59  Aligned_cols=192  Identities=16%  Similarity=0.184  Sum_probs=102.9

Q ss_pred             cccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCchhhhhhhhcccCCccc
Q 005987          151 LAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTIWQEYMHNCKTGLEY  230 (666)
Q Consensus       151 Lvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~~~~e~l~~~~~g~~~  230 (666)
                      |.||.-+.+.|...++........+-| =.|=|+|++||||...++.||+.+--.-.   .|+   +-.++.+.. ...-
T Consensus        84 lfGQHla~~~Vv~alk~~~~n~~p~KP-LvLSfHG~tGTGKN~Va~iiA~n~~~~Gl---~S~---~V~~fvat~-hFP~  155 (344)
T KOG2170|consen   84 LFGQHLAKQLVVNALKSHWANPNPRKP-LVLSFHGWTGTGKNYVAEIIAENLYRGGL---RSP---FVHHFVATL-HFPH  155 (344)
T ss_pred             hhchHHHHHHHHHHHHHHhcCCCCCCC-eEEEecCCCCCchhHHHHHHHHHHHhccc---cch---hHHHhhhhc-cCCC
Confidence            568888888888888876654332222 24557999999999999999998721100   000   000000000 0000


Q ss_pred             cchhH----HHHHH-HHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcC--------CCceE
Q 005987          231 TSKLD----EFENF-VERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRST--------HIPTA  297 (666)
Q Consensus       231 ~s~~~----~f~~f-l~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~--------~~PiV  297 (666)
                      .+.++    +++.. .+.++..            .+.|.|+||+|.+..     .+.++|..+++..        +.-|+
T Consensus       156 ~~~ie~Yk~eL~~~v~~~v~~C------------~rslFIFDE~DKmp~-----gLld~lkpfLdyyp~v~gv~frkaIF  218 (344)
T KOG2170|consen  156 ASKIEDYKEELKNRVRGTVQAC------------QRSLFIFDEVDKLPP-----GLLDVLKPFLDYYPQVSGVDFRKAIF  218 (344)
T ss_pred             hHHHHHHHHHHHHHHHHHHHhc------------CCceEEechhhhcCH-----hHHHHHhhhhccccccccccccceEE
Confidence            11112    22221 1222211            245999999998853     3555565555521        22466


Q ss_pred             EEEecCCCCCCcc--------------chhhhhhH-HH-HHHh--------------hcCeeEEEeCCCCHHHHHHHHHH
Q 005987          298 VVLTECGKADSVD--------------STAQSFEE-LQ-SILV--------------DAGARKVALNPITNGSIKRTLSK  347 (666)
Q Consensus       298 iIit~~~~~~s~d--------------~~~r~l~~-L~-s~L~--------------r~r~~~I~F~p~s~~~i~kiL~~  347 (666)
                      |.+++.+-....+              ...+.+++ |. +..+              +.--..|.|-|+....++..++-
T Consensus       219 IfLSN~gg~eI~~~aL~~~~~g~~re~~~l~~~E~~L~~~~~n~~~~Gl~~S~li~~~lid~fIPFLPLek~hV~~C~r~  298 (344)
T KOG2170|consen  219 IFLSNAGGSEIARIALENARNGKPREQLRLKSFEPALMQSAFNEKAGGLVHSRLISNNLIDHFIPFLPLEKRHVRSCIRA  298 (344)
T ss_pred             EEEcCCcchHHHHHHHHHHHcCCCcccchhhhhhHHHHHhhhccccccccccccchhhHHhhccCcCcccHHHHHHHHHH
Confidence            6666654221110              00111110 00 0000              00123578999999999999999


Q ss_pred             HHHHhCCCCCHHHHHHHHHH
Q 005987          348 ICRQEQYSLSTEQIDLVAQA  367 (666)
Q Consensus       348 I~~~e~i~v~~~~l~~Ia~~  367 (666)
                      -+.++|...+.+.++.+++.
T Consensus       299 el~~rg~~~d~~~~erva~~  318 (344)
T KOG2170|consen  299 ELRKRGLAPDQDFVERVANS  318 (344)
T ss_pred             HHHhcccccchHHHHHHHHh
Confidence            99899988888887777653

>PRK06585 holA DNA polymerase III subunit delta; Reviewed

Probab=97.65  E-value=0.0048  Score=66.60  Aligned_cols=200  Identities=13%  Similarity=0.113  Sum_probs=121.5

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcC------CcEEEEcCCCchhhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLG------ARLYEWDTPTPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSP  252 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg------~~viE~nasd~~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~  252 (666)
                      +++||||+-.-.....+..+.+.+.      ++++.+...+                +.   ....++++.+...+    
T Consensus        21 ~~yll~G~e~~li~~~~~~l~~~~~~~~~~~fn~~~~~~~e----------------~~---~~~~~~~~~~~t~s----   77 (343)
T PRK06585         21 RAVLLYGPDRGLVRERARRLAKSVVPDLDDPFAVVRLDGDD----------------LD---ADPARLEDEANAIS----   77 (343)
T ss_pred             eEEEEeCCchHHHHHHHHHHHHHhcCCCCCCcceeeccHHH----------------hh---cCHHHHHHHHhCCC----
Confidence            6999999999888888888877763      2222222110                00   01345666665443    


Q ss_pred             CCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcCCCceEEEEecCCCCCCccchhhhhhHHHHHHhh-cCeeEE
Q 005987          253 SIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVD-AGARKV  331 (666)
Q Consensus       253 s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r-~r~~~I  331 (666)
                       ++++   +++|+|.+.+.        ...+.|..++.....-.++|+....    .+...+    +...+.. ..+..|
T Consensus        78 -lF~~---~rlViv~~~~~--------~~~~~L~~~l~~~~~~~~lil~~~~----~~~~~k----l~k~~~~~~~~~~v  137 (343)
T PRK06585         78 -LFGG---RRLIWVRAGSK--------NLAAALKALLESPPGDAFIVIEAGD----LKKGSS----LRKLFETAAYAAAI  137 (343)
T ss_pred             -CCCC---ceEEEEECCch--------hHHHHHHHHHcCCCCCcEEEEEcCC----CCcccH----HHHHHhcCCCeeEE
Confidence             2332   46888985432        1223455565553222333443211    111111    2222211 125678


Q ss_pred             EeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCcHHHHHHHHHHHhcCCCCcccccccCCCCCCCccccCCCCC
Q 005987          332 ALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASGGDIRQAITSLQFSSLKQDPMLNLSLSISKPNFPEEKADGHGG  411 (666)
Q Consensus       332 ~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~s~GDIR~AIn~LQf~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~  411 (666)
                      .|.+++..++.+.+...+...|+.+++++++.|++.++||++.+.|-|+-++.-......              .+ .+.
T Consensus       138 ~~~~~~~~~l~~~i~~~~~~~g~~i~~~a~~~L~~~~g~dl~~l~~EleKL~ly~~~~~~--------------It-~ed  202 (343)
T PRK06585        138 PCYADDERDLARLIDDELAEAGLRITPDARALLVALLGGDRLASRNEIEKLALYAHGKGE--------------IT-LDD  202 (343)
T ss_pred             ecCCCCHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHhCCCHHHHHHHHHHHHHhcCCCCC--------------CC-HHH
Confidence            999999999999999999999999999999999999999999999999887764211000              00 011


Q ss_pred             cccccCCccccchHHHHhHHhhCCC
Q 005987          412 FSIQFGRDETLSLFHALGKFLHNKR  436 (666)
Q Consensus       412 ~~~~~~RD~~l~lFhalGkil~~Kr  436 (666)
                      +..+.......++|+.+..++.++.
T Consensus       203 V~~lv~~~~e~~if~l~dai~~~~~  227 (343)
T PRK06585        203 VRAVVGDASALSLDDAADAALAGDL  227 (343)
T ss_pred             HHHHhCCcccccHHHHHHHHHCCCH
Confidence            2234455556788888887777653

>PRK11361 acetoacetate metabolism regulatory protein AtoC; Provisional

Probab=97.64  E-value=0.0022  Score=71.82  Aligned_cols=209  Identities=14%  Similarity=0.182  Sum_probs=109.4

Q ss_pred             ccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcCCCchhhhhhhhcc
Q 005987          148 LEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL---GARLYEWDTPTPTIWQEYMHNC  224 (666)
Q Consensus       148 l~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~nasd~~~~~e~l~~~  224 (666)
                      +..+++......++...+..+..   .  . ..++++|++|+||+++|+++....   +..++.+++.....  +.+...
T Consensus       142 ~~~ii~~S~~~~~~~~~~~~~a~---~--~-~~vli~Ge~GtGK~~lA~~ih~~s~~~~~~~~~i~c~~~~~--~~~~~~  213 (457)
T PRK11361        142 WGHILTNSPAMMDICKDTAKIAL---S--Q-ASVLISGESGTGKELIARAIHYNSRRAKGPFIKVNCAALPE--SLLESE  213 (457)
T ss_pred             ccceecccHHHhHHHHHHHHHcC---C--C-cEEEEEcCCCccHHHHHHHHHHhCCCCCCCeEEEECCCCCH--HHHHHH
Confidence            34578887777787777766432   1  1 469999999999999999997764   46778888764210  000000


Q ss_pred             cCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcCCC----------
Q 005987          225 KTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHI----------  294 (666)
Q Consensus       225 ~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~~~----------  294 (666)
                      ..|.........      ...+.+.+    .  .....+|+|||++.+...     .+..|..+++....          
T Consensus       214 lfg~~~~~~~~~------~~~~~g~~----~--~a~~gtl~ld~i~~l~~~-----~q~~L~~~l~~~~~~~~~~~~~~~  276 (457)
T PRK11361        214 LFGHEKGAFTGA------QTLRQGLF----E--RANEGTLLLDEIGEMPLV-----LQAKLLRILQEREFERIGGHQTIK  276 (457)
T ss_pred             hcCCCCCCCCCC------CCCCCCce----E--ECCCCEEEEechhhCCHH-----HHHHHHHHHhcCcEEeCCCCceee
Confidence            000000000000      00000000    0  011348999999998643     23334444443221          


Q ss_pred             -c-eEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCH--HHHHHH----HHHHHHHhC---CCCCHHHHHH
Q 005987          295 -P-TAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITN--GSIKRT----LSKICRQEQ---YSLSTEQIDL  363 (666)
Q Consensus       295 -P-iViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~--~~i~ki----L~~I~~~e~---i~v~~~~l~~  363 (666)
                       . .||.+++......  .....+.  ..++.+.....|.++|+..  +++..+    |.+.+...+   ..+++++++.
T Consensus       277 ~~~rii~~t~~~l~~~--~~~g~~~--~~l~~~l~~~~i~~ppLreR~~di~~l~~~~l~~~~~~~~~~~~~~~~~a~~~  352 (457)
T PRK11361        277 VDIRIIAATNRDLQAM--VKEGTFR--EDLFYRLNVIHLILPPLRDRREDISLLANHFLQKFSSENQRDIIDIDPMAMSL  352 (457)
T ss_pred             eceEEEEeCCCCHHHH--HHcCCch--HHHHHHhccceecCCChhhchhhHHHHHHHHHHHHHHHcCCCCCCcCHHHHHH
Confidence             1 2333332110000  0000111  1222232356677777763  344433    333333222   4589999999


Q ss_pred             HHHHc-CCcHHHHHHHHHHHhcC
Q 005987          364 VAQAS-GGDIRQAITSLQFSSLK  385 (666)
Q Consensus       364 Ia~~s-~GDIR~AIn~LQf~~~~  385 (666)
                      |.... .|++|..-|.|+-++..
T Consensus       353 L~~~~wpgNv~eL~~~~~~~~~~  375 (457)
T PRK11361        353 LTAWSWPGNIRELSNVIERAVVM  375 (457)
T ss_pred             HHcCCCCCcHHHHHHHHHHHHHh
Confidence            99874 79999999999987754

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

Probab=97.64  E-value=0.00041  Score=64.70  Aligned_cols=47  Identities=21%  Similarity=0.328  Sum_probs=34.1

Q ss_pred             ccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCC
Q 005987          152 AVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGA  204 (666)
Q Consensus       152 vg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~  204 (666)
                      +|....++++++-++....   ..   ..++|+|++|+||+++|+.|...-+.
T Consensus         1 vG~S~~~~~l~~~l~~~a~---~~---~pvli~GE~GtGK~~~A~~lh~~~~~   47 (138)
T PF14532_consen    1 VGKSPAMRRLRRQLERLAK---SS---SPVLITGEPGTGKSLLARALHRYSGR   47 (138)
T ss_dssp             --SCHHHHHHHHHHHHHHC---SS---S-EEEECCTTSSHHHHHHCCHHTTTT
T ss_pred             CCCCHHHHHHHHHHHHHhC---CC---CcEEEEcCCCCCHHHHHHHHHhhcCc
Confidence            3556677788877776543   11   46999999999999999999887653

>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=97.63  E-value=0.0015  Score=66.52  Aligned_cols=65  Identities=22%  Similarity=0.387  Sum_probs=46.7

Q ss_pred             EEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCchhhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCC
Q 005987          180 VLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESK  259 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~  259 (666)
                      .-.++||+|+|||.+++.||+.+|..++.+|+++..             .    ...+.+++.-+...+           
T Consensus        34 ~~~~~GpagtGKtetik~La~~lG~~~~vfnc~~~~-------------~----~~~l~ril~G~~~~G-----------   85 (231)
T PF12774_consen   34 GGALSGPAGTGKTETIKDLARALGRFVVVFNCSEQM-------------D----YQSLSRILKGLAQSG-----------   85 (231)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHCTT--EEEEETTSSS------------------HHHHHHHHHHHHHHT-----------
T ss_pred             CCCCcCCCCCCchhHHHHHHHHhCCeEEEecccccc-------------c----HHHHHHHHHHHhhcC-----------
Confidence            467899999999999999999999999999987622             1    224445554443332           


Q ss_pred             CceEEEEeCCCCCcc
Q 005987          260 SSAILLIDDLPVTNG  274 (666)
Q Consensus       260 ~~~IIlIDEid~l~~  274 (666)
                        .-+++||++++..
T Consensus        86 --aW~cfdefnrl~~   98 (231)
T PF12774_consen   86 --AWLCFDEFNRLSE   98 (231)
T ss_dssp             ---EEEEETCCCSSH
T ss_pred             --chhhhhhhhhhhH
Confidence              4789999999864

>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=97.62  E-value=0.0023  Score=71.01  Aligned_cols=35  Identities=29%  Similarity=0.451  Sum_probs=27.5

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc-----CCcEEEEcCCC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL-----GARLYEWDTPT  213 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel-----g~~viE~nasd  213 (666)
                      ++++|.||+|+||||++..||..+     +..|.-+++..
T Consensus       222 ~~i~~vGptGvGKTTt~~kLA~~~~~~~~g~~V~li~~D~  261 (424)
T PRK05703        222 GVVALVGPTGVGKTTTLAKLAARYALLYGKKKVALITLDT  261 (424)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHHHHhcCCCeEEEEECCc
Confidence            689999999999999998887654     45666666543

>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=97.62  E-value=0.0017  Score=67.56  Aligned_cols=57  Identities=16%  Similarity=0.281  Sum_probs=39.0

Q ss_pred             ccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCC
Q 005987          150 ELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTP  212 (666)
Q Consensus       150 eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nas  212 (666)
                      +|+.-+..++-|.+..+ .+.    . +..++||.|.+|+||+|+++..|--.+++++++..+
T Consensus         9 ~lVlf~~ai~hi~ri~R-vL~----~-~~Gh~LLvG~~GsGr~sl~rLaa~i~~~~~~~i~~~   65 (268)
T PF12780_consen    9 NLVLFDEAIEHIARISR-VLS----Q-PRGHALLVGVGGSGRQSLARLAAFICGYEVFQIEIT   65 (268)
T ss_dssp             -----HHHHHHHHHHHH-HHC----S-TTEEEEEECTTTSCHHHHHHHHHHHTTEEEE-TTTS
T ss_pred             ceeeHHHHHHHHHHHHH-HHc----C-CCCCeEEecCCCccHHHHHHHHHHHhccceEEEEee
Confidence            45667777777666544 332    1 225799999999999999999999899999987643

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.

>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=97.61  E-value=0.003  Score=68.46  Aligned_cols=34  Identities=26%  Similarity=0.373  Sum_probs=27.9

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcCC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL---GARLYEWDTP  212 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel---g~~viE~nas  212 (666)
                      +.++|.||+|+||||++..||..+   |..+.-+.+-
T Consensus       242 ~vI~LVGptGvGKTTTiaKLA~~L~~~GkkVglI~aD  278 (436)
T PRK11889        242 QTIALIGPTGVGKTTTLAKMAWQFHGKKKTVGFITTD  278 (436)
T ss_pred             cEEEEECCCCCcHHHHHHHHHHHHHHcCCcEEEEecC
Confidence            689999999999999999999877   5566655543

>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=97.61  E-value=0.0006  Score=65.97  Aligned_cols=57  Identities=18%  Similarity=0.237  Sum_probs=43.2

Q ss_pred             cccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcCCC
Q 005987          151 LAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL---GARLYEWDTPT  213 (666)
Q Consensus       151 Lvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~nasd  213 (666)
                      |+|....++++.+-++....     .+ .++||+|++||||+.+|+++-+..   +..++.+|++.
T Consensus         1 liG~s~~m~~~~~~~~~~a~-----~~-~pVlI~GE~GtGK~~lA~~IH~~s~r~~~pfi~vnc~~   60 (168)
T PF00158_consen    1 LIGESPAMKRLREQAKRAAS-----SD-LPVLITGETGTGKELLARAIHNNSPRKNGPFISVNCAA   60 (168)
T ss_dssp             SS--SHHHHHHHHHHHHHTT-----ST-S-EEEECSTTSSHHHHHHHHHHCSTTTTS-EEEEETTT
T ss_pred             CEeCCHHHHHHHHHHHHHhC-----CC-CCEEEEcCCCCcHHHHHHHHHHhhhcccCCeEEEehhh
Confidence            57788888999888887543     22 469999999999999999998865   46789999876

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 ....

>COG5271 MDN1 AAA ATPase containing von Willebrand factor type A (vWA) domain [General function prediction only]

Probab=97.61  E-value=0.0015  Score=79.36  Aligned_cols=190  Identities=15%  Similarity=0.195  Sum_probs=113.1

Q ss_pred             cccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCchhhhhhhhcccCCccc
Q 005987          151 LAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTIWQEYMHNCKTGLEY  230 (666)
Q Consensus       151 Lvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~~~~e~l~~~~~g~~~  230 (666)
                      .+.-+-....+.+.++.+..   .+.   ++||.||+.+|||+++..+|++.|-+++.+|+-..+..+++++...+.-. 
T Consensus       867 yIiTPfVqkn~ln~~Ra~s~---~~f---P~LiQGpTSSGKTSMI~yla~~tghkfVRINNHEHTdlqeYiGTyvTdd~-  939 (4600)
T COG5271         867 YIITPFVQKNYLNTMRAASL---SNF---PLLIQGPTSSGKTSMILYLARETGHKFVRINNHEHTDLQEYIGTYVTDDD-  939 (4600)
T ss_pred             eEecHHHHHHHHHHHHHHhh---cCC---cEEEecCCCCCcchHHHHHHHHhCccEEEecCcccchHHHHhhceeecCC-
Confidence            44444444444444443321   233   49999999999999999999999999999999887777777654322110 


Q ss_pred             cchhHHHH-HHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcC-------------CCce
Q 005987          231 TSKLDEFE-NFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRST-------------HIPT  296 (666)
Q Consensus       231 ~s~~~~f~-~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~-------------~~Pi  296 (666)
                       .++ .|+ .++-.+-+             ++--|++||+....     ..+.++|..+++..             +.|-
T Consensus       940 -G~l-sFkEGvLVeAlR-------------~GyWIVLDELNLAp-----TDVLEaLNRLLDDNRelfIPETqevV~PHp~  999 (4600)
T COG5271         940 -GSL-SFKEGVLVEALR-------------RGYWIVLDELNLAP-----TDVLEALNRLLDDNRELFIPETQEVVVPHPN  999 (4600)
T ss_pred             -Cce-eeehhHHHHHHh-------------cCcEEEeeccccCc-----HHHHHHHHHhhccccceecCCcceeeccCCC
Confidence             000 111 12222222             22368999996432     22344455554432             2255


Q ss_pred             EEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHc-CCcHHHH
Q 005987          297 AVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQAS-GGDIRQA  375 (666)
Q Consensus       297 ViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~s-~GDIR~A  375 (666)
                      +.+.++.+++..  +..|..  |...+++ |+..++|..++.+++..+|...     +++.+.....|++.. +=.+|+.
T Consensus      1000 F~lFATQNppg~--YgGRK~--LSrAFRN-RFlE~hFddipedEle~ILh~r-----c~iapSyakKiVeVyr~Ls~rRs 1069 (4600)
T COG5271        1000 FRLFATQNPPGG--YGGRKG--LSRAFRN-RFLEMHFDDIPEDELEEILHGR-----CEIAPSYAKKIVEVYRGLSSRRS 1069 (4600)
T ss_pred             eeEEeecCCCcc--ccchHH--HHHHHHh-hhHhhhcccCcHHHHHHHHhcc-----CccCHHHHHHHHHHHHHhhhhhh
Confidence            566655554332  222211  2222333 6888999999999999999855     457777777777653 2345665


Q ss_pred             HH
Q 005987          376 IT  377 (666)
Q Consensus       376 In  377 (666)
                      ++
T Consensus      1070 ~~ 1071 (4600)
T COG5271        1070 IN 1071 (4600)
T ss_pred             HH
Confidence            55

>PRK07452 DNA polymerase III subunit delta; Validated

Probab=97.60  E-value=0.0037  Score=66.93  Aligned_cols=169  Identities=17%  Similarity=0.203  Sum_probs=102.5

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcC------CcEEEEcCCCchhhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLG------ARLYEWDTPTPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSP  252 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg------~~viE~nasd~~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~  252 (666)
                      +++||||+----+...+..+.+.+.      +.+.+++..+                    .+.+..++..+...+    
T Consensus         2 ~~yll~G~e~~l~~~~~~~l~~~~~~~~~~~fn~~~~d~~~--------------------~~~~~~~~~~~~t~p----   57 (326)
T PRK07452          2 PIYLYWGEDDFALNQAIEKLIDQVVDPEWKSFNYSRLDGDD--------------------ADQAIQALNEAMTPP----   57 (326)
T ss_pred             CEEEEEcChHHHHHHHHHHHHHHhCCchhhhcchhhcCCcc--------------------chHHHHHHHHhcCCC----
Confidence            4799999988777777777776652      1222222111                    112345555553332    


Q ss_pred             CCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcCCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEE
Q 005987          253 SIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVA  332 (666)
Q Consensus       253 s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~  332 (666)
                       +.+   .+++|+|++++...+..  ....+.|..+++......++|+.....   .|...+.    ...+.. .+..+.
T Consensus        58 -ff~---~~rlVvv~~~~~~~~~~--~~~~~~L~~~l~~~~~~~~li~~~~~~---~d~r~k~----~k~l~k-~~~~~~  123 (326)
T PRK07452         58 -FGS---GGRLVWLKNSPLCQGCS--EELLAELERTLPLIPENTHLLLTNTKK---PDGRLKS----TKLLQK-LAEEKE  123 (326)
T ss_pred             -CCC---CceEEEEeCchhhccCC--HHHHHHHHHHHcCCCCCcEEEEEeCCC---cchHHHH----HHHHHH-ceeEEE
Confidence             122   24688999876432111  223345666666533223333322111   1111111    122222 366778


Q ss_pred             eCCC---CHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCcHHHHHHHHHHHhcC
Q 005987          333 LNPI---TNGSIKRTLSKICRQEQYSLSTEQIDLVAQASGGDIRQAITSLQFSSLK  385 (666)
Q Consensus       333 F~p~---s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~s~GDIR~AIn~LQf~~~~  385 (666)
                      |.++   ...++.+.++..+.+.|+.+++++++.|++.++||++.+.|.|+-++.-
T Consensus       124 ~~~~~~~~~~~l~~~i~~~~~~~g~~i~~~a~~~L~~~~g~dl~~l~~EleKL~ly  179 (326)
T PRK07452        124 FSLIPPWDTEGLKQLVERTAQELGVKLTPEAAELLAEAVGNDSRRLYNELEKLALY  179 (326)
T ss_pred             ecCCCcccHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhCccHHHHHHHHHHHHHh
Confidence            8766   4567999999999999999999999999999999999999999988763

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

Probab=97.58  E-value=0.0011  Score=70.48  Aligned_cols=176  Identities=16%  Similarity=0.259  Sum_probs=102.5

Q ss_pred             ccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCchhhhhh----hhc
Q 005987          148 LEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTIWQEY----MHN  223 (666)
Q Consensus       148 l~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~~~~e~----l~~  223 (666)
                      ...+.+++..++.+...+-+.    ....| -+++|+|-.|+|||.+++.+-++++.+-+-+|+-+.-.|...    +..
T Consensus         5 ~~~v~~Re~qi~~L~~Llg~~----~~~~P-S~~~iyG~sgTGKT~~~r~~l~~~n~~~vw~n~~ecft~~~lle~IL~~   79 (438)
T KOG2543|consen    5 EPNVPCRESQIRRLKSLLGNN----SCTIP-SIVHIYGHSGTGKTYLVRQLLRKLNLENVWLNCVECFTYAILLEKILNK   79 (438)
T ss_pred             ccCccchHHHHHHHHHHhCCC----Ccccc-eeEEEeccCCCchhHHHHHHHhhcCCcceeeehHHhccHHHHHHHHHHH
Confidence            345678888898888776531    12344 578999999999999999999999888777776553333222    222


Q ss_pred             c----cCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcCCCceEEE
Q 005987          224 C----KTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHIPTAVV  299 (666)
Q Consensus       224 ~----~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~~~PiViI  299 (666)
                      .    ..|.......+.|.+|+....++.....     ......|++|.+|.+...++  .+...|..+.+-.+.|.+.|
T Consensus        80 ~~~~d~dg~~~~~~~en~~d~i~~l~q~~~~t~-----~d~~~~liLDnad~lrD~~a--~ll~~l~~L~el~~~~~i~i  152 (438)
T KOG2543|consen   80 SQLADKDGDKVEGDAENFSDFIYLLVQWPAATN-----RDQKVFLILDNADALRDMDA--ILLQCLFRLYELLNEPTIVI  152 (438)
T ss_pred             hccCCCchhhhhhHHHHHHHHHHHHHhhHHhhc-----cCceEEEEEcCHHhhhccch--HHHHHHHHHHHHhCCCceEE
Confidence            1    1122222223456666666655443221     12467899999987643221  12234444444444444333


Q ss_pred             EecCCCCCCccchhhhhhHHHHHHh---hcCeeEEEeCCCCHHHHHHHHHH
Q 005987          300 LTECGKADSVDSTAQSFEELQSILV---DAGARKVALNPITNGSIKRTLSK  347 (666)
Q Consensus       300 it~~~~~~s~d~~~r~l~~L~s~L~---r~r~~~I~F~p~s~~~i~kiL~~  347 (666)
                      +.....-            ....+.   ..-...+.|+.++.++++++|.+
T Consensus       153 ils~~~~------------e~~y~~n~g~~~i~~l~fP~Ys~~e~~~Il~~  191 (438)
T KOG2543|consen  153 ILSAPSC------------EKQYLINTGTLEIVVLHFPQYSVEETQVILSR  191 (438)
T ss_pred             EEecccc------------HHHhhcccCCCCceEEecCCCCHHHHHHHHhc
Confidence            3321110            011111   11245789999999999988775

>KOG2228 consensus Origin recognition complex, subunit 4 [Replication, recombination and repair]

Probab=97.58  E-value=0.0018  Score=67.81  Aligned_cols=181  Identities=13%  Similarity=0.215  Sum_probs=92.6

Q ss_pred             cccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHH-HHHH--HcCCc--EEEEcCCCch---hhhhhh-
Q 005987          151 LAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVR-QIAS--HLGAR--LYEWDTPTPT---IWQEYM-  221 (666)
Q Consensus       151 Lvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~-~LAk--elg~~--viE~nasd~~---~~~e~l-  221 (666)
                      |.|+.+....+..|++.-...  |.  .+.+++.||.|+|||.++- .|+.  +.|=.  ++.+|.--..   ...+.. 
T Consensus        26 l~g~~~~~~~l~~~lkqt~~~--gE--snsviiigprgsgkT~li~~~Ls~~q~~~E~~l~v~Lng~~~~dk~al~~I~r  101 (408)
T KOG2228|consen   26 LFGVQDEQKHLSELLKQTILH--GE--SNSVIIIGPRGSGKTILIDTRLSDIQENGENFLLVRLNGELQTDKIALKGITR  101 (408)
T ss_pred             eeehHHHHHHHHHHHHHHHHh--cC--CCceEEEccCCCCceEeeHHHHhhHHhcCCeEEEEEECccchhhHHHHHHHHH
Confidence            678889999999999865442  22  2589999999999999873 3333  45433  3444543211   111110 


Q ss_pred             ----hcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcCCCceE
Q 005987          222 ----HNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHIPTA  297 (666)
Q Consensus       222 ----~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~~~PiV  297 (666)
                          .....+....+..+.+..+++-.+.-..       ..+-++|.|+||+|...+-. .+-+.--|....++.+.|+.
T Consensus       102 ql~~e~~~~~k~~gsfte~l~~lL~~L~~~~~-------~t~~~ViFIldEfDlf~~h~-rQtllYnlfDisqs~r~Pic  173 (408)
T KOG2228|consen  102 QLALELNRIVKSFGSFTENLSKLLEALKKGDE-------TTSGKVIFILDEFDLFAPHS-RQTLLYNLFDISQSARAPIC  173 (408)
T ss_pred             HHHHHHhhhheeecccchhHHHHHHHHhcCCC-------CCCceEEEEeehhhccccch-hhHHHHHHHHHHhhcCCCeE
Confidence                0011122233444445555554433211       12235677788999654321 12221113334455667876


Q ss_pred             EEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHH
Q 005987          298 VVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKIC  349 (666)
Q Consensus       298 iIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~  349 (666)
                      ++-.++- -+..+...   ...++++++  -.+.-+++.+-.++.++++..+
T Consensus       174 iig~Ttr-ld~lE~LE---KRVKSRFsh--r~I~m~~~~~l~~yv~l~r~ll  219 (408)
T KOG2228|consen  174 IIGVTTR-LDILELLE---KRVKSRFSH--RVIFMLPSLPLGDYVDLYRKLL  219 (408)
T ss_pred             EEEeecc-ccHHHHHH---HHHHhhccc--ceeeccCCCChHHHHHHHHHHh
Confidence            5533322 11111111   133555444  1233445556788888887765

>cd03281 ABC_MSH5_euk MutS5 homolog in eukaryotes

Probab=97.57  E-value=0.00037  Score=70.15  Aligned_cols=22  Identities=36%  Similarity=0.641  Sum_probs=20.3

Q ss_pred             cEEEEECCCCchHHHHHHHHHH
Q 005987          179 NVLVITGQAGVGKTATVRQIAS  200 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAk  200 (666)
                      +.++|+||.|+||||+++.++.
T Consensus        30 ~~~~itGpNg~GKStlLk~i~~   51 (213)
T cd03281          30 SIMVITGPNSSGKSVYLKQVAL   51 (213)
T ss_pred             eEEEEECCCCCChHHHHHHHHH
Confidence            6899999999999999999983

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

>TIGR01818 ntrC nitrogen regulation protein NR(I)

Probab=97.56  E-value=0.0049  Score=69.24  Aligned_cols=199  Identities=16%  Similarity=0.236  Sum_probs=112.8

Q ss_pred             cccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcCCCchhhhhhhhccc
Q 005987          149 EELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL---GARLYEWDTPTPTIWQEYMHNCK  225 (666)
Q Consensus       149 ~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~nasd~~~~~e~l~~~~  225 (666)
                      ..+++......++...+.....   ..   ..++++|.+||||+++++++.+..   +..++.+|+.....  +      
T Consensus       134 ~~lig~s~~~~~v~~~i~~~a~---~~---~~vli~Ge~GtGK~~~A~~ih~~~~~~~~~~~~~~c~~~~~--~------  199 (463)
T TIGR01818       134 AELIGEAPAMQEVFRAIGRLSR---SD---ITVLINGESGTGKELVARALHRHSPRANGPFIALNMAAIPK--D------  199 (463)
T ss_pred             cceeecCHHHHHHHHHHHHHhC---cC---CeEEEECCCCCCHHHHHHHHHHhCCCCCCCeEEEeCCCCCH--H------
Confidence            4578887888888777765321   11   368999999999999999998764   45677777654210  0      


Q ss_pred             CCccccchhHHHHHHHHHHHhhcCCCCCCCC---------CCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcCC---
Q 005987          226 TGLEYTSKLDEFENFVERIRRYGSTSPSIPG---------ESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTH---  293 (666)
Q Consensus       226 ~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~---------~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~~---  293 (666)
                                .+...+     ++.....+.+         ....+..|+|||++.+....     +..|..+++.+.   
T Consensus       200 ----------~~~~~l-----fg~~~~~~~~~~~~~~g~~~~a~~gtl~l~ei~~l~~~~-----q~~ll~~l~~~~~~~  259 (463)
T TIGR01818       200 ----------LIESEL-----FGHEKGAFTGANTRRQGRFEQADGGTLFLDEIGDMPLDA-----QTRLLRVLADGEFYR  259 (463)
T ss_pred             ----------HHHHHh-----cCCCCCCCCCcccCCCCcEEECCCCeEEEEchhhCCHHH-----HHHHHHHHhcCcEEE
Confidence                      011100     1100000000         00113479999999886532     223444444432   


Q ss_pred             --------Cc-eEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCC--HHHHHHHHHHHHH----HhC---CC
Q 005987          294 --------IP-TAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPIT--NGSIKRTLSKICR----QEQ---YS  355 (666)
Q Consensus       294 --------~P-iViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s--~~~i~kiL~~I~~----~e~---i~  355 (666)
                              .. .||++++......  .....+.  ..++.+..+..|.++|+.  .+++..++...+.    ..+   ..
T Consensus       260 ~~~~~~~~~~~rii~~~~~~l~~~--~~~~~f~--~~L~~rl~~~~i~lPpLr~R~~Di~~l~~~~l~~~~~~~~~~~~~  335 (463)
T TIGR01818       260 VGGRTPIKVDVRIVAATHQNLEAL--VRQGKFR--EDLFHRLNVIRIHLPPLRERREDIPRLARHFLALAARELDVEPKL  335 (463)
T ss_pred             CCCCceeeeeeEEEEeCCCCHHHH--HHcCCcH--HHHHHHhCcceecCCCcccchhhHHHHHHHHHHHHHHHhCCCCCC
Confidence                    11 2333332111000  0001111  133333345688999988  5666666555443    323   45


Q ss_pred             CCHHHHHHHHHHc-CCcHHHHHHHHHHHhcC
Q 005987          356 LSTEQIDLVAQAS-GGDIRQAITSLQFSSLK  385 (666)
Q Consensus       356 v~~~~l~~Ia~~s-~GDIR~AIn~LQf~~~~  385 (666)
                      +++++++.|.... .|++|..-|.++.++..
T Consensus       336 ~~~~a~~~L~~~~wpgNvreL~~~~~~~~~~  366 (463)
T TIGR01818       336 LDPEALERLKQLRWPGNVRQLENLCRWLTVM  366 (463)
T ss_pred             cCHHHHHHHHhCCCCChHHHHHHHHHHHHHh
Confidence            8999999999874 69999999999988764

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.

>PRK15455 PrkA family serine protein kinase; Provisional

Probab=97.56  E-value=9.3e-05  Score=83.08  Aligned_cols=56  Identities=18%  Similarity=0.328  Sum_probs=46.8

Q ss_pred             CCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc
Q 005987          145 PRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       145 P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      -.-|+|+.|.++.++.|..+|..+.....  ...++|+|.||||+||||+++.||+.+
T Consensus        72 y~fF~d~yGlee~ieriv~~l~~Aa~gl~--~~~~IL~LvGPpG~GKSsLa~~la~~l  127 (644)
T PRK15455         72 YPAFEEFYGMEEAIEQIVSYFRHAAQGLE--EKKQILYLLGPVGGGKSSLAERLKSLM  127 (644)
T ss_pred             ccchhcccCcHHHHHHHHHHHHHHHHhcC--CCCceEEEecCCCCCchHHHHHHHHHH
Confidence            34678899999999999999976655332  234699999999999999999999988

>PF14516 AAA_35: AAA-like domain

Probab=97.55  E-value=0.0053  Score=66.01  Aligned_cols=173  Identities=14%  Similarity=0.162  Sum_probs=95.8

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcCCCc-----hhhhh----hhhcccCCcccc-----------chhH
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL---GARLYEWDTPTP-----TIWQE----YMHNCKTGLEYT-----------SKLD  235 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel---g~~viE~nasd~-----~~~~e----~l~~~~~g~~~~-----------s~~~  235 (666)
                      ..+.|.||..+|||+++..+.+.+   |+.++.++....     ..+..    .+......+...           ....
T Consensus        32 ~~~~I~apRq~GKTSll~~l~~~l~~~~~~~v~id~~~~~~~~~~~~~~f~~~~~~~i~~~L~l~~~l~~~w~~~~~~~~  111 (331)
T PF14516_consen   32 SYIRIKAPRQMGKTSLLLRLLERLQQQGYRCVYIDLQQLGSAIFSDLEQFLRWFCEEISRQLKLDEKLDEYWDEEIGSKI  111 (331)
T ss_pred             CEEEEECcccCCHHHHHHHHHHHHHHCCCEEEEEEeecCCCcccCCHHHHHHHHHHHHHHHcCCChhHHHHHHHhcCChh
Confidence            589999999999999998887665   788777664431     11111    111111111100           1112


Q ss_pred             HHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcc-hhHHHHHHHHHHHHHhcCC-Cc----e-EEEEecCCCCCC
Q 005987          236 EFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNG-RTAFERLRQCLLLLVRSTH-IP----T-AVVLTECGKADS  308 (666)
Q Consensus       236 ~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~-~~~~~~l~~~L~~l~~~~~-~P----i-ViIit~~~~~~s  308 (666)
                      .+..++++.- .        ....++.||+|||+|.+.. ......+...|+.+..... .|    + ++++..+.....
T Consensus       112 ~~~~~~~~~l-l--------~~~~~~lVL~iDEiD~l~~~~~~~~dF~~~LR~~~~~~~~~~~~~~L~li~~~~t~~~~~  182 (331)
T PF14516_consen  112 SCTEYFEEYL-L--------KQIDKPLVLFIDEIDRLFEYPQIADDFFGLLRSWYEQRKNNPIWQKLRLILAGSTEDYII  182 (331)
T ss_pred             hHHHHHHHHH-H--------hcCCCCEEEEEechhhhccCcchHHHHHHHHHHHHHhcccCcccceEEEEEecCcccccc
Confidence            3333443320 0        0113678999999998765 2223445555655554332 11    2 333333211110


Q ss_pred             ccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCcHH
Q 005987          309 VDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASGGDIR  373 (666)
Q Consensus       309 ~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~s~GDIR  373 (666)
                      .+..       .+-+ + -+..|.+.+.+.+++...+++    .+..+++..++.|...++|-.-
T Consensus       183 ~~~~-------~SPF-N-Ig~~i~L~~Ft~~ev~~L~~~----~~~~~~~~~~~~l~~~tgGhP~  234 (331)
T PF14516_consen  183 LDIN-------QSPF-N-IGQPIELPDFTPEEVQELAQR----YGLEFSQEQLEQLMDWTGGHPY  234 (331)
T ss_pred             cCCC-------CCCc-c-cccceeCCCCCHHHHHHHHHh----hhccCCHHHHHHHHHHHCCCHH
Confidence            1100       1111 1 145688999999999887664    4566888889999999999753

>PTZ00202 tuzin; Provisional

Probab=97.55  E-value=0.00082  Score=73.22  Aligned_cols=63  Identities=19%  Similarity=0.245  Sum_probs=50.6

Q ss_pred             CCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcC
Q 005987          144 KPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDT  211 (666)
Q Consensus       144 ~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~na  211 (666)
                      .|....+++|++..+.+|...|....    ...+ ++++|+||+||||||+++.++..++...+..|.
T Consensus       257 lPa~~~~FVGReaEla~Lr~VL~~~d----~~~p-rivvLtG~~G~GKTTLlR~~~~~l~~~qL~vNp  319 (550)
T PTZ00202        257 APAVIRQFVSREAEESWVRQVLRRLD----TAHP-RIVVFTGFRGCGKSSLCRSAVRKEGMPAVFVDV  319 (550)
T ss_pred             CCCCccCCCCcHHHHHHHHHHHhccC----CCCc-eEEEEECCCCCCHHHHHHHHHhcCCceEEEECC
Confidence            68888999999999999998887422    2233 699999999999999999999999855444443

>PRK10536 hypothetical protein; Provisional

Probab=97.54  E-value=0.0015  Score=67.01  Aligned_cols=50  Identities=20%  Similarity=0.201  Sum_probs=34.2

Q ss_pred             CHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc----CCcEEEEcCCC
Q 005987          154 QRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL----GARLYEWDTPT  213 (666)
Q Consensus       154 ~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel----g~~viE~nasd  213 (666)
                      .......+..+|.+      .    ..++++||+|||||+++.++|.+.    .+..+.+..|.
T Consensus        60 ~n~~Q~~~l~al~~------~----~lV~i~G~aGTGKT~La~a~a~~~l~~~~~~kIiI~RP~  113 (262)
T PRK10536         60 RNEAQAHYLKAIES------K----QLIFATGEAGCGKTWISAAKAAEALIHKDVDRIIVTRPV  113 (262)
T ss_pred             CCHHHHHHHHHHhc------C----CeEEEECCCCCCHHHHHHHHHHHHHhcCCeeEEEEeCCC
Confidence            33444555556653      1    489999999999999999999852    34545555443

>TIGR01128 holA DNA polymerase III, delta subunit

Probab=97.54  E-value=0.0024  Score=67.32  Aligned_cols=148  Identities=11%  Similarity=0.120  Sum_probs=95.4

Q ss_pred             ceEEEEeCCCCCcchhHHHHHHHHHHHHHhcCCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHH
Q 005987          261 SAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGS  340 (666)
Q Consensus       261 ~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~  340 (666)
                      ++||+|++++.+.....    .+.|..+++.....+++|+.....    +...+....+...   .+|..+.|.+++..+
T Consensus        47 ~kliii~~~~~~~~~~~----~~~L~~~l~~~~~~~~~i~~~~~~----~~~~~~~k~~~~~---~~~~~i~~~~~~~~~  115 (302)
T TIGR01128        47 RRLVELRNPEGKPGAKG----LKALEEYLANPPPDTLLLIEAPKL----DKRKKLTKWLKAL---KNAQIVECKTPKEQE  115 (302)
T ss_pred             CeEEEEECCCCCCCHHH----HHHHHHHHhcCCCCEEEEEecCCC----CHhHHHHHHHHHh---cCeeEEEecCCCHHH
Confidence            46999999998654322    234555555543333333332111    1111111112221   158999999999999


Q ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHHHHcCCcHHHHHHHHHHHhcCCCCcccccccCCCCCCCccccCCCCCcccccCCcc
Q 005987          341 IKRTLSKICRQEQYSLSTEQIDLVAQASGGDIRQAITSLQFSSLKQDPMLNLSLSISKPNFPEEKADGHGGFSIQFGRDE  420 (666)
Q Consensus       341 i~kiL~~I~~~e~i~v~~~~l~~Ia~~s~GDIR~AIn~LQf~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~~~~~RD~  420 (666)
                      +.+.+...+..+|+.+++++++.|+..++||++.+.|-|+-++.-.... .              .+ .+.+..+...+.
T Consensus       116 ~~~~i~~~~~~~g~~i~~~a~~~l~~~~~~d~~~l~~el~KL~~~~~~~-~--------------It-~e~I~~~~~~~~  179 (302)
T TIGR01128       116 LPRWIQARLKKLGLRIDPDAVQLLAELVEGNLLAIAQELEKLALYAPDG-K--------------IT-LEDVEEAVSDSA  179 (302)
T ss_pred             HHHHHHHHHHHcCCCCCHHHHHHHHHHhCcHHHHHHHHHHHHHhhCCCC-C--------------CC-HHHHHHHHhhhh
Confidence            9999999999999999999999999999999999999998776532110 0              00 011223344455


Q ss_pred             ccchHHHHhHHhhCC
Q 005987          421 TLSLFHALGKFLHNK  435 (666)
Q Consensus       421 ~l~lFhalGkil~~K  435 (666)
                      ..++|..+..++.++
T Consensus       180 ~~~if~l~dal~~~~  194 (302)
T TIGR01128       180 RFNVFDLTDALLEGK  194 (302)
T ss_pred             cCCHHHHHHHHHCCC
Confidence            667888887777765

subunit around DNA forming a DNA sliding clamp.

>PRK14974 cell division protein FtsY; Provisional

Probab=97.54  E-value=0.0044  Score=66.47  Aligned_cols=33  Identities=33%  Similarity=0.419  Sum_probs=27.1

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL---GARLYEWDT  211 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel---g~~viE~na  211 (666)
                      .+++|+||||+||||++..+|..+   |..+.-+++
T Consensus       141 ~vi~~~G~~GvGKTTtiakLA~~l~~~g~~V~li~~  176 (336)
T PRK14974        141 VVIVFVGVNGTGKTTTIAKLAYYLKKNGFSVVIAAG  176 (336)
T ss_pred             eEEEEEcCCCCCHHHHHHHHHHHHHHcCCeEEEecC
Confidence            689999999999999999998876   566655544

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

Probab=97.51  E-value=0.0004  Score=68.94  Aligned_cols=32  Identities=38%  Similarity=0.604  Sum_probs=25.0

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc---CCcEEEEc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL---GARLYEWD  210 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel---g~~viE~n  210 (666)
                      +..+|.||||||||++++.+++.+   |..|+-+.
T Consensus        19 ~~~~l~G~aGtGKT~~l~~~~~~~~~~g~~v~~~a   53 (196)
T PF13604_consen   19 RVSVLQGPAGTGKTTLLKALAEALEAAGKRVIGLA   53 (196)
T ss_dssp             SEEEEEESTTSTHHHHHHHHHHHHHHTT--EEEEE
T ss_pred             eEEEEEECCCCCHHHHHHHHHHHHHhCCCeEEEEC
Confidence            589999999999999999987766   66666554

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

Probab=97.51  E-value=8.1e-05  Score=72.24  Aligned_cols=59  Identities=20%  Similarity=0.404  Sum_probs=37.9

Q ss_pred             ccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCc---EEEEcCCC
Q 005987          150 ELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGAR---LYEWDTPT  213 (666)
Q Consensus       150 eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~---viE~nasd  213 (666)
                      +++|+++.++++...+. ...   +..+ +.++|+||+|+|||++++.++..+.-.   ++.++...
T Consensus         1 ~fvgR~~e~~~l~~~l~-~~~---~~~~-~~~ll~G~~G~GKT~ll~~~~~~~~~~~~~~~~~~~~~   62 (185)
T PF13191_consen    1 QFVGREEEIERLRDLLD-AAQ---SGSP-RNLLLTGESGSGKTSLLRALLDRLAERGGYVISINCDD   62 (185)
T ss_dssp             --TT-HHHHHHHHHTTG-GTS---S------EEE-B-TTSSHHHHHHHHHHHHHHHT--EEEEEEET
T ss_pred             CCCCHHHHHHHHHHHHH-HHH---cCCC-cEEEEECCCCCCHHHHHHHHHHHHHhcCCEEEEEEEec
Confidence            36899999999999986 332   2222 689999999999999999888877322   66555443

>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=97.50  E-value=0.0016  Score=64.63  Aligned_cols=33  Identities=33%  Similarity=0.629  Sum_probs=25.7

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL---GARLYEWDT  211 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel---g~~viE~na  211 (666)
                      ++++|.||+|+||||++-.||..+   +.+|.-++.
T Consensus         2 ~vi~lvGptGvGKTTt~aKLAa~~~~~~~~v~lis~   37 (196)
T PF00448_consen    2 KVIALVGPTGVGKTTTIAKLAARLKLKGKKVALISA   37 (196)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHHHHHTT--EEEEEE
T ss_pred             EEEEEECCCCCchHhHHHHHHHHHhhccccceeecC
Confidence            789999999999999999998876   555554444

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 ....

>PLN02840 tRNA dimethylallyltransferase

Probab=97.48  E-value=0.00098  Score=73.03  Aligned_cols=161  Identities=19%  Similarity=0.209  Sum_probs=87.0

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCchhhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGES  258 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~  258 (666)
                      .+++|.||+|+||||++..||++++.+++..+.-.  .        ..+......-..    .++....           
T Consensus        22 ~vi~I~GptgsGKTtla~~La~~~~~~iis~Ds~q--v--------Yr~~~IgTaKpt----~eE~~~V-----------   76 (421)
T PLN02840         22 KVIVISGPTGAGKSRLALELAKRLNGEIISADSVQ--V--------YRGLDVGSAKPS----LSERKEV-----------   76 (421)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHCCCCeEeccccc--e--------ecceeEEcCCCC----HHHHcCC-----------
Confidence            58999999999999999999999998877654321  1        111111000000    0011000           


Q ss_pred             CCceEEEEeCCCC--CcchhHH-HHHHHHHHHHHhcCCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCC
Q 005987          259 KSSAILLIDDLPV--TNGRTAF-ERLRQCLLLLVRSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNP  335 (666)
Q Consensus       259 ~~~~IIlIDEid~--l~~~~~~-~~l~~~L~~l~~~~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p  335 (666)
                        + =-+||-++-  -.....| +....++..+...++.|+|  ++.++.      +      +++++..     +.+-|
T Consensus        77 --~-Hhlidil~p~e~ySv~~F~~~A~~~I~~i~~rgkiPIv--VGGTGl------Y------l~aLl~G-----~~~~p  134 (421)
T PLN02840         77 --P-HHLIDILHPSDDYSVGAFFDDARRATQDILNRGRVPIV--AGGTGL------Y------LRWYIYG-----KPDVP  134 (421)
T ss_pred             --C-eEeEeecCCCCceeHHHHHHHHHHHHHHHHhcCCCEEE--EcCccH------H------HHHHhcC-----CCCCC
Confidence              1 234554442  2222223 3345667777788888765  455331      1      4454431     23344


Q ss_pred             CCHHHHHHHHHHHHHHhCCCCC-HHHHHHHH--------HHcCCcHHHHHHHHHHHhcCC
Q 005987          336 ITNGSIKRTLSKICRQEQYSLS-TEQIDLVA--------QASGGDIRQAITSLQFSSLKQ  386 (666)
Q Consensus       336 ~s~~~i~kiL~~I~~~e~i~v~-~~~l~~Ia--------~~s~GDIR~AIn~LQf~~~~~  386 (666)
                      ....++++.+...+...+..-. +.+.+.+.        .....|.|+.+..|+.+-..+
T Consensus       135 ~~~~~~r~~l~~~l~~~~~~~g~~~l~~~Ll~~~DP~A~~i~pnD~~Ri~RALEV~~~TG  194 (421)
T PLN02840        135 KSSPEITSEVWSELVDFQKNGDWDAAVELVVNAGDPKARSLPRNDWYRLRRSLEIIKSSG  194 (421)
T ss_pred             CCCHHHHHHHHHHHHHhccccCHHHHHHHHHhccCcHHHhcCCCcHHHHHHHHHHHHHHC
Confidence            5556666666655554321111 12233322        235689999999999986544

>PRK06581 DNA polymerase III subunit delta'; Validated

Probab=97.47  E-value=0.0075  Score=61.03  Aligned_cols=172  Identities=9%  Similarity=0.083  Sum_probs=101.7

Q ss_pred             CCCCccEEEEECCCC-chHHHHHHHHHHHcCCcEEEE-cCCCchhhhhhhhcccCCc--cccchhHHHHHHHHHHHhhcC
Q 005987          174 DKFSTNVLVITGQAG-VGKTATVRQIASHLGARLYEW-DTPTPTIWQEYMHNCKTGL--EYTSKLDEFENFVERIRRYGS  249 (666)
Q Consensus       174 g~~~~k~LLL~GPpG-~GKTtla~~LAkelg~~viE~-nasd~~~~~e~l~~~~~g~--~~~s~~~~f~~fl~~a~~~~~  249 (666)
                      ++.. +..||.|..+ .||..++..+++.+...-++. +.||.....    ....+.  .-.-..++++++.+.+...+ 
T Consensus        12 ~kLs-hAYLfeG~n~~~~~~~~~~f~~~~l~~~~i~~~~HPD~~~I~----pe~~~~~~~~~I~IdqIReL~~~l~~~p-   85 (263)
T PRK06581         12 NKLY-NSWLIEAENIEQALKDLEKFIYIKLFKNSIPLENNPDYHFIA----RETSATSNAKNISIEQIRKLQDFLSKTS-   85 (263)
T ss_pred             Ccch-heeeEeCCChhhHHHHHHHHHHHHHhccCcccCCCCCEEEEe----ccccccccCCcccHHHHHHHHHHHhhCc-
Confidence            5665 7899999998 999999999998884432222 233321110    000000  01124566666665553322 


Q ss_pred             CCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcCCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCee
Q 005987          250 TSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGAR  329 (666)
Q Consensus       250 l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~  329 (666)
                             ..+..+|++|++++.+...     ..++|++.++..+..++++.....       ..+.++.+++     ||.
T Consensus        86 -------~~g~~KViII~~ae~mt~~-----AANALLKtLEEPP~~t~fILit~~-------~~~LLpTIrS-----RCq  141 (263)
T PRK06581         86 -------AISGYKVAIIYSAELMNLN-----AANSCLKILEDAPKNSYIFLITSR-------AASIISTIRS-----RCF  141 (263)
T ss_pred             -------ccCCcEEEEEechHHhCHH-----HHHHHHHhhcCCCCCeEEEEEeCC-------hhhCchhHhh-----ceE
Confidence                   1124679999999988643     334677777776654555443321       2344555554     699


Q ss_pred             EEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCcHHHHHHH
Q 005987          330 KVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASGGDIRQAITS  378 (666)
Q Consensus       330 ~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~s~GDIR~AIn~  378 (666)
                      .+.|+.+............+.-   -.+...++.|.+...-|....+.-
T Consensus       142 ~i~~~~p~~~~~~e~~~~~~~p---~~~~~~l~~i~~~~~~d~~~w~~~  187 (263)
T PRK06581        142 KINVRSSILHAYNELYSQFIQP---IADNKTLDFINRFTTKDRELWLDF  187 (263)
T ss_pred             EEeCCCCCHHHHHHHHHHhccc---ccccHHHHHHHHHhhhhHHHHHHH
Confidence            9999999997777665544322   234556777777766665554433

>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=97.46  E-value=0.00015  Score=71.87  Aligned_cols=46  Identities=22%  Similarity=0.339  Sum_probs=36.1

Q ss_pred             CccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc
Q 005987          147 SLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       147 sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      .|+||+||+...+.+.-...       |.   +.+||.||||+|||++|+.+..-|
T Consensus         1 Df~dI~GQe~aKrAL~iAAa-------G~---h~lLl~GppGtGKTmlA~~l~~lL   46 (206)
T PF01078_consen    1 DFSDIVGQEEAKRALEIAAA-------GG---HHLLLIGPPGTGKTMLARRLPSLL   46 (206)
T ss_dssp             -TCCSSSTHHHHHHHHHHHH-------CC-----EEEES-CCCTHHHHHHHHHHCS
T ss_pred             ChhhhcCcHHHHHHHHHHHc-------CC---CCeEEECCCCCCHHHHHHHHHHhC
Confidence            37899999998888876655       32   589999999999999999999876

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.

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

Probab=97.45  E-value=0.0011  Score=69.62  Aligned_cols=159  Identities=19%  Similarity=0.258  Sum_probs=90.8

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCchhhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGES  258 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~  258 (666)
                      ++++|.||+++|||.++-.||+.+|.+|+..+...  .        ..|....+.-..    .+..   ..         
T Consensus         4 ~~i~I~GPTAsGKT~lai~LAk~~~~eIIs~DSmQ--v--------Yr~mdIGTAKps----~~e~---~~---------   57 (308)
T COG0324           4 KLIVIAGPTASGKTALAIALAKRLGGEIISLDSMQ--V--------YRGLDIGTAKPS----LEEL---AG---------   57 (308)
T ss_pred             cEEEEECCCCcCHHHHHHHHHHHcCCcEEecchhh--h--------cCCCcccCCCCC----HHHH---cC---------
Confidence            68999999999999999999999999998766432  1        122221100000    0111   00         


Q ss_pred             CCceEEEEeCCCCC---cchhHHHHHHHHHHHHHhcCCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCC
Q 005987          259 KSSAILLIDDLPVT---NGRTAFERLRQCLLLLVRSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNP  335 (666)
Q Consensus       259 ~~~~IIlIDEid~l---~~~~~~~~l~~~L~~l~~~~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p  335 (666)
                       -+ =.+||.+|-.   +...........+..+...++.|++  ++.+.            .-+++++.     -...-|
T Consensus        58 -vp-HhliDi~~p~e~ysa~~f~~~a~~~i~~i~~rgk~pIl--VGGTg------------lY~~aL~~-----g~~~~p  116 (308)
T COG0324          58 -VP-HHLIDIRDPTESYSAAEFQRDALAAIDDILARGKLPIL--VGGTG------------LYLKALLE-----GLSLLP  116 (308)
T ss_pred             -CC-EEEecccCccccccHHHHHHHHHHHHHHHHhCCCCcEE--EccHH------------HHHHHHHc-----CCCCCC
Confidence             11 2467877632   2222223344556777777888775  34421            11455432     344455


Q ss_pred             CCHHHHHHHHHHHHHHhCC--------CCCHHHHHHHHHHcCCcHHHHHHHHHHHhcCCC
Q 005987          336 ITNGSIKRTLSKICRQEQY--------SLSTEQIDLVAQASGGDIRQAITSLQFSSLKQD  387 (666)
Q Consensus       336 ~s~~~i~kiL~~I~~~e~i--------~v~~~~l~~Ia~~s~GDIR~AIn~LQf~~~~~~  387 (666)
                      .....++..+...+...+.        .+++....   ..-..|.|+.+..|+.+-..+.
T Consensus       117 ~~~~~~r~~~~~~~~~~g~~~L~~~L~~~Dp~~a~---~i~pnD~~Ri~RALEv~~~tGk  173 (308)
T COG0324         117 EADPEVRRRLEAELAELGNDALHAELKKIDPEAAA---KIHPNDPQRIIRALEVYYLTGK  173 (308)
T ss_pred             CCCHHHHHHHHHHHHhcCHHHHHHHHHhhCHHHHH---hcCCCchhHHHHHHHHHHHHCC
Confidence            6566666666666555442        23333222   2346899999999998876543

>TIGR00174 miaA tRNA isopentenyltransferase (miaA)

Probab=97.44  E-value=0.0011  Score=69.38  Aligned_cols=157  Identities=18%  Similarity=0.270  Sum_probs=84.9

Q ss_pred             EEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCchhhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCC
Q 005987          180 VLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESK  259 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~  259 (666)
                      +++|.||+|+|||+++..||++++..++....-.  .+        .+....+.-..    .++..             .
T Consensus         1 vi~i~G~t~~GKs~la~~l~~~~~~~iis~Ds~q--vY--------~~l~IgTakp~----~~e~~-------------~   53 (287)
T TIGR00174         1 VIFIMGPTAVGKSQLAIQLAKKLNAEIISVDSMQ--IY--------KGMDIGTAKPS----LQERE-------------G   53 (287)
T ss_pred             CEEEECCCCCCHHHHHHHHHHhCCCcEEEechhh--ee--------eeccccCCCCC----HHHHc-------------C
Confidence            3789999999999999999999998887655321  11        11111000000    00000             0


Q ss_pred             CceEEEEeCCC--CCcchhHH-HHHHHHHHHHHhcCCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCC
Q 005987          260 SSAILLIDDLP--VTNGRTAF-ERLRQCLLLLVRSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPI  336 (666)
Q Consensus       260 ~~~IIlIDEid--~l~~~~~~-~~l~~~L~~l~~~~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~  336 (666)
                      -+ --+||-++  .......| +...+++..+...++.|++  ++.++.            -+++++..     +...|.
T Consensus        54 v~-hhlid~~~~~~~~~v~~f~~~a~~~i~~~~~~g~~pi~--vGGTg~------------Yi~all~g-----~~~~p~  113 (287)
T TIGR00174        54 IP-HHLIDILDPSESYSAADFQTLALNAIADITARGKIPLL--VGGTGL------------YLKALLEG-----LSPTPS  113 (287)
T ss_pred             cc-EEEEEEechhheEcHHHHHHHHHHHHHHHHhCCCCEEE--EcCcHH------------HHHHHHcC-----CCCCCC
Confidence            11 13444333  22222222 3344667777777877654  555331            14454431     223344


Q ss_pred             CHHHHHHHHHHHHHHhCC--------CCCHHHHHHHHHHcCCcHHHHHHHHHHHhcCC
Q 005987          337 TNGSIKRTLSKICRQEQY--------SLSTEQIDLVAQASGGDIRQAITSLQFSSLKQ  386 (666)
Q Consensus       337 s~~~i~kiL~~I~~~e~i--------~v~~~~l~~Ia~~s~GDIR~AIn~LQf~~~~~  386 (666)
                      ...++++.+.......+.        .++++...   ....+|.|+.+..|+.+...+
T Consensus       114 ~~~~~r~~l~~~~~~~g~~~l~~~L~~~DP~~a~---~i~~nd~~Ri~RALEi~~~tG  168 (287)
T TIGR00174       114 ADKLIREQLEILAEEQGWDFLYNELKKVDPVAAA---KIHPNDTRRVQRALEVFYATG  168 (287)
T ss_pred             CCHHHHHHHHHHHHHcCHHHHHHHHHhcCHHHHH---hcCCccHHHHHHHHHHHHHHC
Confidence            466677777766555442        23443322   235699999999999876543

Catalyzes the first step in the modification of an adenosine near the anticodon to 2-methylthio-N6-isopentyladenosine.

>TIGR02031 BchD-ChlD magnesium chelatase ATPase subunit D

Probab=97.41  E-value=0.0039  Score=72.11  Aligned_cols=32  Identities=34%  Similarity=0.401  Sum_probs=26.9

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCc--EEEEc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGAR--LYEWD  210 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~--viE~n  210 (666)
                      ..+||.|+||+|||++++.+++.+...  ++++.
T Consensus        17 g~vLl~G~~GtgKs~lar~l~~~~~~~~pfv~i~   50 (589)
T TIGR02031        17 GGVAIRARAGTGKTALARALAEILPPIMPFVELP   50 (589)
T ss_pred             ceEEEEcCCCcHHHHHHHHHHHhCCcCCCeEecC
Confidence            479999999999999999999987643  55554

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.

>TIGR00368 Mg chelatase-related protein

Probab=97.40  E-value=0.00095  Score=75.36  Aligned_cols=47  Identities=19%  Similarity=0.265  Sum_probs=37.7

Q ss_pred             CCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc
Q 005987          146 RSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       146 ~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      ..|+|+.|++..++.+.-.+.       +   ..+++|.||||+|||++++.++..+
T Consensus       189 ~d~~dv~Gq~~~~~al~~aa~-------~---g~~vlliG~pGsGKTtlar~l~~ll  235 (499)
T TIGR00368       189 LDLKDIKGQQHAKRALEIAAA-------G---GHNLLLFGPPGSGKTMLASRLQGIL  235 (499)
T ss_pred             CCHHHhcCcHHHHhhhhhhcc-------C---CCEEEEEecCCCCHHHHHHHHhccc
Confidence            488999999888766654432       1   1579999999999999999999865

The N-terminal end matches very strongly a pfam Mg_chelatase domain.

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

Probab=97.39  E-value=0.001  Score=70.53  Aligned_cols=157  Identities=20%  Similarity=0.291  Sum_probs=85.1

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCchhhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGES  258 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~  258 (666)
                      ++++|+||+|+|||+++..||++++..++..++-.  .        ..++.....-..    .++..             
T Consensus         5 ~~i~i~GptgsGKt~la~~la~~~~~~iis~Ds~Q--v--------y~~l~i~Takp~----~~E~~-------------   57 (307)
T PRK00091          5 KVIVIVGPTASGKTALAIELAKRLNGEIISADSMQ--V--------YRGMDIGTAKPT----AEERA-------------   57 (307)
T ss_pred             eEEEEECCCCcCHHHHHHHHHHhCCCcEEeccccc--e--------eecccccCCCCC----HHHHc-------------
Confidence            58999999999999999999999998776544321  1        111111000000    00000             


Q ss_pred             CCceEEEEeCCC--CCcchhHH-HHHHHHHHHHHhcCCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCC
Q 005987          259 KSSAILLIDDLP--VTNGRTAF-ERLRQCLLLLVRSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNP  335 (666)
Q Consensus       259 ~~~~IIlIDEid--~l~~~~~~-~~l~~~L~~l~~~~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p  335 (666)
                       .-.--+||.++  .......| +.....+..+...++.|+++  +.++      .+      +++++.  +.   ...|
T Consensus        58 -gv~hhlid~~~~~~~~s~~~f~~~a~~~i~~i~~~gk~pIlv--GGt~------~Y------~~al~~--g~---~~~p  117 (307)
T PRK00091         58 -GVPHHLIDILDPTESYSVADFQRDALAAIADILARGKLPILV--GGTG------LY------IKALLE--GL---SPLP  117 (307)
T ss_pred             -CccEEeecccChhhcccHHHHHHHHHHHHHHHHhCCCCEEEE--CcHH------HH------HHHhcc--CC---CCCC
Confidence             00123555443  21222222 33345566677777776654  4321      11      233332  11   2456


Q ss_pred             CCHHHHHHHHHHHHHHhCC--------CCCHHHHHHHHHHcCCcHHHHHHHHHHHhcC
Q 005987          336 ITNGSIKRTLSKICRQEQY--------SLSTEQIDLVAQASGGDIRQAITSLQFSSLK  385 (666)
Q Consensus       336 ~s~~~i~kiL~~I~~~e~i--------~v~~~~l~~Ia~~s~GDIR~AIn~LQf~~~~  385 (666)
                      +....+++.|.......+.        .+++.....   ....|.|+.+..|+.+-..
T Consensus       118 ~~~~~~r~~l~~~~~~~g~~~l~~~L~~~Dp~~a~~---i~~~d~~Ri~RAlEi~~~t  172 (307)
T PRK00091        118 PADPELRAELEALAAEEGWEALHAELAEIDPEAAAR---IHPNDPQRIIRALEVYELT  172 (307)
T ss_pred             CCCHHHHHHHHHHHHhcCHHHHHHHHHhcCHHHHhh---cCCCCCchhHHHHHHHHHH
Confidence            6677788888877665542        133333222   2568999999999987653

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

Probab=97.39  E-value=0.00032  Score=76.03  Aligned_cols=24  Identities=46%  Similarity=0.684  Sum_probs=22.8

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      +++++.|.||||||.++-.+|+++
T Consensus         2 ~v~~I~G~aGTGKTvla~~l~~~l   25 (352)
T PF09848_consen    2 QVILITGGAGTGKTVLALNLAKEL   25 (352)
T ss_pred             eEEEEEecCCcCHHHHHHHHHHHh
Confidence            589999999999999999999998

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

>COG4088 Predicted nucleotide kinase [Nucleotide transport and metabolism]

Probab=97.38  E-value=0.0021  Score=62.98  Aligned_cols=24  Identities=33%  Similarity=0.664  Sum_probs=22.8

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      +.++|+|+||+||||.++-||++|
T Consensus         2 pLiIlTGyPgsGKTtfakeLak~L   25 (261)
T COG4088           2 PLIILTGYPGSGKTTFAKELAKEL   25 (261)
T ss_pred             ceEEEecCCCCCchHHHHHHHHHH
Confidence            379999999999999999999999

>PRK04296 thymidine kinase; Provisional

Probab=97.38  E-value=0.0014  Score=64.61  Aligned_cols=32  Identities=22%  Similarity=0.346  Sum_probs=26.2

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc---CCcEEEEc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL---GARLYEWD  210 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel---g~~viE~n  210 (666)
                      .+.|++||+|+||||++..++..+   |..++-++
T Consensus         3 ~i~litG~~GsGKTT~~l~~~~~~~~~g~~v~i~k   37 (190)
T PRK04296          3 KLEFIYGAMNSGKSTELLQRAYNYEERGMKVLVFK   37 (190)
T ss_pred             EEEEEECCCCCHHHHHHHHHHHHHHHcCCeEEEEe
Confidence            478999999999999998888776   66666554

>PRK12727 flagellar biosynthesis regulator FlhF; Provisional

Probab=97.37  E-value=0.0052  Score=69.07  Aligned_cols=25  Identities=32%  Similarity=0.660  Sum_probs=22.1

Q ss_pred             ccEEEEECCCCchHHHHHHHHHHHc
Q 005987          178 TNVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       178 ~k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      .+++.|.||+|+||||++..||..+
T Consensus       350 G~vIaLVGPtGvGKTTtaakLAa~l  374 (559)
T PRK12727        350 GGVIALVGPTGAGKTTTIAKLAQRF  374 (559)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHH
Confidence            3689999999999999999998764

>PRK00131 aroK shikimate kinase; Reviewed

Probab=97.37  E-value=0.00019  Score=69.06  Aligned_cols=30  Identities=30%  Similarity=0.494  Sum_probs=28.0

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEEE
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLYE  208 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~viE  208 (666)
                      ..++|+|||||||||+++.||+.+|+.++.
T Consensus         5 ~~i~l~G~~GsGKstla~~La~~l~~~~~d   34 (175)
T PRK00131          5 PNIVLIGFMGAGKSTIGRLLAKRLGYDFID   34 (175)
T ss_pred             CeEEEEcCCCCCHHHHHHHHHHHhCCCEEE
Confidence            689999999999999999999999988774

>PRK08485 DNA polymerase III subunit delta'; Validated

Probab=97.37  E-value=0.0033  Score=61.79  Aligned_cols=116  Identities=11%  Similarity=0.117  Sum_probs=80.5

Q ss_pred             hhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcCCCceEEEEecCCCCCCccch
Q 005987          233 KLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHIPTAVVLTECGKADSVDST  312 (666)
Q Consensus       233 ~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~~~PiViIit~~~~~~s~d~~  312 (666)
                      .+++++++++.+...+          ...++ +|++++.+...     ..++|+..++.....++|+.....       .
T Consensus        38 ~Vd~iReii~~~~~~~----------~~~k~-iI~~a~~l~~~-----A~NaLLK~LEEPp~~~~fiL~t~~-------~   94 (206)
T PRK08485         38 KIEDAKEVIAEAYIAE----------SEEKI-IVIAAPSYGIE-----AQNALLKILEEPPKNICFIIVAKS-------K   94 (206)
T ss_pred             CHHHHHHHHHHHhhCC----------CCcEE-EEEchHhhCHH-----HHHHHHHHhcCCCCCeEEEEEeCC-------h
Confidence            3567777777764321          11234 57889877532     334577777776655555554432       2


Q ss_pred             hhhhhHHHHHHhhcCeeE-------------EEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCcHHHHHH
Q 005987          313 AQSFEELQSILVDAGARK-------------VALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASGGDIRQAIT  377 (666)
Q Consensus       313 ~r~l~~L~s~L~r~r~~~-------------I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~s~GDIR~AIn  377 (666)
                      .+.++.+++     ||..             +.|++++..++...|.. +.++++...+++++.|+..+.|.+|.++.
T Consensus        95 ~~llpTI~S-----Rc~~~~~~~~~~~~~l~l~l~~l~~~~i~~~L~~-~~ke~~~~~~ea~~lIa~la~~s~r~~l~  166 (206)
T PRK08485         95 NLLLPTIRS-----RLIIEKRKQKKPVKPLDLDLKKLDLKDIYEFLKE-LEKENKLSKEELKELIESLLKECVKYKIP  166 (206)
T ss_pred             HhCchHHHh-----hheeccccccccccccccccCCCCHHHHHHHHHH-HHHcccccHHHHHHHHHHHHHHHHHHHcC
Confidence            334445554     4765             77999999999999999 78888888889999999999999999864

>PRK08118 topology modulation protein; Reviewed

Probab=97.35  E-value=0.00017  Score=69.66  Aligned_cols=31  Identities=26%  Similarity=0.519  Sum_probs=28.5

Q ss_pred             EEEEECCCCchHHHHHHHHHHHcCCcEEEEc
Q 005987          180 VLVITGQAGVGKTATVRQIASHLGARLYEWD  210 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkelg~~viE~n  210 (666)
                      .+++.||||+||||+++.|++.+++.++.++
T Consensus         3 rI~I~G~~GsGKSTlak~L~~~l~~~~~~lD   33 (167)
T PRK08118          3 KIILIGSGGSGKSTLARQLGEKLNIPVHHLD   33 (167)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCCceecc
Confidence            5899999999999999999999999888765

>COG3829 RocR Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]

Probab=97.33  E-value=0.0091  Score=66.53  Aligned_cols=204  Identities=14%  Similarity=0.215  Sum_probs=116.9

Q ss_pred             ccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcCCCchhhh
Q 005987          142 KYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL---GARLYEWDTPTPTIWQ  218 (666)
Q Consensus       142 KY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~nasd~~~~~  218 (666)
                      -+++-++++|++....+.++..-.+....     .+ -.+||.|.+||||-.+|+++-+.-   +..++.+||..-.   
T Consensus       238 ~~a~y~f~~Iig~S~~m~~~~~~akr~A~-----td-stVLi~GESGTGKElfA~~IH~~S~R~~~PFIaiNCaAiP---  308 (560)
T COG3829         238 LKAKYTFDDIIGESPAMLRVLELAKRIAK-----TD-STVLILGESGTGKELFARAIHNLSPRANGPFIAINCAAIP---  308 (560)
T ss_pred             cccccchhhhccCCHHHHHHHHHHHhhcC-----CC-CcEEEecCCCccHHHHHHHHHhcCcccCCCeEEEecccCC---
Confidence            56677899999999999999888876422     11 469999999999999999987754   6788999986411   


Q ss_pred             hhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCC----------CceEEEEeCCCCCcchhHHHHHHHHHHHH
Q 005987          219 EYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESK----------SSAILLIDDLPVTNGRTAFERLRQCLLLL  288 (666)
Q Consensus       219 e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~----------~~~IIlIDEid~l~~~~~~~~l~~~L~~l  288 (666)
                      +.                   .++ ..-|+.-.+.++|..+          ..--||+||+-.+.-.     ++.-|+..
T Consensus       309 e~-------------------LlE-SELFGye~GAFTGA~~~GK~GlfE~A~gGTLFLDEIgempl~-----LQaKLLRV  363 (560)
T COG3829         309 ET-------------------LLE-SELFGYEKGAFTGASKGGKPGLFELANGGTLFLDEIGEMPLP-----LQAKLLRV  363 (560)
T ss_pred             HH-------------------HHH-HHHhCcCCccccccccCCCCcceeeccCCeEEehhhccCCHH-----HHHHHHHH
Confidence            00                   111 1112222222332211          1236899999877532     22223333


Q ss_pred             HhcC---------CCc-eEEEEecCCCCCCccchhhhhh--HHH-HHHhhcCeeEEEeCCCC--HHHHHHHHHHHHH---
Q 005987          289 VRST---------HIP-TAVVLTECGKADSVDSTAQSFE--ELQ-SILVDAGARKVALNPIT--NGSIKRTLSKICR---  350 (666)
Q Consensus       289 ~~~~---------~~P-iViIit~~~~~~s~d~~~r~l~--~L~-s~L~r~r~~~I~F~p~s--~~~i~kiL~~I~~---  350 (666)
                      ++..         ..| =|-|+++++.+-     ...+.  .+| .+.-|.....|.++|+-  +++|.......+.   
T Consensus       364 LQEkei~rvG~t~~~~vDVRIIAATN~nL-----~~~i~~G~FReDLYYRLNV~~i~iPPLReR~eDI~~L~~~Fl~k~s  438 (560)
T COG3829         364 LQEKEIERVGGTKPIPVDVRIIAATNRNL-----EKMIAEGTFREDLYYRLNVIPITIPPLRERKEDIPLLAEYFLDKFS  438 (560)
T ss_pred             HhhceEEecCCCCceeeEEEEEeccCcCH-----HHHHhcCcchhhheeeeceeeecCCCcccCcchHHHHHHHHHHHHH
Confidence            3332         112 134445444321     11110  011 22222234446666663  2344433333333   


Q ss_pred             -HhC--CC-CCHHHHHHHHHHc-CCcHHHHHHHHHHHhc
Q 005987          351 -QEQ--YS-LSTEQIDLVAQAS-GGDIRQAITSLQFSSL  384 (666)
Q Consensus       351 -~e~--i~-v~~~~l~~Ia~~s-~GDIR~AIn~LQf~~~  384 (666)
                       ..+  ++ ++++++..|.... .|++|..-|.++-+..
T Consensus       439 ~~~~~~v~~ls~~a~~~L~~y~WPGNVRELeNviER~v~  477 (560)
T COG3829         439 RRYGRNVKGLSPDALALLLRYDWPGNVRELENVIERAVN  477 (560)
T ss_pred             HHcCCCcccCCHHHHHHHHhCCCCchHHHHHHHHHHHHh
Confidence             333  33 7899999888763 5999999999998774

>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=97.32  E-value=0.00018  Score=66.92  Aligned_cols=29  Identities=28%  Similarity=0.637  Sum_probs=25.5

Q ss_pred             EEEEECCCCchHHHHHHHHHHHcCCcEEE
Q 005987          180 VLVITGQAGVGKTATVRQIASHLGARLYE  208 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkelg~~viE  208 (666)
                      .++++||||+||||+|+.+++.+++.++.
T Consensus         1 lii~~G~pgsGKSt~a~~l~~~~~~~~i~   29 (143)
T PF13671_consen    1 LIILCGPPGSGKSTLAKRLAKRLGAVVIS   29 (143)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHSTEEEEE
T ss_pred             CEEEECCCCCCHHHHHHHHHHHCCCEEEe
Confidence            47999999999999999999999955553

...

>COG1239 ChlI Mg-chelatase subunit ChlI [Coenzyme metabolism]

Probab=97.31  E-value=0.013  Score=63.61  Aligned_cols=25  Identities=28%  Similarity=0.429  Sum_probs=22.9

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLG  203 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg  203 (666)
                      ..+||.|+.|+||||++|+||.-|.
T Consensus        39 ggvLI~G~kGtaKSt~~Rala~LLp   63 (423)
T COG1239          39 GGALIAGEKGTAKSTLARALADLLP   63 (423)
T ss_pred             ceeEEecCCCccHHHHHHHHHHhCC
Confidence            4699999999999999999999883

>PF10923 DUF2791: P-loop Domain of unknown function (DUF2791); InterPro: IPR021228 This is a family of proteins found in archaea and bacteria

Probab=97.31  E-value=0.053  Score=59.61  Aligned_cols=127  Identities=20%  Similarity=0.253  Sum_probs=74.4

Q ss_pred             CceEEEEeCCCCCc---chhHHHHHHHHHHHHHh---cCCCc-eEEEEecCCCCC-CccchhhhhhHHHHHHhh------
Q 005987          260 SSAILLIDDLPVTN---GRTAFERLRQCLLLLVR---STHIP-TAVVLTECGKAD-SVDSTAQSFEELQSILVD------  325 (666)
Q Consensus       260 ~~~IIlIDEid~l~---~~~~~~~l~~~L~~l~~---~~~~P-iViIit~~~~~~-s~d~~~r~l~~L~s~L~r------  325 (666)
                      +..+|+|||+.++.   ...+.++..+.|+.+++   .++.| +.|+++.+...- ....-...+++|+++|..      
T Consensus       239 ~GLlI~lDE~e~l~kl~~~~~R~~~ye~lr~lidd~~~G~~~gL~~~~~gTPef~eD~rrGv~sY~AL~~RL~~~~~~~~  318 (416)
T PF10923_consen  239 KGLLILLDELENLYKLRNDQAREKNYEALRQLIDDIDQGRAPGLYFVFAGTPEFFEDGRRGVYSYEALAQRLAEEFFADD  318 (416)
T ss_pred             CceEEEEechHHHHhcCChHHHHHHHHHHHHHHHHHhcCCCCceEEEEeeCHHHhhCccccccccHHHHHHHhccccccc
Confidence            46799999998752   22223333344555543   34444 334444432110 000112345566666542      


Q ss_pred             ----cCeeEEEeCCCCHHHHHHHHHHHHHHh------CCCCCHHHHHHHHHHcCC----c--------HHHHHHHHHHHh
Q 005987          326 ----AGARKVALNPITNGSIKRTLSKICRQE------QYSLSTEQIDLVAQASGG----D--------IRQAITSLQFSS  383 (666)
Q Consensus       326 ----~r~~~I~F~p~s~~~i~kiL~~I~~~e------~i~v~~~~l~~Ia~~s~G----D--------IR~AIn~LQf~~  383 (666)
                          ++..+|++.|++++++..++.++..-.      ...++++.|..+++.+.|    +        ||..|+.|..+.
T Consensus       319 ~~~n~~~pvIrL~~l~~eel~~l~~klr~i~a~~~~~~~~v~d~~l~~~~~~~~~r~G~~~~~tPR~~ik~fv~~Ld~~~  398 (416)
T PF10923_consen  319 GFDNLRAPVIRLQPLTPEELLELLEKLRDIYAEAYGYESRVDDEELKAFAQHVAGRLGGDVFVTPREFIKDFVDVLDILE  398 (416)
T ss_pred             cccCccCceecCCCCCHHHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHhccCcccccCHHHHHHHHHHHHHHHH
Confidence                245679999999999999999887642      246889999888866433    2        455666665555


Q ss_pred             cCC
Q 005987          384 LKQ  386 (666)
Q Consensus       384 ~~~  386 (666)
                      ..+
T Consensus       399 q~p  401 (416)
T PF10923_consen  399 QNP  401 (416)
T ss_pred             HCC
Confidence            443

Some of the proteins in this family are annotated as being methyl-accepting chemotaxis proteins and ATP/GTP binding proteins.

>COG1102 Cmk Cytidylate kinase [Nucleotide transport and metabolism]

Probab=97.30  E-value=0.00019  Score=67.59  Aligned_cols=29  Identities=45%  Similarity=0.788  Sum_probs=26.5

Q ss_pred             EEEEECCCCchHHHHHHHHHHHcCCcEEE
Q 005987          180 VLVITGQAGVGKTATVRQIASHLGARLYE  208 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkelg~~viE  208 (666)
                      .+.+.|||||||||+++.||+.+|++++.
T Consensus         2 ~ItIsG~pGsG~TTva~~lAe~~gl~~vs   30 (179)
T COG1102           2 VITISGLPGSGKTTVARELAEHLGLKLVS   30 (179)
T ss_pred             EEEeccCCCCChhHHHHHHHHHhCCceee
Confidence            47799999999999999999999998873

>COG1936 Predicted nucleotide kinase (related to CMP and AMP kinases) [Nucleotide transport and metabolism]

Probab=97.30  E-value=0.00017  Score=68.73  Aligned_cols=30  Identities=37%  Similarity=0.689  Sum_probs=27.9

Q ss_pred             EEEEECCCCchHHHHHHHHHHHcCCcEEEEc
Q 005987          180 VLVITGQAGVGKTATVRQIASHLGARLYEWD  210 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkelg~~viE~n  210 (666)
                      .++++|.|||||||+++.|+ ++|+.+++++
T Consensus         2 ~I~ITGTPGvGKTT~~~~L~-~lg~~~i~l~   31 (180)
T COG1936           2 LIAITGTPGVGKTTVCKLLR-ELGYKVIELN   31 (180)
T ss_pred             eEEEeCCCCCchHHHHHHHH-HhCCceeeHH
Confidence            58899999999999999999 9999999876

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

Probab=97.29  E-value=0.0044  Score=68.27  Aligned_cols=124  Identities=13%  Similarity=0.231  Sum_probs=74.1

Q ss_pred             EEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCchhhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCC
Q 005987          180 VLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESK  259 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~  259 (666)
                      +.+|+||.+|||||+++.+.+.+.-.++.++--|....            .....+.+..+. .+  +.        .  
T Consensus        39 i~~i~GpR~~GKTtll~~l~~~~~~~~iy~~~~d~~~~------------~~~l~d~~~~~~-~~--~~--------~--   93 (398)
T COG1373          39 IILILGPRQVGKTTLLKLLIKGLLEEIIYINFDDLRLD------------RIELLDLLRAYI-EL--KE--------R--   93 (398)
T ss_pred             EEEEECCccccHHHHHHHHHhhCCcceEEEEecchhcc------------hhhHHHHHHHHH-Hh--hc--------c--
Confidence            89999999999999999988887555666665442110            000111112111 11  11        0  


Q ss_pred             CceEEEEeCCCCCcchhHHHHHHHHHHHHHhcCCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHH
Q 005987          260 SSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNG  339 (666)
Q Consensus       260 ~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~  339 (666)
                      .+..|++||+++..      .....+..+.+.+.. -|+|++.....        ....+.+.|.. |...+.+-|++-.
T Consensus        94 ~~~yifLDEIq~v~------~W~~~lk~l~d~~~~-~v~itgsss~l--------l~~~~~~~L~G-R~~~~~l~PlSF~  157 (398)
T COG1373          94 EKSYIFLDEIQNVP------DWERALKYLYDRGNL-DVLITGSSSSL--------LSKEISESLAG-RGKDLELYPLSFR  157 (398)
T ss_pred             CCceEEEecccCch------hHHHHHHHHHccccc-eEEEECCchhh--------hccchhhhcCC-CceeEEECCCCHH
Confidence            24589999999863      244456777777755 34554442211        11123344443 5888999999998


Q ss_pred             HHHHH
Q 005987          340 SIKRT  344 (666)
Q Consensus       340 ~i~ki  344 (666)
                      +....
T Consensus       158 Efl~~  162 (398)
T COG1373         158 EFLKL  162 (398)
T ss_pred             HHHhh
Confidence            88764

>PF00519 PPV_E1_C: Papillomavirus helicase; InterPro: IPR001177 Papillomaviruses are a large family of DNA tumour viruses which give rise to warts in their host species

Probab=97.29  E-value=0.001  Score=71.16  Aligned_cols=40  Identities=20%  Similarity=0.272  Sum_probs=33.5

Q ss_pred             CCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCC
Q 005987          174 DKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPT  213 (666)
Q Consensus       174 g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd  213 (666)
                      |.+.++.++|+|||+||||..+..|.+-++..|+..-++.
T Consensus       258 g~PKKnClvi~GPPdTGKS~F~~SLi~Fl~GkViSf~Ns~  297 (432)
T PF00519_consen  258 GIPKKNCLVIYGPPDTGKSMFCMSLIKFLKGKVISFVNSK  297 (432)
T ss_dssp             TBTTSSEEEEESSCCCSHHHHHHHHHHHHTSEEE-GGGTT
T ss_pred             CCCcccEEEEECCCCCchhHHHHHHHHHhCCEEEEecCCC
Confidence            5566678999999999999999999999999999764443

The helicase E1 protein is an ATP-dependent DNA helicase required for initiation of viral DNA replication []. It forms a complex with the viral E2 protein, which is a site-specific DNA-binding transcriptional activator. The E1-E2 complex binds to the replication origin which contains binding sites for both proteins []. The E1 protein is a 70 kDa polypeptide with a central DNA-binding domain and a C-terminal ATPase/helicase domain. It binds specific 18 bp DNA sequences at the origin of replication, melts the DNA duplex and functions as a 3' to 5' helicase []. In addition to E2 it also interacts with DNA polymerase alpha and replication protein A to effect DNA replication. The DNA-binding domain forms a five-stranded antiparallel beta sheet bordered by four loosely packed alpha helices on one side and two tightly packed helices on the other []. Two structural modules within this domain, an extended loop and a helix, contain conserved residues and are critical for DNA binding. In solution E1 is a monomer, but binds DNA as a dimer. Recruitment of more E1 subunits to the complex leads to melting of the origin and ultimately to the formation of an E1 hexamer with helicase activity []. The entry represents the C-terminal region of E1, containing both the DNA-binding and ATPase/helical domains.; GO: 0003677 DNA binding, 0004003 ATP-dependent DNA helicase activity, 0005524 ATP binding, 0006260 DNA replication; PDB: 1TUE_K 1R9W_A 2V9P_B 2GXA_I 1KSX_J 1KSY_A 1F08_B.

>PRK10365 transcriptional regulatory protein ZraR; Provisional

Probab=97.27  E-value=0.011  Score=65.85  Aligned_cols=201  Identities=13%  Similarity=0.185  Sum_probs=105.6

Q ss_pred             ccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcCCCchhhhhhhhcccC
Q 005987          150 ELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL---GARLYEWDTPTPTIWQEYMHNCKT  226 (666)
Q Consensus       150 eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~nasd~~~~~e~l~~~~~  226 (666)
                      .+++....+..+..-+....    .  ....++++|.+|+||+++++++....   +..++.+++....  .+       
T Consensus       140 ~lig~s~~~~~~~~~i~~~~----~--~~~~vli~ge~g~gk~~~a~~ih~~s~~~~~~~i~~~c~~~~--~~-------  204 (441)
T PRK10365        140 GMVGKSPAMQHLLSEIALVA----P--SEATVLIHGDSGTGKELVARAIHASSARSEKPLVTLNCAALN--ES-------  204 (441)
T ss_pred             ceEecCHHHHHHHHHHhhcc----C--CCCeEEEEecCCCCHHHHHHHHHHcCCCCCCCeeeeeCCCCC--HH-------
Confidence            45666666666655444221    1  12468999999999999999997654   4568888876421  00       


Q ss_pred             CccccchhHHHHHHHHHHHhhcCCCC---CCCC--CCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcCCC-------
Q 005987          227 GLEYTSKLDEFENFVERIRRYGSTSP---SIPG--ESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHI-------  294 (666)
Q Consensus       227 g~~~~s~~~~f~~fl~~a~~~~~l~~---s~~~--~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~~~-------  294 (666)
                               .+...+-... .+....   ...|  ....+.+|+|||++.+...     .+..|..+++.+..       
T Consensus       205 ---------~~~~~lfg~~-~~~~~~~~~~~~g~~~~a~~gtl~ldei~~l~~~-----~q~~l~~~l~~~~~~~~~~~~  269 (441)
T PRK10365        205 ---------LLESELFGHE-KGAFTGADKRREGRFVEADGGTLFLDEIGDISPM-----MQVRLLRAIQEREVQRVGSNQ  269 (441)
T ss_pred             ---------HHHHHhcCCC-CCCcCCCCcCCCCceeECCCCEEEEeccccCCHH-----HHHHHHHHHccCcEEeCCCCc
Confidence                     1111110000 000000   0000  0012347999999998653     22234444444321       


Q ss_pred             ----c-eEEEEecCCCCCCccc-hhhhhhHHHHHHhhcCeeEEEeCCCCHH--HHHHHHHHH----HHHhC---CCCCHH
Q 005987          295 ----P-TAVVLTECGKADSVDS-TAQSFEELQSILVDAGARKVALNPITNG--SIKRTLSKI----CRQEQ---YSLSTE  359 (666)
Q Consensus       295 ----P-iViIit~~~~~~s~d~-~~r~l~~L~s~L~r~r~~~I~F~p~s~~--~i~kiL~~I----~~~e~---i~v~~~  359 (666)
                          . .+|++++...   .+. ....+  .+.++.+.....|.++|+...  ++..+....    +...+   ..++++
T Consensus       270 ~~~~~~rii~~t~~~~---~~~~~~~~~--~~~l~~~l~~~~i~~ppLreR~~Di~~l~~~~l~~~~~~~~~~~~~~~~~  344 (441)
T PRK10365        270 TISVDVRLIAATHRDL---AAEVNAGRF--RQDLYYRLNVVAIEVPSLRQRREDIPLLAGHFLQRFAERNRKAVKGFTPQ  344 (441)
T ss_pred             eeeeceEEEEeCCCCH---HHHHHcCCc--hHHHHHHhccceecCCChhhcchhHHHHHHHHHHHHHHHhCCCCCCcCHH
Confidence                1 2333332211   000 00011  122222323556777777542  444443333    33222   348999


Q ss_pred             HHHHHHHHc-CCcHHHHHHHHHHHhcC
Q 005987          360 QIDLVAQAS-GGDIRQAITSLQFSSLK  385 (666)
Q Consensus       360 ~l~~Ia~~s-~GDIR~AIn~LQf~~~~  385 (666)
                      +++.|.... .|++|...|.++.++..
T Consensus       345 a~~~L~~~~wpgN~reL~~~~~~~~~~  371 (441)
T PRK10365        345 AMDLLIHYDWPGNIRELENAVERAVVL  371 (441)
T ss_pred             HHHHHHhCCCCCHHHHHHHHHHHHHHh
Confidence            999999887 89999999999987753

>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=97.27  E-value=0.0029  Score=68.72  Aligned_cols=25  Identities=36%  Similarity=0.610  Sum_probs=22.5

Q ss_pred             ccEEEEECCCCchHHHHHHHHHHHc
Q 005987          178 TNVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       178 ~k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      +.+++|.||+|+||||++..||..+
T Consensus       137 g~ii~lvGptGvGKTTtiakLA~~~  161 (374)
T PRK14722        137 GGVFALMGPTGVGKTTTTAKLAARC  161 (374)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHH
Confidence            3689999999999999999999864

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

Probab=97.27  E-value=0.0024  Score=67.25  Aligned_cols=156  Identities=15%  Similarity=0.174  Sum_probs=83.1

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCchhhhhhhhcccCCccccc-hhHHHHHHHHHHHhhcCCCCCCCCC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTIWQEYMHNCKTGLEYTS-KLDEFENFVERIRRYGSTSPSIPGE  257 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~~~~e~l~~~~~g~~~~s-~~~~f~~fl~~a~~~~~l~~s~~~~  257 (666)
                      ++++|.||+|+|||.++-.||+. +.+++..++-  ..|        .|..... +..     .++....          
T Consensus         5 ~ii~I~GpTasGKS~LAl~LA~~-~~eIIsaDS~--QvY--------r~ldIgTaKpt-----~eE~~~i----------   58 (300)
T PRK14729          5 KIVFIFGPTAVGKSNILFHFPKG-KAEIINVDSI--QVY--------KEFDIASCKPS-----KELRKHI----------   58 (300)
T ss_pred             cEEEEECCCccCHHHHHHHHHHh-CCcEEeccHH--HHH--------CCCceecCCCC-----HHHHcCC----------
Confidence            58999999999999999999999 4455533321  111        1111100 000     0000000          


Q ss_pred             CCCceEEEEeCCCCC--cchhHH-HHHHHHHHHHHhcCCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeC
Q 005987          258 SKSSAILLIDDLPVT--NGRTAF-ERLRQCLLLLVRSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALN  334 (666)
Q Consensus       258 ~~~~~IIlIDEid~l--~~~~~~-~~l~~~L~~l~~~~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~  334 (666)
                         + =-+||-++-.  .....| +...+++..+...++.|+|  |+.++.      +      +++++.     -+.+.
T Consensus        59 ---~-Hhlid~~~p~e~~sv~~f~~~a~~~i~~i~~~gk~Pil--vGGTgl------Y------i~all~-----gl~~~  115 (300)
T PRK14729         59 ---K-HHLVDFLEPIKEYNLGIFYKEALKIIKELRQQKKIPIF--VGGSAF------Y------FKHLKY-----GLPST  115 (300)
T ss_pred             ---C-eeeeeccCCCCceeHHHHHHHHHHHHHHHHHCCCCEEE--EeCchH------H------HHHHHc-----CCCCC
Confidence               1 1355655421  122223 2344566777777777754  555331      1      445442     12334


Q ss_pred             CCCHHHHHHHHHHHHHHhCC--------CCCHHHHHHHHHHcCCcHHHHHHHHHHHhcCC
Q 005987          335 PITNGSIKRTLSKICRQEQY--------SLSTEQIDLVAQASGGDIRQAITSLQFSSLKQ  386 (666)
Q Consensus       335 p~s~~~i~kiL~~I~~~e~i--------~v~~~~l~~Ia~~s~GDIR~AIn~LQf~~~~~  386 (666)
                      |+....++..+...+..+|.        .+++....   ....+|.|+.+..|+.+...+
T Consensus       116 p~~~~~~r~~~~~~~~~~g~~~l~~~L~~~DP~~A~---~i~pnd~~Ri~RALEv~~~tG  172 (300)
T PRK14729        116 PPVSSKIRIYVNNLFTLKGKSYLLEELKRVDFIRYE---SINKNDIYRIKRSLEVYYQTG  172 (300)
T ss_pred             CCCCHHHHHHHHHHHHhcCHHHHHHHHHhcCHHHHh---hCCcCCHHHHHHHHHHHHHhC
Confidence            55566677767666555441        23333222   225699999999999986544

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

Probab=97.27  E-value=0.00099  Score=69.27  Aligned_cols=60  Identities=27%  Similarity=0.457  Sum_probs=44.4

Q ss_pred             CCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcC---CcEEEEcCCC
Q 005987          145 PRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLG---ARLYEWDTPT  213 (666)
Q Consensus       145 P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg---~~viE~nasd  213 (666)
                      +.+++++-..+..++.++.++..      .   ...++|+||+|+||||+++++...+.   ..++.+..+.
T Consensus        56 ~~~l~~lg~~~~~~~~l~~~~~~------~---~GlilisG~tGSGKTT~l~all~~i~~~~~~iitiEdp~  118 (264)
T cd01129          56 ILDLEKLGLKPENLEIFRKLLEK------P---HGIILVTGPTGSGKTTTLYSALSELNTPEKNIITVEDPV  118 (264)
T ss_pred             CCCHHHcCCCHHHHHHHHHHHhc------C---CCEEEEECCCCCcHHHHHHHHHhhhCCCCCeEEEECCCc
Confidence            45778887777777777666653      1   14799999999999999999988773   3466665443

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.

>cd01121 Sms Sms (bacterial radA) DNA repair protein

Probab=97.27  E-value=0.002  Score=70.19  Aligned_cols=39  Identities=26%  Similarity=0.480  Sum_probs=30.1

Q ss_pred             CCCCccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcCC
Q 005987          174 DKFSTNVLVITGQAGVGKTATVRQIASHL---GARLYEWDTP  212 (666)
Q Consensus       174 g~~~~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~nas  212 (666)
                      |-.+...++|+||||+||||++..+|..+   +..++.+...
T Consensus        78 Gi~~GslvLI~G~pG~GKStLllq~a~~~a~~g~~VlYvs~E  119 (372)
T cd01121          78 GLVPGSVILIGGDPGIGKSTLLLQVAARLAKRGGKVLYVSGE  119 (372)
T ss_pred             CccCCeEEEEEeCCCCCHHHHHHHHHHHHHhcCCeEEEEECC
Confidence            34445789999999999999999998765   4567666543

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.

>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=97.26  E-value=0.0022  Score=62.50  Aligned_cols=32  Identities=22%  Similarity=0.158  Sum_probs=25.3

Q ss_pred             EEEEECCCCchHHHHHHHHHHHc---CCcEEEEcC
Q 005987          180 VLVITGQAGVGKTATVRQIASHL---GARLYEWDT  211 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkel---g~~viE~na  211 (666)
                      ++||+||||+|||+++..++.+.   |..++.+..
T Consensus         1 ~~li~G~~G~GKT~l~~~~~~~~~~~g~~v~~~s~   35 (187)
T cd01124           1 STLLSGGPGTGKTTFALQFLYAGLARGEPGLYVTL   35 (187)
T ss_pred             CEEEEcCCCCCHHHHHHHHHHHHHHCCCcEEEEEC
Confidence            37899999999999998877654   666766654

A related protein is found in archaea.

>KOG3347 consensus Predicted nucleotide kinase/nuclear protein involved oxidative stress response [Nucleotide transport and metabolism]

Probab=97.26  E-value=0.00023  Score=66.12  Aligned_cols=32  Identities=25%  Similarity=0.473  Sum_probs=29.2

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEEEEc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLYEWD  210 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~viE~n  210 (666)
                      ..+|++|-|||||||++..||..+|++.+++.
T Consensus         8 PNILvtGTPG~GKstl~~~lae~~~~~~i~is   39 (176)
T KOG3347|consen    8 PNILVTGTPGTGKSTLAERLAEKTGLEYIEIS   39 (176)
T ss_pred             CCEEEeCCCCCCchhHHHHHHHHhCCceEehh
Confidence            36999999999999999999999999988765

>PHA02624 large T antigen; Provisional

Probab=97.24  E-value=0.00056  Score=77.30  Aligned_cols=40  Identities=15%  Similarity=0.243  Sum_probs=34.9

Q ss_pred             CCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCC
Q 005987          174 DKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPT  213 (666)
Q Consensus       174 g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd  213 (666)
                      |.+..+.++|+||||+||||++.+|++.+|..++.+|.|.
T Consensus       427 giPKk~~il~~GPpnTGKTtf~~sLl~~L~G~vlsVNsPt  466 (647)
T PHA02624        427 NVPKRRYWLFKGPVNSGKTTLAAALLDLCGGKSLNVNCPP  466 (647)
T ss_pred             cCCCCeEEEEECCCCCCHHHHHHHHHHHcCCeEEEeeCCc
Confidence            4444579999999999999999999999988888888775

>PRK13765 ATP-dependent protease Lon; Provisional

Probab=97.23  E-value=0.00036  Score=80.74  Aligned_cols=52  Identities=19%  Similarity=0.323  Sum_probs=45.3

Q ss_pred             cCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCC
Q 005987          143 YKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGA  204 (666)
Q Consensus       143 Y~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~  204 (666)
                      -.|+.+++++||++.++.|..++..      +    +.++|+|||||||||+++++|+.+..
T Consensus        25 ~~~~~~~~vigq~~a~~~L~~~~~~------~----~~~l~~G~~G~GKttla~~l~~~l~~   76 (637)
T PRK13765         25 VPERLIDQVIGQEHAVEVIKKAAKQ------R----RHVMMIGSPGTGKSMLAKAMAELLPK   76 (637)
T ss_pred             cCcccHHHcCChHHHHHHHHHHHHh------C----CeEEEECCCCCcHHHHHHHHHHHcCh
Confidence            3478999999999999999888775      2    37999999999999999999998853

>cd03283 ABC_MutS-like MutS-like homolog in eukaryotes

Probab=97.23  E-value=0.0044  Score=61.67  Aligned_cols=22  Identities=36%  Similarity=0.505  Sum_probs=20.5

Q ss_pred             cEEEEECCCCchHHHHHHHHHH
Q 005987          179 NVLVITGQAGVGKTATVRQIAS  200 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAk  200 (666)
                      +.++|+||+|+||||+++.++.
T Consensus        26 ~~~~ltGpNg~GKSTllr~i~~   47 (199)
T cd03283          26 NGILITGSNMSGKSTFLRTIGV   47 (199)
T ss_pred             cEEEEECCCCCChHHHHHHHHH
Confidence            5899999999999999999984

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

>PRK12726 flagellar biosynthesis regulator FlhF; Provisional

Probab=97.22  E-value=0.016  Score=62.79  Aligned_cols=36  Identities=31%  Similarity=0.417  Sum_probs=29.1

Q ss_pred             ccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcCCC
Q 005987          178 TNVLVITGQAGVGKTATVRQIASHL---GARLYEWDTPT  213 (666)
Q Consensus       178 ~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~nasd  213 (666)
                      +++++|.||+||||||++..||..+   |..+.-+++-.
T Consensus       206 ~~ii~lvGptGvGKTTt~akLA~~l~~~g~~V~lItaDt  244 (407)
T PRK12726        206 HRIISLIGQTGVGKTTTLVKLGWQLLKQNRTVGFITTDT  244 (407)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEeCCc
Confidence            4789999999999999999999866   66666665543

>PRK03839 putative kinase; Provisional

Probab=97.20  E-value=0.00032  Score=68.37  Aligned_cols=31  Identities=35%  Similarity=0.625  Sum_probs=27.6

Q ss_pred             EEEEECCCCchHHHHHHHHHHHcCCcEEEEc
Q 005987          180 VLVITGQAGVGKTATVRQIASHLGARLYEWD  210 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkelg~~viE~n  210 (666)
                      .++|.|+||+||||+++.||+.+++.++...
T Consensus         2 ~I~l~G~pGsGKsT~~~~La~~~~~~~id~d   32 (180)
T PRK03839          2 IIAITGTPGVGKTTVSKLLAEKLGYEYVDLT   32 (180)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCcEEehh
Confidence            4889999999999999999999998887543

>PRK11823 DNA repair protein RadA; Provisional

Probab=97.20  E-value=0.0018  Score=72.34  Aligned_cols=40  Identities=25%  Similarity=0.459  Sum_probs=31.4

Q ss_pred             CCCCccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcCCC
Q 005987          174 DKFSTNVLVITGQAGVGKTATVRQIASHL---GARLYEWDTPT  213 (666)
Q Consensus       174 g~~~~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~nasd  213 (666)
                      |-++...++|+||||+||||++..+|..+   +..++.+..-+
T Consensus        76 Gi~~Gs~~lI~G~pG~GKTtL~lq~a~~~a~~g~~vlYvs~Ee  118 (446)
T PRK11823         76 GLVPGSVVLIGGDPGIGKSTLLLQVAARLAAAGGKVLYVSGEE  118 (446)
T ss_pred             CccCCEEEEEECCCCCCHHHHHHHHHHHHHhcCCeEEEEEccc
Confidence            44455689999999999999999998866   66777776543

>smart00350 MCM minichromosome maintenance proteins

Probab=97.19  E-value=0.011  Score=67.34  Aligned_cols=24  Identities=13%  Similarity=0.347  Sum_probs=22.4

Q ss_pred             EEEEECCCCchHHHHHHHHHHHcC
Q 005987          180 VLVITGQAGVGKTATVRQIASHLG  203 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkelg  203 (666)
                      ++||.|+||+|||++++.+++...
T Consensus       238 ~vLL~G~pGtGKs~lar~l~~~~~  261 (509)
T smart00350      238 NILLLGDPGTAKSQLLKYVEKTAP  261 (509)
T ss_pred             eEEEeCCCChhHHHHHHHHHHHcC
Confidence            699999999999999999999764

>KOG0745 consensus Putative ATP-dependent Clp-type protease (AAA+ ATPase superfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=97.18  E-value=0.00081  Score=72.32  Aligned_cols=98  Identities=20%  Similarity=0.300  Sum_probs=58.2

Q ss_pred             ccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCchhhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCC
Q 005987          178 TNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGE  257 (666)
Q Consensus       178 ~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~  257 (666)
                      +..+||.||+|+|||.+++.||+-++..+.--.+..-+.      +...|-.+   ..-+..++..+ .|..-       
T Consensus       226 KSNvLllGPtGsGKTllaqTLAr~ldVPfaIcDcTtLTQ------AGYVGeDV---Esvi~KLl~~A-~~nVe-------  288 (564)
T KOG0745|consen  226 KSNVLLLGPTGSGKTLLAQTLARVLDVPFAICDCTTLTQ------AGYVGEDV---ESVIQKLLQEA-EYNVE-------  288 (564)
T ss_pred             cccEEEECCCCCchhHHHHHHHHHhCCCeEEecccchhh------cccccccH---HHHHHHHHHHc-cCCHH-------
Confidence            357999999999999999999999998877666554110      11112111   11223333332 12100       


Q ss_pred             CCCceEEEEeCCCCCcch--------h-HHHHHHHHHHHHHhcC
Q 005987          258 SKSSAILLIDDLPVTNGR--------T-AFERLRQCLLLLVRST  292 (666)
Q Consensus       258 ~~~~~IIlIDEid~l~~~--------~-~~~~l~~~L~~l~~~~  292 (666)
                      .-..-|++|||+|.+...        + .-+++++.|+.+++.+
T Consensus       289 kAQqGIVflDEvDKi~~~~~~i~~~RDVsGEGVQQaLLKllEGt  332 (564)
T KOG0745|consen  289 KAQQGIVFLDEVDKITKKAESIHTSRDVSGEGVQQALLKLLEGT  332 (564)
T ss_pred             HHhcCeEEEehhhhhcccCccccccccccchhHHHHHHHHhccc
Confidence            012349999999976411        0 1145777888888754

>PF08519 RFC1: Replication factor RFC1 C terminal domain; InterPro: IPR013725 This is the C-terminal domain of replication factor C, RFC1

Probab=97.17  E-value=0.00038  Score=66.21  Aligned_cols=93  Identities=18%  Similarity=0.141  Sum_probs=38.5

Q ss_pred             hhHhhhccccccCccccccchhHHHHHHHHHHHHHHHhhhCCCCCCCCcccccCCcchhhhhhhHHHHHHHHHhhhcccc
Q 005987          506 LSDADLLLASFRGRLVRYNEADNVLQSAAASVAARGVLFGNSHPVPPRWHAIRKPKLWRVDQSSLQKKKELLKKKFMAWD  585 (666)
Q Consensus       506 LS~aD~l~~~~~~~~~~~~~~~~~l~~~a~sva~RGv~~~n~~p~~~~~~~~~~P~~~~~~~~~~~~~~~~~~~~~~~~~  585 (666)
                      +|++|++.+.+|+.++ |    +++..+|..-||+...+...+.   ....+.||+|+..+++..+++ .++.....+  
T Consensus         1 IS~gDlv~~~Ir~~q~-W----sLlP~~a~~S~V~P~~~~~g~~---~~~~~~FP~wLGknS~~~K~~-Rll~el~~h--   69 (155)
T PF08519_consen    1 ISDGDLVDRQIRSTQQ-W----SLLPTHAFFSCVLPASFMRGSM---SGERPNFPSWLGKNSKQNKNK-RLLQELQSH--   69 (155)
T ss_dssp             HHHHHHHHHHHTT-SS-G----GGHHHHHHHHTHHHHHTT-EE----SS------SHHHHHHHHHHHH-HHHHHHHTT--
T ss_pred             CcHHHHHHHHhhcCCc-h----hhhHHHHHHHhhhhHHHhcCCC---CcccCCCcHHHHHHhHHHHHH-HHHHHHHHH--
Confidence            6899999999988644 5    3566666655566554433331   224677999999998766544 343332222  


Q ss_pred             CCcccccccCCCCCchhhhhhhhhhhhHHhh
Q 005987          586 GSISADVYNGSSSSDVSVLATEYAPALKWLG  616 (666)
Q Consensus       586 g~~~~~~~~~~~~~~~~~~~~e~lP~l~~i~  616 (666)
                             ++.....+..+++.+|+|+|+...
T Consensus        70 -------~~~~~s~~~~~v~~~Ylp~L~~~l   93 (155)
T PF08519_consen   70 -------MRLKTSASKSEVRLDYLPLLRQKL   93 (155)
T ss_dssp             -------TTT---------------------
T ss_pred             -------hcccccCCHHHHHHHHHHHHHHHH
Confidence                   223334556789999999999754

RFC complexes hydrolyse ATP and load sliding clamps such as PCNA (proliferating cell nuclear antigen) onto double-stranded DNA. RFC1 is essential for RFC function in vivo [, ]. ; GO: 0003689 DNA clamp loader activity, 0005524 ATP binding, 0006260 DNA replication, 0005663 DNA replication factor C complex; PDB: 1SXJ_A.

>COG4619 ABC-type uncharacterized transport system, ATPase component [General function prediction only]

Probab=97.16  E-value=0.0031  Score=60.05  Aligned_cols=24  Identities=33%  Similarity=0.643  Sum_probs=22.1

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      -.++|+||+||||||+.+.+|.-.
T Consensus        30 e~iaitGPSG~GKStllk~va~Li   53 (223)
T COG4619          30 EFIAITGPSGCGKSTLLKIVASLI   53 (223)
T ss_pred             ceEEEeCCCCccHHHHHHHHHhcc
Confidence            468999999999999999999976

>TIGR03499 FlhF flagellar biosynthetic protein FlhF

Probab=97.16  E-value=0.0034  Score=65.97  Aligned_cols=57  Identities=28%  Similarity=0.350  Sum_probs=37.3

Q ss_pred             HHHHHHHHHHHhhcCCC--C--CCCccEEEEECCCCchHHHHHHHHHHHc----C-CcEEEEcCCC
Q 005987          157 KVEEVRAWFEERLGDSK--D--KFSTNVLVITGQAGVGKTATVRQIASHL----G-ARLYEWDTPT  213 (666)
Q Consensus       157 ~i~el~~wL~~~~~~~~--g--~~~~k~LLL~GPpG~GKTtla~~LAkel----g-~~viE~nasd  213 (666)
                      ..+.+..+|...+....  .  ...+++++|.||+|+||||++..||..+    | ..|.-+..-.
T Consensus       169 ~~~~~~~~l~~~l~~~~~~~~~~~~~~vi~~vGptGvGKTTt~~kLa~~~~~~~g~~~V~li~~D~  234 (282)
T TIGR03499       169 AWRWLREALEKMLPVKPEEDEILEQGGVIALVGPTGVGKTTTLAKLAARFVLEHGNKKVALITTDT  234 (282)
T ss_pred             HHHHHHHHHHHHhccCCccccccCCCeEEEEECCCCCCHHHHHHHHHHHHHHHcCCCeEEEEECCc
Confidence            34556666655543111  1  1123689999999999999999998876    4 5666666543

>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=97.13  E-value=0.0033  Score=68.23  Aligned_cols=27  Identities=26%  Similarity=0.283  Sum_probs=24.1

Q ss_pred             CccEEEEECCCCchHHHHHHHHHHHcC
Q 005987          177 STNVLVITGQAGVGKTATVRQIASHLG  203 (666)
Q Consensus       177 ~~k~LLL~GPpG~GKTtla~~LAkelg  203 (666)
                      +++.|+|+||+|+|||.++-.+...+-
T Consensus        61 ~~~GlYl~G~vG~GKT~Lmd~f~~~lp   87 (362)
T PF03969_consen   61 PPKGLYLWGPVGRGKTMLMDLFYDSLP   87 (362)
T ss_pred             CCceEEEECCCCCchhHHHHHHHHhCC
Confidence            448999999999999999999988874

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

>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=97.12  E-value=0.00081  Score=70.01  Aligned_cols=64  Identities=25%  Similarity=0.453  Sum_probs=47.7

Q ss_pred             CCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcC---CcEEEEcCCC
Q 005987          144 KPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLG---ARLYEWDTPT  213 (666)
Q Consensus       144 ~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg---~~viE~nasd  213 (666)
                      .+-++++|.......+++.++|.....   +   ...++++||+|+||||++.+++..+.   ..++.+..+.
T Consensus        99 ~~~sle~l~~~~~~~~~~~~~l~~~v~---~---~~~ili~G~tGSGKTT~l~all~~i~~~~~~iv~iEd~~  165 (270)
T PF00437_consen   99 KPFSLEDLGESGSIPEEIAEFLRSAVR---G---RGNILISGPTGSGKTTLLNALLEEIPPEDERIVTIEDPP  165 (270)
T ss_dssp             S--CHCCCCHTHHCHHHHHHHHHHCHH---T---TEEEEEEESTTSSHHHHHHHHHHHCHTTTSEEEEEESSS
T ss_pred             ccccHhhccCchhhHHHHHHHHhhccc---c---ceEEEEECCCccccchHHHHHhhhccccccceEEecccc
Confidence            344788898888878888888886433   1   15899999999999999999999883   4555555443

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 ....

>PRK14737 gmk guanylate kinase; Provisional

Probab=97.12  E-value=0.013  Score=57.76  Aligned_cols=25  Identities=20%  Similarity=0.453  Sum_probs=23.0

Q ss_pred             ccEEEEECCCCchHHHHHHHHHHHc
Q 005987          178 TNVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       178 ~k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      +++++|+||+|+||||+++.|.++.
T Consensus         4 ~~~ivl~GpsG~GK~tl~~~l~~~~   28 (186)
T PRK14737          4 PKLFIISSVAGGGKSTIIQALLEEH   28 (186)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHhcC
Confidence            3789999999999999999999876

>PRK13947 shikimate kinase; Provisional

Probab=97.12  E-value=0.00044  Score=66.60  Aligned_cols=31  Identities=29%  Similarity=0.462  Sum_probs=28.0

Q ss_pred             EEEEECCCCchHHHHHHHHHHHcCCcEEEEc
Q 005987          180 VLVITGQAGVGKTATVRQIASHLGARLYEWD  210 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkelg~~viE~n  210 (666)
                      .++|.|+|||||||+++.||+.+|+.++...
T Consensus         3 ~I~l~G~~GsGKst~a~~La~~lg~~~id~d   33 (171)
T PRK13947          3 NIVLIGFMGTGKTTVGKRVATTLSFGFIDTD   33 (171)
T ss_pred             eEEEEcCCCCCHHHHHHHHHHHhCCCEEECc
Confidence            5899999999999999999999999887543

>PRK12724 flagellar biosynthesis regulator FlhF; Provisional

Probab=97.11  E-value=0.017  Score=63.34  Aligned_cols=56  Identities=25%  Similarity=0.445  Sum_probs=35.4

Q ss_pred             HHHHHHHHHHHHhhcCCC------CCCCccEEEEECCCCchHHHHHHHHHHHc----CCcEEEEcC
Q 005987          156 KKVEEVRAWFEERLGDSK------DKFSTNVLVITGQAGVGKTATVRQIASHL----GARLYEWDT  211 (666)
Q Consensus       156 k~i~el~~wL~~~~~~~~------g~~~~k~LLL~GPpG~GKTtla~~LAkel----g~~viE~na  211 (666)
                      ...+.+.++|...+....      +...+.+++|.||+|+||||++..||..+    |..+.-+..
T Consensus       195 ~~~~~l~~~L~~~l~~~~~~~~~~g~~~~~vi~lvGptGvGKTTtaaKLA~~~~~~~G~~V~Lit~  260 (432)
T PRK12724        195 NVTERAVTYLEERVSVDSDLFSGTGKNQRKVVFFVGPTGSGKTTSIAKLAAKYFLHMGKSVSLYTT  260 (432)
T ss_pred             HHHHHHHHHHHHhcccchhhhhhcccCCCeEEEEECCCCCCHHHHHHHHHHHHHHhcCCeEEEecc
Confidence            344556666655442111      11233579999999999999999999754    445554443

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

Probab=97.11  E-value=0.0016  Score=72.02  Aligned_cols=62  Identities=21%  Similarity=0.356  Sum_probs=48.6

Q ss_pred             ccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCC---cEEEEcCC
Q 005987          142 KYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGA---RLYEWDTP  212 (666)
Q Consensus       142 KY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~---~viE~nas  212 (666)
                      .+.+-++++|...+.....+..+++.         |..++|++||+|+||||+.+++.++++-   .++.+.-|
T Consensus       231 ~~~~l~l~~Lg~~~~~~~~~~~~~~~---------p~GliLvTGPTGSGKTTTLY~~L~~ln~~~~nI~TiEDP  295 (500)
T COG2804         231 DQVILDLEKLGMSPFQLARLLRLLNR---------PQGLILVTGPTGSGKTTTLYAALSELNTPERNIITIEDP  295 (500)
T ss_pred             ccccCCHHHhCCCHHHHHHHHHHHhC---------CCeEEEEeCCCCCCHHHHHHHHHHHhcCCCceEEEeeCC
Confidence            33477889999999999998888874         2268999999999999999999999843   34444433

>cd01131 PilT Pilus retraction ATPase PilT

Probab=97.10  E-value=0.0011  Score=65.80  Aligned_cols=25  Identities=24%  Similarity=0.569  Sum_probs=22.7

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLG  203 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg  203 (666)
                      ..++|+||+|+||||++++++..+.
T Consensus         2 GlilI~GptGSGKTTll~~ll~~~~   26 (198)
T cd01131           2 GLVLVTGPTGSGKSTTLAAMIDYIN   26 (198)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHhh
Confidence            4799999999999999999998884

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.

>PRK06762 hypothetical protein; Provisional

Probab=97.10  E-value=0.00056  Score=65.64  Aligned_cols=32  Identities=28%  Similarity=0.522  Sum_probs=27.2

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEEEEc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLYEWD  210 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~viE~n  210 (666)
                      ..++|+|+||+||||+++.|++.++..++.++
T Consensus         3 ~li~i~G~~GsGKST~A~~L~~~l~~~~~~i~   34 (166)
T PRK06762          3 TLIIIRGNSGSGKTTIAKQLQERLGRGTLLVS   34 (166)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhCCCeEEec
Confidence            68999999999999999999999965554444

>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=97.10  E-value=0.01  Score=57.26  Aligned_cols=34  Identities=35%  Similarity=0.533  Sum_probs=28.2

Q ss_pred             EEEEECCCCchHHHHHHHHHHHc---CCcEEEEcCCC
Q 005987          180 VLVITGQAGVGKTATVRQIASHL---GARLYEWDTPT  213 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkel---g~~viE~nasd  213 (666)
                      +++++||||+||||++..+|..+   |..+.-+++..
T Consensus         2 ~~~~~G~~G~GKTt~~~~la~~~~~~g~~v~~i~~D~   38 (173)
T cd03115           2 VILLVGLQGVGKTTTAAKLALYLKKKGKKVLLVAADT   38 (173)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHCCCcEEEEEcCC
Confidence            58899999999999999998876   67777766543

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.

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

Probab=97.09  E-value=0.0015  Score=67.20  Aligned_cols=26  Identities=23%  Similarity=0.291  Sum_probs=23.4

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGA  204 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~  204 (666)
                      ..++|.||+||||||+++.+++.+..
T Consensus        17 qr~~I~G~~G~GKTTLlr~I~n~l~~   42 (249)
T cd01128          17 QRGLIVAPPKAGKTTLLQSIANAITK   42 (249)
T ss_pred             CEEEEECCCCCCHHHHHHHHHhcccc
Confidence            47999999999999999999998754

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.

>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]

Probab=97.08  E-value=0.012  Score=68.65  Aligned_cols=203  Identities=18%  Similarity=0.294  Sum_probs=116.8

Q ss_pred             cCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc--CCcEE--EEcCCC--chh
Q 005987          143 YKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL--GARLY--EWDTPT--PTI  216 (666)
Q Consensus       143 Y~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel--g~~vi--E~nasd--~~~  216 (666)
                      .+|.-....+.+++.+..+....           ..+.+||+-|.|.||||++-.++...  +..|.  .+..+|  +.-
T Consensus        13 ~~P~~~~~~v~R~rL~~~L~~~~-----------~~RL~li~APAGfGKttl~aq~~~~~~~~~~v~Wlslde~dndp~r   81 (894)
T COG2909          13 VRPVRPDNYVVRPRLLDRLRRAN-----------DYRLILISAPAGFGKTTLLAQWRELAADGAAVAWLSLDESDNDPAR   81 (894)
T ss_pred             CCCCCcccccccHHHHHHHhcCC-----------CceEEEEeCCCCCcHHHHHHHHHHhcCcccceeEeecCCccCCHHH
Confidence            35566777888888777764321           23799999999999999999988633  33332  223332  111


Q ss_pred             hhhhhhccc----C--C---------ccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHH
Q 005987          217 WQEYMHNCK----T--G---------LEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERL  281 (666)
Q Consensus       217 ~~e~l~~~~----~--g---------~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l  281 (666)
                      +..++....    .  |         ..+.+...-|..++.++..|.           .|..++|||.+.+...    .+
T Consensus        82 F~~yLi~al~~~~p~~~~~a~~l~q~~~~~~l~~l~~~L~~Ela~~~-----------~pl~LVlDDyHli~~~----~l  146 (894)
T COG2909          82 FLSYLIAALQQATPTLGDEAQTLLQKHQYVSLESLLSSLLNELASYE-----------GPLYLVLDDYHLISDP----AL  146 (894)
T ss_pred             HHHHHHHHHHHhCccccHHHHHHHHhcccccHHHHHHHHHHHHHhhc-----------CceEEEeccccccCcc----cH
Confidence            222221100    0  0         011223334566666666664           4679999999987654    24


Q ss_pred             HHHHHHHHhcCCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHH
Q 005987          282 RQCLLLLVRSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQI  361 (666)
Q Consensus       282 ~~~L~~l~~~~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l  361 (666)
                      ..+|..+++...--+.++++....+.-.--..|    ++..+--.+...+.   .+.++....+...   -+..++...+
T Consensus       147 ~~~l~fLl~~~P~~l~lvv~SR~rP~l~la~lR----lr~~llEi~~~~Lr---f~~eE~~~fl~~~---~~l~Ld~~~~  216 (894)
T COG2909         147 HEALRFLLKHAPENLTLVVTSRSRPQLGLARLR----LRDELLEIGSEELR---FDTEEAAAFLNDR---GSLPLDAADL  216 (894)
T ss_pred             HHHHHHHHHhCCCCeEEEEEeccCCCCccccee----ehhhHHhcChHhhc---CChHHHHHHHHHc---CCCCCChHHH
Confidence            556777887776556677776544321100111    11111000122233   3566766666532   3478899999


Q ss_pred             HHHHHHcCCcHHHHHHHHHHHhcC
Q 005987          362 DLVAQASGGDIRQAITSLQFSSLK  385 (666)
Q Consensus       362 ~~Ia~~s~GDIR~AIn~LQf~~~~  385 (666)
                      +.|.+.+.|=+-    .||.+++.
T Consensus       217 ~~L~~~teGW~~----al~L~aLa  236 (894)
T COG2909         217 KALYDRTEGWAA----ALQLIALA  236 (894)
T ss_pred             HHHHhhcccHHH----HHHHHHHH
Confidence            999999999654    45555543

>PRK00625 shikimate kinase; Provisional

Probab=97.07  E-value=0.00054  Score=66.59  Aligned_cols=31  Identities=26%  Similarity=0.433  Sum_probs=28.2

Q ss_pred             EEEEECCCCchHHHHHHHHHHHcCCcEEEEc
Q 005987          180 VLVITGQAGVGKTATVRQIASHLGARLYEWD  210 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkelg~~viE~n  210 (666)
                      .++|+|+||+||||+++.||+.+++.++..+
T Consensus         2 ~I~LiG~pGsGKTT~~k~La~~l~~~~id~D   32 (173)
T PRK00625          2 QIFLCGLPTVGKTSFGKALAKFLSLPFFDTD   32 (173)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCCEEEhh
Confidence            4899999999999999999999999888654

>TIGR02688 conserved hypothetical protein TIGR02688

Probab=97.07  E-value=0.0057  Score=66.81  Aligned_cols=23  Identities=22%  Similarity=0.329  Sum_probs=20.7

Q ss_pred             cEEEEECCCCchHHHHHHHHHHH
Q 005987          179 NVLVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAke  201 (666)
                      -++++.||+|||||+++.+++..
T Consensus       210 ~Nli~lGp~GTGKThla~~l~~~  232 (449)
T TIGR02688       210 YNLIELGPKGTGKSYIYNNLSPY  232 (449)
T ss_pred             CcEEEECCCCCCHHHHHHHHhHH
Confidence            46999999999999999988776

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.

>COG1116 TauB ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]

Probab=97.05  E-value=0.0043  Score=62.91  Aligned_cols=24  Identities=33%  Similarity=0.519  Sum_probs=21.9

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      -.+-|.||+||||||+.+++|--.
T Consensus        30 EfvsilGpSGcGKSTLLriiAGL~   53 (248)
T COG1116          30 EFVAILGPSGCGKSTLLRLIAGLE   53 (248)
T ss_pred             CEEEEECCCCCCHHHHHHHHhCCC
Confidence            479999999999999999999865

>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=97.05  E-value=0.03  Score=59.63  Aligned_cols=86  Identities=17%  Similarity=0.218  Sum_probs=49.4

Q ss_pred             CCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcCCCceEEEEecCCCCCCccchhhhh----------hHHHHHHhhcC
Q 005987          258 SKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHIPTAVVLTECGKADSVDSTAQSF----------EELQSILVDAG  327 (666)
Q Consensus       258 ~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~~~PiViIit~~~~~~s~d~~~r~l----------~~L~s~L~r~r  327 (666)
                      .+.+.||+|||+|++..... ..+.+.+..++...++ +++++.|...      ..+.+          ..-...|+..-
T Consensus       170 ~~~~iViiIDdLDR~~~~~i-~~~l~~ik~~~~~~~i-~~Il~~D~~~------l~~ai~~~~~~~~~~~~~~~yLeKii  241 (325)
T PF07693_consen  170 SKKRIVIIIDDLDRCSPEEI-VELLEAIKLLLDFPNI-IFILAFDPEI------LEKAIEKNYGEGFDEIDGREYLEKII  241 (325)
T ss_pred             CCceEEEEEcchhcCCcHHH-HHHHHHHHHhcCCCCe-EEEEEecHHH------HHHHHHhhcCcccccccHHHHHHhhc
Confidence            35678999999999976543 3344555555554332 3344444211      00000          01133344422


Q ss_pred             eeEEEeCCCCHHHHHHHHHHHHHH
Q 005987          328 ARKVALNPITNGSIKRTLSKICRQ  351 (666)
Q Consensus       328 ~~~I~F~p~s~~~i~kiL~~I~~~  351 (666)
                      -..+.++++....+.+.+...+..
T Consensus       242 q~~~~lP~~~~~~~~~~~~~~~~~  265 (325)
T PF07693_consen  242 QVPFSLPPPSPSDLERYLNELLES  265 (325)
T ss_pred             CeEEEeCCCCHHHHHHHHHHHHHH
Confidence            345888999999999888887544

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 [].

>TIGR01359 UMP_CMP_kin_fam UMP-CMP kinase family

Probab=97.04  E-value=0.00052  Score=66.90  Aligned_cols=30  Identities=23%  Similarity=0.391  Sum_probs=26.2

Q ss_pred             EEEEECCCCchHHHHHHHHHHHcCCcEEEE
Q 005987          180 VLVITGQAGVGKTATVRQIASHLGARLYEW  209 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkelg~~viE~  209 (666)
                      +++|.||||+||||+++.||+.+|+..+..
T Consensus         1 ~i~i~G~pGsGKst~a~~la~~~~~~~is~   30 (183)
T TIGR01359         1 VVFVLGGPGSGKGTQCAKIVENFGFTHLSA   30 (183)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHcCCeEEEC
Confidence            378999999999999999999999766543

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.

>TIGR02237 recomb_radB DNA repair and recombination protein RadB

Probab=97.03  E-value=0.0045  Score=61.73  Aligned_cols=39  Identities=26%  Similarity=0.277  Sum_probs=30.8

Q ss_pred             CCCCccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcCC
Q 005987          174 DKFSTNVLVITGQAGVGKTATVRQIASHL---GARLYEWDTP  212 (666)
Q Consensus       174 g~~~~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~nas  212 (666)
                      |-++..+.+|+||||+|||+++..+|.+.   |..++.+..-
T Consensus         8 Gi~~g~i~~i~G~~GsGKT~l~~~~~~~~~~~g~~v~yi~~e   49 (209)
T TIGR02237         8 GVERGTITQIYGPPGSGKTNICMILAVNAARQGKKVVYIDTE   49 (209)
T ss_pred             CCCCCeEEEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEECC
Confidence            44446799999999999999999888654   6677777664

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

>TIGR01618 phage_P_loop phage nucleotide-binding protein

Probab=97.03  E-value=0.00082  Score=67.71  Aligned_cols=21  Identities=38%  Similarity=0.752  Sum_probs=19.6

Q ss_pred             cEEEEECCCCchHHHHHHHHH
Q 005987          179 NVLVITGQAGVGKTATVRQIA  199 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LA  199 (666)
                      ..+||||+||+||||+|+.++
T Consensus        13 ~~~liyG~~G~GKtt~a~~~~   33 (220)
T TIGR01618        13 NMYLIYGKPGTGKTSTIKYLP   33 (220)
T ss_pred             cEEEEECCCCCCHHHHHHhcC
Confidence            579999999999999999987

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.

>cd00464 SK Shikimate kinase (SK) is the fifth enzyme in the shikimate pathway, a seven-step biosynthetic pathway which converts erythrose-4-phosphate to chorismic acid, found in bacteria, fungi and plants

Probab=97.03  E-value=0.00054  Score=64.55  Aligned_cols=29  Identities=34%  Similarity=0.559  Sum_probs=26.6

Q ss_pred             EEEECCCCchHHHHHHHHHHHcCCcEEEE
Q 005987          181 LVITGQAGVGKTATVRQIASHLGARLYEW  209 (666)
Q Consensus       181 LLL~GPpG~GKTtla~~LAkelg~~viE~  209 (666)
                      ++|+||||+||||+++.||+.+|+.++..
T Consensus         2 i~l~G~~GsGKstla~~la~~l~~~~~~~   30 (154)
T cd00464           2 IVLIGMMGAGKTTVGRLLAKALGLPFVDL   30 (154)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHhCCCEEEc
Confidence            78999999999999999999999987743

Chorismic acid is a important intermediate in the synthesis of aromatic compounds, such as aromatic amino acids, p-aminobenzoic acid, folate and ubiquinone. Shikimate kinase catalyses the phosphorylation of the 3-hydroxyl group of shikimic acid using ATP.

>cd03282 ABC_MSH4_euk MutS4 homolog in eukaryotes

Probab=97.03  E-value=0.0057  Score=61.11  Aligned_cols=22  Identities=36%  Similarity=0.474  Sum_probs=20.1

Q ss_pred             cEEEEECCCCchHHHHHHHHHH
Q 005987          179 NVLVITGQAGVGKTATVRQIAS  200 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAk  200 (666)
                      +.++|+||.|+||||+++.++.
T Consensus        30 ~~~~l~G~n~~GKstll~~i~~   51 (204)
T cd03282          30 RFHIITGPNMSGKSTYLKQIAL   51 (204)
T ss_pred             cEEEEECCCCCCHHHHHHHHHH
Confidence            6899999999999999999873

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

>cd02021 GntK Gluconate kinase (GntK) catalyzes the phosphoryl transfer from ATP to gluconate

Probab=97.03  E-value=0.00055  Score=64.48  Aligned_cols=29  Identities=31%  Similarity=0.653  Sum_probs=25.7

Q ss_pred             EEEEECCCCchHHHHHHHHHHHcCCcEEE
Q 005987          180 VLVITGQAGVGKTATVRQIASHLGARLYE  208 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkelg~~viE  208 (666)
                      +++|+||||+||||+++.|++.++..++.
T Consensus         1 li~l~G~~GsGKST~a~~l~~~~~~~~i~   29 (150)
T cd02021           1 IIVVMGVSGSGKSTVGKALAERLGAPFID   29 (150)
T ss_pred             CEEEEcCCCCCHHHHHHHHHhhcCCEEEe
Confidence            47899999999999999999999876653

The resulting product gluconate-6-phoshate is an important precursor of gluconate metabolism. GntK acts as a dimmer composed of two identical subunits.

>PRK09361 radB DNA repair and recombination protein RadB; Provisional

Probab=97.02  E-value=0.0055  Score=61.93  Aligned_cols=39  Identities=28%  Similarity=0.295  Sum_probs=30.6

Q ss_pred             CCCCccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcCC
Q 005987          174 DKFSTNVLVITGQAGVGKTATVRQIASHL---GARLYEWDTP  212 (666)
Q Consensus       174 g~~~~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~nas  212 (666)
                      |-+...+.+|+||||+|||+++..+|.+.   +..++.+..-
T Consensus        19 Gi~~g~i~~i~G~~GsGKT~l~~~la~~~~~~~~~v~yi~~e   60 (225)
T PRK09361         19 GFERGTITQIYGPPGSGKTNICLQLAVEAAKNGKKVIYIDTE   60 (225)
T ss_pred             CCCCCeEEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEECC
Confidence            33445689999999999999999998755   6777766654

>TIGR02533 type_II_gspE general secretory pathway protein E

Probab=97.02  E-value=0.0021  Score=72.46  Aligned_cols=62  Identities=21%  Similarity=0.355  Sum_probs=46.5

Q ss_pred             cCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcC---CcEEEEcCCC
Q 005987          143 YKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLG---ARLYEWDTPT  213 (666)
Q Consensus       143 Y~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg---~~viE~nasd  213 (666)
                      ..+.++++|-..++.++.++..+..         +...++++||+|+||||+++++.+++.   ..++.+..|.
T Consensus       216 ~~~~~l~~Lg~~~~~~~~l~~~~~~---------~~GlilitGptGSGKTTtL~a~L~~l~~~~~~iiTiEDpv  280 (486)
T TIGR02533       216 AVRLDLETLGMSPELLSRFERLIRR---------PHGIILVTGPTGSGKTTTLYAALSRLNTPERNILTVEDPV  280 (486)
T ss_pred             cCCCCHHHcCCCHHHHHHHHHHHhc---------CCCEEEEEcCCCCCHHHHHHHHHhccCCCCCcEEEEcCCe
Confidence            3566888888888888888776653         114799999999999999998888773   3466665443

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

>PRK05629 hypothetical protein; Validated

Probab=97.02  E-value=0.052  Score=58.04  Aligned_cols=93  Identities=6%  Similarity=-0.011  Sum_probs=72.4

Q ss_pred             CeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCcHHHHHHHHHHHhcCCCCcccccccCCCCCCCcccc
Q 005987          327 GARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASGGDIRQAITSLQFSSLKQDPMLNLSLSISKPNFPEEKA  406 (666)
Q Consensus       327 r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~s~GDIR~AIn~LQf~~~~~~~~~~~~~~~~~~~~~k~~~  406 (666)
                      .+..+.|.++.+.++.+.+...+...|+++++++++.|++.+++|+..+-+-|+-++...+...                
T Consensus       117 ~~~~ve~~~~~~~~l~~wi~~~~~~~g~~i~~~A~~~L~~~~g~dl~~l~~EleKL~~~~~~~I----------------  180 (318)
T PRK05629        117 IAVVHEAAKLKPRERPGWVTQEFKNHGVRPTPDVVHALLEGVGSDLRELASAISQLVEDTQGNV----------------  180 (318)
T ss_pred             cceEeeCCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHCccHHHHHHHHHHHHhcCCCCc----------------
Confidence            3778999999999999999999999999999999999999999999999999997775321110                


Q ss_pred             CCCCCcccccCCccccchHHHHhHHhhCCC
Q 005987          407 DGHGGFSIQFGRDETLSLFHALGKFLHNKR  436 (666)
Q Consensus       407 ~~~~~~~~~~~RD~~l~lFhalGkil~~Kr  436 (666)
                      + ...+..+.......++|+.+..++.++.
T Consensus       181 t-~e~V~~~v~~~~~~~iF~l~dAv~~g~~  209 (318)
T PRK05629        181 T-VEKVRAYYVGVAEVSGFDIADLACAGQV  209 (318)
T ss_pred             C-HHHHHHHhCCCccchHHHHHHHHHcCCH
Confidence            0 0112234445566789988888887763

>TIGR00764 lon_rel lon-related putative ATP-dependent protease

Probab=97.01  E-value=0.00094  Score=77.36  Aligned_cols=48  Identities=21%  Similarity=0.374  Sum_probs=41.1

Q ss_pred             CccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCC
Q 005987          147 SLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGA  204 (666)
Q Consensus       147 sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~  204 (666)
                      -+++++||++.++.++..+..      +    ++++|+||||||||++++++|+.++.
T Consensus        16 ~~~~viG~~~a~~~l~~a~~~------~----~~~ll~G~pG~GKT~la~~la~~l~~   63 (608)
T TIGR00764        16 LIDQVIGQEEAVEIIKKAAKQ------K----RNVLLIGEPGVGKSMLAKAMAELLPD   63 (608)
T ss_pred             hHhhccCHHHHHHHHHHHHHc------C----CCEEEECCCCCCHHHHHHHHHHHcCc
Confidence            467899999999888887764      2    36889999999999999999999954

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

>TIGR01360 aden_kin_iso1 adenylate kinase, isozyme 1 subfamily

Probab=97.00  E-value=0.00067  Score=66.21  Aligned_cols=30  Identities=23%  Similarity=0.454  Sum_probs=27.1

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEEE
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLYE  208 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~viE  208 (666)
                      ++++|.||||+||||+++.||+.+|+..+.
T Consensus         4 ~ii~i~G~~GsGKsTl~~~l~~~~g~~~~~   33 (188)
T TIGR01360         4 KIIFIVGGPGSGKGTQCEKIVEKYGFTHLS   33 (188)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHhCCcEEe
Confidence            489999999999999999999999877664

Members of this family are adenylate kinase, EC 2.7.4.3. This clade is found only in eukaryotes and includes human adenylate kinase isozyme 1 (myokinase). Within the adenylate kinase superfamily, this set appears specifically closely related to a subfamily of eukaryotic UMP-CMP kinases (TIGR01359), rather than to the large clade of bacterial, archaeal, and eukaryotic adenylate kinase family members in TIGR01351.

>PRK14531 adenylate kinase; Provisional

Probab=97.00  E-value=0.00067  Score=66.46  Aligned_cols=30  Identities=23%  Similarity=0.423  Sum_probs=26.9

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEEE
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLYE  208 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~viE  208 (666)
                      +.++|.||||+||||+++.||+.+|+..+.
T Consensus         3 ~~i~i~G~pGsGKsT~~~~la~~~g~~~is   32 (183)
T PRK14531          3 QRLLFLGPPGAGKGTQAARLCAAHGLRHLS   32 (183)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHhCCCeEe
Confidence            468999999999999999999999987664

>PRK08154 anaerobic benzoate catabolism transcriptional regulator; Reviewed

Probab=97.00  E-value=0.0014  Score=69.82  Aligned_cols=55  Identities=24%  Similarity=0.384  Sum_probs=40.5

Q ss_pred             CHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEE
Q 005987          154 QRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYE  208 (666)
Q Consensus       154 ~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE  208 (666)
                      .++..+.+...++..+.....--+...++|+|++||||||+++.||+.+|+.++.
T Consensus       109 ~~~~~~~~~~~l~~~~~~~~~~~~~~~I~l~G~~GsGKStvg~~La~~Lg~~~id  163 (309)
T PRK08154        109 SPAQLARVRDALSGMLGAGRRAARRRRIALIGLRGAGKSTLGRMLAARLGVPFVE  163 (309)
T ss_pred             CHHHHHHHHHHHHHHHhhhhhccCCCEEEEECCCCCCHHHHHHHHHHHcCCCEEe
Confidence            5556666666666544432211233689999999999999999999999999884

>PRK14532 adenylate kinase; Provisional

Probab=96.99  E-value=0.00067  Score=66.56  Aligned_cols=30  Identities=17%  Similarity=0.298  Sum_probs=26.6

Q ss_pred             EEEEECCCCchHHHHHHHHHHHcCCcEEEE
Q 005987          180 VLVITGQAGVGKTATVRQIASHLGARLYEW  209 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkelg~~viE~  209 (666)
                      .++|.||||+||||+++.||+.+|+..+..
T Consensus         2 ~i~~~G~pGsGKsT~a~~la~~~g~~~is~   31 (188)
T PRK14532          2 NLILFGPPAAGKGTQAKRLVEERGMVQLST   31 (188)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHcCCeEEeC
Confidence            388999999999999999999999877643

>PRK07261 topology modulation protein; Provisional

Probab=96.98  E-value=0.00076  Score=65.40  Aligned_cols=31  Identities=26%  Similarity=0.532  Sum_probs=27.4

Q ss_pred             EEEEECCCCchHHHHHHHHHHHcCCcEEEEc
Q 005987          180 VLVITGQAGVGKTATVRQIASHLGARLYEWD  210 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkelg~~viE~n  210 (666)
                      .++|.||||+||||+++.|++.+++.++..+
T Consensus         2 ri~i~G~~GsGKSTla~~l~~~~~~~~i~~D   32 (171)
T PRK07261          2 KIAIIGYSGSGKSTLARKLSQHYNCPVLHLD   32 (171)
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHhCCCeEecC
Confidence            4889999999999999999999988877643

>PRK13949 shikimate kinase; Provisional

Probab=96.97  E-value=0.0007  Score=65.53  Aligned_cols=31  Identities=29%  Similarity=0.517  Sum_probs=27.7

Q ss_pred             EEEEECCCCchHHHHHHHHHHHcCCcEEEEc
Q 005987          180 VLVITGQAGVGKTATVRQIASHLGARLYEWD  210 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkelg~~viE~n  210 (666)
                      .++|.||||+||||+++.||+.+++.++..+
T Consensus         3 ~I~liG~~GsGKstl~~~La~~l~~~~id~D   33 (169)
T PRK13949          3 RIFLVGYMGAGKTTLGKALARELGLSFIDLD   33 (169)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHcCCCeeccc
Confidence            5899999999999999999999998877543

>cd02020 CMPK Cytidine monophosphate kinase (CMPK) catalyzes the reversible phosphorylation of cytidine monophosphate (CMP) to produce cytidine diphosphate (CDP), using ATP as the preferred phosphoryl donor

Probab=96.97  E-value=0.00067  Score=63.24  Aligned_cols=31  Identities=29%  Similarity=0.551  Sum_probs=27.2

Q ss_pred             EEEEECCCCchHHHHHHHHHHHcCCcEEEEc
Q 005987          180 VLVITGQAGVGKTATVRQIASHLGARLYEWD  210 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkelg~~viE~n  210 (666)
                      +++|+|||||||||+++.||+.+|+.++...
T Consensus         1 ~I~i~G~~GsGKst~a~~la~~~~~~~~~~~   31 (147)
T cd02020           1 IIAIDGPAGSGKSTVAKLLAKKLGLPYLDTG   31 (147)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHhCCceeccc
Confidence            3789999999999999999999998876543

>cd00227 CPT Chloramphenicol (Cm) phosphotransferase (CPT)

Probab=96.97  E-value=0.00065  Score=65.97  Aligned_cols=29  Identities=21%  Similarity=0.483  Sum_probs=25.7

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEE
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLY  207 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~vi  207 (666)
                      ++++|+||||+||||+++.|++.++...+
T Consensus         3 ~~i~l~G~~gsGKst~a~~l~~~~~~~~~   31 (175)
T cd00227           3 RIIILNGGSSAGKSSIARALQSVLAEPWL   31 (175)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHhhCCCcc
Confidence            68999999999999999999999865443

Cm-inactivating enzyme; modifies the primary (C-3) hydroxyl of the antibiotic. Related structurally to shikimate kinase II.

>PRK08533 flagellar accessory protein FlaH; Reviewed

Probab=96.95  E-value=0.01  Score=60.48  Aligned_cols=35  Identities=20%  Similarity=0.344  Sum_probs=25.9

Q ss_pred             CccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcC
Q 005987          177 STNVLVITGQAGVGKTATVRQIASHL---GARLYEWDT  211 (666)
Q Consensus       177 ~~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~na  211 (666)
                      +...++|.|||||||||++..++..+   |..++.+..
T Consensus        23 ~g~~~~i~G~~G~GKTtl~~~~~~~~~~~g~~~~yi~~   60 (230)
T PRK08533         23 AGSLILIEGDESTGKSILSQRLAYGFLQNGYSVSYVST   60 (230)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHHhCCCcEEEEeC
Confidence            34689999999999999975554433   666666654

>TIGR02782 TrbB_P P-type conjugative transfer ATPase TrbB

Probab=96.94  E-value=0.0015  Score=69.06  Aligned_cols=62  Identities=15%  Similarity=0.215  Sum_probs=38.8

Q ss_pred             CCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc-----CCcEEEEcC
Q 005987          144 KPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL-----GARLYEWDT  211 (666)
Q Consensus       144 ~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel-----g~~viE~na  211 (666)
                      .|-++++|+-..-.-.+...+|..+..   +   .+.+|++||+|+||||++++|+..+     +..++.+..
T Consensus       104 ~~~tl~~l~~~g~~~~~~~~~L~~~v~---~---~~~ilI~G~tGSGKTTll~al~~~i~~~~~~~ri~tiEd  170 (299)
T TIGR02782       104 AVFTLDDYVEAGIMTAAQRDVLREAVL---A---RKNILVVGGTGSGKTTLANALLAEIAKNDPTDRVVIIED  170 (299)
T ss_pred             CCCCHHHHHhcCCCCHHHHHHHHHHHH---c---CCeEEEECCCCCCHHHHHHHHHHHhhccCCCceEEEECC
Confidence            345677775322221233344444432   1   1479999999999999999999987     345555543

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.

>cd01394 radB RadB

Probab=96.94  E-value=0.009  Score=60.00  Aligned_cols=38  Identities=29%  Similarity=0.309  Sum_probs=30.4

Q ss_pred             CCCCccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcC
Q 005987          174 DKFSTNVLVITGQAGVGKTATVRQIASHL---GARLYEWDT  211 (666)
Q Consensus       174 g~~~~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~na  211 (666)
                      |-++..+++|+||||+|||+++..+|.+.   |..++.+..
T Consensus        15 Gi~~g~i~~i~G~~GsGKT~l~~~~a~~~~~~g~~v~yi~~   55 (218)
T cd01394          15 GVERGTVTQVYGPPGTGKTNIAIQLAVETAGQGKKVAYIDT   55 (218)
T ss_pred             CccCCeEEEEECCCCCCHHHHHHHHHHHHHhcCCeEEEEEC
Confidence            44455789999999999999999998775   567777754

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

>PRK10416 signal recognition particle-docking protein FtsY; Provisional

Probab=96.94  E-value=0.046  Score=58.40  Aligned_cols=34  Identities=29%  Similarity=0.495  Sum_probs=28.1

Q ss_pred             ccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcC
Q 005987          178 TNVLVITGQAGVGKTATVRQIASHL---GARLYEWDT  211 (666)
Q Consensus       178 ~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~na  211 (666)
                      +.+++|.||+|+||||++..||..+   |..|.-+.+
T Consensus       114 ~~vi~lvGpnGsGKTTt~~kLA~~l~~~g~~V~Li~~  150 (318)
T PRK10416        114 PFVILVVGVNGVGKTTTIGKLAHKYKAQGKKVLLAAG  150 (318)
T ss_pred             CeEEEEECCCCCcHHHHHHHHHHHHHhcCCeEEEEec
Confidence            4689999999999999999999877   566665554

>PRK10436 hypothetical protein; Provisional

Probab=96.93  E-value=0.0034  Score=70.26  Aligned_cols=60  Identities=22%  Similarity=0.417  Sum_probs=45.7

Q ss_pred             CCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcC---CcEEEEcCCC
Q 005987          145 PRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLG---ARLYEWDTPT  213 (666)
Q Consensus       145 P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg---~~viE~nasd  213 (666)
                      +.++++|-..+..++.++..+..         +..++|++||+|+||||+++++.++++   ..++.+..|.
T Consensus       194 ~~~L~~LG~~~~~~~~l~~~~~~---------~~GliLvtGpTGSGKTTtL~a~l~~~~~~~~~i~TiEDPv  256 (462)
T PRK10436        194 ALDLETLGMTPAQLAQFRQALQQ---------PQGLILVTGPTGSGKTVTLYSALQTLNTAQINICSVEDPV  256 (462)
T ss_pred             CCCHHHcCcCHHHHHHHHHHHHh---------cCCeEEEECCCCCChHHHHHHHHHhhCCCCCEEEEecCCc
Confidence            45788888888888888777654         125899999999999999998888873   4566665554

>PF02562 PhoH: PhoH-like protein; InterPro: IPR003714 PhoH is a cytoplasmic protein and predicted ATPase that is induced by phosphate starvation and belongings to the phosphate regulon (pho) in Escherichia coli []

Probab=96.93  E-value=0.0071  Score=60.26  Aligned_cols=24  Identities=33%  Similarity=0.531  Sum_probs=20.1

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      +.+++.||+|||||.+|-+.|.++
T Consensus        20 ~~v~~~G~AGTGKT~LA~a~Al~~   43 (205)
T PF02562_consen   20 DLVIVNGPAGTGKTFLALAAALEL   43 (205)
T ss_dssp             SEEEEE--TTSSTTHHHHHHHHHH
T ss_pred             CeEEEECCCCCcHHHHHHHHHHHH
Confidence            589999999999999999998776

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

>cd03243 ABC_MutS_homologs The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch

Probab=96.93  E-value=0.0046  Score=61.50  Aligned_cols=22  Identities=36%  Similarity=0.498  Sum_probs=20.4

Q ss_pred             cEEEEECCCCchHHHHHHHHHH
Q 005987          179 NVLVITGQAGVGKTATVRQIAS  200 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAk  200 (666)
                      ..++|+||.|+||||+++.++.
T Consensus        30 ~~~~l~G~Ng~GKStll~~i~~   51 (202)
T cd03243          30 RLLLITGPNMGGKSTYLRSIGL   51 (202)
T ss_pred             eEEEEECCCCCccHHHHHHHHH
Confidence            5899999999999999999993

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

>PRK06696 uridine kinase; Validated

Probab=96.93  E-value=0.002  Score=65.25  Aligned_cols=52  Identities=15%  Similarity=0.215  Sum_probs=39.3

Q ss_pred             CHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEc
Q 005987          154 QRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL---GARLYEWD  210 (666)
Q Consensus       154 ~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~n  210 (666)
                      +++.+++|.+++.....   ++  +.++.|.|++|+||||+|+.|++.+   |..++.+.
T Consensus         3 ~~~~~~~la~~~~~~~~---~~--~~iI~I~G~sgsGKSTlA~~L~~~l~~~g~~v~~~~   57 (223)
T PRK06696          3 RKQLIKELAEHILTLNL---TR--PLRVAIDGITASGKTTFADELAEEIKKRGRPVIRAS   57 (223)
T ss_pred             HHHHHHHHHHHHHHhCC---CC--ceEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEec
Confidence            46677888888764211   22  2589999999999999999999999   66666544

>TIGR00150 HI0065_YjeE ATPase, YjeE family

Probab=96.92  E-value=0.002  Score=59.66  Aligned_cols=52  Identities=27%  Similarity=0.436  Sum_probs=36.1

Q ss_pred             HHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCC
Q 005987          155 RKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPT  213 (666)
Q Consensus       155 ~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd  213 (666)
                      .+....+-..|...+.      +..+++|.|+.|+||||+++.+++.+|.. -+++.|.
T Consensus         5 ~~~t~~l~~~l~~~l~------~~~~i~l~G~lGaGKTtl~~~l~~~lg~~-~~v~SPT   56 (133)
T TIGR00150         5 EKAMDKFGKAFAKPLD------FGTVVLLKGDLGAGKTTLVQGLLQGLGIQ-GNVTSPT   56 (133)
T ss_pred             HHHHHHHHHHHHHhCC------CCCEEEEEcCCCCCHHHHHHHHHHHcCCC-CcccCCC
Confidence            3444555555554432      22589999999999999999999999864 2344443

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.

>smart00534 MUTSac ATPase domain of DNA mismatch repair MUTS family

Probab=96.92  E-value=0.012  Score=57.67  Aligned_cols=19  Identities=37%  Similarity=0.588  Sum_probs=18.1

Q ss_pred             EEEECCCCchHHHHHHHHH
Q 005987          181 LVITGQAGVGKTATVRQIA  199 (666)
Q Consensus       181 LLL~GPpG~GKTtla~~LA  199 (666)
                      ++|+||.|.||||+++.++
T Consensus         2 ~~ltG~N~~GKst~l~~i~   20 (185)
T smart00534        2 VIITGPNMGGKSTYLRQVG   20 (185)
T ss_pred             EEEECCCCCcHHHHHHHHH
Confidence            7899999999999999998

>PRK14530 adenylate kinase; Provisional

Probab=96.91  E-value=0.00088  Score=67.37  Aligned_cols=31  Identities=19%  Similarity=0.364  Sum_probs=27.3

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEEEE
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLYEW  209 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~viE~  209 (666)
                      +.++|.||||+||||+++.||+.+|+..+..
T Consensus         4 ~~I~i~G~pGsGKsT~~~~La~~~~~~~i~~   34 (215)
T PRK14530          4 PRILLLGAPGAGKGTQSSNLAEEFGVEHVTT   34 (215)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHhCCeEEec
Confidence            4688999999999999999999999876643

>cd03280 ABC_MutS2 MutS2 homologs in bacteria and eukaryotes

Probab=96.90  E-value=0.0052  Score=61.07  Aligned_cols=22  Identities=45%  Similarity=0.629  Sum_probs=20.3

Q ss_pred             cEEEEECCCCchHHHHHHHHHH
Q 005987          179 NVLVITGQAGVGKTATVRQIAS  200 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAk  200 (666)
                      +.++|+||.|+||||+.+.++.
T Consensus        29 ~~~~ltG~Ng~GKStll~~i~~   50 (200)
T cd03280          29 RVLVITGPNAGGKTVTLKTLGL   50 (200)
T ss_pred             eEEEEECCCCCChHHHHHHHHH
Confidence            5799999999999999999983

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

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

Probab=96.89  E-value=0.068  Score=56.93  Aligned_cols=49  Identities=8%  Similarity=0.091  Sum_probs=39.6

Q ss_pred             eeEEEeCCCCHHHHHHHHHHHHHHhCC---CCCHHHHHHHHHHcCCcHHHHH
Q 005987          328 ARKVALNPITNGSIKRTLSKICRQEQY---SLSTEQIDLVAQASGGDIRQAI  376 (666)
Q Consensus       328 ~~~I~F~p~s~~~i~kiL~~I~~~e~i---~v~~~~l~~Ia~~s~GDIR~AI  376 (666)
                      +..|.+.+++.++++.++.......-+   ..++...+.+...++|+.|...
T Consensus       256 ~~~i~v~~~s~~E~~~ll~yy~~~~~l~~~~~~~~~~e~~~~~s~GNp~el~  307 (309)
T PF10236_consen  256 VKPIEVPRLSKEEARSLLEYYADSGWLRSRVDEELVLEKLFLSSNGNPRELE  307 (309)
T ss_pred             CceEEeCCCCHHHHHHHHHHHHHCCccccCCCCHHHHHHHHHhcCCCHHHhc
Confidence            458999999999999999988776544   3466788888888999998754

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).

>TIGR01420 pilT_fam pilus retraction protein PilT

Probab=96.89  E-value=0.0036  Score=67.64  Aligned_cols=34  Identities=21%  Similarity=0.546  Sum_probs=26.9

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcC----CcEEEEcCC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLG----ARLYEWDTP  212 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg----~~viE~nas  212 (666)
                      ..++|+||+|+||||+++++++.+.    ..++.+..+
T Consensus       123 g~ili~G~tGSGKTT~l~al~~~i~~~~~~~i~tiEdp  160 (343)
T TIGR01420       123 GLILVTGPTGSGKSTTLASMIDYINKNAAGHIITIEDP  160 (343)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHhhCcCCCCEEEEEcCC
Confidence            5899999999999999999998774    345555443

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.

>COG1220 HslU ATP-dependent protease HslVU (ClpYQ), ATPase subunit [Posttranslational modification, protein turnover, chaperones]

Probab=96.89  E-value=0.0015  Score=68.35  Aligned_cols=63  Identities=22%  Similarity=0.364  Sum_probs=49.3

Q ss_pred             cccCHHHHHHHHHHHHHhhcCC------CCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCC
Q 005987          151 LAVQRKKVEEVRAWFEERLGDS------KDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPT  213 (666)
Q Consensus       151 Lvg~~k~i~el~~wL~~~~~~~------~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd  213 (666)
                      ++||+++.+.|.-.|.+.....      +...-++.+|+.||+|+|||..||.||+-.+..++-+.+.-
T Consensus        17 IIGQ~~AKkaVAIALRNR~RR~qL~~~lr~EV~PKNILMIGpTGVGKTEIARRLAkl~~aPFiKVEATK   85 (444)
T COG1220          17 IIGQDEAKKAVAIALRNRWRRMQLEEELRDEVTPKNILMIGPTGVGKTEIARRLAKLAGAPFIKVEATK   85 (444)
T ss_pred             hcCcHHHHHHHHHHHHHHHHHHhcCHHHhhccCccceEEECCCCCcHHHHHHHHHHHhCCCeEEEEeee
Confidence            6899999998887776432210      12233478999999999999999999999999999888764

>PRK06217 hypothetical protein; Validated

Probab=96.88  E-value=0.001  Score=65.15  Aligned_cols=31  Identities=29%  Similarity=0.358  Sum_probs=28.1

Q ss_pred             EEEEECCCCchHHHHHHHHHHHcCCcEEEEc
Q 005987          180 VLVITGQAGVGKTATVRQIASHLGARLYEWD  210 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkelg~~viE~n  210 (666)
                      .++|.|+||+||||+++.|++.+|+.+++.+
T Consensus         3 ~I~i~G~~GsGKSTla~~L~~~l~~~~~~~D   33 (183)
T PRK06217          3 RIHITGASGSGTTTLGAALAERLDIPHLDTD   33 (183)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHcCCcEEEcC
Confidence            5899999999999999999999998877654

>TIGR01313 therm_gnt_kin carbohydrate kinase, thermoresistant glucokinase family

Probab=96.87  E-value=0.00085  Score=64.17  Aligned_cols=27  Identities=37%  Similarity=0.671  Sum_probs=24.1

Q ss_pred             EEEECCCCchHHHHHHHHHHHcCCcEE
Q 005987          181 LVITGQAGVGKTATVRQIASHLGARLY  207 (666)
Q Consensus       181 LLL~GPpG~GKTtla~~LAkelg~~vi  207 (666)
                      ++|.||+||||||+++.|++.++..++
T Consensus         1 i~l~G~~GsGKSTla~~l~~~l~~~~v   27 (163)
T TIGR01313         1 FVLMGVAGSGKSTIASALAHRLGAKFI   27 (163)
T ss_pred             CEEECCCCCCHHHHHHHHHHhcCCeEE
Confidence            478999999999999999999986655

This model represents a subfamily of proteins that includes thermoresistant and thermosensitve isozymes of gluconate kinase (gluconokinase) in E. coli and other related proteins; members of this family are often named by similarity to the thermostable isozyme. These proteins show homology to shikimate kinases and adenylate kinases but not to gluconate kinases from the FGGY family of carbohydrate kinases.

>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=96.85  E-value=0.00096  Score=65.50  Aligned_cols=29  Identities=21%  Similarity=0.394  Sum_probs=26.4

Q ss_pred             EEEECCCCchHHHHHHHHHHHcCCcEEEE
Q 005987          181 LVITGQAGVGKTATVRQIASHLGARLYEW  209 (666)
Q Consensus       181 LLL~GPpG~GKTtla~~LAkelg~~viE~  209 (666)
                      ++|.||||+||||+++.||+.+|+.++..
T Consensus         2 I~i~G~pGsGKst~a~~La~~~~~~~i~~   30 (194)
T cd01428           2 ILLLGPPGSGKGTQAERLAKKYGLPHIST   30 (194)
T ss_pred             EEEECCCCCCHHHHHHHHHHHcCCeEEEC
Confidence            78999999999999999999999877653

This enzyme is required for the biosynthesis of ADP and is essential for homeostasis of adenosine phosphates.

>cd03287 ABC_MSH3_euk MutS3 homolog in eukaryotes

Probab=96.85  E-value=0.014  Score=59.14  Aligned_cols=22  Identities=36%  Similarity=0.460  Sum_probs=20.5

Q ss_pred             cEEEEECCCCchHHHHHHHHHH
Q 005987          179 NVLVITGQAGVGKTATVRQIAS  200 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAk  200 (666)
                      +.++|+||.|+||||+.+.++-
T Consensus        32 ~~~~itG~N~~GKStll~~i~~   53 (222)
T cd03287          32 YCQIITGPNMGGKSSYIRQVAL   53 (222)
T ss_pred             cEEEEECCCCCCHHHHHHHHHH
Confidence            5799999999999999999987

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

>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=96.85  E-value=0.009  Score=56.75  Aligned_cols=25  Identities=32%  Similarity=0.602  Sum_probs=22.8

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLG  203 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg  203 (666)
                      ..+.|.||+|+||||++++++..+.
T Consensus        26 ~~~~i~G~nGsGKStll~~l~g~~~   50 (157)
T cd00267          26 EIVALVGPNGSGKSTLLRAIAGLLK   50 (157)
T ss_pred             CEEEEECCCCCCHHHHHHHHhCCCC
Confidence            5899999999999999999998763

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.

>TIGR00064 ftsY signal recognition particle-docking protein FtsY

Probab=96.84  E-value=0.07  Score=55.74  Aligned_cols=34  Identities=35%  Similarity=0.567  Sum_probs=27.6

Q ss_pred             ccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcC
Q 005987          178 TNVLVITGQAGVGKTATVRQIASHL---GARLYEWDT  211 (666)
Q Consensus       178 ~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~na  211 (666)
                      ++.++|+||+|+||||++..||..+   |.+|.-+.+
T Consensus        72 ~~vi~l~G~~G~GKTTt~akLA~~l~~~g~~V~li~~  108 (272)
T TIGR00064        72 PNVILFVGVNGVGKTTTIAKLANKLKKQGKSVLLAAG  108 (272)
T ss_pred             CeEEEEECCCCCcHHHHHHHHHHHHHhcCCEEEEEeC
Confidence            3689999999999999999998877   666655544

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.

>PF13245 AAA_19: Part of AAA domain

Probab=96.83  E-value=0.0011  Score=55.35  Aligned_cols=24  Identities=42%  Similarity=0.688  Sum_probs=17.8

Q ss_pred             cEEEEECCCCchHHHHH-HHHHHHc
Q 005987          179 NVLVITGQAGVGKTATV-RQIASHL  202 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla-~~LAkel  202 (666)
                      +.+++.||||+|||+++ +.++..+
T Consensus        11 ~~~vv~g~pGtGKT~~~~~~i~~l~   35 (76)
T PF13245_consen   11 PLFVVQGPPGTGKTTTLAARIAELL   35 (76)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHH
Confidence            57888999999999554 5555544

>PRK04040 adenylate kinase; Provisional

Probab=96.83  E-value=0.0011  Score=65.33  Aligned_cols=29  Identities=34%  Similarity=0.598  Sum_probs=26.1

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc--CCcEE
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL--GARLY  207 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel--g~~vi  207 (666)
                      +.++|+|+|||||||+++.|++.+  ++.++
T Consensus         3 ~~i~v~G~pG~GKtt~~~~l~~~l~~~~~~~   33 (188)
T PRK04040          3 KVVVVTGVPGVGKTTVLNKALEKLKEDYKIV   33 (188)
T ss_pred             eEEEEEeCCCCCHHHHHHHHHHHhccCCeEE
Confidence            589999999999999999999999  66654

>cd00046 DEXDc DEAD-like helicases superfamily

Probab=96.82  E-value=0.0039  Score=56.33  Aligned_cols=24  Identities=21%  Similarity=0.184  Sum_probs=21.4

Q ss_pred             EEEEECCCCchHHHHHHHHHHHcC
Q 005987          180 VLVITGQAGVGKTATVRQIASHLG  203 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkelg  203 (666)
                      .++++||+|+|||+++..++.++.
T Consensus         2 ~~~i~~~~G~GKT~~~~~~~~~~~   25 (144)
T cd00046           2 DVLLAAPTGSGKTLAALLPILELL   25 (144)
T ss_pred             CEEEECCCCCchhHHHHHHHHHHH
Confidence            589999999999999988888773

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

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

Probab=96.81  E-value=0.014  Score=58.82  Aligned_cols=39  Identities=28%  Similarity=0.306  Sum_probs=29.7

Q ss_pred             CCCCccEEEEECCCCchHHHHHHHHHHHc---C------CcEEEEcCC
Q 005987          174 DKFSTNVLVITGQAGVGKTATVRQIASHL---G------ARLYEWDTP  212 (666)
Q Consensus       174 g~~~~k~LLL~GPpG~GKTtla~~LAkel---g------~~viE~nas  212 (666)
                      |-++..+..|+||||+|||+++..+|...   +      ..++.+...
T Consensus        15 G~~~g~v~~I~G~~GsGKT~l~~~ia~~~~~~~~~~g~~~~v~yi~~e   62 (226)
T cd01393          15 GIPTGRITEIFGEFGSGKTQLCLQLAVEAQLPGELGGLEGKVVYIDTE   62 (226)
T ss_pred             CCcCCcEEEEeCCCCCChhHHHHHHHHHhhcccccCCCcceEEEEecC
Confidence            44455799999999999999999888763   3      566666554

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.

>PRK06547 hypothetical protein; Provisional

Probab=96.81  E-value=0.0013  Score=63.98  Aligned_cols=31  Identities=29%  Similarity=0.475  Sum_probs=27.8

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEEEE
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLYEW  209 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~viE~  209 (666)
                      ..++|+||+|+||||+++.||+.++..++..
T Consensus        16 ~~i~i~G~~GsGKTt~a~~l~~~~~~~~~~~   46 (172)
T PRK06547         16 ITVLIDGRSGSGKTTLAGALAARTGFQLVHL   46 (172)
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHhCCCeecc
Confidence            5899999999999999999999998877754

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

Probab=96.81  E-value=0.055  Score=58.78  Aligned_cols=26  Identities=35%  Similarity=0.618  Sum_probs=22.9

Q ss_pred             ccEEEEECCCCchHHHHHHHHHHHcC
Q 005987          178 TNVLVITGQAGVGKTATVRQIASHLG  203 (666)
Q Consensus       178 ~k~LLL~GPpG~GKTtla~~LAkelg  203 (666)
                      ++++.|.||+|+||||++-.||..+.
T Consensus       203 ~~vi~LVGPTGVGKTTTlAKLAar~~  228 (407)
T COG1419         203 KRVIALVGPTGVGKTTTLAKLAARYV  228 (407)
T ss_pred             CcEEEEECCCCCcHHHHHHHHHHHHH
Confidence            47999999999999999888887764

>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=96.80  E-value=0.0022  Score=68.31  Aligned_cols=53  Identities=17%  Similarity=0.301  Sum_probs=45.4

Q ss_pred             cccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcC
Q 005987          149 EELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLG  203 (666)
Q Consensus       149 ~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg  203 (666)
                      +++.|-++.++++.++++++-..  .....++|+|.||+|+||||+++.|.+-+.
T Consensus        61 ~~~~G~~~~i~~lV~~fk~AA~g--~~~~krIl~L~GPvg~GKSsl~~~Lk~~le  113 (358)
T PF08298_consen   61 DEFYGMEETIERLVNYFKSAAQG--LEERKRILLLLGPVGGGKSSLAELLKRGLE  113 (358)
T ss_pred             ccccCcHHHHHHHHHHHHHHHhc--cCccceEEEEECCCCCCHHHHHHHHHHHhh
Confidence            48999999999999999976653  334458999999999999999999999873

PrkA possesses the A-motif of nucleotide-binding proteins and exhibits distant homology to eukaryotic protein kinases []. Note that many of these are hypothetical.

>TIGR03574 selen_PSTK L-seryl-tRNA(Sec) kinase, archaeal

Probab=96.80  E-value=0.0082  Score=61.75  Aligned_cols=31  Identities=26%  Similarity=0.521  Sum_probs=26.1

Q ss_pred             EEEEECCCCchHHHHHHHHHHHc---CCcEEEEc
Q 005987          180 VLVITGQAGVGKTATVRQIASHL---GARLYEWD  210 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkel---g~~viE~n  210 (666)
                      .++|+|+||+||||+++.||+.+   ++.++.++
T Consensus         1 LIvl~G~pGSGKST~a~~La~~l~~~~~~v~~i~   34 (249)
T TIGR03574         1 LIILTGLPGVGKSTFSKELAKKLSEKNIDVIILG   34 (249)
T ss_pred             CEEEEcCCCCCHHHHHHHHHHHHHHcCCceEEEc
Confidence            37899999999999999999987   56666554

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.

>PF01443 Viral_helicase1: Viral (Superfamily 1) RNA helicase; InterPro: IPR000606 This entry includes RNA and DNA helicases

Probab=96.80  E-value=0.0017  Score=65.75  Aligned_cols=22  Identities=23%  Similarity=0.573  Sum_probs=20.4

Q ss_pred             EEEECCCCchHHHHHHHHHHHc
Q 005987          181 LVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       181 LLL~GPpG~GKTtla~~LAkel  202 (666)
                      +++.|+|||||||+++.+++..
T Consensus         1 ~vv~G~pGsGKSt~i~~~~~~~   22 (234)
T PF01443_consen    1 IVVHGVPGSGKSTLIKKLLKDR   22 (234)
T ss_pred             CEEEcCCCCCHHHHHHHHHHhc
Confidence            4799999999999999999985

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

>TIGR02012 tigrfam_recA protein RecA

Probab=96.80  E-value=0.012  Score=62.61  Aligned_cols=39  Identities=18%  Similarity=0.148  Sum_probs=29.2

Q ss_pred             CCCCccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcCC
Q 005987          174 DKFSTNVLVITGQAGVGKTATVRQIASHL---GARLYEWDTP  212 (666)
Q Consensus       174 g~~~~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~nas  212 (666)
                      |-++.++++|+||||+||||++..++.+.   |..++.+.+.
T Consensus        51 Glp~G~iteI~G~~GsGKTtLaL~~~~~~~~~g~~v~yId~E   92 (321)
T TIGR02012        51 GLPRGRIIEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAE   92 (321)
T ss_pred             CCcCCeEEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEEccc
Confidence            44555799999999999999987766554   6666666543

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.

>PRK14528 adenylate kinase; Provisional

Probab=96.77  E-value=0.0013  Score=64.63  Aligned_cols=31  Identities=16%  Similarity=0.321  Sum_probs=27.3

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEEEE
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLYEW  209 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~viE~  209 (666)
                      +.+++.||||+||||+++.||+.+|+.++..
T Consensus         2 ~~i~i~G~pGsGKtt~a~~la~~~~~~~is~   32 (186)
T PRK14528          2 KNIIFMGPPGAGKGTQAKILCERLSIPQIST   32 (186)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHhCCCeeeC
Confidence            3589999999999999999999999877643

>PRK01184 hypothetical protein; Provisional

Probab=96.76  E-value=0.0013  Score=64.18  Aligned_cols=30  Identities=23%  Similarity=0.427  Sum_probs=26.0

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEEEE
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLYEW  209 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~viE~  209 (666)
                      .+++|+||||+||||+++ +++++|+.++..
T Consensus         2 ~~i~l~G~~GsGKsT~a~-~~~~~g~~~i~~   31 (184)
T PRK01184          2 KIIGVVGMPGSGKGEFSK-IAREMGIPVVVM   31 (184)
T ss_pred             cEEEEECCCCCCHHHHHH-HHHHcCCcEEEh
Confidence            478999999999999987 789999887654

>PRK02496 adk adenylate kinase; Provisional

Probab=96.76  E-value=0.0013  Score=64.43  Aligned_cols=30  Identities=27%  Similarity=0.340  Sum_probs=26.7

Q ss_pred             EEEEECCCCchHHHHHHHHHHHcCCcEEEE
Q 005987          180 VLVITGQAGVGKTATVRQIASHLGARLYEW  209 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkelg~~viE~  209 (666)
                      .++|.||||+||||+++.||+.+|+..+..
T Consensus         3 ~i~i~G~pGsGKst~a~~la~~~~~~~i~~   32 (184)
T PRK02496          3 RLIFLGPPGAGKGTQAVVLAEHLHIPHIST   32 (184)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCcEEEh
Confidence            488999999999999999999999877643

>PRK14527 adenylate kinase; Provisional

Probab=96.76  E-value=0.0011  Score=65.34  Aligned_cols=30  Identities=27%  Similarity=0.551  Sum_probs=26.9

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEEE
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLYE  208 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~viE  208 (666)
                      .++++.||||+||||+++.||+.+++..+.
T Consensus         7 ~~i~i~G~pGsGKsT~a~~La~~~~~~~is   36 (191)
T PRK14527          7 KVVIFLGPPGAGKGTQAERLAQELGLKKLS   36 (191)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHhCCCCCC
Confidence            689999999999999999999999876553

>PRK13946 shikimate kinase; Provisional

Probab=96.74  E-value=0.0014  Score=64.21  Aligned_cols=31  Identities=29%  Similarity=0.529  Sum_probs=28.4

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEEEE
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLYEW  209 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~viE~  209 (666)
                      +.++|.|++||||||+++.||+.+|+.++..
T Consensus        11 ~~I~l~G~~GsGKsti~~~LA~~Lg~~~id~   41 (184)
T PRK13946         11 RTVVLVGLMGAGKSTVGRRLATMLGLPFLDA   41 (184)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHcCCCeECc
Confidence            6899999999999999999999999987743

>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=96.73  E-value=0.013  Score=61.16  Aligned_cols=32  Identities=19%  Similarity=0.378  Sum_probs=22.9

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc---CCcEEEEc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL---GARLYEWD  210 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel---g~~viE~n  210 (666)
                      +.++|+|.||+||||+++.|++.+   +.+++.++
T Consensus         2 pLiil~G~P~SGKTt~a~~L~~~~~~~~~~v~~i~   36 (270)
T PF08433_consen    2 PLIILCGLPCSGKTTRAKELKKYLEEKGKEVVIIS   36 (270)
T ss_dssp             -EEEEE--TTSSHHHHHHHHHHHHHHTT--EEEE-
T ss_pred             EEEEEEcCCCCcHHHHHHHHHHHHHhcCCEEEEEc
Confidence            379999999999999999999976   56666665

The Elongator complex has histone acetyltransferase activity. ; PDB: 3ADB_B 3ADC_B 3A4M_B 3A4N_B 3AM1_A 3A4L_B 3ADD_A.

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

Probab=96.73  E-value=0.0013  Score=65.93  Aligned_cols=23  Identities=39%  Similarity=0.684  Sum_probs=18.5

Q ss_pred             EEEEECCCCchHHHHHHHHHHHc
Q 005987          180 VLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      +.++.||||||||+++..++..+
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            59999999999998887777766

>TIGR02538 type_IV_pilB type IV-A pilus assembly ATPase PilB

Probab=96.72  E-value=0.005  Score=70.95  Aligned_cols=61  Identities=15%  Similarity=0.275  Sum_probs=46.1

Q ss_pred             CCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcC---CcEEEEcCCC
Q 005987          144 KPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLG---ARLYEWDTPT  213 (666)
Q Consensus       144 ~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg---~~viE~nasd  213 (666)
                      .+.++++|-..+..++.+...+...         ..++|++||+|+||||+++++.++++   ..++.+..|.
T Consensus       291 ~~~~l~~lg~~~~~~~~l~~~~~~~---------~Glilv~G~tGSGKTTtl~a~l~~~~~~~~~i~tiEdpv  354 (564)
T TIGR02538       291 AQLDIDKLGFEPDQKALFLEAIHKP---------QGMVLVTGPTGSGKTVSLYTALNILNTEEVNISTAEDPV  354 (564)
T ss_pred             ccCCHHHcCCCHHHHHHHHHHHHhc---------CCeEEEECCCCCCHHHHHHHHHHhhCCCCceEEEecCCc
Confidence            3457888888888888887776541         14899999999999999999888874   3455555443

This model describes a protein of type IV pilus biogenesis designated PilB in Pseudomonas aeruginosa but PilF in Neisseria gonorrhoeae; the more common usage, reflected here, is PilB. This protein is an ATPase involved in protein export for pilin assembly and is closely related to GspE (TIGR02533) of type II secretion, also called the main terminal branch of the general secretion pathway. Note that type IV pilus systems are often divided into type IV-A and IV-B, with the latter group including bundle-forming pilus, mannose-sensitive hemagglutinin, etc. Members of this family are found in type IV-A systems.

>cd00984 DnaB_C DnaB helicase C terminal domain

Probab=96.71  E-value=0.018  Score=58.68  Aligned_cols=40  Identities=20%  Similarity=0.336  Sum_probs=30.4

Q ss_pred             CCCCccEEEEECCCCchHHHHHHHHHHHc----CCcEEEEcCCC
Q 005987          174 DKFSTNVLVITGQAGVGKTATVRQIASHL----GARLYEWDTPT  213 (666)
Q Consensus       174 g~~~~k~LLL~GPpG~GKTtla~~LAkel----g~~viE~nasd  213 (666)
                      |-.+...++|.||||+|||+++..+|..+    |..++.++.-.
T Consensus         9 Gl~~G~l~lI~G~~G~GKT~~~~~~~~~~~~~~g~~vly~s~E~   52 (242)
T cd00984           9 GLQPGDLIIIAARPSMGKTAFALNIAENIAKKQGKPVLFFSLEM   52 (242)
T ss_pred             CCCCCeEEEEEeCCCCCHHHHHHHHHHHHHHhCCCceEEEeCCC
Confidence            44455689999999999999987776654    77877776443

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.

>PTZ00088 adenylate kinase 1; Provisional

Probab=96.71  E-value=0.0014  Score=66.59  Aligned_cols=31  Identities=19%  Similarity=0.309  Sum_probs=27.7

Q ss_pred             EEEEECCCCchHHHHHHHHHHHcCCcEEEEc
Q 005987          180 VLVITGQAGVGKTATVRQIASHLGARLYEWD  210 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkelg~~viE~n  210 (666)
                      .++|.||||+||||+++.||+.+|+.++...
T Consensus         8 rIvl~G~PGsGK~T~a~~La~~~g~~~is~g   38 (229)
T PTZ00088          8 KIVLFGAPGVGKGTFAEILSKKENLKHINMG   38 (229)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHhCCcEEECC
Confidence            3899999999999999999999998877654

>COG1126 GlnQ ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]

Probab=96.70  E-value=0.01  Score=58.88  Aligned_cols=41  Identities=12%  Similarity=0.189  Sum_probs=28.0

Q ss_pred             CceEEEEeCCCCCcchhHHHHHHHHHHHHHhcCCCceEEEEec
Q 005987          260 SSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHIPTAVVLTE  302 (666)
Q Consensus       260 ~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~~~PiViIit~  302 (666)
                      .|.++|+||.-..-...-.+.+.+++..+.+.+.  +.+|+|.
T Consensus       154 ~P~vmLFDEPTSALDPElv~EVL~vm~~LA~eGm--TMivVTH  194 (240)
T COG1126         154 DPKVMLFDEPTSALDPELVGEVLDVMKDLAEEGM--TMIIVTH  194 (240)
T ss_pred             CCCEEeecCCcccCCHHHHHHHHHHHHHHHHcCC--eEEEEec
Confidence            4789999998654444455667777888877774  4455553

>PRK03731 aroL shikimate kinase II; Reviewed

Probab=96.70  E-value=0.0017  Score=62.60  Aligned_cols=31  Identities=32%  Similarity=0.471  Sum_probs=27.7

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEEEE
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLYEW  209 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~viE~  209 (666)
                      +.++|+|++||||||+++.||+.+|+.++..
T Consensus         3 ~~i~~~G~~GsGKst~~~~la~~lg~~~~d~   33 (171)
T PRK03731          3 QPLFLVGARGCGKTTVGMALAQALGYRFVDT   33 (171)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHhCCCEEEc
Confidence            3588899999999999999999999987754

>PLN02200 adenylate kinase family protein

Probab=96.69  E-value=0.0017  Score=66.34  Aligned_cols=29  Identities=21%  Similarity=0.397  Sum_probs=26.3

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEE
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLY  207 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~vi  207 (666)
                      .+++|.||||+||||+++.||+.+|+..+
T Consensus        44 ~ii~I~G~PGSGKsT~a~~La~~~g~~hi   72 (234)
T PLN02200         44 FITFVLGGPGSGKGTQCEKIVETFGFKHL   72 (234)
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHhCCeEE
Confidence            57999999999999999999999987654

>PRK05800 cobU adenosylcobinamide kinase/adenosylcobinamide-phosphate guanylyltransferase; Validated

Probab=96.69  E-value=0.0078  Score=58.34  Aligned_cols=33  Identities=24%  Similarity=0.411  Sum_probs=28.7

Q ss_pred             EEEEECCCCchHHHHHHHHHHHcCCcEEEEcCC
Q 005987          180 VLVITGQAGVGKTATVRQIASHLGARLYEWDTP  212 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkelg~~viE~nas  212 (666)
                      .++++||||+|||+++..++.+++..++.+...
T Consensus         3 ~ili~G~~~sGKS~~a~~l~~~~~~~~~~iat~   35 (170)
T PRK05800          3 LILVTGGARSGKSRFAERLAAQSGLQVLYIATA   35 (170)
T ss_pred             EEEEECCCCccHHHHHHHHHHHcCCCcEeCcCC
Confidence            689999999999999999999988777766553

>TIGR01448 recD_rel helicase, putative, RecD/TraA family

Probab=96.69  E-value=0.021  Score=67.77  Aligned_cols=35  Identities=34%  Similarity=0.503  Sum_probs=26.2

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc---C-CcEEEEcCCC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL---G-ARLYEWDTPT  213 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel---g-~~viE~nasd  213 (666)
                      +.++|+|+|||||||+++++.+.+   + ..-+.+.+|.
T Consensus       339 ~~~iitGgpGTGKTt~l~~i~~~~~~~~~~~~v~l~ApT  377 (720)
T TIGR01448       339 KVVILTGGPGTGKTTITRAIIELAEELGGLLPVGLAAPT  377 (720)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHHcCCCceEEEEeCc
Confidence            589999999999999999987765   3 1234445554

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.

>PRK13948 shikimate kinase; Provisional

Probab=96.68  E-value=0.002  Score=63.16  Aligned_cols=33  Identities=18%  Similarity=0.285  Sum_probs=29.5

Q ss_pred             ccEEEEECCCCchHHHHHHHHHHHcCCcEEEEc
Q 005987          178 TNVLVITGQAGVGKTATVRQIASHLGARLYEWD  210 (666)
Q Consensus       178 ~k~LLL~GPpG~GKTtla~~LAkelg~~viE~n  210 (666)
                      +..++|.|++||||||+++.||+.+|+.++..+
T Consensus        10 ~~~I~LiG~~GsGKSTvg~~La~~lg~~~iD~D   42 (182)
T PRK13948         10 VTWVALAGFMGTGKSRIGWELSRALMLHFIDTD   42 (182)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHcCCCEEECC
Confidence            368999999999999999999999999888543

>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=96.68  E-value=0.022  Score=55.54  Aligned_cols=24  Identities=42%  Similarity=0.681  Sum_probs=22.2

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      ..+.|.||+|+||||++++++..+
T Consensus        26 e~~~l~G~nGsGKSTLl~~l~Gl~   49 (177)
T cd03222          26 EVIGIVGPNGTGKTTAVKILAGQL   49 (177)
T ss_pred             CEEEEECCCCChHHHHHHHHHcCC
Confidence            589999999999999999999875

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.

>TIGR00959 ffh signal recognition particle protein

Probab=96.67  E-value=0.17  Score=56.15  Aligned_cols=36  Identities=28%  Similarity=0.418  Sum_probs=28.5

Q ss_pred             ccEEEEECCCCchHHHHHHHHHHHc----CCcEEEEcCCC
Q 005987          178 TNVLVITGQAGVGKTATVRQIASHL----GARLYEWDTPT  213 (666)
Q Consensus       178 ~k~LLL~GPpG~GKTtla~~LAkel----g~~viE~nasd  213 (666)
                      +.+++++||+|+||||++..||..+    |..+.-+.+-.
T Consensus        99 p~vi~~vG~~GsGKTTtaakLA~~l~~~~g~kV~lV~~D~  138 (428)
T TIGR00959        99 PTVILMVGLQGSGKTTTCGKLAYYLKKKQGKKVLLVACDL  138 (428)
T ss_pred             CEEEEEECCCCCcHHHHHHHHHHHHHHhCCCeEEEEeccc
Confidence            3689999999999999988888764    56676666543

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.

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

Probab=96.67  E-value=0.017  Score=55.85  Aligned_cols=33  Identities=27%  Similarity=0.452  Sum_probs=27.9

Q ss_pred             EEEEECCCCchHHHHHHHHHHHcCCcEEEEcCC
Q 005987          180 VLVITGQAGVGKTATVRQIASHLGARLYEWDTP  212 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkelg~~viE~nas  212 (666)
                      +.|++||+|+|||++|..+|...+.+++.+...
T Consensus         1 ~~li~G~~~sGKS~~a~~~~~~~~~~~~y~at~   33 (169)
T cd00544           1 IILVTGGARSGKSRFAERLAAELGGPVTYIATA   33 (169)
T ss_pred             CEEEECCCCCCHHHHHHHHHHhcCCCeEEEEcc
Confidence            368999999999999999999877777777544

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.

>PRK09862 putative ATP-dependent protease; Provisional

Probab=96.67  E-value=0.015  Score=65.69  Aligned_cols=47  Identities=21%  Similarity=0.285  Sum_probs=35.4

Q ss_pred             CCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc
Q 005987          146 RSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       146 ~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      ..+.++.|++..++.+.-.+.       +   .++++|.||||+|||++++.++..+
T Consensus       188 ~d~~~v~Gq~~~~~al~laa~-------~---G~~llliG~~GsGKTtLak~L~gll  234 (506)
T PRK09862        188 HDLSDVIGQEQGKRGLEITAA-------G---GHNLLLIGPPGTGKTMLASRINGLL  234 (506)
T ss_pred             cCeEEEECcHHHHhhhheecc-------C---CcEEEEECCCCCcHHHHHHHHhccC
Confidence            478888888776655432111       1   2689999999999999999999876

>COG1117 PstB ABC-type phosphate transport system, ATPase component [Inorganic ion transport and metabolism]

Probab=96.66  E-value=0.015  Score=57.65  Aligned_cols=24  Identities=25%  Similarity=0.445  Sum_probs=21.5

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      ++--|.||+||||||++|++-+-.
T Consensus        34 ~VTAlIGPSGcGKST~LR~lNRmn   57 (253)
T COG1117          34 KVTALIGPSGCGKSTLLRCLNRMN   57 (253)
T ss_pred             ceEEEECCCCcCHHHHHHHHHhhc
Confidence            678899999999999999997764

>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=96.65  E-value=0.002  Score=52.61  Aligned_cols=22  Identities=36%  Similarity=0.735  Sum_probs=20.7

Q ss_pred             EEEECCCCchHHHHHHHHHHHc
Q 005987          181 LVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       181 LLL~GPpG~GKTtla~~LAkel  202 (666)
                      +.+.|+||+||||+++.|++.+
T Consensus         2 i~i~G~~gsGKst~~~~l~~~l   23 (69)
T cd02019           2 IAITGGSGSGKSTVAKKLAEQL   23 (69)
T ss_pred             EEEECCCCCCHHHHHHHHHHHh
Confidence            6789999999999999999996

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.

>cd04138 H_N_K_Ras_like H-Ras/N-Ras/K-Ras subfamily

Probab=96.65  E-value=0.036  Score=51.85  Aligned_cols=21  Identities=43%  Similarity=0.691  Sum_probs=19.0

Q ss_pred             EEEECCCCchHHHHHHHHHHH
Q 005987          181 LVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       181 LLL~GPpG~GKTtla~~LAke  201 (666)
                      +++.|++|+||||+++.++..
T Consensus         4 i~iiG~~~vGKTsl~~~~~~~   24 (162)
T cd04138           4 LVVVGAGGVGKSALTIQLIQN   24 (162)
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            788899999999999999864

H-Ras, N-Ras, and K-Ras4A/4B are the prototypical members of the Ras family. These isoforms generate distinct signal outputs despite interacting with a common set of activators and effectors, and are strongly associated with oncogenic progression in tumor initiation. Mutated versions of Ras that are insensitive to GAP stimulation (and are therefore constitutively active) are found in a significant fraction of human cancers. Many Ras guanine nucleotide exchange factors (GEFs) have been identified. They are sequestered in the cytosol until activation by growth factors triggers recruitment to the plasma membrane or Golgi, where the GEF colocalizes with Ras. Active (GTP-bound) Ras interacts with several effector proteins that stimulate a variety of diverse cytoplasmic signaling activities. Some are known to positively mediate the oncogenic properties of Ras, including Raf, phosphatidylinositol 3-kinase (PI3K), RalGEFs, and Tiam1.

>COG0703 AroK Shikimate kinase [Amino acid transport and metabolism]

Probab=96.65  E-value=0.0016  Score=62.76  Aligned_cols=31  Identities=26%  Similarity=0.365  Sum_probs=27.9

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEEEE
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLYEW  209 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~viE~  209 (666)
                      +.++|.|++|+||||+.+.||+.|++.++-.
T Consensus         3 ~~IvLiG~mGaGKSTIGr~LAk~L~~~F~D~   33 (172)
T COG0703           3 MNIVLIGFMGAGKSTIGRALAKALNLPFIDT   33 (172)
T ss_pred             ccEEEEcCCCCCHhHHHHHHHHHcCCCcccc
Confidence            4699999999999999999999999987743

>TIGR01447 recD exodeoxyribonuclease V, alpha subunit

Probab=96.64  E-value=0.011  Score=68.35  Aligned_cols=24  Identities=46%  Similarity=0.625  Sum_probs=20.9

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      +..+|+|+|||||||++..+...+
T Consensus       161 ~~~vitGgpGTGKTt~v~~ll~~l  184 (586)
T TIGR01447       161 NFSLITGGPGTGKTTTVARLLLAL  184 (586)
T ss_pred             CeEEEEcCCCCCHHHHHHHHHHHH
Confidence            589999999999999988876654

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.

>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=96.64  E-value=0.0013  Score=59.57  Aligned_cols=22  Identities=36%  Similarity=0.643  Sum_probs=21.0

Q ss_pred             EEEECCCCchHHHHHHHHHHHc
Q 005987          181 LVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       181 LLL~GPpG~GKTtla~~LAkel  202 (666)
                      ++|+|+||+||||+++.|++.+
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            5899999999999999999998

...

>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=96.64  E-value=0.027  Score=54.92  Aligned_cols=23  Identities=30%  Similarity=0.433  Sum_probs=20.6

Q ss_pred             cEEEEECCCCchHHHHHHHHHHH
Q 005987          179 NVLVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAke  201 (666)
                      ..+.|.||+||||||+.++++..
T Consensus        22 ~~~~l~G~nG~GKSTLl~~il~~   44 (176)
T cd03238          22 VLVVVTGVSGSGKSTLVNEGLYA   44 (176)
T ss_pred             CEEEEECCCCCCHHHHHHHHhhc
Confidence            58999999999999999998643

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.

>PRK04182 cytidylate kinase; Provisional

Probab=96.63  E-value=0.0019  Score=62.50  Aligned_cols=29  Identities=34%  Similarity=0.634  Sum_probs=26.4

Q ss_pred             EEEEECCCCchHHHHHHHHHHHcCCcEEE
Q 005987          180 VLVITGQAGVGKTATVRQIASHLGARLYE  208 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkelg~~viE  208 (666)
                      +++|+|++||||||+++.||+.+|+.++.
T Consensus         2 ~I~i~G~~GsGKstia~~la~~lg~~~id   30 (180)
T PRK04182          2 IITISGPPGSGKTTVARLLAEKLGLKHVS   30 (180)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHcCCcEec
Confidence            58999999999999999999999987663

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

Probab=96.63  E-value=0.0017  Score=71.28  Aligned_cols=48  Identities=17%  Similarity=0.276  Sum_probs=39.5

Q ss_pred             CCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc
Q 005987          145 PRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       145 P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      ...|.|+.||+...+.+.-...       |.   +.|||+||||||||.+|+.+..-|
T Consensus       175 ~~D~~DV~GQ~~AKrAleiAAA-------Gg---HnLl~~GpPGtGKTmla~Rl~~lL  222 (490)
T COG0606         175 APDFKDVKGQEQAKRALEIAAA-------GG---HNLLLVGPPGTGKTMLASRLPGLL  222 (490)
T ss_pred             CcchhhhcCcHHHHHHHHHHHh-------cC---CcEEEecCCCCchHHhhhhhcccC
Confidence            4489999999999888766544       22   679999999999999999887765

>COG3604 FhlA Transcriptional regulator containing GAF, AAA-type ATPase, and DNA binding domains [Transcription / Signal transduction mechanisms]

Probab=96.62  E-value=0.075  Score=58.79  Aligned_cols=208  Identities=16%  Similarity=0.213  Sum_probs=111.9

Q ss_pred             CccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcCCCch-hh--hhh
Q 005987          147 SLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL---GARLYEWDTPTPT-IW--QEY  220 (666)
Q Consensus       147 sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~nasd~~-~~--~e~  220 (666)
                      .+.+++|+...+.++.+-++-...   ..   -.+||.|.+||||--.|++|-+.-   +-.++.+|+..-. ..  .|.
T Consensus       221 ~~~~iIG~S~am~~ll~~i~~VA~---Sd---~tVLi~GETGtGKElvAraIH~~S~R~~kPfV~~NCAAlPesLlESEL  294 (550)
T COG3604         221 EVGGIIGRSPAMRQLLKEIEVVAK---SD---STVLIRGETGTGKELVARAIHQLSPRRDKPFVKLNCAALPESLLESEL  294 (550)
T ss_pred             ccccceecCHHHHHHHHHHHHHhc---CC---CeEEEecCCCccHHHHHHHHHhhCcccCCCceeeeccccchHHHHHHH
Confidence            467899999999999988875432   11   369999999999999999987764   4567888886411 10  111


Q ss_pred             hhcccCCccccchhHHHHH-HHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcCC------
Q 005987          221 MHNCKTGLEYTSKLDEFEN-FVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTH------  293 (666)
Q Consensus       221 l~~~~~g~~~~s~~~~f~~-fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~~------  293 (666)
                      +.. ..|        .|.. +-.+..+|..    .     .+--||+|||-.+.-.     ++.-|+..++.+.      
T Consensus       295 FGH-eKG--------AFTGA~~~r~GrFEl----A-----dGGTLFLDEIGelPL~-----lQaKLLRvLQegEieRvG~  351 (550)
T COG3604         295 FGH-EKG--------AFTGAINTRRGRFEL----A-----DGGTLFLDEIGELPLA-----LQAKLLRVLQEGEIERVGG  351 (550)
T ss_pred             hcc-ccc--------ccccchhccCcceee----c-----CCCeEechhhccCCHH-----HHHHHHHHHhhcceeecCC
Confidence            111 001        0000 0111111110    0     1236899999876532     2222333333321      


Q ss_pred             -Cce---EEEEecCCCCCCccchhhhhhHHHH-HHhhcCeeEEEeCCCCH-----HHHH-HHHHHHHHHhC---CCCCHH
Q 005987          294 -IPT---AVVLTECGKADSVDSTAQSFEELQS-ILVDAGARKVALNPITN-----GSIK-RTLSKICRQEQ---YSLSTE  359 (666)
Q Consensus       294 -~Pi---ViIit~~~~~~s~d~~~r~l~~L~s-~L~r~r~~~I~F~p~s~-----~~i~-kiL~~I~~~e~---i~v~~~  359 (666)
                       .|+   |-|+++++.+-..--...   ..++ +.-|....-|.++|+-.     -.+. .++++++...|   +.++++
T Consensus       352 ~r~ikVDVRiIAATNRDL~~~V~~G---~FRaDLYyRLsV~Pl~lPPLRER~~DIplLA~~Fle~~~~~~gr~~l~ls~~  428 (550)
T COG3604         352 DRTIKVDVRVIAATNRDLEEMVRDG---EFRADLYYRLSVFPLELPPLRERPEDIPLLAGYFLEKFRRRLGRAILSLSAE  428 (550)
T ss_pred             CceeEEEEEEEeccchhHHHHHHcC---cchhhhhhcccccccCCCCcccCCccHHHHHHHHHHHHHHhcCCcccccCHH
Confidence             121   233344332100000000   0111 11121233355555532     2233 34555555544   468999


Q ss_pred             HHHHHHHH-cCCcHHHHHHHHHHHhcCC
Q 005987          360 QIDLVAQA-SGGDIRQAITSLQFSSLKQ  386 (666)
Q Consensus       360 ~l~~Ia~~-s~GDIR~AIn~LQf~~~~~  386 (666)
                      +++.|... -.|++|...|.++-+++..
T Consensus       429 Al~~L~~y~wPGNVRELen~veRavlla  456 (550)
T COG3604         429 ALELLSSYEWPGNVRELENVVERAVLLA  456 (550)
T ss_pred             HHHHHHcCCCCCcHHHHHHHHHHHHHHh
Confidence            99999876 4699999999999988743

>PRK05057 aroK shikimate kinase I; Reviewed

Probab=96.61  E-value=0.0023  Score=62.15  Aligned_cols=32  Identities=31%  Similarity=0.586  Sum_probs=28.4

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEEEEc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLYEWD  210 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~viE~n  210 (666)
                      +.++|.||+|+||||+++.||+.+++.++...
T Consensus         5 ~~I~liG~~GaGKStl~~~La~~l~~~~vd~D   36 (172)
T PRK05057          5 RNIFLVGPMGAGKSTIGRQLAQQLNMEFYDSD   36 (172)
T ss_pred             CEEEEECCCCcCHHHHHHHHHHHcCCcEEECC
Confidence            47999999999999999999999998877543

>TIGR01351 adk adenylate kinases

Probab=96.61  E-value=0.0019  Score=64.69  Aligned_cols=29  Identities=31%  Similarity=0.468  Sum_probs=26.2

Q ss_pred             EEEECCCCchHHHHHHHHHHHcCCcEEEE
Q 005987          181 LVITGQAGVGKTATVRQIASHLGARLYEW  209 (666)
Q Consensus       181 LLL~GPpG~GKTtla~~LAkelg~~viE~  209 (666)
                      ++|.||||+||||+++.||+.+|+.++..
T Consensus         2 I~i~G~pGsGKsT~a~~La~~~g~~~is~   30 (210)
T TIGR01351         2 LVLLGPPGSGKGTQAKRIAEKYGLPHIST   30 (210)
T ss_pred             EEEECCCCCCHHHHHHHHHHHcCCCeeeh
Confidence            78999999999999999999999877753

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.

>smart00173 RAS Ras subfamily of RAS small GTPases

Probab=96.60  E-value=0.036  Score=52.39  Aligned_cols=21  Identities=43%  Similarity=0.621  Sum_probs=18.9

Q ss_pred             EEEECCCCchHHHHHHHHHHH
Q 005987          181 LVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       181 LLL~GPpG~GKTtla~~LAke  201 (666)
                      +++.|++|+||||++..+...
T Consensus         3 i~v~G~~~~GKTsli~~~~~~   23 (164)
T smart00173        3 LVVLGSGGVGKSALTIQFVQG   23 (164)
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            678899999999999999864

Similar in fold and function to the bacterial EF-Tu GTPase. p21Ras couples receptor Tyr kinases and G protein receptors to protein kinase cascades

>KOG1970 consensus Checkpoint RAD17-RFC complex, RAD17/RAD24 component [Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]

Probab=96.60  E-value=0.00047  Score=76.17  Aligned_cols=46  Identities=35%  Similarity=0.518  Sum_probs=40.0

Q ss_pred             ccchhhhhhhhcccccccccccccCcccccCccccccccccccccCCCCccccccccc
Q 005987            4 SLSFEKFDEVLNGSKVSNVIWNQENDSALGSSSTQQLWTDKYKLCSLEEPDVQKKNVE   61 (666)
Q Consensus         4 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   61 (666)
                      +..|+.|++..+   |.         .+.......++|++||+|+.+|||+||||||.
T Consensus        47 ~~d~~a~~d~~~---~~---------l~~~~~d~~elW~eKy~P~t~eeLAVHkkKI~   92 (634)
T KOG1970|consen   47 EEDFEAFDDEES---VH---------LNNEKEDEFELWVEKYKPRTLEELAVHKKKIS   92 (634)
T ss_pred             hhhhhhhchhhh---cc---------cCCCCccccchhHHhcCcccHHHHhhhHHhHH
Confidence            567888888877   66         67777888999999999999999999999986

>PRK00279 adk adenylate kinase; Reviewed

Probab=96.59  E-value=0.002  Score=64.76  Aligned_cols=30  Identities=27%  Similarity=0.398  Sum_probs=26.9

Q ss_pred             EEEEECCCCchHHHHHHHHHHHcCCcEEEE
Q 005987          180 VLVITGQAGVGKTATVRQIASHLGARLYEW  209 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkelg~~viE~  209 (666)
                      .+++.||||+||||+++.||+.+|+..+..
T Consensus         2 ~I~v~G~pGsGKsT~a~~la~~~~~~~is~   31 (215)
T PRK00279          2 RLILLGPPGAGKGTQAKFIAEKYGIPHIST   31 (215)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCcEEEC
Confidence            388999999999999999999999877753

>PRK13900 type IV secretion system ATPase VirB11; Provisional

Probab=96.59  E-value=0.067  Score=57.52  Aligned_cols=44  Identities=20%  Similarity=0.373  Sum_probs=31.4

Q ss_pred             HHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcC--CcEEEE
Q 005987          160 EVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLG--ARLYEW  209 (666)
Q Consensus       160 el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg--~~viE~  209 (666)
                      .+..+|..+..   ++   +.+|++||+|+||||++++|+..+.  ..++.+
T Consensus       148 ~~~~~L~~~v~---~~---~nili~G~tgSGKTTll~aL~~~ip~~~ri~ti  193 (332)
T PRK13900        148 KIKEFLEHAVI---SK---KNIIISGGTSTGKTTFTNAALREIPAIERLITV  193 (332)
T ss_pred             HHHHHHHHHHH---cC---CcEEEECCCCCCHHHHHHHHHhhCCCCCeEEEe
Confidence            34555554443   21   5799999999999999999999884  344443

>TIGR00416 sms DNA repair protein RadA

Probab=96.59  E-value=0.01  Score=66.53  Aligned_cols=38  Identities=21%  Similarity=0.402  Sum_probs=29.7

Q ss_pred             CCCCccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcC
Q 005987          174 DKFSTNVLVITGQAGVGKTATVRQIASHL---GARLYEWDT  211 (666)
Q Consensus       174 g~~~~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~na  211 (666)
                      |-++...++|+|+||+||||++..+|..+   +..++.+..
T Consensus        90 Gi~~GsvilI~G~pGsGKTTL~lq~a~~~a~~g~kvlYvs~  130 (454)
T TIGR00416        90 GIVPGSLILIGGDPGIGKSTLLLQVACQLAKNQMKVLYVSG  130 (454)
T ss_pred             CccCCeEEEEEcCCCCCHHHHHHHHHHHHHhcCCcEEEEEC
Confidence            44555789999999999999999887765   456666654

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)).

>TIGR00767 rho transcription termination factor Rho

Probab=96.57  E-value=0.0065  Score=66.10  Aligned_cols=25  Identities=24%  Similarity=0.310  Sum_probs=22.8

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLG  203 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg  203 (666)
                      ..++|.||||+||||+++.+++.+.
T Consensus       169 q~~~IvG~~g~GKTtL~~~i~~~I~  193 (415)
T TIGR00767       169 QRGLIVAPPKAGKTVLLQKIAQAIT  193 (415)
T ss_pred             CEEEEECCCCCChhHHHHHHHHhhc
Confidence            5799999999999999999999863

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

>cd04139 RalA_RalB RalA/RalB subfamily

Probab=96.57  E-value=0.07  Score=50.07  Aligned_cols=21  Identities=33%  Similarity=0.582  Sum_probs=19.0

Q ss_pred             EEEECCCCchHHHHHHHHHHH
Q 005987          181 LVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       181 LLL~GPpG~GKTtla~~LAke  201 (666)
                      +++.|+||+||||+++.+...
T Consensus         3 i~~~G~~~~GKTsl~~~l~~~   23 (164)
T cd04139           3 VIVVGAGGVGKSALTLQFMYD   23 (164)
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            789999999999999999754

The Ral (Ras-like) subfamily consists of the highly homologous RalA and RalB. Ral proteins are believed to play a crucial role in tumorigenesis, metastasis, endocytosis, and actin cytoskeleton dynamics. Despite their high sequence similarity (80% sequence identity), nonoverlapping and opposing functions have been assigned to RalA and RalBs in tumor migration. In human bladder and prostate cancer cells, RalB promotes migration while RalA inhibits it. A Ral-specific set of GEFs has been identified that are activated by Ras binding. This RalGEF activity is enhanced by Ras binding to another of its target proteins, phosphatidylinositol 3-kinase (PI3K). Ral effectors include RLIP76/RalBP1, a Rac/cdc42 GAP, and the exocyst (Sec6/8) complex, a heterooctomeric protein complex that is involved in tethering vesicles to specific sites on the plasma membrane prior to exocytosis. In rat kidney cells, RalB is required for functional assembly of the exo

>cd03216 ABC_Carb_Monos_I This family represents the domain I of the carbohydrate uptake proteins that transport only monosaccharides (Monos)

Probab=96.57  E-value=0.021  Score=54.84  Aligned_cols=24  Identities=21%  Similarity=0.475  Sum_probs=22.2

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      ..+.|.||+|+||||++++++..+
T Consensus        27 e~~~l~G~nGsGKSTLl~~i~G~~   50 (163)
T cd03216          27 EVHALLGENGAGKSTLMKILSGLY   50 (163)
T ss_pred             CEEEEECCCCCCHHHHHHHHhCCC
Confidence            589999999999999999999875

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.

>cd00983 recA RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response

Probab=96.56  E-value=0.017  Score=61.51  Aligned_cols=38  Identities=18%  Similarity=0.185  Sum_probs=29.4

Q ss_pred             CCCCccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcC
Q 005987          174 DKFSTNVLVITGQAGVGKTATVRQIASHL---GARLYEWDT  211 (666)
Q Consensus       174 g~~~~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~na  211 (666)
                      |-++.++..|+||||+||||++..++.+.   |..++.+.+
T Consensus        51 Glp~G~iteI~Gp~GsGKTtLal~~~~~~~~~g~~~vyId~   91 (325)
T cd00983          51 GYPKGRIIEIYGPESSGKTTLALHAIAEAQKLGGTVAFIDA   91 (325)
T ss_pred             CccCCeEEEEECCCCCCHHHHHHHHHHHHHHcCCCEEEECc
Confidence            44455689999999999999998877544   667776665

RecA couples ATP hydrolysis to DNA strand exchange.

>PLN02748 tRNA dimethylallyltransferase

Probab=96.54  E-value=0.035  Score=62.02  Aligned_cols=32  Identities=31%  Similarity=0.537  Sum_probs=28.4

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEEEEc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLYEWD  210 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~viE~n  210 (666)
                      ++++|.||+|+|||+++..||+.++++++...
T Consensus        23 ~~i~i~GptgsGKs~la~~la~~~~~eii~~D   54 (468)
T PLN02748         23 KVVVVMGPTGSGKSKLAVDLASHFPVEIINAD   54 (468)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHhcCeeEEcCc
Confidence            58999999999999999999999998777443

>TIGR02173 cyt_kin_arch cytidylate kinase, putative

Probab=96.53  E-value=0.0024  Score=61.21  Aligned_cols=29  Identities=31%  Similarity=0.609  Sum_probs=26.3

Q ss_pred             EEEEECCCCchHHHHHHHHHHHcCCcEEE
Q 005987          180 VLVITGQAGVGKTATVRQIASHLGARLYE  208 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkelg~~viE  208 (666)
                      +++|+|++|+||||+++.||+.+|+.++.
T Consensus         2 iI~i~G~~GSGKstia~~la~~lg~~~~~   30 (171)
T TIGR02173         2 IITISGPPGSGKTTVAKILAEKLSLKLIS   30 (171)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHcCCceec
Confidence            58999999999999999999999987653

Proteins in this family are believed to be cytidylate kinase. Members of this family are found in the archaea and in spirochaetes, and differ considerably from the common bacterial form of cytidylate kinase described by TIGR00017.

>PRK14723 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=96.52  E-value=0.1  Score=61.58  Aligned_cols=25  Identities=40%  Similarity=0.644  Sum_probs=22.5

Q ss_pred             ccEEEEECCCCchHHHHHHHHHHHc
Q 005987          178 TNVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       178 ~k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      +++++|.||+|+||||++..||..+
T Consensus       185 g~Vi~lVGpnGvGKTTTiaKLA~~~  209 (767)
T PRK14723        185 GGVLALVGPTGVGKTTTTAKLAARC  209 (767)
T ss_pred             CeEEEEECCCCCcHHHHHHHHHhhH
Confidence            3689999999999999999999765

>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=96.52  E-value=0.02  Score=53.79  Aligned_cols=24  Identities=29%  Similarity=0.580  Sum_probs=22.4

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      .++.|.||+|+||||++++++..+
T Consensus        27 e~~~i~G~nGsGKStLl~~l~G~~   50 (144)
T cd03221          27 DRIGLVGRNGAGKSTLLKLIAGEL   50 (144)
T ss_pred             CEEEEECCCCCCHHHHHHHHcCCC
Confidence            589999999999999999999876

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.

>PHA02530 pseT polynucleotide kinase; Provisional

Probab=96.51  E-value=0.0024  Score=67.44  Aligned_cols=29  Identities=24%  Similarity=0.359  Sum_probs=25.5

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc-CCcEE
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL-GARLY  207 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel-g~~vi  207 (666)
                      ++++|.|||||||||+++.|++.+ ++.++
T Consensus         3 ~liil~G~pGSGKSTla~~L~~~~~~~~~l   32 (300)
T PHA02530          3 KIILTVGVPGSGKSTWAREFAAKNPKAVNV   32 (300)
T ss_pred             EEEEEEcCCCCCHHHHHHHHHHHCCCCEEE
Confidence            589999999999999999999999 55444

>PRK10078 ribose 1,5-bisphosphokinase; Provisional

Probab=96.50  E-value=0.0023  Score=62.86  Aligned_cols=29  Identities=17%  Similarity=0.392  Sum_probs=25.4

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEE
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLY  207 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~vi  207 (666)
                      .+++|.||+|+||||+++.|+..++..+.
T Consensus         3 ~~i~l~G~sGsGKsTl~~~l~~~~~~~~~   31 (186)
T PRK10078          3 KLIWLMGPSGSGKDSLLAALRQREQTQLL   31 (186)
T ss_pred             cEEEEECCCCCCHHHHHHHHhccCCCeEE
Confidence            47999999999999999999998876543

>TIGR02525 plasmid_TraJ plasmid transfer ATPase TraJ

Probab=96.50  E-value=0.0087  Score=65.12  Aligned_cols=34  Identities=26%  Similarity=0.580  Sum_probs=27.5

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcC-----CcEEEEcCC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLG-----ARLYEWDTP  212 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg-----~~viE~nas  212 (666)
                      ..+|++||+|+||||+++++++.+.     ..++.+..+
T Consensus       150 GlilI~G~TGSGKTT~l~al~~~i~~~~~~~~IvtiEdp  188 (372)
T TIGR02525       150 GLGLICGETGSGKSTLAASIYQHCGETYPDRKIVTYEDP  188 (372)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHhcCCCceEEEEecC
Confidence            4789999999999999999998872     456666544

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).

>PRK12339 2-phosphoglycerate kinase; Provisional

Probab=96.50  E-value=0.0026  Score=63.13  Aligned_cols=29  Identities=34%  Similarity=0.460  Sum_probs=26.3

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEE
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLY  207 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~vi  207 (666)
                      .+++++|+||+||||+++.||.++|+.++
T Consensus         4 ~~i~i~G~~G~GKst~a~~l~~~~~~~~~   32 (197)
T PRK12339          4 TIHFIGGIPGVGKTSISGYIARHRAIDIV   32 (197)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHhcCCeEE
Confidence            58999999999999999999999987553

>smart00072 GuKc Guanylate kinase homologues

Probab=96.49  E-value=0.032  Score=54.58  Aligned_cols=24  Identities=25%  Similarity=0.595  Sum_probs=22.7

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      ++++|.||+|+||+|++..|+++.
T Consensus         3 r~ivl~Gpsg~GK~tl~~~L~~~~   26 (184)
T smart00072        3 RPIVLSGPSGVGKGTLLAELIQEI   26 (184)
T ss_pred             cEEEEECCCCCCHHHHHHHHHhcC
Confidence            689999999999999999999986

Active enzymes catalyze ATP-dependent phosphorylation of GMP to GDP. Structure resembles that of adenylate kinase. So-called membrane-associated guanylate kinase homologues (MAGUKs) do not possess guanylate kinase activities; instead at least some possess protein-binding functions.

>cd03284 ABC_MutS1 MutS1 homolog in eukaryotes

Probab=96.48  E-value=0.021  Score=57.57  Aligned_cols=22  Identities=41%  Similarity=0.628  Sum_probs=20.2

Q ss_pred             cEEEEECCCCchHHHHHHHHHH
Q 005987          179 NVLVITGQAGVGKTATVRQIAS  200 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAk  200 (666)
                      +.++|+||+|+||||+.+.++.
T Consensus        31 ~~~~l~Gpn~sGKstllr~i~~   52 (216)
T cd03284          31 QILLITGPNMAGKSTYLRQVAL   52 (216)
T ss_pred             eEEEEECCCCCChHHHHHHHHH
Confidence            5899999999999999999874

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

>COG3265 GntK Gluconate kinase [Carbohydrate transport and metabolism]

Probab=96.48  E-value=0.024  Score=52.94  Aligned_cols=26  Identities=35%  Similarity=0.595  Sum_probs=23.9

Q ss_pred             CCCCchHHHHHHHHHHHcCCcEEEEc
Q 005987          185 GQAGVGKTATVRQIASHLGARLYEWD  210 (666)
Q Consensus       185 GPpG~GKTtla~~LAkelg~~viE~n  210 (666)
                      |.+||||||++.+||+++|+.+++-.
T Consensus         2 GVsG~GKStvg~~lA~~lg~~fidGD   27 (161)
T COG3265           2 GVSGSGKSTVGSALAERLGAKFIDGD   27 (161)
T ss_pred             CCCccCHHHHHHHHHHHcCCceeccc
Confidence            89999999999999999999988744

>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=96.47  E-value=0.054  Score=55.32  Aligned_cols=33  Identities=30%  Similarity=0.375  Sum_probs=24.7

Q ss_pred             EEEEECCCCchHHHHHHHHHHHcC--CcEEEEcCC
Q 005987          180 VLVITGQAGVGKTATVRQIASHLG--ARLYEWDTP  212 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkelg--~~viE~nas  212 (666)
                      .+++.||+|+|||+++..|...+.  +..+.+-++
T Consensus        15 r~viIG~sGSGKT~li~~lL~~~~~~f~~I~l~t~   49 (241)
T PF04665_consen   15 RMVIIGKSGSGKTTLIKSLLYYLRHKFDHIFLITP   49 (241)
T ss_pred             eEEEECCCCCCHHHHHHHHHHhhcccCCEEEEEec
Confidence            488999999999999998888773  344444333

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

>PF13521 AAA_28: AAA domain; PDB: 1LW7_A

Probab=96.47  E-value=0.0025  Score=61.02  Aligned_cols=26  Identities=35%  Similarity=0.578  Sum_probs=21.3

Q ss_pred             EEEECCCCchHHHHHHHHHHHcCCcEE
Q 005987          181 LVITGQAGVGKTATVRQIASHLGARLY  207 (666)
Q Consensus       181 LLL~GPpG~GKTtla~~LAkelg~~vi  207 (666)
                      ++|+|+|||||||+++.|++. |+.++
T Consensus         2 I~i~G~~stGKTTL~~~L~~~-g~~~v   27 (163)
T PF13521_consen    2 IVITGGPSTGKTTLIEALAAR-GYPVV   27 (163)
T ss_dssp             EEEE--TTSHHHHHHHHHHHH-T-EEE
T ss_pred             EEEECCCCCCHHHHHHHHHHc-CCeEE
Confidence            789999999999999999999 88766

>PRK10867 signal recognition particle protein; Provisional

Probab=96.46  E-value=0.15  Score=56.59  Aligned_cols=36  Identities=25%  Similarity=0.397  Sum_probs=28.5

Q ss_pred             ccEEEEECCCCchHHHHHHHHHHHc----CCcEEEEcCCC
Q 005987          178 TNVLVITGQAGVGKTATVRQIASHL----GARLYEWDTPT  213 (666)
Q Consensus       178 ~k~LLL~GPpG~GKTtla~~LAkel----g~~viE~nasd  213 (666)
                      +.+++++||+|+||||++..||..+    |..+.-+.+-.
T Consensus       100 p~vI~~vG~~GsGKTTtaakLA~~l~~~~G~kV~lV~~D~  139 (433)
T PRK10867        100 PTVIMMVGLQGAGKTTTAGKLAKYLKKKKKKKVLLVAADV  139 (433)
T ss_pred             CEEEEEECCCCCcHHHHHHHHHHHHHHhcCCcEEEEEccc
Confidence            3789999999999999888888755    66676666543

>PF00488 MutS_V: MutS domain V C-terminus

Probab=96.45  E-value=0.048  Score=55.70  Aligned_cols=24  Identities=29%  Similarity=0.505  Sum_probs=21.4

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      +.+||+||...||||+++.+|-..
T Consensus        44 ~~~iiTGpN~sGKSt~lk~i~~~~   67 (235)
T PF00488_consen   44 RIIIITGPNMSGKSTFLKQIGLIV   67 (235)
T ss_dssp             SEEEEESSTTSSHHHHHHHHHHHH
T ss_pred             eEEEEeCCCccchhhHHHHHHHHh
Confidence            689999999999999999987653

; InterPro: IPR000432 Mismatch repair contributes to the overall fidelity of DNA replication and is essential for combating the adverse effects of damage to the genome. It involves the correction of mismatched base pairs that have been missed by the proofreading element of the DNA polymerase complex. The post-replicative Mismatch Repair System (MMRS) of Escherichia coli involves MutS (Mutator S), MutL and MutH proteins, and acts to correct point mutations or small insertion/deletion loops produced during DNA replication []. MutS and MutL are involved in preventing recombination between partially homologous DNA sequences. The assembly of MMRS is initiated by MutS, which recognises and binds to mispaired nucleotides and allows further action of MutL and MutH to eliminate a portion of newly synthesized DNA strand containing the mispaired base []. MutS can also collaborate with methyltransferases in the repair of O(6)-methylguanine damage, which would otherwise pair with thymine during replication to create an O(6)mG:T mismatch []. MutS exists as a dimer, where the two monomers have different conformations and form a heterodimer at the structural level []. Only one monomer recognises the mismatch specifically and has ADP bound. Non-specific major groove DNA-binding domains from both monomers embrace the DNA in a clamp-like structure. Mismatch binding induces ATP uptake and a conformational change in the MutS protein, resulting in a clamp that translocates on DNA. MutS is a modular protein with a complex structure [], and is composed of: N-terminal mismatch-recognition domain, which is similar in structure to tRNA endonuclease. Connector domain, which is similar in structure to Holliday junction resolvase ruvC. Core domain, which is composed of two separate subdomains that join together to form a helical bundle; from within the core domain, two helices act as levers that extend towards (but do not touch) the DNA. Clamp domain, which is inserted between the two subdomains of the core domain at the top of the lever helices; the clamp domain has a beta-sheet structure. ATPase domain (connected to the core domain), which has a classical Walker A motif. HTH (helix-turn-helix) domain, which is involved in dimer contacts. The MutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair. Homologues of MutS have been found in many species including eukaryotes (MSH 1, 2, 3, 4, 5, and 6 proteins), archaea and bacteria, and together these proteins have been grouped into the MutS family. Although many of these proteins have similar activities to the E. coli MutS, there is significant diversity of function among the MutS family members. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein [].This diversity is even seen within species, where many species encode multiple MutS homologues with distinct functions []. Inter-species homologues may have arisen through frequent ancient horizontal gene transfer of MutS (and MutL) from bacteria to archaea and eukaryotes via endosymbiotic ancestors of mitochondria and chloroplasts []. This entry represents the C-terminal domain found in proteins in the MutS family of DNA mismatch repair proteins. The C-terminal region of MutS is comprised of the ATPase domain and the HTH (helix-turn-helix) domain, the latter being involved in dimer contacts. Yeast MSH3 [], bacterial proteins involved in DNA mismatch repair, and the predicted protein product of the Rep-3 gene of mouse share extensive sequence similarity. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein. ; GO: 0005524 ATP binding, 0030983 mismatched DNA binding, 0006298 mismatch repair; PDB: 1FW6_A 1EWQ_A 1EWR_B 1NNE_B 2WTU_A 1OH7_A 1OH5_B 1W7A_B 1NG9_A 1OH8_B ....

>TIGR01425 SRP54_euk signal recognition particle protein SRP54

Probab=96.45  E-value=0.26  Score=54.60  Aligned_cols=35  Identities=29%  Similarity=0.347  Sum_probs=29.4

Q ss_pred             ccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcCC
Q 005987          178 TNVLVITGQAGVGKTATVRQIASHL---GARLYEWDTP  212 (666)
Q Consensus       178 ~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~nas  212 (666)
                      +++++|+||+|+||||++..||..+   |..|.-+.+-
T Consensus       100 ~~vi~lvG~~GvGKTTtaaKLA~~l~~~G~kV~lV~~D  137 (429)
T TIGR01425       100 QNVIMFVGLQGSGKTTTCTKLAYYYQRKGFKPCLVCAD  137 (429)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEcCc
Confidence            3689999999999999999999877   7777766653

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.

>PRK10875 recD exonuclease V subunit alpha; Provisional

Probab=96.45  E-value=0.013  Score=67.87  Aligned_cols=35  Identities=34%  Similarity=0.507  Sum_probs=26.4

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc---C---CcEEEEcCCC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL---G---ARLYEWDTPT  213 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel---g---~~viE~nasd  213 (666)
                      +..+|+|+|||||||+++.+...+   +   ...+-+-+|.
T Consensus       168 ~~~vItGgpGTGKTt~v~~ll~~l~~~~~~~~~~i~l~APT  208 (615)
T PRK10875        168 RISVISGGPGTGKTTTVAKLLAALIQLADGERCRIRLAAPT  208 (615)
T ss_pred             CeEEEEeCCCCCHHHHHHHHHHHHHHhcCCCCcEEEEECCc
Confidence            589999999999999998877655   1   1245556665

>PRK09376 rho transcription termination factor Rho; Provisional

Probab=96.44  E-value=0.007  Score=65.65  Aligned_cols=25  Identities=24%  Similarity=0.316  Sum_probs=21.8

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLG  203 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg  203 (666)
                      .-.+|.|||||||||+++.+++.+.
T Consensus       170 QR~lIvgppGvGKTTLaK~Ian~I~  194 (416)
T PRK09376        170 QRGLIVAPPKAGKTVLLQNIANSIT  194 (416)
T ss_pred             ceEEEeCCCCCChhHHHHHHHHHHH
Confidence            3578889999999999999999873

>TIGR02322 phosphon_PhnN phosphonate metabolism protein/1,5-bisphosphokinase (PRPP-forming) PhnN

Probab=96.43  E-value=0.0026  Score=61.83  Aligned_cols=26  Identities=19%  Similarity=0.454  Sum_probs=23.5

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGA  204 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~  204 (666)
                      +.++|.||+|+||||+++.|+..++.
T Consensus         2 ~~~~i~G~sGsGKttl~~~l~~~~~~   27 (179)
T TIGR02322         2 RLIYVVGPSGAGKDTLLDYARARLAG   27 (179)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHcCc
Confidence            47899999999999999999998754

Members of this family resemble PhnN of phosphonate utilization operons, where different such operons confer the ability to use somewhat different profiles of C-P bond-containing compounds (see PubMed:15231805), including phosphites as well as phosphonates. PhnN in E. coli shows considerable homology to guanylate kinases (EC 2.7.4.8), and has actually been shown to act as a ribose 1,5-bisphosphokinase (PRPP forming). This suggests an analogous kinase reaction for phosphonate metabolism, converting 5-phosphoalpha-1-(methylphosphono)ribose to methylphosphono-PRPP.

>PRK05973 replicative DNA helicase; Provisional

Probab=96.43  E-value=0.023  Score=57.96  Aligned_cols=37  Identities=16%  Similarity=0.186  Sum_probs=27.9

Q ss_pred             CCCCccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEc
Q 005987          174 DKFSTNVLVITGQAGVGKTATVRQIASHL---GARLYEWD  210 (666)
Q Consensus       174 g~~~~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~n  210 (666)
                      |-++...+||.|+||+|||+++..+|.+.   |..++.+.
T Consensus        60 Gl~~Gsl~LIaG~PG~GKT~lalqfa~~~a~~Ge~vlyfS   99 (237)
T PRK05973         60 QLKPGDLVLLGARPGHGKTLLGLELAVEAMKSGRTGVFFT   99 (237)
T ss_pred             CCCCCCEEEEEeCCCCCHHHHHHHHHHHHHhcCCeEEEEE
Confidence            33445689999999999999988777654   66665554

>PF06144 DNA_pol3_delta: DNA polymerase III, delta subunit; InterPro: IPR010372 DNA polymerase III, delta subunit (2

Probab=96.42  E-value=0.015  Score=55.95  Aligned_cols=113  Identities=12%  Similarity=0.218  Sum_probs=64.8

Q ss_pred             ceEEEEeCCCCCcchhHHHHHHHHHHHHHhcCCCc-eEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHH
Q 005987          261 SAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHIP-TAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNG  339 (666)
Q Consensus       261 ~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~~~P-iViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~  339 (666)
                      +++|+|.+++-+... .-....+.|..++.....- ++++++. +.   .+...+    +...+.. .+.++.|.++...
T Consensus        58 ~klvii~~~~~l~~~-~~~~~~~~l~~~l~~~~~~~~lii~~~-~~---~~~~~k----~~k~l~~-~~~~~~~~~~~~~  127 (172)
T PF06144_consen   58 KKLVIIKNAPFLKDK-LKKKEIKALIEYLSNPPPDCILIIFSE-EK---LDKRKK----LYKALKK-QAIVIECKKPKEQ  127 (172)
T ss_dssp             EEEEEEE-----TT--S-TTHHHHHHHHTTT--SSEEEEEEES--S-----HHHH----HHHHHTT-TEEEEEE----TT
T ss_pred             CeEEEEecCcccccc-ccHHHHHHHHHHHhCCCCCEEEEEEeC-Cc---hhhhhh----HHHHHhc-ccceEEecCCCHH
Confidence            579999998432100 0011223355555543222 3333333 11   111122    2333333 5888999999999


Q ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCcHHHHHHHHHHHh
Q 005987          340 SIKRTLSKICRQEQYSLSTEQIDLVAQASGGDIRQAITSLQFSS  383 (666)
Q Consensus       340 ~i~kiL~~I~~~e~i~v~~~~l~~Ia~~s~GDIR~AIn~LQf~~  383 (666)
                      ++...++..+.+.|+.+++++++.|++..++|++.+.+.|+-++
T Consensus       128 ~~~~~i~~~~~~~g~~i~~~a~~~L~~~~~~d~~~l~~EleKL~  171 (172)
T PF06144_consen  128 ELPRWIKERAKKNGLKIDPDAAQYLIERVGNDLSLLQNELEKLS  171 (172)
T ss_dssp             THHHHHHHHHHHTT-EE-HHHHHHHHHHHTT-HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCCCHHHHHHHHHHhChHHHHHHHHHHHhc
Confidence            99999999999999999999999999999999999999998765

7.7.7 from EC) is required for, along with delta' subunit, the assembly of the processivity factor beta(2) onto primed DNA in the DNA polymerase III holoenzyme-catalysed reaction []. The delta subunit is also known as HolA.; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication, 0009360 DNA polymerase III complex; PDB: 3GLG_F 1XXH_A 1JQL_B 3GLF_F 1JQJ_C 3GLI_F.

>cd01867 Rab8_Rab10_Rab13_like Rab8/Sec4/Ypt2

Probab=96.41  E-value=0.1  Score=49.65  Aligned_cols=22  Identities=27%  Similarity=0.595  Sum_probs=19.8

Q ss_pred             EEEEECCCCchHHHHHHHHHHH
Q 005987          180 VLVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAke  201 (666)
                      -+++.|++|+|||+++..++..
T Consensus         5 ki~vvG~~~~GKSsl~~~~~~~   26 (167)
T cd01867           5 KLLLIGDSGVGKSCLLLRFSED   26 (167)
T ss_pred             EEEEECCCCCCHHHHHHHHhhC
Confidence            4899999999999999999864

Rab8/Sec4/Ypt2 are known or suspected to be involved in post-Golgi transport to the plasma membrane. It is likely that these Rabs have functions that are specific to the mammalian lineage and have no orthologs in plants. Rab8 modulates polarized membrane transport through reorganization of actin and microtubules, induces the formation of new surface extensions, and has an important role in directed membrane transport to cell surfaces. The Ypt2 gene of the fission yeast Schizosaccharomyces pombe encodes a member of the Ypt/Rab family of small GTP-binding proteins, related in sequence to Sec4p of Saccharomyces cerevisiae but closer to mammalian Rab8. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhi

>cd03286 ABC_MSH6_euk MutS6 homolog in eukaryotes

Probab=96.41  E-value=0.079  Score=53.48  Aligned_cols=23  Identities=30%  Similarity=0.482  Sum_probs=20.3

Q ss_pred             cEEEEECCCCchHHHHHHHHHHH
Q 005987          179 NVLVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAke  201 (666)
                      +.++|+||.|.|||++.+.++--
T Consensus        31 ~~~~itG~n~~gKs~~l~~i~~~   53 (218)
T cd03286          31 RILVLTGPNMGGKSTLLRTVCLA   53 (218)
T ss_pred             cEEEEECCCCCchHHHHHHHHHH
Confidence            58999999999999998887664

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

>cd00876 Ras Ras family

Probab=96.40  E-value=0.069  Score=49.82  Aligned_cols=21  Identities=38%  Similarity=0.589  Sum_probs=19.0

Q ss_pred             EEEECCCCchHHHHHHHHHHH
Q 005987          181 LVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       181 LLL~GPpG~GKTtla~~LAke  201 (666)
                      +++.||+|+||||++..+...
T Consensus         2 i~i~G~~~~GKTsli~~l~~~   22 (160)
T cd00876           2 VVVLGAGGVGKSAITIQFVKG   22 (160)
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            789999999999999998754

The Ras family of the Ras superfamily includes classical N-Ras, H-Ras, and K-Ras, as well as R-Ras, Rap, Ral, Rheb, Rhes, ARHI, RERG, Rin/Rit, RSR1, RRP22, Ras2, Ras-dva, and RGK proteins. Ras proteins regulate cell growth, proliferation and differentiation. Ras is activated by guanine nucleotide exchange factors (GEFs) that release GDP and allow GTP binding. Many RasGEFs have been identified. These are sequestered in the cytosol until activation by growth factors triggers recruitment to the plasma membrane or Golgi, where the GEF colocalizes with Ras. Active GTP-bound Ras interacts with several effector proteins: among the best characterized are the Raf kinases, phosphatidylinositol 3-kinase (PI3K), RalGEFs and NORE/MST1. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of m

>PRK08233 hypothetical protein; Provisional

Probab=96.40  E-value=0.0037  Score=60.56  Aligned_cols=30  Identities=20%  Similarity=0.388  Sum_probs=25.3

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcC-CcEEE
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLG-ARLYE  208 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg-~~viE  208 (666)
                      .++.|.|+||+||||++..||..++ ..++.
T Consensus         4 ~iI~I~G~~GsGKtTla~~L~~~l~~~~~~~   34 (182)
T PRK08233          4 KIITIAAVSGGGKTTLTERLTHKLKNSKALY   34 (182)
T ss_pred             eEEEEECCCCCCHHHHHHHHHhhCCCCceEE
Confidence            5789999999999999999999995 33443

>PRK14721 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=96.40  E-value=0.12  Score=57.11  Aligned_cols=25  Identities=36%  Similarity=0.587  Sum_probs=22.3

Q ss_pred             ccEEEEECCCCchHHHHHHHHHHHc
Q 005987          178 TNVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       178 ~k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      +..+.|.||+|+||||++..||..+
T Consensus       191 g~vi~lvGpnG~GKTTtlakLA~~~  215 (420)
T PRK14721        191 GGVYALIGPTGVGKTTTTAKLAARA  215 (420)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHH
Confidence            3689999999999999999998764

>PRK06995 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=96.39  E-value=0.036  Score=62.21  Aligned_cols=24  Identities=38%  Similarity=0.650  Sum_probs=22.3

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      ++++|.||+|+||||++..||..+
T Consensus       257 ~Vi~LvGpnGvGKTTTiaKLA~~~  280 (484)
T PRK06995        257 GVFALMGPTGVGKTTTTAKLAARC  280 (484)
T ss_pred             cEEEEECCCCccHHHHHHHHHHHH
Confidence            689999999999999999999766

>PRK14526 adenylate kinase; Provisional

Probab=96.39  E-value=0.0029  Score=63.50  Aligned_cols=28  Identities=25%  Similarity=0.385  Sum_probs=25.1

Q ss_pred             EEEECCCCchHHHHHHHHHHHcCCcEEE
Q 005987          181 LVITGQAGVGKTATVRQIASHLGARLYE  208 (666)
Q Consensus       181 LLL~GPpG~GKTtla~~LAkelg~~viE  208 (666)
                      ++|.||||+||||+++.||+.+++..+.
T Consensus         3 i~l~G~pGsGKsT~a~~La~~~~~~~is   30 (211)
T PRK14526          3 LVFLGPPGSGKGTIAKILSNELNYYHIS   30 (211)
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCCceee
Confidence            7899999999999999999999876653

>PRK08487 DNA polymerase III subunit delta; Validated

Probab=96.39  E-value=0.36  Score=51.80  Aligned_cols=90  Identities=12%  Similarity=0.079  Sum_probs=70.3

Q ss_pred             eeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCcHHHHHHHHHHHhcCCCCcccccccCCCCCCCccccC
Q 005987          328 ARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASGGDIRQAITSLQFSSLKQDPMLNLSLSISKPNFPEEKAD  407 (666)
Q Consensus       328 ~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~s~GDIR~AIn~LQf~~~~~~~~~~~~~~~~~~~~~k~~~~  407 (666)
                      ...|.|.+++..++.+.+...+.+.|+.+++++++.|+..+++|+..+.+-|+-+++-.....                 
T Consensus       127 ~~~v~~~~~~~~~l~~~i~~~~~~~g~~i~~~a~~~L~~~~g~dl~~l~~ELeKL~ly~~~It-----------------  189 (328)
T PRK08487        127 AVFVRFFKPNAREALELLQERAKELGLDIDQNALNHLYFIHNEDLALAANELEKLAILNEPIT-----------------  189 (328)
T ss_pred             ceEEEeeCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCcHHHHHHHHHHHHHHhcCCCC-----------------
Confidence            457899999999999999999999999999999999999999999999999988876432110                 


Q ss_pred             CCCCcccccCCccccchHHHHhHHhhCC
Q 005987          408 GHGGFSIQFGRDETLSLFHALGKFLHNK  435 (666)
Q Consensus       408 ~~~~~~~~~~RD~~l~lFhalGkil~~K  435 (666)
                       .+.+..+..+....++|+.+..++.++
T Consensus       190 -~edV~~~v~~~~e~~vF~l~dai~~g~  216 (328)
T PRK08487        190 -LKDIQELVFGLGSVSFEDFFEKLLNKK  216 (328)
T ss_pred             -HHHHHHHhcccccccHHHHHHHHHCCC
Confidence             011223344555677888777777665

>TIGR03877 thermo_KaiC_1 KaiC domain protein, Ph0284 family

Probab=96.38  E-value=0.053  Score=55.37  Aligned_cols=38  Identities=21%  Similarity=0.180  Sum_probs=27.4

Q ss_pred             CCCCccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcC
Q 005987          174 DKFSTNVLVITGQAGVGKTATVRQIASHL---GARLYEWDT  211 (666)
Q Consensus       174 g~~~~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~na  211 (666)
                      |-++...+||+||||+|||+++..++.+.   |-.++.+..
T Consensus        17 G~~~gs~~lI~G~pGsGKT~la~~~l~~~~~~ge~~lyvs~   57 (237)
T TIGR03877        17 GIPERNVVLLSGGPGTGKSIFSQQFLWNGLQMGEPGIYVAL   57 (237)
T ss_pred             CCcCCeEEEEEcCCCCCHHHHHHHHHHHHHHcCCcEEEEEe
Confidence            44455789999999999999987665542   555655543

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.

>cd04160 Arfrp1 Arfrp1 subfamily

Probab=96.36  E-value=0.062  Score=50.91  Aligned_cols=22  Identities=27%  Similarity=0.472  Sum_probs=19.7

Q ss_pred             EEEECCCCchHHHHHHHHHHHc
Q 005987          181 LVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       181 LLL~GPpG~GKTtla~~LAkel  202 (666)
                      ++|.|++|+||||++..+....
T Consensus         2 i~~vG~~~~GKstLi~~l~~~~   23 (167)
T cd04160           2 VLILGLDNAGKTTFLEQLKTLF   23 (167)
T ss_pred             EEEEecCCCCHHHHHHHHhhhc
Confidence            7899999999999999997654

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.

>PRK06731 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=96.36  E-value=0.11  Score=54.08  Aligned_cols=33  Identities=27%  Similarity=0.391  Sum_probs=26.5

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL---GARLYEWDT  211 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel---g~~viE~na  211 (666)
                      ..++|.||+|+||||++..++..+   +..+..+.+
T Consensus        76 ~~i~~~G~~g~GKTtl~~~l~~~l~~~~~~v~~i~~  111 (270)
T PRK06731         76 QTIALIGPTGVGKTTTLAKMAWQFHGKKKTVGFITT  111 (270)
T ss_pred             CEEEEECCCCCcHHHHHHHHHHHHHHcCCeEEEEec
Confidence            589999999999999999998886   344554444

>cd01123 Rad51_DMC1_radA Rad51_DMC1_radA,B

Probab=96.36  E-value=0.029  Score=56.92  Aligned_cols=39  Identities=26%  Similarity=0.265  Sum_probs=29.0

Q ss_pred             CCCCccEEEEECCCCchHHHHHHHHHHHc---------CCcEEEEcCC
Q 005987          174 DKFSTNVLVITGQAGVGKTATVRQIASHL---------GARLYEWDTP  212 (666)
Q Consensus       174 g~~~~k~LLL~GPpG~GKTtla~~LAkel---------g~~viE~nas  212 (666)
                      |-++..++.|+||||||||+++..+|...         +..++.+..-
T Consensus        15 Gi~~g~i~~i~G~~GsGKT~l~~~l~~~~~~~~~~~g~~~~viyi~~e   62 (235)
T cd01123          15 GIETGSITEIFGEFGSGKTQLCHQLAVTVQLPIELGGLEGKAVYIDTE   62 (235)
T ss_pred             CCCCCeEEEEECCCCCCHHHHHHHHHHHeeCccccCCCCccEEEEeCC
Confidence            33445789999999999999999887553         2466666543

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 .

>cd04145 M_R_Ras_like M-Ras/R-Ras-like subfamily

Probab=96.36  E-value=0.07  Score=50.24  Aligned_cols=22  Identities=41%  Similarity=0.573  Sum_probs=19.5

Q ss_pred             EEEEECCCCchHHHHHHHHHHH
Q 005987          180 VLVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAke  201 (666)
                      .+++.|++|+||||++..+...
T Consensus         4 ki~i~G~~~~GKtsl~~~~~~~   25 (164)
T cd04145           4 KLVVVGGGGVGKSALTIQFIQS   25 (164)
T ss_pred             EEEEECCCCCcHHHHHHHHHhC
Confidence            4889999999999999988764

This subfamily contains R-Ras2/TC21, M-Ras/R-Ras3, and related members of the Ras family. M-Ras is expressed in lympho-hematopoetic cells. It interacts with some of the known Ras effectors, but appears to also have its own effectors. Expression of mutated M-Ras leads to transformation of several types of cell lines, including hematopoietic cells, mammary epithelial cells, and fibroblasts. Overexpression of M-Ras is observed in carcinomas from breast, uterus, thyroid, stomach, colon, kidney, lung, and rectum. In addition, expression of a constitutively active M-Ras mutant in murine bone marrow induces a malignant mast cell leukemia that is distinct from the monocytic leukemia induced by H-Ras. TC21, along with H-Ras, has been shown to regulate the branching morphogenesis of ureteric bud cell branching in mice. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an ali

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

Probab=96.35  E-value=0.055  Score=52.79  Aligned_cols=24  Identities=25%  Similarity=0.497  Sum_probs=22.4

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      -.++|+||+|.||||+++.+..+.
T Consensus        29 ef~fl~GpSGAGKSTllkLi~~~e   52 (223)
T COG2884          29 EFVFLTGPSGAGKSTLLKLIYGEE   52 (223)
T ss_pred             eEEEEECCCCCCHHHHHHHHHhhh
Confidence            479999999999999999999987

>TIGR03878 thermo_KaiC_2 KaiC domain protein, AF_0795 family

Probab=96.35  E-value=0.023  Score=58.99  Aligned_cols=37  Identities=27%  Similarity=0.257  Sum_probs=27.4

Q ss_pred             CCCCccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEc
Q 005987          174 DKFSTNVLVITGQAGVGKTATVRQIASHL---GARLYEWD  210 (666)
Q Consensus       174 g~~~~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~n  210 (666)
                      |-++....+++||||+|||+++..+|.+.   |..++.+.
T Consensus        32 Gip~gs~~lI~G~pGtGKT~l~~qf~~~~a~~Ge~vlyis   71 (259)
T TIGR03878        32 GIPAYSVINITGVSDTGKSLMVEQFAVTQASRGNPVLFVT   71 (259)
T ss_pred             CeECCcEEEEEcCCCCCHHHHHHHHHHHHHhCCCcEEEEE
Confidence            33455789999999999999998876643   55555544

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

>cd04137 RheB Rheb (Ras Homolog Enriched in Brain) subfamily

Probab=96.34  E-value=0.083  Score=50.86  Aligned_cols=23  Identities=22%  Similarity=0.364  Sum_probs=20.1

Q ss_pred             cEEEEECCCCchHHHHHHHHHHH
Q 005987          179 NVLVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAke  201 (666)
                      +.++|.|+||+||||+++.+...
T Consensus         2 ~kv~l~G~~g~GKTtl~~~~~~~   24 (180)
T cd04137           2 RKIAVLGSRSVGKSSLTVQFVEG   24 (180)
T ss_pred             eEEEEECCCCCCHHHHHHHHHhC
Confidence            35889999999999999988854

Rheb was initially identified in rat brain, where its expression is elevated by seizures or by long-term potentiation. It is expressed ubiquitously, with elevated levels in muscle and brain. Rheb functions as an important mediator between the tuberous sclerosis complex proteins, TSC1 and TSC2, and the mammalian target of rapamycin (TOR) kinase to stimulate cell growth. TOR kinase regulates cell growth by controlling nutrient availability, growth factors, and the energy status of the cell. TSC1 and TSC2 form a dimeric complex that has tumor suppressor activity, and TSC2 is a GTPase activating protein (GAP) for Rheb. The TSC1/TSC2 complex inhibits the activation of TOR kinase through Rheb. Rheb has also been shown to induce the formation of large cytoplasmic vacuoles in a process that is dependent on the GTPase cycle of Rheb, but independent of the TOR kinase, suggesting Rheb plays a role in endocytic trafficking that le

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

Probab=96.34  E-value=0.014  Score=63.59  Aligned_cols=26  Identities=31%  Similarity=0.473  Sum_probs=23.3

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGA  204 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~  204 (666)
                      ..+.|+||+|||||+++++|...+..
T Consensus        23 ~~~fv~G~~GtGKs~l~~~i~~~~~~   48 (364)
T PF05970_consen   23 LNFFVTGPAGTGKSFLIKAIIDYLRS   48 (364)
T ss_pred             cEEEEEcCCCCChhHHHHHHHHHhcc
Confidence            57999999999999999999988843

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

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

Probab=96.34  E-value=0.03  Score=58.12  Aligned_cols=37  Identities=30%  Similarity=0.440  Sum_probs=28.9

Q ss_pred             CCccEEEEECCCCchHHHHHHHHHHHc----CCcEEEEcCC
Q 005987          176 FSTNVLVITGQAGVGKTATVRQIASHL----GARLYEWDTP  212 (666)
Q Consensus       176 ~~~k~LLL~GPpG~GKTtla~~LAkel----g~~viE~nas  212 (666)
                      .+...++|.||||+|||+++..+|..+    |..++.+..-
T Consensus        28 ~~g~~~~i~g~~G~GKT~l~~~~~~~~~~~~g~~vl~iS~E   68 (271)
T cd01122          28 RKGELIILTAGTGVGKTTFLREYALDLITQHGVRVGTISLE   68 (271)
T ss_pred             cCCcEEEEEcCCCCCHHHHHHHHHHHHHHhcCceEEEEEcc
Confidence            344689999999999999998877664    6777776543

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

>PLN02674 adenylate kinase

Probab=96.33  E-value=0.0073  Score=61.88  Aligned_cols=30  Identities=20%  Similarity=0.258  Sum_probs=26.5

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEEE
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLYE  208 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~viE  208 (666)
                      ..++|.||||+||+|.++.||+.+|+..+.
T Consensus        32 ~~i~l~G~PGsGKgT~a~~La~~~~~~his   61 (244)
T PLN02674         32 KRLILIGPPGSGKGTQSPIIKDEYCLCHLA   61 (244)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHcCCcEEc
Confidence            468899999999999999999999976653

>KOG1808 consensus AAA ATPase containing von Willebrand factor type A (vWA) domain [General function prediction only]

Probab=96.33  E-value=0.016  Score=73.14  Aligned_cols=46  Identities=26%  Similarity=0.494  Sum_probs=40.7

Q ss_pred             CCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCchhhhhhhh
Q 005987          174 DKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTIWQEYMH  222 (666)
Q Consensus       174 g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~~~~e~l~  222 (666)
                      |+.|   +||.||.|||||+++.-+|+..|.+++++|.-....+++++.
T Consensus       439 ~~~p---illqG~tssGKtsii~~la~~~g~~~vrinnhehtd~qeyig  484 (1856)
T KOG1808|consen  439 GKFP---ILLQGPTSSGKTSIIKELARATGKNIVRINNHEHTDLQEYIG  484 (1856)
T ss_pred             CCCC---eEEecCcCcCchhHHHHHHHHhccCceehhccccchHHHHHH
Confidence            5544   999999999999999999999999999999888777777765

>PLN02199 shikimate kinase

Probab=96.33  E-value=0.0047  Score=64.53  Aligned_cols=32  Identities=25%  Similarity=0.505  Sum_probs=28.8

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEEEEc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLYEWD  210 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~viE~n  210 (666)
                      +.++|.|++|+||||+++.||+.+|+.++-.+
T Consensus       103 ~~I~LIG~~GSGKSTVgr~LA~~Lg~~fIDtD  134 (303)
T PLN02199        103 RSMYLVGMMGSGKTTVGKLMSKVLGYTFFDCD  134 (303)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHhCCCEEehH
Confidence            57999999999999999999999999888543

>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=96.33  E-value=0.047  Score=52.54  Aligned_cols=24  Identities=38%  Similarity=0.630  Sum_probs=22.5

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      ..+.|.||+|+||||++++++..+
T Consensus        28 e~~~i~G~nGsGKSTLl~~l~G~~   51 (166)
T cd03223          28 DRLLITGPSGTGKSSLFRALAGLW   51 (166)
T ss_pred             CEEEEECCCCCCHHHHHHHHhcCC
Confidence            589999999999999999999876

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

>cd02027 APSK Adenosine 5'-phosphosulfate kinase (APSK) catalyzes the phosphorylation of adenosine 5'-phosphosulfate to form 3'-phosphoadenosine 5'-phosphosulfate (PAPS)

Probab=96.32  E-value=0.0042  Score=58.78  Aligned_cols=31  Identities=35%  Similarity=0.655  Sum_probs=26.7

Q ss_pred             EEEEECCCCchHHHHHHHHHHHc---CCcEEEEc
Q 005987          180 VLVITGQAGVGKTATVRQIASHL---GARLYEWD  210 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkel---g~~viE~n  210 (666)
                      +++|+|+||+||||+++.|+..+   ++.++.++
T Consensus         1 ~i~i~G~~GsGKSTla~~L~~~l~~~g~~~~~i~   34 (149)
T cd02027           1 VIWLTGLSGSGKSTIARALEEKLFQRGRPVYVLD   34 (149)
T ss_pred             CEEEEcCCCCCHHHHHHHHHHHHHHcCCCEEEEc
Confidence            37899999999999999999998   66666665

The end-product PAPS is a biologically "activated" sulfate form important for the assimilation of inorganic sulfate.

>PRK00889 adenylylsulfate kinase; Provisional

Probab=96.32  E-value=0.0053  Score=59.49  Aligned_cols=34  Identities=32%  Similarity=0.420  Sum_probs=27.7

Q ss_pred             ccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcC
Q 005987          178 TNVLVITGQAGVGKTATVRQIASHL---GARLYEWDT  211 (666)
Q Consensus       178 ~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~na  211 (666)
                      +.+++|+|+||+||||+++.||..+   |..+..++.
T Consensus         4 g~~i~~~G~~GsGKST~a~~la~~l~~~g~~v~~id~   40 (175)
T PRK00889          4 GVTVWFTGLSGAGKTTIARALAEKLREAGYPVEVLDG   40 (175)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEcC
Confidence            3689999999999999999999988   445555543

>PRK07914 hypothetical protein; Reviewed

Probab=96.32  E-value=0.074  Score=56.90  Aligned_cols=146  Identities=11%  Similarity=0.121  Sum_probs=93.9

Q ss_pred             ceEEEEeCCCCCcchhHHHHHHHHHHHHHhcCCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCC-CHH
Q 005987          261 SAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPI-TNG  339 (666)
Q Consensus       261 ~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~-s~~  339 (666)
                      +++|+|++......     ...+.|..+++......++|+...+..    ...+.+..|+    ..++..|.|.++ ...
T Consensus        65 rRlV~v~~~~~~~~-----~~~~~l~~~l~~~~~~t~lil~~~~~~----~~kk~~K~L~----k~g~~~v~~~~~~~~~  131 (320)
T PRK07914         65 ERVVVLEAAAEAGK-----DAAALILSAAADLPPGTVLVVVHSGGG----RAKALANQLR----KLGAEVHPCARITKAA  131 (320)
T ss_pred             ceEEEEeChHhccH-----HHHHHHHHHHhCCCCCeEEEEEecCCc----chhHHHHHHH----HCCCEEEecCCCCCHH
Confidence            46899998643321     123346666665433233333321111    1111122232    225668999999 999


Q ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCcHHHHHHHHHHHhcCCCCcccccccCCCCCCCccccCCCCCcccccCCc
Q 005987          340 SIKRTLSKICRQEQYSLSTEQIDLVAQASGGDIRQAITSLQFSSLKQDPMLNLSLSISKPNFPEEKADGHGGFSIQFGRD  419 (666)
Q Consensus       340 ~i~kiL~~I~~~e~i~v~~~~l~~Ia~~s~GDIR~AIn~LQf~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~~~~~RD  419 (666)
                      ++.+.+...+...|+.+++++++.|++..+||+..+-+-|+-++...+....                 .+.+..+..+.
T Consensus       132 ~l~~wi~~~a~~~g~~i~~~A~~~L~~~~g~dl~~l~~EleKL~~~~~~~It-----------------~e~V~~~v~~~  194 (320)
T PRK07914        132 ERADFVRKEFRSLRVKVDDDTVTALLDAVGSDLRELASACSQLVADTGGAVD-----------------AAAVRRYHSGK  194 (320)
T ss_pred             HHHHHHHHHHHHcCCCCCHHHHHHHHHHHCccHHHHHHHHHHHhcCCCCCcC-----------------HHHHHHHcCCC
Confidence            9999999999999999999999999999999999999999877652211110                 01123344556


Q ss_pred             cccchHHHHhHHhhCCC
Q 005987          420 ETLSLFHALGKFLHNKR  436 (666)
Q Consensus       420 ~~l~lFhalGkil~~Kr  436 (666)
                      ...++|+.+..++.++.
T Consensus       195 ~~~~vf~L~dAi~~g~~  211 (320)
T PRK07914        195 AEVKGFDIADKAVAGDV  211 (320)
T ss_pred             eechHHHHHHHHHCCCH
Confidence            67788888888877653

>cd03237 ABC_RNaseL_inhibitor_domain2 The ATPase domain 2 of RNase L inhibitor

Probab=96.30  E-value=0.041  Score=56.58  Aligned_cols=24  Identities=38%  Similarity=0.631  Sum_probs=22.4

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      .++.|.||+|+||||++++|+..+
T Consensus        26 e~~~i~G~NGsGKSTLlk~L~G~~   49 (246)
T cd03237          26 EVIGILGPNGIGKTTFIKMLAGVL   49 (246)
T ss_pred             CEEEEECCCCCCHHHHHHHHhCCC
Confidence            589999999999999999999876

The ABC ATPase, RNase L inhibitor (RLI), is a key enzyme in ribosomal biogenesis, formation of translation preinitiation complexes, and assembly of HIV capsids. 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 of more than 48%. The high degree of evolutionary conservation suggests that RLI performs a central role in archaeal and eukaryotic physiology.

>PRK06067 flagellar accessory protein FlaH; Validated

Probab=96.28  E-value=0.033  Score=56.64  Aligned_cols=38  Identities=24%  Similarity=0.380  Sum_probs=29.4

Q ss_pred             CCCCccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcC
Q 005987          174 DKFSTNVLVITGQAGVGKTATVRQIASHL---GARLYEWDT  211 (666)
Q Consensus       174 g~~~~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~na  211 (666)
                      |-++..+++++||||+|||+++..++.+.   |..++.+..
T Consensus        21 G~~~g~~~~i~G~~GsGKt~l~~~~~~~~~~~g~~~~y~~~   61 (234)
T PRK06067         21 GIPFPSLILIEGDHGTGKSVLSQQFVYGALKQGKKVYVITT   61 (234)
T ss_pred             CCcCCcEEEEECCCCCChHHHHHHHHHHHHhCCCEEEEEEc
Confidence            44456789999999999999999997653   566666554

>cd01866 Rab2 Rab2 subfamily

Probab=96.28  E-value=0.13  Score=49.15  Aligned_cols=22  Identities=32%  Similarity=0.582  Sum_probs=19.8

Q ss_pred             EEEEECCCCchHHHHHHHHHHH
Q 005987          180 VLVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAke  201 (666)
                      -+++.|+||+|||+++..++..
T Consensus         6 ki~vvG~~~vGKSsLl~~l~~~   27 (168)
T cd01866           6 KYIIIGDTGVGKSCLLLQFTDK   27 (168)
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            4899999999999999999864

Rab2 is localized on cis-Golgi membranes and interacts with Golgi matrix proteins. Rab2 is also implicated in the maturation of vesicular tubular clusters (VTCs), which are microtubule-associated intermediates in transport between the ER and Golgi apparatus. In plants, Rab2 regulates vesicle trafficking between the ER and the Golgi bodies and is important to pollen tube growth. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key featur

>cd04119 RJL RJL (RabJ-Like) subfamily

Probab=96.27  E-value=0.084  Score=49.69  Aligned_cols=22  Identities=23%  Similarity=0.543  Sum_probs=19.7

Q ss_pred             EEEECCCCchHHHHHHHHHHHc
Q 005987          181 LVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       181 LLL~GPpG~GKTtla~~LAkel  202 (666)
                      +++.|++|+||||++..++..-
T Consensus         3 i~~vG~~~vGKTsli~~l~~~~   24 (168)
T cd04119           3 VISMGNSGVGKSCIIKRYCEGR   24 (168)
T ss_pred             EEEECCCCCCHHHHHHHHHhCC
Confidence            7899999999999999998753

RJLs are found in many protists and as chimeras with C-terminal DNAJ domains in deuterostome metazoa. They are not found in plants, fungi, and protostome metazoa, suggesting a horizontal gene transfer between protists and deuterostome metazoa. RJLs lack any known membrane targeting signal and contain a degenerate phosphate/magnesium-binding 3 (PM3) motif, suggesting an impaired ability to hydrolyze GTP. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization.

>cd01869 Rab1_Ypt1 Rab1/Ypt1 subfamily

Probab=96.27  E-value=0.12  Score=49.01  Aligned_cols=22  Identities=32%  Similarity=0.619  Sum_probs=19.1

Q ss_pred             EEEEECCCCchHHHHHHHHHHH
Q 005987          180 VLVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAke  201 (666)
                      -+++.|++||||||++..++..
T Consensus         4 ki~i~G~~~vGKSsli~~~~~~   25 (166)
T cd01869           4 KLLLIGDSGVGKSCLLLRFADD   25 (166)
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            3788899999999999998753

Rab1 is found in every eukaryote and is a key regulatory component for the transport of vesicles from the ER to the Golgi apparatus. Studies on mutations of Ypt1, the yeast homolog of Rab1, showed that this protein is necessary for the budding of vesicles of the ER as well as for their transport to, and fusion with, the Golgi apparatus. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to t

>COG1122 CbiO ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]

Probab=96.27  E-value=0.034  Score=56.76  Aligned_cols=24  Identities=21%  Similarity=0.486  Sum_probs=21.8

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      ..++|.||+|+||||+++.++--+
T Consensus        31 e~~~i~G~nGsGKSTL~~~l~GLl   54 (235)
T COG1122          31 ERVLLIGPNGSGKSTLLKLLNGLL   54 (235)
T ss_pred             CEEEEECCCCCCHHHHHHHHcCcC
Confidence            579999999999999999998766

>COG0563 Adk Adenylate kinase and related kinases [Nucleotide transport and metabolism]

Probab=96.26  E-value=0.004  Score=60.82  Aligned_cols=28  Identities=29%  Similarity=0.550  Sum_probs=24.1

Q ss_pred             EEEEECCCCchHHHHHHHHHHHcCCcEE
Q 005987          180 VLVITGQAGVGKTATVRQIASHLGARLY  207 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkelg~~vi  207 (666)
                      .++|-||||+||||+|+.||+.+++.-+
T Consensus         2 riiilG~pGaGK~T~A~~La~~~~i~hl   29 (178)
T COG0563           2 RILILGPPGAGKSTLAKKLAKKLGLPHL   29 (178)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHhCCcEE
Confidence            4889999999999999999999765443

>KOG1051 consensus Chaperone HSP104 and related ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones]

Probab=96.26  E-value=0.023  Score=67.42  Aligned_cols=166  Identities=16%  Similarity=0.216  Sum_probs=96.1

Q ss_pred             ccccccC-HHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcC----------CcEEEEcCCCchh
Q 005987          148 LEELAVQ-RKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLG----------ARLYEWDTPTPTI  216 (666)
Q Consensus       148 l~eLvg~-~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg----------~~viE~nasd~~~  216 (666)
                      ++-++|. +..++.+.+.|....       . +.-+|.|.||+|||+++.-+|+.+-          ..++.++-     
T Consensus       185 ldPvigr~deeirRvi~iL~Rrt-------k-~NPvLVG~~gvgktaiv~gla~ri~~G~vp~~l~~~~l~~l~~-----  251 (898)
T KOG1051|consen  185 LDPVIGRHDEEIRRVIEILSRKT-------K-NNPVLVGEPGVGKTAIVEGLAQRIATGDVPETLKDKKLIALDF-----  251 (898)
T ss_pred             CCCccCCchHHHHHHHHHHhccC-------C-CCceEEecCCCCchhHHHHHHHHhhcCCCCccccccceEEEEh-----
Confidence            4556676 888888888876522       1 4678999999999999999999871          11111111     


Q ss_pred             hhhhhhcccCCcccc-chhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhH---HHHHHHHHHHHHhcC
Q 005987          217 WQEYMHNCKTGLEYT-SKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTA---FERLRQCLLLLVRST  292 (666)
Q Consensus       217 ~~e~l~~~~~g~~~~-s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~---~~~l~~~L~~l~~~~  292 (666)
                           .....|..+. .....++..+.++..           .+.+.||+|||++-+.+...   .....+.|...+..+
T Consensus       252 -----g~l~aGa~~rge~E~rlk~l~k~v~~-----------~~~gvILfigelh~lvg~g~~~~~~d~~nlLkp~L~rg  315 (898)
T KOG1051|consen  252 -----GSLVAGAKRRGEFEERLKELLKEVES-----------GGGGVILFLGELHWLVGSGSNYGAIDAANLLKPLLARG  315 (898)
T ss_pred             -----hhcccCcccchHHHHHHHHHHHHHhc-----------CCCcEEEEecceeeeecCCCcchHHHHHHhhHHHHhcC
Confidence                 1112333332 122344555554432           13468999999997543211   112334455556666


Q ss_pred             CCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHH
Q 005987          293 HIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQ  351 (666)
Q Consensus       293 ~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~  351 (666)
                      .   +.+|+.++    .+.+.+.++. .+.+++ +...+..+-|+......+|......
T Consensus       316 ~---l~~IGatT----~e~Y~k~iek-dPalEr-rw~l~~v~~pS~~~~~~iL~~l~~~  365 (898)
T KOG1051|consen  316 G---LWCIGATT----LETYRKCIEK-DPALER-RWQLVLVPIPSVENLSLILPGLSER  365 (898)
T ss_pred             C---eEEEeccc----HHHHHHHHhh-Ccchhh-CcceeEeccCcccchhhhhhhhhhh
Confidence            5   56666543    2245555554 334454 5777888888876656566555444

>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=96.25  E-value=0.0035  Score=59.21  Aligned_cols=27  Identities=26%  Similarity=0.407  Sum_probs=24.0

Q ss_pred             EECCCCchHHHHHHHHHHHcCCcEEEE
Q 005987          183 ITGQAGVGKTATVRQIASHLGARLYEW  209 (666)
Q Consensus       183 L~GPpG~GKTtla~~LAkelg~~viE~  209 (666)
                      |.||||+||||+++.||+.+|+..+..
T Consensus         1 i~G~PgsGK~t~~~~la~~~~~~~is~   27 (151)
T PF00406_consen    1 ILGPPGSGKGTQAKRLAKRYGLVHISV   27 (151)
T ss_dssp             EEESTTSSHHHHHHHHHHHHTSEEEEH
T ss_pred             CcCCCCCChHHHHHHHHHhcCcceech
Confidence            579999999999999999999876653

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 ....

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

Probab=96.25  E-value=0.015  Score=58.79  Aligned_cols=39  Identities=23%  Similarity=0.253  Sum_probs=27.8

Q ss_pred             CCCCccEEEEECCCCchHHHHHHHHHHHc----CCcEEEEcCC
Q 005987          174 DKFSTNVLVITGQAGVGKTATVRQIASHL----GARLYEWDTP  212 (666)
Q Consensus       174 g~~~~k~LLL~GPpG~GKTtla~~LAkel----g~~viE~nas  212 (666)
                      |-++...+|++||||+|||+++..++.+.    |-.++.+...
T Consensus        15 Gip~gs~~li~G~~GsGKT~l~~q~l~~~~~~~ge~vlyvs~e   57 (226)
T PF06745_consen   15 GIPKGSVVLISGPPGSGKTTLALQFLYNGLKNFGEKVLYVSFE   57 (226)
T ss_dssp             SEETTSEEEEEESTTSSHHHHHHHHHHHHHHHHT--EEEEESS
T ss_pred             CCCCCcEEEEEeCCCCCcHHHHHHHHHHhhhhcCCcEEEEEec
Confidence            44455789999999999999988766433    7777776643

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 ....

>COG1125 OpuBA ABC-type proline/glycine betaine transport systems, ATPase components [Amino acid transport and metabolism]

Probab=96.24  E-value=0.031  Score=56.86  Aligned_cols=24  Identities=38%  Similarity=0.653  Sum_probs=21.4

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      -.++|.||+||||||+.+.+-+-+
T Consensus        28 ef~vliGpSGsGKTTtLkMINrLi   51 (309)
T COG1125          28 EFLVLIGPSGSGKTTTLKMINRLI   51 (309)
T ss_pred             eEEEEECCCCCcHHHHHHHHhccc
Confidence            479999999999999999987765

>TIGR02524 dot_icm_DotB Dot/Icm secretion system ATPase DotB

Probab=96.23  E-value=0.013  Score=63.56  Aligned_cols=24  Identities=33%  Similarity=0.605  Sum_probs=22.7

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      ..++++||+|+||||+++++++++
T Consensus       135 glilI~GpTGSGKTTtL~aLl~~i  158 (358)
T TIGR02524       135 GIVFITGATGSGKSTLLAAIIREL  158 (358)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHH
Confidence            589999999999999999999987

Members of this protein family are the DotB component of Dot/Icm secretion systems, as found in obligate intracellular pathogens Legionella pneumophila and Coxiella burnetii. While this system resembles type IV secretion systems and has been called a form of type IV, the liturature now seems to favor calling this the Dot/Icm system. This family is most closely related to TraJ proteins of plasmid transfer, rather than to proteins of other type IV secretion systems.

>PLN02165 adenylate isopentenyltransferase

Probab=96.23  E-value=0.0048  Score=65.73  Aligned_cols=30  Identities=27%  Similarity=0.500  Sum_probs=27.4

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEEE
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLYE  208 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~viE  208 (666)
                      ++++|.||+|+|||+++..||+.++++++.
T Consensus        44 ~iivIiGPTGSGKStLA~~LA~~l~~eIIs   73 (334)
T PLN02165         44 KVVVIMGATGSGKSRLSVDLATRFPSEIIN   73 (334)
T ss_pred             CEEEEECCCCCcHHHHHHHHHHHcCCceec
Confidence            589999999999999999999999987664

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

Probab=96.22  E-value=0.0036  Score=61.45  Aligned_cols=24  Identities=25%  Similarity=0.548  Sum_probs=22.5

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      ..++|.||+|+||||++++++..+
T Consensus        26 ~~i~I~G~tGSGKTTll~aL~~~i   49 (186)
T cd01130          26 KNILISGGTGSGKTTLLNALLAFI   49 (186)
T ss_pred             CEEEEECCCCCCHHHHHHHHHhhc
Confidence            589999999999999999999887

The homohexamer, VirB11 is one of eleven Vir proteins, which are required for T-pilus biogenesis and virulence in the transfer of T-DNA from the Ti (tumor-inducing) plasmid of bacterial to plant cells. The pilus is a fibrous cell surface organelle, which mediates adhesion between bacteria during conjugative transfer or between bacteria and host eukaryotic cells during infection. VirB11- related ATPases include the archaeal flagella biosynthesis protein and the pilus assembly proteins CpaF/TadA and TrbB. This alignment contains the C-terminal domain, which is the ATPase.

>PTZ00293 thymidine kinase; Provisional

Probab=96.22  E-value=0.035  Score=55.49  Aligned_cols=33  Identities=21%  Similarity=0.194  Sum_probs=25.8

Q ss_pred             cEEEEECCCCchHHH-HHHHHHHHc--CCcEEEEcC
Q 005987          179 NVLVITGQAGVGKTA-TVRQIASHL--GARLYEWDT  211 (666)
Q Consensus       179 k~LLL~GPpG~GKTt-la~~LAkel--g~~viE~na  211 (666)
                      ++-+++||-|+|||| |++.+.+..  |..++-+..
T Consensus         5 ~i~vi~GpMfSGKTteLLr~i~~y~~ag~kv~~~kp   40 (211)
T PTZ00293          5 TISVIIGPMFSGKTTELMRLVKRFTYSEKKCVVIKY   40 (211)
T ss_pred             EEEEEECCCCChHHHHHHHHHHHHHHcCCceEEEEe
Confidence            578999999999999 888876644  566666644

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

Probab=96.21  E-value=0.005  Score=60.99  Aligned_cols=33  Identities=36%  Similarity=0.530  Sum_probs=26.9

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEEEEcC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLYEWDT  211 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~viE~na  211 (666)
                      ++++|.||+|+|||.++-.+|+++|..|+..+.
T Consensus         2 ~v~~i~GpT~tGKt~~ai~lA~~~g~pvI~~Dr   34 (233)
T PF01745_consen    2 KVYLIVGPTGTGKTALAIALAQKTGAPVISLDR   34 (233)
T ss_dssp             EEEEEE-STTSSHHHHHHHHHHHH--EEEEE-S
T ss_pred             cEEEEECCCCCChhHHHHHHHHHhCCCEEEecc
Confidence            579999999999999999999999999998764

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

>cd03233 ABC_PDR_domain1 The pleiotropic drug resistance (PDR) family of ATP-binding cassette (ABC) transporters

Probab=96.20  E-value=0.041  Score=54.68  Aligned_cols=25  Identities=16%  Similarity=0.473  Sum_probs=22.8

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLG  203 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg  203 (666)
                      ..+.|.||+|+||||++++|+..+.
T Consensus        34 e~~~i~G~nGsGKSTLl~~l~G~~~   58 (202)
T cd03233          34 EMVLVLGRPGSGCSTLLKALANRTE   58 (202)
T ss_pred             cEEEEECCCCCCHHHHHHHhcccCC
Confidence            5899999999999999999998764

PDR is a well-described phenomenon occurring in fungi and shares several similarities with processes in bacteria and higher eukaryotes. This PDR subfamily represents domain I of its (ABC-IM)2 organization. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds including sugars, ions, peptides, and more complex organic molecules. 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.

>PRK14712 conjugal transfer nickase/helicase TraI; Provisional

Probab=96.19  E-value=0.12  Score=65.37  Aligned_cols=165  Identities=19%  Similarity=0.286  Sum_probs=80.3

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc-------CCcEEEEcCCCchhhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL-------GARLYEWDTPTPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTS  251 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel-------g~~viE~nasd~~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~  251 (666)
                      +.++|.|.|||||||+++.+...+       ++.|+-+ +|...-. ..+..  .|+. ..   -+..||.....+... 
T Consensus       853 r~~~IqG~AGTGKTT~l~~i~~~~~~l~e~~g~~V~gl-APTgkAa-~~L~e--~Gi~-A~---TIasfL~~~~~~~~~-  923 (1623)
T PRK14712        853 RFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRVVGL-GPTHRAV-GEMRS--AGVD-AQ---TLASFLHDTQLQQRS-  923 (1623)
T ss_pred             ceEEEEeCCCCCHHHHHHHHHHHHHHHhhccCceEEEE-echHHHH-HHHHH--hCch-Hh---hHHHHhccccchhhc-
Confidence            689999999999999987775532       4555544 4432211 11211  2332 12   233444321100000 


Q ss_pred             CCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcCCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEE
Q 005987          252 PSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKV  331 (666)
Q Consensus       252 ~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I  331 (666)
                        .........||||||+-+++... +..    |..++.... -.|++++|.....+... ..   +++.++.+.++..+
T Consensus       924 --~~~~~~~~~llIVDEASMV~~~~-m~~----ll~~~~~~g-arvVLVGD~~QL~sV~a-G~---~F~~lq~~~~~~ta  991 (1623)
T PRK14712        924 --GETPDFSNTLFLLDESSMVGNTD-MAR----AYALIAAGG-GRAVASGDTDQLQAIAP-GQ---PFRLQQTRSAADVV  991 (1623)
T ss_pred             --ccCCCCCCcEEEEEccccccHHH-HHH----HHHhhhhCC-CEEEEEcchhhcCCCCC-CH---HHHHHHHcCCCCeE
Confidence              00000124699999999876432 222    333334322 25677888643332221 11   12222222123333


Q ss_pred             EeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCcHHHHHHHHHH
Q 005987          332 ALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASGGDIRQAITSLQF  381 (666)
Q Consensus       332 ~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~s~GDIR~AIn~LQf  381 (666)
                      .+..+        .+         -.++....+.....|++..|+..|+-
T Consensus       992 ~L~eI--------~R---------Q~~elr~AV~~~~~g~~~~AL~~L~~ 1024 (1623)
T PRK14712        992 IMKEI--------VR---------QTPELREAVYSLINRDVERALSGLER 1024 (1623)
T ss_pred             EeCee--------ec---------CCHHHHHHHHHHHcCCHHHHHHHHhh
Confidence            32211        11         13445556666677888888888863

>smart00175 RAB Rab subfamily of small GTPases

Probab=96.18  E-value=0.097  Score=49.19  Aligned_cols=21  Identities=24%  Similarity=0.661  Sum_probs=19.2

Q ss_pred             EEEECCCCchHHHHHHHHHHH
Q 005987          181 LVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       181 LLL~GPpG~GKTtla~~LAke  201 (666)
                      +++.|+||+||||+++.+...
T Consensus         3 v~v~G~~~~GKTtli~~l~~~   23 (164)
T smart00175        3 IILIGDSGVGKSSLLSRFTDG   23 (164)
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            789999999999999999765

Rab GTPases are implicated in vesicle trafficking.

>PRK12338 hypothetical protein; Provisional

Probab=96.18  E-value=0.0047  Score=65.44  Aligned_cols=29  Identities=24%  Similarity=0.489  Sum_probs=26.4

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEE
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLY  207 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~vi  207 (666)
                      .+++++|+||+||||+++.||+.+|+..+
T Consensus         5 ~ii~i~G~sGsGKST~a~~la~~l~~~~~   33 (319)
T PRK12338          5 YVILIGSASGIGKSTIASELARTLNIKHL   33 (319)
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHCCCeEE
Confidence            58999999999999999999999997643

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

Probab=96.18  E-value=0.03  Score=58.23  Aligned_cols=34  Identities=21%  Similarity=0.540  Sum_probs=26.9

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcC----CcEEEEcCC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLG----ARLYEWDTP  212 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg----~~viE~nas  212 (666)
                      ..+|++||+|+||||++-++-..++    ..++.+..|
T Consensus       126 GLILVTGpTGSGKSTTlAamId~iN~~~~~HIlTIEDP  163 (353)
T COG2805         126 GLILVTGPTGSGKSTTLAAMIDYINKHKAKHILTIEDP  163 (353)
T ss_pred             ceEEEeCCCCCcHHHHHHHHHHHHhccCCcceEEecCc
Confidence            5899999999999999988887774    455555544

>COG1134 TagH ABC-type polysaccharide/polyol phosphate transport system, ATPase component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]

Probab=96.17  E-value=0.016  Score=58.62  Aligned_cols=25  Identities=28%  Similarity=0.428  Sum_probs=22.4

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLG  203 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg  203 (666)
                      -.+=|.|++|+||||+.+.||..+-
T Consensus        54 e~vGiiG~NGaGKSTLlkliaGi~~   78 (249)
T COG1134          54 ERVGIIGHNGAGKSTLLKLIAGIYK   78 (249)
T ss_pred             CEEEEECCCCCcHHHHHHHHhCccC
Confidence            3688999999999999999999873

>cd03230 ABC_DR_subfamily_A This family of ATP-binding proteins belongs to a multisubunit transporter involved in drug resistance (BcrA and DrrA), nodulation, lipid transport, and lantibiotic immunity

Probab=96.16  E-value=0.029  Score=54.23  Aligned_cols=24  Identities=29%  Similarity=0.498  Sum_probs=22.3

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      ..+.|.||+|+||||+++++|..+
T Consensus        27 e~~~i~G~nGsGKStLl~~l~G~~   50 (173)
T cd03230          27 EIYGLLGPNGAGKTTLIKIILGLL   50 (173)
T ss_pred             cEEEEECCCCCCHHHHHHHHhCCC
Confidence            589999999999999999999875

In bacteria and archaea, these transporters usually include an ATP-binding protein and one or two integral membrane proteins. Eukaryote systems of the ABCA subfamily display ABC domains that are quite similar to this family. The ATP-binding domain shows the highest similarity between all members of the ABC transporter 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.

>PRK12608 transcription termination factor Rho; Provisional

Probab=96.15  E-value=0.015  Score=62.88  Aligned_cols=25  Identities=28%  Similarity=0.347  Sum_probs=22.3

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLG  203 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg  203 (666)
                      .-.+|+|||||||||+++.+|+.+.
T Consensus       134 QR~LIvG~pGtGKTTLl~~la~~i~  158 (380)
T PRK12608        134 QRGLIVAPPRAGKTVLLQQIAAAVA  158 (380)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHHH
Confidence            3589999999999999999999873

>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=96.14  E-value=0.059  Score=52.10  Aligned_cols=24  Identities=38%  Similarity=0.551  Sum_probs=22.4

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      ..+.|.||+|+||||++++|+..+
T Consensus        29 e~~~i~G~nGsGKStLl~~l~G~~   52 (173)
T cd03246          29 ESLAIIGPSGSGKSTLARLILGLL   52 (173)
T ss_pred             CEEEEECCCCCCHHHHHHHHHhcc
Confidence            589999999999999999999876

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

>cd00154 Rab Rab family

Probab=96.14  E-value=0.16  Score=46.83  Aligned_cols=22  Identities=32%  Similarity=0.581  Sum_probs=19.4

Q ss_pred             EEEECCCCchHHHHHHHHHHHc
Q 005987          181 LVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       181 LLL~GPpG~GKTtla~~LAkel  202 (666)
                      +++.|+||+||||++..+...-
T Consensus         3 i~~~G~~~~GKStl~~~l~~~~   24 (159)
T cd00154           3 IVLIGDSGVGKTSLLLRFVDGK   24 (159)
T ss_pred             EEEECCCCCCHHHHHHHHHhCc
Confidence            7899999999999999987653

Rab GTPases form the largest family within the Ras superfamily. There are at least 60 Rab genes in the human genome, and a number of Rab GTPases are conserved from yeast to humans. Rab GTPases are small, monomeric proteins that function as molecular switches to regulate vesicle trafficking pathways. The different Rab GTPases are localized to the cytosolic face of specific intracellular membranes, where they regulate distinct steps in membrane traffic pathways. In the GTP-bound form, Rab GTPases recruit specific sets of effector proteins onto membranes. Through their effectors, Rab GTPases regulate vesicle formation, actin- and tubulin-dependent vesicle movement, and membrane fusion. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide di

>PRK09354 recA recombinase A; Provisional

Probab=96.14  E-value=0.047  Score=58.74  Aligned_cols=39  Identities=18%  Similarity=0.140  Sum_probs=29.4

Q ss_pred             CCCCccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcCC
Q 005987          174 DKFSTNVLVITGQAGVGKTATVRQIASHL---GARLYEWDTP  212 (666)
Q Consensus       174 g~~~~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~nas  212 (666)
                      |-++.++.+|+||||+||||++..++.+.   |..++.+.+.
T Consensus        56 Gip~G~IteI~G~~GsGKTtLal~~~~~~~~~G~~~~yId~E   97 (349)
T PRK09354         56 GLPRGRIVEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAE   97 (349)
T ss_pred             CCcCCeEEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEECCc
Confidence            44555789999999999999998776543   6666666543

>PRK05541 adenylylsulfate kinase; Provisional

Probab=96.13  E-value=0.0045  Score=60.06  Aligned_cols=25  Identities=40%  Similarity=0.546  Sum_probs=23.5

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLG  203 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg  203 (666)
                      ..++|+|++|+||||+++.|++.+.
T Consensus         8 ~~I~i~G~~GsGKst~a~~l~~~l~   32 (176)
T PRK05541          8 YVIWITGLAGSGKTTIAKALYERLK   32 (176)
T ss_pred             CEEEEEcCCCCCHHHHHHHHHHHHH
Confidence            5899999999999999999999985

>cd04177 RSR1 RSR1 subgroup

Probab=96.12  E-value=0.089  Score=50.15  Aligned_cols=23  Identities=35%  Similarity=0.589  Sum_probs=20.1

Q ss_pred             EEEEECCCCchHHHHHHHHHHHc
Q 005987          180 VLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      .++|.|+||+||||+++.+++..
T Consensus         3 ki~liG~~~~GKTsli~~~~~~~   25 (168)
T cd04177           3 KIVVLGAGGVGKSALTVQFVQNV   25 (168)
T ss_pred             EEEEECCCCCCHHHHHHHHHhCC
Confidence            38899999999999999998654

RSR1/Bud1p is a member of the Rap subfamily of the Ras family that is found in fungi. In budding yeasts, RSR1 is involved in selecting a site for bud growth on the cell cortex, which directs the establishment of cell polarization. The Rho family GTPase cdc42 and its GEF, cdc24, then establish an axis of polarized growth by organizing the actin cytoskeleton and secretory apparatus at the bud site. It is believed that cdc42 interacts directly with RSR1 in vivo. In filamentous fungi, polar growth occurs at the tips of hypha and at novel growth sites along the extending hypha. In Ashbya gossypii, RSR1 is a key regulator of hyphal growth, localizing at the tip region and regulating in apical polarization of the actin cytoskeleton. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key featu

>COG0529 CysC Adenylylsulfate kinase and related kinases [Inorganic ion transport and metabolism]

Probab=96.11  E-value=0.073  Score=51.30  Aligned_cols=33  Identities=30%  Similarity=0.529  Sum_probs=28.9

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL---GARLYEWDT  211 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel---g~~viE~na  211 (666)
                      ..+.|+|.+|+||||+|.+|++.|   |+.+.-+..
T Consensus        24 ~viW~TGLSGsGKSTiA~ale~~L~~~G~~~y~LDG   59 (197)
T COG0529          24 AVIWFTGLSGSGKSTIANALEEKLFAKGYHVYLLDG   59 (197)
T ss_pred             eEEEeecCCCCCHHHHHHHHHHHHHHcCCeEEEecC
Confidence            589999999999999999999987   777776654

>TIGR02768 TraA_Ti Ti-type conjugative transfer relaxase TraA

Probab=96.11  E-value=0.03  Score=66.63  Aligned_cols=34  Identities=24%  Similarity=0.454  Sum_probs=27.0

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcCCC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL---GARLYEWDTPT  213 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel---g~~viE~nasd  213 (666)
                      +..+|+|+|||||||+++++...+   |+.|+-+ +|.
T Consensus       369 ~~~il~G~aGTGKTtll~~i~~~~~~~g~~V~~~-ApT  405 (744)
T TIGR02768       369 DIAVVVGRAGTGKSTMLKAAREAWEAAGYRVIGA-ALS  405 (744)
T ss_pred             CEEEEEecCCCCHHHHHHHHHHHHHhCCCeEEEE-eCc
Confidence            589999999999999999987654   7776654 443

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.

>cd04136 Rap_like Rap-like subfamily

Probab=96.10  E-value=0.1  Score=49.06  Aligned_cols=22  Identities=36%  Similarity=0.540  Sum_probs=19.1

Q ss_pred             EEEEECCCCchHHHHHHHHHHH
Q 005987          180 VLVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAke  201 (666)
                      -+++.|+||+||||++..++..
T Consensus         3 ki~i~G~~~vGKTsl~~~~~~~   24 (163)
T cd04136           3 KVVVLGSGGVGKSALTVQFVQG   24 (163)
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            3788899999999999988854

The Rap subfamily consists of the Rap1, Rap2, and RSR1. Rap subfamily proteins perform different cellular functions, depending on the isoform and its subcellular localization. For example, in rat salivary gland, neutrophils, and platelets, Rap1 localizes to secretory granules and is believed to regulate exocytosis or the formation of secretory granules. Rap1 has also been shown to localize in the Golgi of rat fibroblasts, zymogen granules, plasma membrane, and microsomal membrane of the pancreatic acini, as well as in the endocytic compartment of skeletal muscle cells and fibroblasts. Rap1 localizes in the nucleus of human oropharyngeal squamous cell carcinomas (SCCs) and cell lines. Rap1 plays a role in phagocytosis by controlling the binding of adhesion receptors (typically integrins) to their ligands. In yeast, Rap1 has been implicated in multiple functions, including activation and silencing of transcription and maintenance of telomeres.

>PRK09825 idnK D-gluconate kinase; Provisional

Probab=96.06  E-value=0.0065  Score=59.23  Aligned_cols=27  Identities=26%  Similarity=0.465  Sum_probs=24.8

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGAR  205 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~  205 (666)
                      .+++|.||+|+||||+++.++..++..
T Consensus         4 e~i~l~G~sGsGKSTl~~~la~~l~~~   30 (176)
T PRK09825          4 ESYILMGVSGSGKSLIGSKIAALFSAK   30 (176)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHhcCCE
Confidence            579999999999999999999998864

>PRK05907 hypothetical protein; Provisional

Probab=96.05  E-value=0.88  Score=48.52  Aligned_cols=91  Identities=12%  Similarity=0.039  Sum_probs=69.9

Q ss_pred             EEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHc-CCcHHHHHHHHHHHhcCCCCcccccccCCCCCCCccccCCC
Q 005987          331 VALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQAS-GGDIRQAITSLQFSSLKQDPMLNLSLSISKPNFPEEKADGH  409 (666)
Q Consensus       331 I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~s-~GDIR~AIn~LQf~~~~~~~~~~~~~~~~~~~~~k~~~~~~  409 (666)
                      +.|.++...++.+.+...+.++|..+++++++.++..+ +||+..+.+-|+-+++-.....              +.+ .
T Consensus       129 ~e~~~l~e~~L~~Wi~~~~~~~g~~i~~~a~~~L~~~~~~~nL~~l~~EleKL~ly~g~~~--------------~It-~  193 (311)
T PRK05907        129 GEWFADRDKRIAQLLIQRAKELGISCSLGLASLFVSKFPQTGLFEILSEFQKLLCQMGKKE--------------SLE-A  193 (311)
T ss_pred             cccCCCCHHHHHHHHHHHHHHcCCCcCHHHHHHHHHHccCCCHHHHHHHHHHHHHhcCCCC--------------eEC-H
Confidence            48999999999999999999999999999999999999 6999999999998876321100              000 0


Q ss_pred             CCcccccCCccccchHHHHhHHhhCCC
Q 005987          410 GGFSIQFGRDETLSLFHALGKFLHNKR  436 (666)
Q Consensus       410 ~~~~~~~~RD~~l~lFhalGkil~~Kr  436 (666)
                      +.+..+..+-..-++|+-+..|+.++.
T Consensus       194 e~V~~lv~~s~e~nIF~L~dai~~~~~  220 (311)
T PRK05907        194 SDIQSFVVKKEAASLWKLRDALLRRDR  220 (311)
T ss_pred             HHHHHHhcCcccccHHHHHHHHHccCH
Confidence            112344566667889998888887664

>cd01672 TMPK Thymidine monophosphate kinase (TMPK), also known as thymidylate kinase, catalyzes the phosphorylation of thymidine monophosphate (TMP) to thymidine diphosphate (TDP) utilizing ATP as its preferred phophoryl donor

Probab=96.05  E-value=0.0081  Score=58.82  Aligned_cols=34  Identities=29%  Similarity=0.463  Sum_probs=29.2

Q ss_pred             EEEEECCCCchHHHHHHHHHHHc---CCcEEEEcCCC
Q 005987          180 VLVITGQAGVGKTATVRQIASHL---GARLYEWDTPT  213 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkel---g~~viE~nasd  213 (666)
                      .++|.||+|+||||+++.|++.+   |+.++....+.
T Consensus         2 ~I~ieG~~GsGKtT~~~~L~~~l~~~g~~v~~~~~~~   38 (200)
T cd01672           2 FIVFEGIDGAGKTTLIELLAERLEARGYEVVLTREPG   38 (200)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEeCCC
Confidence            68899999999999999999998   77777665544

TMPK represents the rate-limiting step in either de novo or salvage biosynthesis of thymidine triphosphate (TTP).

>PF03193 DUF258: Protein of unknown function, DUF258; InterPro: IPR004881 This entry contains Escherichia coli (strain K12) RsgA, which may play a role in 30S ribosomal subunit biogenesis

Probab=96.05  E-value=0.0045  Score=59.21  Aligned_cols=45  Identities=22%  Similarity=0.398  Sum_probs=31.2

Q ss_pred             HHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEc
Q 005987          155 RKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWD  210 (666)
Q Consensus       155 ~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~n  210 (666)
                      ..-+++|+.+|+.           +..+|.||+|+||||++..|.......+-++.
T Consensus        23 ~~g~~~l~~~l~~-----------k~~vl~G~SGvGKSSLiN~L~~~~~~~t~~is   67 (161)
T PF03193_consen   23 GEGIEELKELLKG-----------KTSVLLGQSGVGKSSLINALLPEAKQKTGEIS   67 (161)
T ss_dssp             TTTHHHHHHHHTT-----------SEEEEECSTTSSHHHHHHHHHTSS----S---
T ss_pred             CcCHHHHHHHhcC-----------CEEEEECCCCCCHHHHHHHHHhhcchhhhhhh
Confidence            3456777777764           58999999999999999999887755444433

RsgA is an unusual circulary permuted GTPase that catalyzes rapid hydrolysis of GTP with a slow catalytic turnover. It is dispensible for viability, but important for overall fitness. The intrinsic GTPase activity is stimulated by the presence of 30S (160-fold increase in kcat) or 70S (96 fold increase in kcat) ribosomes []. The GTPase is inhibited by aminoglycoside antibiotics such as neomycin and paromycin [] streptomycin and spectinomycin []. This inhibition is not due to competition for binding sites on the 30S or 70S ribosome []. ; GO: 0003924 GTPase activity, 0005525 GTP binding; PDB: 2YKR_W 2YV5_A 1T9H_A 2RCN_A 4A2I_V 1U0L_B.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	666
2chg_A	226	Replication Factor C Domains 1 And 2 Length = 226		1e-06
2chq_A	319	Replication Factor C Adpnp Complex Length = 319		2e-06
1sxj_A	516	Crystal Structure Of The Eukaryotic Clamp Loader (R		3e-05

>pdb|2CHG|A Chain A, Replication Factor C Domains 1 And 2 Length = 226

Iteration: 1
 Score = 51.6 bits (122), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 54/246 (21%), Positives = 103/246 (41%), Gaps = 47/246 (19%)
Query: 137 QLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVR 196
           ++W EKY+PR+L+E+  Q + ++ ++ + E +        +   L+ +G  G GKTAT  
Sbjct: 5   EIWVEKYRPRTLDEVVGQDEVIQRLKGYVERK--------NIPHLLFSGPPGTGKTATAI 56
Query: 197 QIASHLGARLYEWDTPTPTIWQEYMHNCKTGLEYTSKLDE--FENFVERIRRYGSTSPSI 254
            +A  L                 +  N +      +  DE   +    +I+ +  T+P I
Sbjct: 57  ALARDL-----------------FGENWRDNFIEMNASDERGIDVVRHKIKEFARTAP-I 98
Query: 255 PGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHIPTAVVLTECGKADSVDSTAQ 314
            G       L   D    + + A   LR+ + +  +S           C    S +  ++
Sbjct: 99  GGAPFKIIFLDEADALTADAQAA---LRRTMEMYSKS-----------CRFILSCNYVSR 144
Query: 315 SFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASGGDIRQ 374
             E +QS             P+   ++K+ L +IC +E   ++ + ++ +   SGGD R+
Sbjct: 145 IIEPIQS-----RCAVFRFKPVPKEAMKKRLLEICEKEGVKITEDGLEALIYISGGDFRK 199
Query: 375 AITSLQ 380
           AI +LQ
Sbjct: 200 AINALQ 205

>pdb|2CHQ|A Chain A, Replication Factor C Adpnp Complex Length = 319

Iteration: 1
 Score = 51.2 bits (121), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 55/248 (22%), Positives = 104/248 (41%), Gaps = 51/248 (20%)
Query: 137 QLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNV--LVITGQAGVGKTAT 194
           ++W EKY+PR+L+E+  Q + ++ ++ + E +          N+  L+ +G  G GKTAT
Sbjct: 5   EIWVEKYRPRTLDEVVGQDEVIQRLKGYVERK----------NIPHLLFSGPPGTGKTAT 54
Query: 195 VRQIASHLGARLYEWDTPTPTIWQEYMHNCKTGLEYTSKLDE--FENFVERIRRYGSTSP 252
              +A  L                 +  N +      +  DE   +    +I+ +  T+P
Sbjct: 55  AIALARDL-----------------FGENWRDNFIEMNASDERGIDVVRHKIKEFARTAP 97
Query: 253 SIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHIPTAVVLTECGKADSVDST 312
            I G       L   D    + + A   LR+ + +  +S           C    S +  
Sbjct: 98  -IGGAPFKIIFLDEADALTADAQAA---LRRTMEMYSKS-----------CRFILSCNYV 142
Query: 313 AQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASGGDI 372
           ++  E +QS             P+   ++K+ L +IC +E   ++ + ++ +   SGGD 
Sbjct: 143 SRIIEPIQS-----RCAVFRFKPVPKEAMKKRLLEICEKEGVKITEDGLEALIYISGGDF 197
Query: 373 RQAITSLQ 380
           R+AI +LQ
Sbjct: 198 RKAINALQ 205

>pdb|1SXJ|A Chain A, Crystal Structure Of The Eukaryotic Clamp Loader (Replication Factor C, Rfc) Bound To The Dna Sliding Clamp (Proliferating Cell Nuclear Antigen, Pcna) Length = 516

Iteration: 1
 Score = 47.4 bits (111), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 55/260 (21%), Positives = 100/260 (38%), Gaps = 45/260 (17%)
Query: 134 STQQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFST---------NVLVIT 184
           ++ +LW  KY P +L+++   +  V +++ W        K+ F              ++ 
Sbjct: 24  ASDKLWTVKYAPTNLQQVCGNKGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLY 83
Query: 185 GQAGVGKTATVRQIASHLGARLYEW---DTPTPTIWQEYMHNCKTGLEYTSKLDEFENFV 241
           G  G+GKT     +A  LG  + E    D  + T+        K  L+  S +  F    
Sbjct: 84  GPPGIGKTTAAHLVAQELGYDILEQNASDVRSKTLLNA---GVKNALDNMSVVGYF---- 136
Query: 242 ERIRRYGSTSPSIPGESKSSAILLIDDLPVTNG--RTAFERLRQCLLLLVRSTHIPTAVV 299
               ++   + ++ G+     ++++D++   +G  R    +L Q      R T  P  ++
Sbjct: 137 ----KHNEEAQNLNGK---HFVIIMDEVDGMSGGDRGGVGQLAQ----FCRKTSTPLILI 185
Query: 300 LTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTE 359
             E                   + +D   R+   N     SIK  L  I  +E++ L   
Sbjct: 186 CNE--------RNLPKMRPFDRVCLDIQFRRPDAN-----SIKSRLMTIAIREKFKLDPN 232
Query: 360 QIDLVAQASGGDIRQAITSL 379
            ID + Q + GDIRQ I  L
Sbjct: 233 VIDRLIQTTRGDIRQVINLL 252

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	666
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	2e-27
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-18
1sxj_E	354	Activator 1 40 kDa subunit; clamp loader, processi	8e-12
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	1e-06
1sxj_C	340	Activator 1 40 kDa subunit; clamp loader, processi	2e-06
1sxj_C	340	Activator 1 40 kDa subunit; clamp loader, processi	9e-04
2chg_A	226	Replication factor C small subunit; DNA-binding pr	4e-06
2chg_A	226	Replication factor C small subunit; DNA-binding pr	2e-05
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	5e-06
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	2e-05
2chq_A	319	Replication factor C small subunit; DNA-binding pr	8e-06
2chq_A	319	Replication factor C small subunit; DNA-binding pr	2e-05
1sxj_B	323	Activator 1 37 kDa subunit; clamp loader, processi	2e-05
1sxj_B	323	Activator 1 37 kDa subunit; clamp loader, processi	5e-04
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	4e-05
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	3e-04

>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 =  115 bits (290), Expect = 2e-27
 Identities = 78/453 (17%), Positives = 141/453 (31%), Gaps = 94/453 (20%)

Query: 127 DSASASSSTQQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTN------- 179
                  ++ +LW  KY P +L+++   +  V +++ W        K+ F          
Sbjct: 17  LFQGPHMASDKLWTVKYAPTNLQQVCGNKGSVMKLKNWLANWENSKKNSFKHAGKDGSGV 76

Query: 180 --VLVITGQAGVGKTATVRQIASHLGARLYEW---DTPTPTIWQEYMHNCKTGLEYTSKL 234
               ++ G  G+GKT     +A  LG  + E    D  + T+    +   K  L+  S  
Sbjct: 77  FRAAMLYGPPGIGKTTAAHLVAQELGYDILEQNASDVRSKTLLNAGV---KNALDNMS-- 131

Query: 235 DEFENFVERIRRYGSTSPSIPGESKSSAILLID--DLPVTNGRTAFERLRQCLLLLVRST 292
                    +  Y   +      +    ++++D  D      R    +L Q      R T
Sbjct: 132 ---------VVGYFKHNEEAQNLNGKHFVIIMDEVDGMSGGDRGGVGQLAQ----FCRKT 178

Query: 293 HIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQE 352
             P  ++L  C      +           +        +        SIK  L  I  +E
Sbjct: 179 STP--LILI-CN-----ERNLPKMRPFDRV-----CLDIQFRRPDANSIKSRLMTIAIRE 225

Query: 353 QYSLSTEQIDLVAQASGGDIRQAITSLQFSSLKQDPMLNLSLSISKPNFPEEKADGHGGF 412
           ++ L    ID + Q + GDIRQ I  L   S           +I+  N  E         
Sbjct: 226 KFKLDPNVIDRLIQTTRGDIRQVINLLSTISTTTK-------TINHENINEISKAWE--- 275

Query: 413 SIQFGRDETLSLFHALGKFLHNKRETDNLVKMDQDAFVVKDKFSRLPLKMDAPEKVLSQA 472
                ++  L  F    K L  +  +D    +    F + DK +      D         
Sbjct: 276 -----KNIALKPFDIAHKMLDGQIYSD----IGSRNFTLNDKIALYFDDFDF-------- 318

Query: 473 HGQARPVLDFLHENFLDFISEDA------IDDAWAVASYLSDADLLLASFRGRLVRYNEA 526
                     + EN+L             ++     A+ +S  D++      + +R +E 
Sbjct: 319 ------TPLMIQENYLSTRPSVLKPGQSHLEAVAEAANCISLGDIVE-----KKIRSSEQ 367

Query: 527 DNVL---QSAAASVAARGVLFGN--SHPVPPRW 554
              L    +  +SV     + G+         W
Sbjct: 368 LWSLLPLHAVLSSVYPASKVAGHMAGRINFTAW 400

>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 = 88.4 bits (218), Expect = 3e-18
 Identities = 92/639 (14%), Positives = 224/639 (35%), Gaps = 145/639 (22%)

Query: 35  SSTQQLWTDKYK--LCSLEEP---DVQKKNVEHF----LTPSRFEGLVNPKRDLALGSSS 85
           +   Q    +YK  L   E+    +   K+V+      L+    + ++  K  +   S +
Sbjct: 11  TGEHQY---QYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAV---SGT 64

Query: 86  RQQLWTNKNKPCSLEEHAIQ---KENVGRFLTPSRFEGLVNPDHDSASASSSTQQLW--A 140
            +  WT  +K   + +  ++   + N    ++P + E    P   +        +L+   
Sbjct: 65  LRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTE-QRQPSMMTRMYIEQRDRLYNDN 123

Query: 141 EKYKPRSLEELAVQR-KKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKT----ATV 195
           + +   +     V R +   ++R    E L  +K+      ++I G  G GKT       
Sbjct: 124 QVFAKYN-----VSRLQPYLKLRQALLE-LRPAKN------VLIDGVLGSGKTWVALDVC 171

Query: 196 RQ--IASHLGARLYEW------DTPTPTI------WQEYMHNCKTGLEYTSKL-DEFENF 240
               +   +  +++ W      ++P   +        +   N  +  +++S +     + 
Sbjct: 172 LSYKVQCKMDFKIF-WLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSI 230

Query: 241 VERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRT--AFERLRQC-LLLLVRSTHIPTA 297
              +RR       +  +   + +L++ +  V N +   AF     C +LL  R   + T 
Sbjct: 231 QAELRRL------LKSKPYENCLLVLLN--VQNAKAWNAFN--LSCKILLTTRFKQV-TD 279

Query: 298 VVLTECGKADSVDSTAQSF--EELQSILVD-AGARKVAL-------NPITNGSIKRTLSK 347
            +        S+D  + +   +E++S+L+     R   L       NP     I  ++  
Sbjct: 280 FLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRD 339

Query: 348 -ICRQEQYS-LSTEQIDLVAQASGGDIRQAITSLQFSSLKQDPMLNLSLSISKPNFPE-- 403
            +   + +  ++ +++  + ++S       +  L+ +  ++   +   LS+    FP   
Sbjct: 340 GLATWDNWKHVNCDKLTTIIESS-------LNVLEPAEYRK---MFDRLSV----FPPSA 385

Query: 404 ---EKADGHGGFSIQFGRDETLSLFHALGKFLHNKRETDNLVKMDQDAFVVKDKFSRLP- 459
                       S+ +       +   + K LH       LV+        K+    +P 
Sbjct: 386 HIPTIL-----LSLIWFDVIKSDVMVVVNK-LHKYS----LVEKQP-----KESTISIPS 430

Query: 460 --LKMDAPEKVLSQAHGQARPVLDF--LHENF-LDFISEDAIDDAWAVASYLS------D 508
             L++    +     H   R ++D   + + F  D +    +D  +   S++       +
Sbjct: 431 IYLELKVKLENEYALH---RSIVDHYNIPKTFDSDDLIPPYLDQYF--YSHIGHHLKNIE 485

Query: 509 ADLLLASFRGRLVRYNEADNVLQSAAASVAARGVL-------------FGNSHPVPPRWH 555
               +  FR   + +   +  ++  + +  A G +               ++ P   R  
Sbjct: 486 HPERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSILNTLQQLKFYKPYICDNDPKYERLV 545

Query: 556 AIRKPKLWRVDQSSLQKK-KELLKKKFMAWDGSISADVY 593
                 L +++++ +  K  +LL+   MA D +I  + +
Sbjct: 546 NAILDFLPKIEENLICSKYTDLLRIALMAEDEAIFEEAH 584

>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 Length = 354

 Score = 66.1 bits (161), Expect = 8e-12
 Identities = 46/292 (15%), Positives = 99/292 (33%), Gaps = 55/292 (18%)

Query: 137 QLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVR 196
            LW +KY+P+SL  L+   +    +++  ++             L++ G  G GK     
Sbjct: 2   SLWVDKYRPKSLNALSHNEELTNFLKSLSDQ-------PRDLPHLLLYGPNGTGKKTRCM 54

Query: 197 QIASHL-GARLYEWDTPTPTIWQEYMHNCKTGLEYTSKLDEF------------ENFV-- 241
            +   + G  +Y          ++++      LE       +            +  V  
Sbjct: 55  ALLESIFGPGVYR----LKIDVRQFVTASNRKLELNVVSSPYHLEITPSDMGNNDRIVIQ 110

Query: 242 ERIRRYGSTSPSIPGESKSSA-----ILLIDDLPVTNGRTAFERLRQCLLLLVRST---H 293
           E ++           +SK         ++I++            L +     +R T   +
Sbjct: 111 ELLKEVAQMEQVDFQDSKDGLAHRYKCVIINE---------ANSLTKDAQAALRRTMEKY 161

Query: 294 IPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQ 353
                ++  C     + +  +S               +     ++  I   LS +   E+
Sbjct: 162 SKNIRLIMVCDSMSPIIAPIKSQ-----------CLLIRCPAPSDSEISTILSDVVTNER 210

Query: 354 YSLSTEQ-IDLVAQASGGDIRQAITSLQFSSLKQDPMLNLSLSISKPNFPEE 404
             L T+  +  +AQAS G++R ++  L+  +L  +  L  S  I KP++   
Sbjct: 211 IQLETKDILKRIAQASNGNLRVSLLMLESMALNNELALKSSSPIIKPDWIIV 262

>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 Length = 353

 Score = 50.2 bits (120), Expect = 1e-06
 Identities = 14/67 (20%), Positives = 26/67 (38%), Gaps = 1/67 (1%)

Query: 334 NPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASGGDIRQAITSLQFSSLKQDPMLNLS 393
             +   +    L  I  QE        ++ +   S GD+R+ IT LQ +S     + +  
Sbjct: 190 KALDASNAIDRLRFISEQENVKCDDGVLERILDISAGDLRRGITLLQSASKGAQYLGD-G 248

Query: 394 LSISKPN 400
            +I+   
Sbjct: 249 KNITSTQ 255

>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 Length = 340

 Score = 49.4 bits (118), Expect = 2e-06
 Identities = 14/62 (22%), Positives = 27/62 (43%)

Query: 334 NPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASGGDIRQAITSLQFSSLKQDPMLNLS 393
            P+   +I+R ++ +   E+  LS      + + S GD+R+ +  LQ      D      
Sbjct: 167 QPLPQEAIERRIANVLVHEKLKLSPNAEKALIELSNGDMRRVLNVLQSCKATLDNPDEDE 226

Query: 394 LS 395
           +S
Sbjct: 227 IS 228

>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 Length = 340

 Score = 40.9 bits (96), Expect = 9e-04
 Identities = 22/81 (27%), Positives = 34/81 (41%), Gaps = 8/81 (9%)

Query: 128 SASASSSTQQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQA 187
           S    S     W EKY+P +L+E+  Q     EV       +    D+     L+  G  
Sbjct: 4   STEKRSKENLPWVEKYRPETLDEVYGQ----NEVI----TTVRKFVDEGKLPHLLFYGPP 55

Query: 188 GVGKTATVRQIASHLGARLYE 208
           G GKT+T+  +A  +  + Y 
Sbjct: 56  GTGKTSTIVALAREIYGKNYS 76

>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} Length = 226

 Score = 47.6 bits (114), Expect = 4e-06
 Identities = 21/76 (27%), Positives = 39/76 (51%), Gaps = 12/76 (15%)

Query: 134 STQQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNV--LVITGQAGVGK 191
              ++W EKY+PR+L+E+  Q + ++ ++ + E +          N+  L+ +G  G GK
Sbjct: 2   ENFEIWVEKYRPRTLDEVVGQDEVIQRLKGYVERK----------NIPHLLFSGPPGTGK 51

Query: 192 TATVRQIASHLGARLY 207
           TAT   +A  L    +
Sbjct: 52  TATAIALARDLFGENW 67

>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} Length = 226

 Score = 45.7 bits (109), Expect = 2e-05
 Identities = 15/47 (31%), Positives = 29/47 (61%)

Query: 334 NPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASGGDIRQAITSLQ 380
            P+   ++K+ L +IC +E   ++ + ++ +   SGGD R+AI +LQ
Sbjct: 159 KPVPKEAMKKRLLEICEKEGVKITEDGLEALIYISGGDFRKAINALQ 205

>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 Length = 327

 Score = 48.1 bits (115), Expect = 5e-06
 Identities = 14/55 (25%), Positives = 25/55 (45%)

Query: 334 NPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASGGDIRQAITSLQFSSLKQDP 388
            P+ +  I + L  I   E   L+ E +  +   + GD+R+AI  LQ ++     
Sbjct: 167 RPLRDEDIAKRLRYIAENEGLELTEEGLQAILYIAEGDMRRAINILQAAAALDKK 221

>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 Length = 327

 Score = 46.2 bits (110), Expect = 2e-05
 Identities = 17/75 (22%), Positives = 34/75 (45%), Gaps = 12/75 (16%)

Query: 136 QQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNV--LVITGQAGVGKTA 193
           ++ W EKY+P+ L+++  Q   V+ ++ + +            ++  L+  G  GVGKT 
Sbjct: 12  EKPWVEKYRPQRLDDIVGQEHIVKRLKHYVKTG----------SMPHLLFAGPPGVGKTT 61

Query: 194 TVRQIASHLGARLYE 208
               +A  L    + 
Sbjct: 62  AALALARELFGENWR 76

>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 Length = 319

 Score = 47.3 bits (113), Expect = 8e-06
 Identities = 21/77 (27%), Positives = 39/77 (50%), Gaps = 12/77 (15%)

Query: 134 STQQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNV--LVITGQAGVGK 191
              ++W EKY+PR+L+E+  Q + ++ ++ + E +          N+  L+ +G  G GK
Sbjct: 2   ENFEIWVEKYRPRTLDEVVGQDEVIQRLKGYVERK----------NIPHLLFSGPPGTGK 51

Query: 192 TATVRQIASHLGARLYE 208
           TAT   +A  L    + 
Sbjct: 52  TATAIALARDLFGENWR 68

>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 Length = 319

 Score = 46.2 bits (110), Expect = 2e-05
 Identities = 15/47 (31%), Positives = 29/47 (61%)

Query: 334 NPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASGGDIRQAITSLQ 380
            P+   ++K+ L +IC +E   ++ + ++ +   SGGD R+AI +LQ
Sbjct: 159 KPVPKEAMKKRLLEICEKEGVKITEDGLEALIYISGGDFRKAINALQ 205

>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 Length = 323

 Score = 46.2 bits (110), Expect = 2e-05
 Identities = 11/47 (23%), Positives = 27/47 (57%)

Query: 334 NPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASGGDIRQAITSLQ 380
           + +++  + + L +I + E    + + ++ +   + GD+RQAI +LQ
Sbjct: 164 SKLSDEDVLKRLLQIIKLEDVKYTNDGLEAIIFTAEGDMRQAINNLQ 210

>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 Length = 323

 Score = 41.6 bits (98), Expect = 5e-04
 Identities = 23/79 (29%), Positives = 38/79 (48%), Gaps = 8/79 (10%)

Query: 130 SASSSTQQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGV 189
           S + S Q  W EKY+P+ L ++       +E     ++     KD    +++ I+G  G+
Sbjct: 2   SKTLSLQLPWVEKYRPQVLSDIVGN----KETIDRLQQIA---KDGNMPHMI-ISGMPGI 53

Query: 190 GKTATVRQIASHLGARLYE 208
           GKT +V  +A  L  R Y 
Sbjct: 54  GKTTSVHCLAHELLGRSYA 72

>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* Length = 324

 Score = 45.4 bits (108), Expect = 4e-05
 Identities = 11/83 (13%), Positives = 32/83 (38%), Gaps = 7/83 (8%)

Query: 126 HDSASASSSTQQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITG 185
             S    +  + +  +KY+P +++E  +     E  ++        +      ++++ + 
Sbjct: 3   GGSMITVNEKEHILEQKYRPSTIDECILPAFDKETFKSI-------TSKGKIPHIILHSP 55

Query: 186 QAGVGKTATVRQIASHLGARLYE 208
             G GKT   + +   + A +  
Sbjct: 56  SPGTGKTTVAKALCHDVNADMMF 78

>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 = 42.4 bits (99), Expect = 3e-04
 Identities = 34/236 (14%), Positives = 71/236 (30%), Gaps = 27/236 (11%)

Query: 156 KKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL--GARLYEWDTPT 213
             + +        + +       + L   G  G GKT   + I + +    +  E     
Sbjct: 27  DILRDAAIAIRYFVKNEV---KFSNL-FLGLTGTGKTFVSKYIFNEIEEVKKEDEEYKDV 82

Query: 214 PTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSI----PGESKSSAILLIDDL 269
              +        T     S L          +   +    I     G     AI+ +D++
Sbjct: 83  KQAYVNCREVGGTPQAVLSSLAGKLTGFSVPKHGINLGEYIDKIKNGTRNIRAIIYLDEV 142

Query: 270 PVTNGRTAFERLRQCLLLLVRSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGAR 329
                R   + +   L  L+RS    + ++++         +     + ++  ++ +   
Sbjct: 143 DTLVKRRGGDIV---LYQLLRSDANISVIMIS---------NDINVRDYMEPRVLSSLGP 190

Query: 330 KVALNPITNGSIKRTLSKICRQEQY--SLSTEQIDLVAQ---ASGGDIRQAITSLQ 380
            V   P     +K  LSK         +   E +  +A       GD R+A+  L 
Sbjct: 191 SVIFKPYDAEQLKFILSKYAEYGLIKGTYDDEILSYIAAISAKEHGDARKAVNLLF 246

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	666
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	100.0
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	99.93
1sxj_E	354	Activator 1 40 kDa subunit; clamp loader, processi	99.9
1sxj_C	340	Activator 1 40 kDa subunit; clamp loader, processi	99.88
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	99.87
2chq_A	319	Replication factor C small subunit; DNA-binding pr	99.87
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	99.86
1sxj_B	323	Activator 1 37 kDa subunit; clamp loader, processi	99.85
2chg_A	226	Replication factor C small subunit; DNA-binding pr	99.84
3pvs_A	447	Replication-associated recombination protein A; ma	99.83
1jr3_A	373	DNA polymerase III subunit gamma; processivity, pr	99.83
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	99.83
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	99.81
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	99.77
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	99.75
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	99.74
1hqc_A	324	RUVB; extended AAA-ATPase domain, complex with nuc	99.73
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	99.73
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	99.72
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	99.72
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	99.7
4b4t_J	405	26S protease regulatory subunit 8 homolog; hydrola	99.69
3bos_A	242	Putative DNA replication factor; P-loop containing	99.69
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	99.68
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	99.68
1in4_A	334	RUVB, holliday junction DNA helicase RUVB; AAA+-cl	99.68
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	99.68
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	99.67
4b4t_M	434	26S protease regulatory subunit 6A; hydrolase, AAA	99.67
4b4t_I	437	26S protease regulatory subunit 4 homolog; hydrola	99.66
4b4t_H	467	26S protease regulatory subunit 7 homolog; hydrola	99.66
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	99.66
4b4t_L	437	26S protease subunit RPT4; hydrolase, AAA-atpases,	99.65
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	99.64
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	99.64
4b4t_K	428	26S protease regulatory subunit 6B homolog; hydrol	99.64
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	99.63
1a5t_A	334	Delta prime, HOLB; zinc finger, DNA replication; 2	99.62
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	99.61
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	99.6
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	99.6
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	99.58
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	99.57
2z4s_A	440	Chromosomal replication initiator protein DNAA; AA	99.56
2gno_A	305	DNA polymerase III, gamma subunit-related protein;	99.56
1ofh_A	310	ATP-dependent HSL protease ATP-binding subunit HSL	99.55
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	99.53
3pxg_A	468	Negative regulator of genetic competence CLPC/MEC;	99.53
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	99.51
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	99.5
2ce7_A	476	Cell division protein FTSH; metalloprotease; HET:	99.49
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	99.46
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	99.45
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	99.43
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	99.42
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	99.41
2r44_A	331	Uncharacterized protein; putative ATPase, structur	99.41
2r62_A	268	Cell division protease FTSH homolog; ATPase domain	99.41
1w5s_A	412	Origin recognition complex subunit 2 ORC2; replica	99.4
4fcw_A	311	Chaperone protein CLPB; AAA domain; HET: ADP; 2.35	99.4
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	99.36
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	99.35
2bjv_A	265	PSP operon transcriptional activator; AAA, transcr	99.34
1ixz_A	254	ATP-dependent metalloprotease FTSH; AAA domain fol	99.33
2dhr_A	499	FTSH; AAA+ protein, hexameric Zn metalloprotease,	99.32
1um8_A	376	ATP-dependent CLP protease ATP-binding subunit CL;	99.32
3m6a_A	543	ATP-dependent protease LA 1; alpha, beta, ATP-bind	99.3
1iy2_A	278	ATP-dependent metalloprotease FTSH; AAA domain fol	99.29
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	99.26
1jr3_D	343	DNA polymerase III, delta subunit; processivity, p	99.24
3hws_A	363	ATP-dependent CLP protease ATP-binding subunit CL;	99.23
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	99.23
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	99.22
1ojl_A	304	Transcriptional regulatory protein ZRAR; response	99.22
1g8p_A	350	Magnesium-chelatase 38 kDa subunit; parallel beta	99.18
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	99.15
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	99.13
2qen_A	350	Walker-type ATPase; unknown function; HET: ADP; 2.	99.07
1g41_A	444	Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dep	99.06
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	99.05
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	98.95
3n70_A	145	Transport activator; sigma-54, ntpase, PSI, MCSG,	98.94
3k1j_A	604	LON protease, ATP-dependent protease LON; ATP-bind	98.92
3nbx_X	500	ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structu	98.89
3co5_A	143	Putative two-component system transcriptional RES	98.86
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	98.84
1u0j_A	267	DNA replication protein; AAA+ protein, P-loop atpa	98.82
2fna_A	357	Conserved hypothetical protein; structural genomic	98.79
1tue_A	212	Replication protein E1; helicase, replication, E1E	98.78
2qgz_A	308	Helicase loader, putative primosome component; str	98.54
3upu_A	459	ATP-dependent DNA helicase DDA; RECA-like domain,	98.52
2kjq_A	149	DNAA-related protein; solution structure, NESG, st	98.51
3dzd_A	368	Transcriptional regulator (NTRC family); sigma43 a	98.41
4akg_A	2695	Glutathione S-transferase class-MU 26 kDa isozyme	98.38
1ny5_A	387	Transcriptional regulator (NTRC family); AAA+ ATPa	98.26
3f9v_A	595	Minichromosome maintenance protein MCM; replicativ	98.18
1ye8_A	178	Protein THEP1, hypothetical UPF0334 kinase-like pr	98.11
1z6t_A	591	APAF-1, apoptotic protease activating factor 1; ca	97.91
2vhj_A	331	Ntpase P4, P4; non- hydrolysable ATP analogue, hyd	97.82
2cvh_A	220	DNA repair and recombination protein RADB; filamen	97.79
3vkg_A	3245	Dynein heavy chain, cytoplasmic; AAA+ protein, mol	97.77
2w0m_A	235	SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus	97.63
4akg_A	2695	Glutathione S-transferase class-MU 26 kDa isozyme	97.62
2a5y_B	549	CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis	97.62
3foz_A	316	TRNA delta(2)-isopentenylpyrophosphate transferas;	97.6
3crm_A	323	TRNA delta(2)-isopentenylpyrophosphate transferase	97.54
3sfz_A	1249	APAF-1, apoptotic peptidase activating factor 1; a	97.49
3exa_A	322	TRNA delta(2)-isopentenylpyrophosphate transferase	97.43
2orw_A	184	Thymidine kinase; TMTK, TP4A, transferase; HET: 4T	97.38
2b8t_A	223	Thymidine kinase; deoxyribonucleoside kinase, zinc	97.38
3trf_A	185	Shikimate kinase, SK; amino acid biosynthesis, tra	97.37
1n0w_A	243	DNA repair protein RAD51 homolog 1; DNA repair, ho	97.37
3dm5_A	443	SRP54, signal recognition 54 kDa protein; protein-	97.35
2i3b_A	189	HCR-ntpase, human cancer-related ntpase; AAA, ross	97.35
3hr8_A	356	Protein RECA; alpha and beta proteins (A/B, A+B),	97.34
1qhx_A	178	CPT, protein (chloramphenicol phosphotransferase);	97.34
3kb2_A	173	SPBC2 prophage-derived uncharacterized protein YOR	97.29
2rhm_A	193	Putative kinase; P-loop containing nucleoside trip	97.25
3vaa_A	199	Shikimate kinase, SK; structural genomics, center	97.24
1gvn_B	287	Zeta; postsegregational killing system, plasmid; 1	97.24
1zuh_A	168	Shikimate kinase; alpha-beta protein, transferase;	97.18
1kag_A	173	SKI, shikimate kinase I; transferase, structural g	97.16
1via_A	175	Shikimate kinase; structural genomics, transferase	97.13
2iyv_A	184	Shikimate kinase, SK; transferase, aromatic amino	97.13
3iij_A	180	Coilin-interacting nuclear ATPase protein; alpha a	97.12
2fz4_A	237	DNA repair protein RAD25; RECA-like domain, DNA da	97.11
3lw7_A	179	Adenylate kinase related protein (ADKA-like); AMP,	97.1
2dr3_A	247	UPF0273 protein PH0284; RECA superfamily ATPase, h	97.07
2ze6_A	253	Isopentenyl transferase; crown GALL tumor, cytokin	97.06
1xp8_A	366	RECA protein, recombinase A; recombination, radior	97.06
1e6c_A	173	Shikimate kinase; phosphoryl transfer, ADP, shikim	97.05
2zr9_A	349	Protein RECA, recombinase A; recombination, RECA m	97.05
3t61_A	202	Gluconokinase; PSI-biology, structural genomics, p	97.04
1ly1_A	181	Polynucleotide kinase; PNK, phosphatase, transfera	97.04
1u94_A	356	RECA protein, recombinase A; homologous recombinat	97.04
2cdn_A	201	Adenylate kinase; phosphoryl transfer, associative	97.03
3cm0_A	186	Adenylate kinase; ATP-binding, cytoplasm, nucleoti	97.03
1tev_A	196	UMP-CMP kinase; ploop, NMP binding region, LID reg	97.02
2vli_A	183	Antibiotic resistance protein; transferase, tunica	97.01
2c95_A	196	Adenylate kinase 1; transferase, AP4A, nucleotide	97.01
1y63_A	184	LMAJ004144AAA protein; structural genomics, protei	97.01
1kht_A	192	Adenylate kinase; phosphotransferase, signaling pr	97.0
3be4_A	217	Adenylate kinase; malaria, cryptosporidium parvum	97.0
4eun_A	200	Thermoresistant glucokinase; putative sugar kinase	97.0
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	96.98
2bwj_A	199	Adenylate kinase 5; phosphoryl transfer reaction,	96.98
2p5t_B	253	PEZT; postsegregational killing system, phosphoryl	96.97
1qf9_A	194	UMP/CMP kinase, protein (uridylmonophosphate/cytid	96.97
3umf_A	217	Adenylate kinase; rossmann fold, transferase; 2.05	96.95
1cr0_A	296	DNA primase/helicase; RECA-type protein fold, tran	96.95
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	96.94
2r8r_A	228	Sensor protein; KDPD, PFAM02702, MCSG, structural	96.93
1knq_A	175	Gluconate kinase; ALFA/beta structure, transferase	96.92
3cmw_A	1706	Protein RECA, recombinase A; homologous recombinat	96.91
3io5_A	333	Recombination and repair protein; storage dimer, i	96.9
3kl4_A	433	SRP54, signal recognition 54 kDa protein; signal r	96.89
3dl0_A	216	Adenylate kinase; phosphotransferase, zinc coordin	96.89
3fb4_A	216	Adenylate kinase; psychrophIle, phosphotransferase	96.88
1ukz_A	203	Uridylate kinase; transferase; HET: ADP AMP; 1.90A	96.88
2pez_A	179	Bifunctional 3'-phosphoadenosine 5'- phosphosulfat	96.87
2pt5_A	168	Shikimate kinase, SK; aromatic amino acid biosynth	96.87
1pzn_A	349	RAD51, DNA repair and recombination protein RAD51,	96.85
1v5w_A	343	DMC1, meiotic recombination protein DMC1/LIM15 hom	96.85
1zd8_A	227	GTP:AMP phosphotransferase mitochondrial; ATP:AMP	96.85
2ehv_A	251	Hypothetical protein PH0186; KAIC, RECA ATPase, un	96.84
1aky_A	220	Adenylate kinase; ATP:AMP phosphotransferase, myok	96.84
2r6a_A	454	DNAB helicase, replicative helicase; replication,	96.82
2z43_A	324	DNA repair and recombination protein RADA; archaea	96.8
3zvl_A	416	Bifunctional polynucleotide phosphatase/kinase; hy	96.8
3jvv_A	356	Twitching mobility protein; hexameric P-loop ATPas	96.77
3tlx_A	243	Adenylate kinase 2; structural genomics, structura	96.75
1vma_A	306	Cell division protein FTSY; TM0570, structural gen	96.75
1xx6_A	191	Thymidine kinase; NESG, northeast structural genom	96.74
2q6t_A	444	DNAB replication FORK helicase; hydrolase; 2.90A {	96.74
3sr0_A	206	Adenylate kinase; phosphoryl transfer analogue, AL	96.73
1cke_A	227	CK, MSSA, protein (cytidine monophosphate kinase);	96.72
1ak2_A	233	Adenylate kinase isoenzyme-2; nucleoside monophosp	96.72
1zp6_A	191	Hypothetical protein ATU3015; alpha-beta protein.,	96.7
2z0h_A	197	DTMP kinase, thymidylate kinase; ATP-binding, nucl	96.69
2px0_A	296	Flagellar biosynthesis protein FLHF; SRP GTPase, f	96.69
1nks_A	194	Adenylate kinase; thermophilic, transferase; HET:	96.67
1zak_A	222	Adenylate kinase; ATP:AMP-phosphotransferase, tran	96.66
2v54_A	204	DTMP kinase, thymidylate kinase; nucleotide biosyn	96.66
2pbr_A	195	DTMP kinase, thymidylate kinase; transferase, nucl	96.66
1kgd_A	180	CASK, peripheral plasma membrane CASK; maguk, guan	96.65
2jaq_A	205	Deoxyguanosine kinase; transferase, deoxyribonucle	96.64
1e4v_A	214	Adenylate kinase; transferase(phosphotransferase);	96.64
2plr_A	213	DTMP kinase, probable thymidylate kinase; TMP-bind	96.6
2ga8_A	359	Hypothetical 39.9 kDa protein; YFR007W, YFH7, unkn	96.6
2xb4_A	223	Adenylate kinase; ATP-binding, nucleotide-binding,	96.59
3lda_A	400	DNA repair protein RAD51; DNA binding protein, ATP	96.59
3b6e_A	216	Interferon-induced helicase C domain-containing P;	96.58
2if2_A	204	Dephospho-COA kinase; alpha-beta protein, structur	96.57
3bh0_A	315	DNAB-like replicative helicase; ATPase, replicatio	96.55
3ake_A	208	Cytidylate kinase; CMP kinase, CMP complex, open c	96.53
3uie_A	200	Adenylyl-sulfate kinase 1, chloroplastic; rossmann	96.53
2efe_B	181	Small GTP-binding protein-like; GEF, GTPase, VPS9,	96.52
3lxx_A	239	GTPase IMAP family member 4; structural genomics c	96.51
3r20_A	233	Cytidylate kinase; structural genomics, seattle st	96.5
2bbw_A	246	Adenylate kinase 4, AK4; nucleotide kinase, nucleo	96.5
1u8z_A	168	RAS-related protein RAL-A; GNP, GTP, GMPPNP, GPPNH	96.5
3a4m_A	260	L-seryl-tRNA(SEC) kinase; P-loop motif, walker A m	96.48
3nwj_A	250	ATSK2; P loop, shikimate, nucleoside monophosphate	96.48
1jjv_A	206	Dephospho-COA kinase; P-loop nucleotide-binding fo	96.47
2a9k_A	187	RAS-related protein RAL-A; bacterial ADP-ribosyltr	96.47
3clv_A	208	RAB5 protein, putative; malaria, GTPase, structura	96.46
1w4r_A	195	Thymidine kinase; type II, human, cytosolic, phosp	96.45
1kao_A	167	RAP2A; GTP-binding protein, small G protein, GDP,	96.44
2bdt_A	189	BH3686; alpha-beta protein, structural genomics, P	96.43
3a8t_A	339	Adenylate isopentenyltransferase; rossmann fold pr	96.41
4eaq_A	229	DTMP kinase, thymidylate kinase; structural genomi	96.41
3t5g_A	181	GTP-binding protein RHEB; immunoglobulin-like beta	96.4
2grj_A	192	Dephospho-COA kinase; TM1387, EC 2.7.1.24, dephosp	96.38
2i1q_A	322	DNA repair and recombination protein RADA; ATPase,	96.37
4e22_A	252	Cytidylate kinase; P-loop, CMP/ATP binding, transf	96.36
2qor_A	204	Guanylate kinase; phosphotransferase, purine metab	96.35
1rz3_A	201	Hypothetical protein rbstp0775; MCSG, structural g	96.31
2bov_A	206	RAla, RAS-related protein RAL-A; C3BOT, exoenzyme,	96.31
2ce2_X	166	GTPase HRAS; signaling protein, guanine nucleotide	96.31
1v43_A	372	Sugar-binding transport ATP-binding protein; ATPas	96.3
1svm_A	377	Large T antigen; AAA+ fold, viral protein; HET: AT	96.29
2wwf_A	212	Thymidilate kinase, putative; transferase, malaria	96.29
3tau_A	208	Guanylate kinase, GMP kinase; structural genomics,	96.25
1ex7_A	186	Guanylate kinase; substrate-induced FIT, domain mo	96.24
3cmw_A	1706	Protein RECA, recombinase A; homologous recombinat	96.23
1vht_A	218	Dephospho-COA kinase; structural genomics, transfe	96.23
2fg5_A	192	RAB-22B, RAS-related protein RAB-31; G-protein, GT	96.22
1uf9_A	203	TT1252 protein; P-loop, nucleotide binding domain,	96.21
4dsu_A	189	GTPase KRAS, isoform 2B; small G-protein, signalin	96.21
3con_A	190	GTPase NRAS; structural genomics consortium, SGC,	96.2
1nn5_A	215	Similar to deoxythymidylate kinase (thymidylate K;	96.17
3a00_A	186	Guanylate kinase, GMP kinase; domain movement, dim	96.17
3vkw_A	446	Replicase large subunit; alpha/beta domain, helica	96.16
4a1f_A	338	DNAB helicase, replicative DNA helicase; hydrolase	96.14
3bgw_A	444	DNAB-like replicative helicase; ATPase, replicatio	96.13
3oes_A	201	GTPase rhebl1; small GTPase, structural genomics,	96.12
1ltq_A	301	Polynucleotide kinase; phosphatase, alpha/beta, P-	96.11
3tr0_A	205	Guanylate kinase, GMP kinase; purines, pyrimidines	96.1
3dz8_A	191	RAS-related protein RAB-3B; GDP, GTPase, structura	96.09
1ek0_A	170	Protein (GTP-binding protein YPT51); vesicular tra	96.08
3d3q_A	340	TRNA delta(2)-isopentenylpyrophosphate transferase	96.07
2h92_A	219	Cytidylate kinase; rossmann fold, transferase; HET	96.05
2j41_A	207	Guanylate kinase; GMP, GMK, transferase, ATP-bindi	96.04
1q3t_A	236	Cytidylate kinase; nucleotide monophosphate kinase	96.04
2j9r_A	214	Thymidine kinase; TK1, DNK, lasso, transferase, AT	96.03
1uj2_A	252	Uridine-cytidine kinase 2; alpha/beta mononucleoti	96.0
3fdi_A	201	Uncharacterized protein; cytidylate kinase like pr	96.0
3ney_A	197	55 kDa erythrocyte membrane protein; structural ge	95.99
1c1y_A	167	RAS-related protein RAP-1A; GTP-binding proteins,	95.98
1r2q_A	170	RAS-related protein RAB-5A; GTPase, GNP, atomic re	95.98
1q57_A	503	DNA primase/helicase; dntpase, DNA replication, tr	95.97
2qt1_A	207	Nicotinamide riboside kinase 1; non-protein kinase	95.97
2yvu_A	186	Probable adenylyl-sulfate kinase; transferase, str	95.95
3bc1_A	195	RAS-related protein RAB-27A; RAB27, GTPase, RAB, s	95.95
2f6r_A	281	COA synthase, bifunctional coenzyme A synthase; 18	95.93
3kkq_A	183	RAS-related protein M-RAS; GTP-binding, GTPase, si	95.92
2h57_A	190	ADP-ribosylation factor-like protein 6; GTP, GTPas	95.91
2gf9_A	189	RAS-related protein RAB-3D; G-protein, structural	95.9
1odf_A	290	YGR205W, hypothetical 33.3 kDa protein in ADE3-Ser	95.9
2hup_A	201	RAS-related protein RAB-43; G-protein, GDP, struct	95.89
3eph_A	409	TRNA isopentenyltransferase; transferase, alternat	95.89
1z08_A	170	RAS-related protein RAB-21; RAB GTPase, vesicular	95.86
3q85_A	169	GTP-binding protein REM 2; G-domain, CAV2 beta, si	95.84
1lvg_A	198	Guanylate kinase, GMP kinase; transferase; HET: AD	95.83
1nrj_B	218	SR-beta, signal recognition particle receptor beta	95.83
3c8u_A	208	Fructokinase; YP_612366.1, putative fructose trans	95.82
1zd9_A	188	ADP-ribosylation factor-like 10B; transport protei	95.81
3tkl_A	196	RAS-related protein RAB-1A; vesicle trafficking, p	95.8
2fn4_A	181	P23, RAS-related protein R-RAS; GDP/GTP binding, G	95.79
3tui_C	366	Methionine import ATP-binding protein METN; ABC-tr	95.77
2zts_A	251	Putative uncharacterized protein PH0186; KAIC like	95.75
1ls1_A	295	Signal recognition particle protein; FFH, SRP54, S	95.75
1z06_A	189	RAS-related protein RAB-33B; RAB GTPase, RAB33B GT	95.75
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	95.72
3q72_A	166	GTP-binding protein RAD; G-domain, CAV2 beta, sign	95.72
1j8m_F	297	SRP54, signal recognition 54 kDa protein; signalin	95.72
2oil_A	193	CATX-8, RAS-related protein RAB-25; G-protein, GDP	95.7
2y8e_A	179	RAB-protein 6, GH09086P, RAB6; hydrolase, nucleoti	95.66
1zu4_A	320	FTSY; GTPase, signal recognition particle, SRP, re	95.64
1wms_A	177	RAB-9, RAB9, RAS-related protein RAB-9A; GTPase, p	95.62
1m7g_A	211	Adenylylsulfate kinase; APS kinase, transferase, s	95.59
3asz_A	211	Uridine kinase; cytidine phosphorylation, transfer	95.59
1zbd_A	203	Rabphilin-3A; G protein, effector, RABCDR, synapti	95.59
2atv_A	196	RERG, RAS-like estrogen-regulated growth inhibitor	95.58
1z2a_A	168	RAS-related protein RAB-23; RAB GTPase, vesicular	95.58
2fu5_C	183	RAS-related protein RAB-8A; MSS4:RAB8 protein comp	95.57
1upt_A	171	ARL1, ADP-ribosylation factor-like protein 1; hydr	95.54
1ksh_A	186	ARF-like protein 2; small GTPase, small GTP-bindin	95.53
1s96_A	219	Guanylate kinase, GMP kinase; E.coli, dimer, SAD,	95.52
4b3f_X	646	DNA-binding protein smubp-2; hydrolase, helicase;	95.51
1z0f_A	179	RAB14, member RAS oncogene family; RAB GTPase, ves	95.5
2qmh_A	205	HPR kinase/phosphorylase; V267F mutation, ATP-bind	95.47
3hdt_A	223	Putative kinase; structura genomics, PSI-2, protei	95.47
3f8t_A	506	Predicted ATPase involved in replication control,	95.45
2a5j_A	191	RAS-related protein RAB-2B; GTPase, signal transdu	95.45
1z0j_A	170	RAB-22, RAS-related protein RAB-22A; RAB GTPase, R	95.44
1znw_A	207	Guanylate kinase, GMP kinase; ATP:GMP-phosphotrans	95.41
1p9r_A	418	General secretion pathway protein E; bacterial typ	95.4
3e70_C	328	DPA, signal recognition particle receptor; FTSY, S	95.4
1gtv_A	214	TMK, thymidylate kinase; transferase, transferase	95.39
1z6g_A	218	Guanylate kinase; structural genomics, SGC, struct	95.38
3c5c_A	187	RAS-like protein 12; GDP, GTPase, structural genom	95.37
3vkg_A	3245	Dynein heavy chain, cytoplasmic; AAA+ protein, mol	95.34
1g16_A	170	RAS-related protein SEC4; G protein RAB, signaling	95.34
3t1o_A	198	Gliding protein MGLA; G domain containing protein,	95.29
1htw_A	158	HI0065; nucleotide-binding fold, structural genomi	95.28
4gp7_A	171	Metallophosphoesterase; polynucleotide kinase phos	95.27
2f9l_A	199	RAB11B, member RAS oncogene family; RAB11B GTPase,	95.26
3thx_B	918	DNA mismatch repair protein MSH3; ABC family ATPas	95.23
3thx_A	934	DNA mismatch repair protein MSH2; ABC family ATPas	95.21
3gmt_A	230	Adenylate kinase; ssgcid, ATP-BIN cytoplasm, nucle	95.2
3reg_A	194	RHO-like small GTPase; cytoskeleton, nucleotide-bi	95.18
3lnc_A	231	Guanylate kinase, GMP kinase; ALS collaborative cr	95.14
3lxw_A	247	GTPase IMAP family member 1; immunity, structural	95.14
4a74_A	231	DNA repair and recombination protein RADA; hydrola	95.13
2ew1_A	201	RAS-related protein RAB-30; G-protein, GTP analogu	95.11
2eyu_A	261	Twitching motility protein PILT; pilus retraction	95.1
4edh_A	213	DTMP kinase, thymidylate kinase; structural genomi	95.1
3b9q_A	302	Chloroplast SRP receptor homolog, alpha subunit CP	95.09
1fzq_A	181	ADP-ribosylation factor-like protein 3; protein-GD	95.08
2nzj_A	175	GTP-binding protein REM 1; GDP/GTP binding, GTP hy	95.05
2bme_A	186	RAB4A, RAS-related protein RAB4A; GTP-binding prot	95.04
3ihw_A	184	Centg3; RAS, centaurin, GTPase, structural genomic	95.03
1x6v_B	630	Bifunctional 3'-phosphoadenosine 5'- phosphosulfat	95.0
1r8s_A	164	ADP-ribosylation factor 1; protein transport/excha	95.0
1xjc_A	169	MOBB protein homolog; structural genomics, midwest	95.0
3tqc_A	321	Pantothenate kinase; biosynthesis of cofactors, pr	94.98
3pqc_A	195	Probable GTP-binding protein ENGB; rossmann fold,	94.97
3tw8_B	181	RAS-related protein RAB-35; longin domain, RAB GTP	94.94
2p5s_A	199	RAS and EF-hand domain containing; G-protein, RAB,	94.92
2ffh_A	425	Protein (FFH); SRP54, signal recognition particle,	94.92
2orv_A	234	Thymidine kinase; TP4A (P1-(5'-adenosyl)P4-(5'- (2	94.91
1x3s_A	195	RAS-related protein RAB-18; GTPase, GNP, structura	94.91
2e87_A	357	Hypothetical protein PH1320; GTP-binding, GTPase,	94.87
2jeo_A	245	Uridine-cytidine kinase 1; UCK, transferase, ATP-b	94.86
2xxa_A	433	Signal recognition particle protein; protein trans	94.86
2yc2_C	208	IFT27, small RAB-related GTPase; transport protein	94.83
2og2_A	359	Putative signal recognition particle receptor; nuc	94.83
2wsm_A	221	Hydrogenase expression/formation protein (HYPB); m	94.81
2v9p_A	305	Replication protein E1; AAA+ molecular motor, DNA	94.78
2g6b_A	180	RAS-related protein RAB-26; G-protein, GTP analogu	94.77
3v9p_A	227	DTMP kinase, thymidylate kinase; ssgcid, STRU geno	94.77
4dhe_A	223	Probable GTP-binding protein ENGB; melioidosis, RA	94.77
4bas_A	199	ADP-ribosylation factor, putative (small GTPase, p	94.77
1a7j_A	290	Phosphoribulokinase; transferase, calvin cycle; 2.	94.75
3e1s_A	574	Exodeoxyribonuclease V, subunit RECD; alpha and be	94.73
1np6_A	174	Molybdopterin-guanine dinucleotide biosynthesis pr	94.7
1m2o_B	190	GTP-binding protein SAR1, GTP binding protein; zin	94.69
2lkc_A	178	Translation initiation factor IF-2; NMR {Geobacill	94.69
2f7s_A	217	C25KG, RAS-related protein RAB-27B; G-protein, str	94.67
1rj9_A	304	FTSY, signal recognition protein; SRP-GTPase domai	94.65
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	94.62
3e2i_A	219	Thymidine kinase; Zn-binding, ATP-binding, DNA syn	94.62
2erx_A	172	GTP-binding protein DI-RAS2; GTP hydrolysis, trans	94.6
2bcg_Y	206	Protein YP2, GTP-binding protein YPT1; RABGTPase,	94.56
2ocp_A	241	DGK, deoxyguanosine kinase; protein-nucleotide com	94.54
3cbq_A	195	GTP-binding protein REM 2; FLJ38964A, structural g	94.5
3llu_A	196	RAS-related GTP-binding protein C; structural geno	94.42
2hxs_A	178	RAB-26, RAS-related protein RAB-28; GTPase, signal	94.36
4dkx_A	216	RAS-related protein RAB-6A; GTP binding fold, memb	94.36
2gco_A	201	H9, RHO-related GTP-binding protein RHOC; GTPase,s	94.32
1g5t_A	196	COB(I)alamin adenosyltransferase; P-loop protein,	94.31
2ewv_A	372	Twitching motility protein PILT; pilus retraction	94.3
2v3c_C	432	SRP54, signal recognition 54 kDa protein; nucleoti	94.3
2gk6_A	624	Regulator of nonsense transcripts 1; UPF1, helicas	94.27
1p5z_B	263	DCK, deoxycytidine kinase; nucleoside kinase, P-lo	94.25
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	94.22
3tif_A	235	Uncharacterized ABC transporter ATP-binding prote;	94.22
1nlf_A	279	Regulatory protein REPA; replicative DNA helicase	94.17
1wb9_A	800	DNA mismatch repair protein MUTS; DNA-binding, ATP	94.14
2oap_1	511	GSPE-2, type II secretion system protein; hexameri	94.14
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	94.13
3lv8_A	236	DTMP kinase, thymidylate kinase; structural genomi	94.13
2qu8_A	228	Putative nucleolar GTP-binding protein 1; GTPase,	94.13
2pcj_A	224	ABC transporter, lipoprotein-releasing system ATP-	94.13
3kta_A	182	Chromosome segregation protein SMC; structural mai	94.09
2o52_A	200	RAS-related protein RAB-4B; G-protein, GDP, struct	94.09
2gf0_A	199	GTP-binding protein DI-RAS1; GDP/GTP binding, GTP	94.06
3tmk_A	216	Thymidylate kinase; phosphotransferase; HET: T5A;	94.05
1g8f_A	511	Sulfate adenylyltransferase; alpha-beta protein, b	94.03
2cbz_A	237	Multidrug resistance-associated protein 1; ABC pro	94.01
3aez_A	312	Pantothenate kinase; transferase, homodimer, COA b	94.0
1sq5_A	308	Pantothenate kinase; P-loop, transferase; HET: PAU	93.98
2ged_A	193	SR-beta, signal recognition particle receptor beta	93.94
2f1r_A	171	Molybdopterin-guanine dinucleotide biosynthesis pr	93.92
3cpj_B	223	GTP-binding protein YPT31/YPT8; RAB GTPase, prenyl	93.92
3b85_A	208	Phosphate starvation-inducible protein; PHOH2, ATP	93.92
3q3j_B	214	RHO-related GTP-binding protein RHO6; RAS-binding	93.91
2hf9_A	226	Probable hydrogenase nickel incorporation protein	93.9
2axn_A	520	6-phosphofructo-2-kinase/fructose-2,6- biphosphata	93.87
1b0u_A	262	Histidine permease; ABC transporter, transport pro	93.82
2onk_A	240	Molybdate/tungstate ABC transporter, ATP-binding p	93.79
1svi_A	195	GTP-binding protein YSXC; ENGB, GTPase, GDP, hydro	93.78
1sgw_A	214	Putative ABC transporter; structural genomics, P p	93.73
4tmk_A	213	Protein (thymidylate kinase); ATP:DTMP phosphotran	93.73
3fvq_A	359	Fe(3+) IONS import ATP-binding protein FBPC; nucle	93.73
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	93.72
2r2a_A	199	Uncharacterized protein; zonular occludens toxin,	93.71
2zu0_C	267	Probable ATP-dependent transporter SUFC; iron-sulf	93.71
1c9k_A	180	COBU, adenosylcobinamide kinase; alpha/beta struct	93.71
2d2e_A	250	SUFC protein; ABC-ATPase, SUF protein, 310-helix,	93.7
3tqf_A	181	HPR(Ser) kinase; transferase, hydrolase; 2.80A {Co	93.7
2h17_A	181	ADP-ribosylation factor-like protein 5A; GDP, GTPa	93.68
2pze_A	229	Cystic fibrosis transmembrane conductance regulat;	93.65
1g6h_A	257	High-affinity branched-chain amino acid transport	93.63
3p32_A	355	Probable GTPase RV1496/MT1543; structural genomics	93.61
1ji0_A	240	ABC transporter; ATP binding protein, structural g	93.6
3gfo_A	275	Cobalt import ATP-binding protein CBIO 1; structur	93.59
1ewq_A	765	DNA mismatch repair protein MUTS; multiple domains	93.59
2olj_A	263	Amino acid ABC transporter; ABC domain, ATPase, hy	93.56
3d31_A	348	Sulfate/molybdate ABC transporter, ATP-binding pro	93.55
2ff7_A	247	Alpha-hemolysin translocation ATP-binding protein	93.55
2wjy_A	800	Regulator of nonsense transcripts 1; nonsense medi	93.54
1mv5_A	243	LMRA, multidrug resistance ABC transporter ATP-bin	93.54
2iut_A	574	DNA translocase FTSK; nucleotide-binding, chromoso	93.51
1z47_A	355	CYSA, putative ABC-transporter ATP-binding protein	93.5
2it1_A	362	362AA long hypothetical maltose/maltodextrin trans	93.5
3rlf_A	381	Maltose/maltodextrin import ATP-binding protein M;	93.49
2b6h_A	192	ADP-ribosylation factor 5; membrane trafficking, G	93.47
1zj6_A	187	ADP-ribosylation factor-like protein 5; ARL, GTP-b	93.46
2qi9_C	249	Vitamin B12 import ATP-binding protein BTUD; inner	93.44
2yyz_A	359	Sugar ABC transporter, ATP-binding protein; sugar	93.44
2ixe_A	271	Antigen peptide transporter 1; ABC ATPase, hydrola	93.4
2ghi_A	260	Transport protein; multidrug resistance protein, M	93.39
1vpl_A	256	ABC transporter, ATP-binding protein; TM0544, stru	93.39
1m8p_A	573	Sulfate adenylyltransferase; rossmann fold, phosph	93.35
2ihy_A	279	ABC transporter, ATP-binding protein; ATPase, ABC	93.35
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	93.34
2yv5_A	302	YJEQ protein; hydrolase, GTPase, permutation, stru	93.34
4g1u_C	266	Hemin import ATP-binding protein HMUV; membrane tr	93.33
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	93.33
1g29_1	372	MALK, maltose transport protein MALK; ATPase, acti	93.26
1lw7_A	365	Transcriptional regulator NADR; NMN, NMN adenylyl	93.26
2yz2_A	266	Putative ABC transporter ATP-binding protein TM_0;	93.19
2nq2_C	253	Hypothetical ABC transporter ATP-binding protein H	93.19
1oxx_K	353	GLCV, glucose, ABC transporter, ATP binding protei	93.18
1u0l_A	301	Probable GTPase ENGC; permutation, OB-fold, zinc-f	93.18
4i1u_A	210	Dephospho-COA kinase; structural genomics, niaid,	93.16
2yhs_A	503	FTSY, cell division protein FTSY; cell cycle, prot	93.1
3ld9_A	223	DTMP kinase, thymidylate kinase; ssgcid, NIH, niai	93.08
2il1_A	192	RAB12; G-protein, GDP, GTPase, predicted, structur	93.07
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	93.07
1w36_D	608	RECD, exodeoxyribonuclease V alpha chain; recombin	93.03
2rcn_A	358	Probable GTPase ENGC; YJEQ, circularly permuted, G	93.03
3iev_A	308	GTP-binding protein ERA; ERA, GTPase, KH domain, a	93.01
2gza_A	361	Type IV secretion system protein VIRB11; ATPase, h	93.0
4hlc_A	205	DTMP kinase, thymidylate kinase; TMK, MRSA, pipiri	92.98
3cr8_A	552	Sulfate adenylyltranferase, adenylylsulfate kinase	92.94
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	92.92
3sop_A	270	Neuronal-specific septin-3; hydrolase; HET: GDP; 2	92.86
3gd7_A	390	Fusion complex of cystic fibrosis transmembrane co	92.85
2pjz_A	263	Hypothetical protein ST1066; ATP binding protein,	92.84
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	92.83
1oix_A	191	RAS-related protein RAB-11A; small G protein, intr	92.83
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	92.8
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	92.79
3def_A	262	T7I23.11 protein; chloroplast, TOC33, GTPase, hydr	92.68
2xzl_A	802	ATP-dependent helicase NAM7; hydrolase-RNA complex	92.64
1tq4_A	413	IIGP1, interferon-inducible GTPase; interferon gam	92.64
3szr_A	608	Interferon-induced GTP-binding protein MX1; interf	92.61
2j37_W	504	Signal recognition particle 54 kDa protein (SRP54)	92.59
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	92.55
2o8b_B	1022	DNA mismatch repair protein MSH6; DNA damage respo	92.48
1f2t_A	149	RAD50 ABC-ATPase; DNA double-strand break repair,	92.46
2dyk_A	161	GTP-binding protein; GTPase, ribosome-binding prot	92.45
2bbs_A	290	Cystic fibrosis transmembrane conductance regulato	92.45
1dek_A	241	Deoxynucleoside monophosphate kinase; transferase,	92.39
2vp4_A	230	Deoxynucleoside kinase; ATP-binding, DNA synthesis	92.39
2pt7_A	330	CAG-ALFA; ATPase, protein-protein complex, type IV	92.36
3hjn_A	197	DTMP kinase, thymidylate kinase; ATP-binding, nucl	92.34
2zej_A	184	Dardarin, leucine-rich repeat kinase 2; parkinson'	92.26
4f4c_A	1321	Multidrug resistance protein PGP-1; ABC transporte	92.12
2wji_A	165	Ferrous iron transport protein B homolog; membrane	92.08
1bif_A	469	6-phosphofructo-2-kinase/ fructose-2,6-bisphospha;	92.07
3nh6_A	306	ATP-binding cassette SUB-family B member 6, mitoc;	92.05
1yrb_A	262	ATP(GTP)binding protein; GTPase, P-loop, rossman f	91.92
2obl_A	347	ESCN; ATPase, hydrolase; 1.80A {Escherichia coli O	91.86
3r7w_A	307	Gtpase1, GTP-binding protein GTR1; RAG gtpases, GT	91.76
3ch4_B	202	Pmkase, phosphomevalonate kinase; parallel beta-sh	91.76
2z83_A	459	Helicase/nucleoside triphosphatase; hydrolase, mem	91.71
2qm8_A	337	GTPase/ATPase; G protein, G3E, metallochaperone, c	91.71
2wjg_A	188	FEOB, ferrous iron transport protein B homolog; me	91.35
1ky3_A	182	GTP-binding protein YPT7P; vesicular traffic, GTP	91.29
2gks_A	546	Bifunctional SAT/APS kinase; transferase, sulfuryl	91.26
2dpy_A	438	FLII, flagellum-specific ATP synthase; beta barrel	91.24
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	91.18
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	91.14
2www_A	349	Methylmalonic aciduria type A protein, mitochondri	91.08
2zpa_A	671	Uncharacterized protein YPFI; RNA modification enz	91.03
1nij_A	318	Hypothetical protein YJIA; structural genomics, P-	90.87
2npi_A	460	Protein CLP1; CLP1-PCF11 complex, ATP binding, ter	90.87
3ug7_A	349	Arsenical pump-driving ATPase; tail-anchored, memb	90.7
3cio_A	299	ETK, tyrosine-protein kinase ETK; WZC, escherichia	90.64
2gj8_A	172	MNME, tRNA modification GTPase TRME; G-domain dime	90.62
1pui_A	210	ENGB, probable GTP-binding protein ENGB; structura	90.58
3bfv_A	271	CAPA1, CAPB2, membrane protein CAPA1, protein tyro	90.54
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	90.53
1m7b_A	184	RND3/RHOE small GTP-binding protein; small GTPase,	90.52
3qks_A	203	DNA double-strand break repair RAD50 ATPase; RECA-	90.47
1udx_A	416	The GTP-binding protein OBG; TGS domain, riken str	90.46

>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=100.00  E-value=6.9e-41  Score=377.70  Aligned_cols=402  Identities=16%  Similarity=0.171  Sum_probs=270.5

Q ss_pred             CCCCccccccCCCCccccccCHHHHHHHHHHHHHhhcCC---------CCCCCccEEEEECCCCchHHHHHHHHHHHcCC
Q 005987          134 STQQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDS---------KDKFSTNVLVITGQAGVGKTATVRQIASHLGA  204 (666)
Q Consensus       134 ~~~~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~---------~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~  204 (666)
                      ....+|++||+|+++++|+|+++.+++|..|++.|....         .+..+.+.+||+||||||||++|+++|+++++
T Consensus        24 ~~~~lW~ekyrP~~~~dliG~~~~~~~L~~~l~~~~~~~~~~~~~~g~~~~~~~~~lLL~GppGtGKTtla~~la~~l~~  103 (516)
T 1sxj_A           24 ASDKLWTVKYAPTNLQQVCGNKGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAAHLVAQELGY  103 (516)
T ss_dssp             --CCCHHHHTCCSSGGGCCSCHHHHHHHHHHHHTHHHHHHTTTCCCCTTSTTSCSEEEEECSTTSSHHHHHHHHHHHTTC
T ss_pred             ccCCCcccccCCCCHHHhcCCHHHHHHHHHHHHHhHhhchhhccccCccCCCCCcEEEEECCCCCCHHHHHHHHHHHcCC
Confidence            457899999999999999999999999999999764211         01113378999999999999999999999999


Q ss_pred             cEEEEcCCCchhhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCC------CCCCCceEEEEeCCCCCcchhHH
Q 005987          205 RLYEWDTPTPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIP------GESKSSAILLIDDLPVTNGRTAF  278 (666)
Q Consensus       205 ~viE~nasd~~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~------~~~~~~~IIlIDEid~l~~~~~~  278 (666)
                      .++++++++.....                 .+...+..+.....+...+.      .....+.||||||+|.+..... 
T Consensus       104 ~~i~in~s~~~~~~-----------------~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~vliIDEid~l~~~~~-  165 (516)
T 1sxj_A          104 DILEQNASDVRSKT-----------------LLNAGVKNALDNMSVVGYFKHNEEAQNLNGKHFVIIMDEVDGMSGGDR-  165 (516)
T ss_dssp             EEEEECTTSCCCHH-----------------HHHHTGGGGTTBCCSTTTTTC----CCSSTTSEEEEECSGGGCCTTST-
T ss_pred             CEEEEeCCCcchHH-----------------HHHHHHHHHhccccHHHHHhhhhhhhhccCCCeEEEEECCCccchhhH-
Confidence            99999998743210                 00000000000000000000      0123567999999998865321 


Q ss_pred             HHHHHHHHHHHhcCCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCH
Q 005987          279 ERLRQCLLLLVRSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLST  358 (666)
Q Consensus       279 ~~l~~~L~~l~~~~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~  358 (666)
                       .....|..+++..+.|+|+++++...        ..+..+    .+ +|..|.|++++.+++.++|..+|..+++.+++
T Consensus       166 -~~l~~L~~~l~~~~~~iIli~~~~~~--------~~l~~l----~~-r~~~i~f~~~~~~~~~~~L~~i~~~~~~~i~~  231 (516)
T 1sxj_A          166 -GGVGQLAQFCRKTSTPLILICNERNL--------PKMRPF----DR-VCLDIQFRRPDANSIKSRLMTIAIREKFKLDP  231 (516)
T ss_dssp             -THHHHHHHHHHHCSSCEEEEESCTTS--------STTGGG----TT-TSEEEECCCCCHHHHHHHHHHHHHHHTCCCCT
T ss_pred             -HHHHHHHHHHHhcCCCEEEEEcCCCC--------ccchhh----Hh-ceEEEEeCCCCHHHHHHHHHHHHHHcCCCCCH
Confidence             12344667777788888887765321        122222    22 68999999999999999999999999999999


Q ss_pred             HHHHHHHHHcCCcHHHHHHHHHHHhcCCCCcccccccCCCCCCCccccCCCCCcccccCCccccchHHHHhHHhhCCCCC
Q 005987          359 EQIDLVAQASGGDIRQAITSLQFSSLKQDPMLNLSLSISKPNFPEEKADGHGGFSIQFGRDETLSLFHALGKFLHNKRET  438 (666)
Q Consensus       359 ~~l~~Ia~~s~GDIR~AIn~LQf~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~~~~~RD~~l~lFhalGkil~~Kr~~  438 (666)
                      ++++.|++.++||+|.+++.||+++........          ...     ........||..+++|+++++||++++..
T Consensus       232 ~~l~~la~~s~GdiR~~i~~L~~~~~~~~~It~----------~~v-----~~~~~~~~~~~~~~~f~~~~~il~~~~~~  296 (516)
T 1sxj_A          232 NVIDRLIQTTRGDIRQVINLLSTISTTTKTINH----------ENI-----NEISKAWEKNIALKPFDIAHKMLDGQIYS  296 (516)
T ss_dssp             THHHHHHHHTTTCHHHHHHHHTHHHHHSSCCCT----------THH-----HHHHHHHHTTTTSHHHHHHHHHTBGGGTS
T ss_pred             HHHHHHHHHcCCcHHHHHHHHHHHHhcCCCCch----------HHH-----HHHHHhhccCCCCCHHHHHHHHhcCCccc
Confidence            999999999999999999999999864322110          000     00011234888999999999999988643


Q ss_pred             CccccccccchhhhhccccCCCCCCChHHHHHhcCCChhHHHHHHHhhcCCCCC------cchHHHHHHHHHHhhHhhhc
Q 005987          439 DNLVKMDQDAFVVKDKFSRLPLKMDAPEKVLSQAHGQARPVLDFLHENFLDFIS------EDAIDDAWAVASYLSDADLL  512 (666)
Q Consensus       439 ~~~~~~~~~~~~~~~~~~r~pl~~~~pE~vl~~~~~~~~~~~~~LhENy~~f~~------d~~i~~~~~~~d~LS~aD~l  512 (666)
                      ....    .              ....++.++....+++.+..||||||+.+++      +..+++++.++|+||++|++
T Consensus       297 ~~~~----~--------------~~~~~~~~~~~~~~~~~~~~~i~eNy~~~~p~~~~~~~~~l~~~~~a~d~ls~~D~~  358 (516)
T 1sxj_A          297 DIGS----R--------------NFTLNDKIALYFDDFDFTPLMIQENYLSTRPSVLKPGQSHLEAVAEAANCISLGDIV  358 (516)
T ss_dssp             TTGG----G--------------TSCHHHHHHHHTTSTTTHHHHHHHHSSSSEESCCCTTCCHHHHHHHHHHHHHHHHHH
T ss_pred             cccc----c--------------CCCHHHhhhhhccCHHHHHHHHHHHhhhccccccCCchhHHHHHHHHHHHHhHHHHH
Confidence            3210    0              0123456677777999999999999988763      13699999999999999999


Q ss_pred             cccccCccccccchhHHHHHHHHHHHHHHHhhhCCCCCCCCcccccCCcchhhhhhhHHHHHHHHHhhhccccCCccccc
Q 005987          513 LASFRGRLVRYNEADNVLQSAAASVAARGVLFGNSHPVPPRWHAIRKPKLWRVDQSSLQKKKELLKKKFMAWDGSISADV  592 (666)
Q Consensus       513 ~~~~~~~~~~~~~~~~~l~~~a~sva~RGv~~~n~~p~~~~~~~~~~P~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~  592 (666)
                      .+++++..+.|.    ++..++...+++...+....    .+.++++|+||+.+++..+++ ++++.....         
T Consensus       359 ~~~i~~~~q~~~----l~~~~~~~~~v~p~~~~~g~----~~~~~~fp~~~~~~s~~~k~~-r~~~~l~~~---------  420 (516)
T 1sxj_A          359 EKKIRSSEQLWS----LLPLHAVLSSVYPASKVAGH----MAGRINFTAWLGQNSKSAKYY-RLLQEIHYH---------  420 (516)
T ss_dssp             HHHHTTCSSCGG----GHHHHHHHHTHHHHHTTCEE----CSSCCCCCSHHHHHHHHHHHH-HHHHHHHTT---------
T ss_pred             HHHHccCCCCcc----cchhhHhhhhhccHHHhCCC----CCCCCcCCHHHhhhchhhHHH-HHHHHHHHH---------
Confidence            998876223453    33333332223322121111    135799999999987665433 333332222         


Q ss_pred             ccCCCCCchhhhhhhhhhhhHHhhcC
Q 005987          593 YNGSSSSDVSVLATEYAPALKWLGNR  618 (666)
Q Consensus       593 ~~~~~~~~~~~~~~e~lP~l~~i~~~  618 (666)
                      .+...+.+..+++++|||+|..+..+
T Consensus       421 ~~~~~~~~~~~~~~~~lp~l~~~~~~  446 (516)
T 1sxj_A          421 TRLGTSTXXXXXXXXXXXXXXXXXXX  446 (516)
T ss_dssp             TTTCCCHHHHHTTTHHHHHHHHSCCC
T ss_pred             hhhhhccccccccccccccccccccc
Confidence            12223344558999999999998653

>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=99.93  E-value=2.5e-24  Score=227.78  Aligned_cols=283  Identities=14%  Similarity=0.227  Sum_probs=185.2

Q ss_pred             CCCccccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCc
Q 005987          135 TQQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTP  214 (666)
Q Consensus       135 ~~~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~  214 (666)
                      ...+|++||+|+++++++|+++.++.++.|++.      ++.+ +.+|++||||||||++++++|++++..++++++++.
T Consensus        12 ~~~~~~~k~rP~~~~~ivg~~~~~~~l~~~l~~------~~~~-~~~L~~G~~G~GKT~la~~la~~l~~~~~~i~~~~~   84 (324)
T 3u61_B           12 KEHILEQKYRPSTIDECILPAFDKETFKSITSK------GKIP-HIILHSPSPGTGKTTVAKALCHDVNADMMFVNGSDC   84 (324)
T ss_dssp             TCSSHHHHSCCCSTTTSCCCHHHHHHHHHHHHT------TCCC-SEEEECSSTTSSHHHHHHHHHHHTTEEEEEEETTTC
T ss_pred             ccchHHHhhCCCCHHHHhCcHHHHHHHHHHHHc------CCCC-eEEEeeCcCCCCHHHHHHHHHHHhCCCEEEEccccc
Confidence            467999999999999999999999999999985      5555 689999999999999999999999999999998652


Q ss_pred             hhhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcCCC
Q 005987          215 TIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHI  294 (666)
Q Consensus       215 ~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~~~  294 (666)
                                  +      .+.++..+.........       .+.+.||||||++.+.+....+.+...+....  ...
T Consensus        85 ------------~------~~~i~~~~~~~~~~~~~-------~~~~~vliiDEi~~l~~~~~~~~L~~~le~~~--~~~  137 (324)
T 3u61_B           85 ------------K------IDFVRGPLTNFASAASF-------DGRQKVIVIDEFDRSGLAESQRHLRSFMEAYS--SNC  137 (324)
T ss_dssp             ------------C------HHHHHTHHHHHHHBCCC-------SSCEEEEEEESCCCGGGHHHHHHHHHHHHHHG--GGC
T ss_pred             ------------C------HHHHHHHHHHHHhhccc-------CCCCeEEEEECCcccCcHHHHHHHHHHHHhCC--CCc
Confidence                        1      22334444433222211       12467999999999863333343433333221  122


Q ss_pred             ceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHH-------HHHHHHHHHHHhCCCCCH-HHHHHHHH
Q 005987          295 PTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGS-------IKRTLSKICRQEQYSLST-EQIDLVAQ  366 (666)
Q Consensus       295 PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~-------i~kiL~~I~~~e~i~v~~-~~l~~Ia~  366 (666)
                       .+|++++.        ..+..+.|.+     ||..|.|++|+.++       +.+.+..++..+++.+++ ++++.|+.
T Consensus       138 -~iI~~~n~--------~~~l~~~l~s-----R~~~i~~~~~~~~e~~~il~~~~~~l~~~~~~~~~~~~~~~~~~~l~~  203 (324)
T 3u61_B          138 -SIIITANN--------IDGIIKPLQS-----RCRVITFGQPTDEDKIEMMKQMIRRLTEICKHEGIAIADMKVVAALVK  203 (324)
T ss_dssp             -EEEEEESS--------GGGSCTTHHH-----HSEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHTCCBSCHHHHHHHHH
T ss_pred             -EEEEEeCC--------ccccCHHHHh-----hCcEEEeCCCCHHHHHHHHHHHHHHHHHHHHHcCCCCCcHHHHHHHHH
Confidence             33333331        1122333443     47899999999876       566677788889999988 99999999


Q ss_pred             HcCCcHHHHHHHHHHHhcCCCCcccccccCCCCCCCccccCCCCCcccccCCccccchHHHHhHHhhCCCCCCccccccc
Q 005987          367 ASGGDIRQAITSLQFSSLKQDPMLNLSLSISKPNFPEEKADGHGGFSIQFGRDETLSLFHALGKFLHNKRETDNLVKMDQ  446 (666)
Q Consensus       367 ~s~GDIR~AIn~LQf~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~~~~~RD~~l~lFhalGkil~~Kr~~~~~~~~~~  446 (666)
                      .++||+|.|+|.||.++..+ .. .                . +.+..+...  .-.+|..+..+ .++....       
T Consensus       204 ~~~gd~R~a~~~L~~~~~~~-~i-~----------------~-~~v~~~~~~--~~~i~~~~~~~-~~~~~~~-------  254 (324)
T 3u61_B          204 KNFPDFRKTIGELDSYSSKG-VL-D----------------A-GILSLVTND--RGAIDDVLESL-KNKDVKQ-------  254 (324)
T ss_dssp             HTCSCTTHHHHHHHHHGGGT-CB-C----------------C---------------CHHHHHHH-HTTCHHH-------
T ss_pred             hCCCCHHHHHHHHHHHhccC-CC-C----------------H-HHHHHHhCC--HHHHHHHHHHH-HcCCHHH-------
Confidence            99999999999999998221 11 0                0 001111111  12344443333 2221000       


Q ss_pred             cchhhhhccccCCCCCCChHHHHHhcCCChhHHHHHHHhhcCCCCCcchHHHHHHHHHHhhHhhhcccc
Q 005987          447 DAFVVKDKFSRLPLKMDAPEKVLSQAHGQARPVLDFLHENFLDFISEDAIDDAWAVASYLSDADLLLAS  515 (666)
Q Consensus       447 ~~~~~~~~~~r~pl~~~~pE~vl~~~~~~~~~~~~~LhENy~~f~~d~~i~~~~~~~d~LS~aD~l~~~  515 (666)
                          ..              ..+...-.++..++..|++++..-++   .+....++++|+.+|..+..
T Consensus       255 ----a~--------------~~~~~l~~~~~~i~~~l~~~~~~~~~---~~~l~~i~~~l~~~d~~l~~  302 (324)
T 3u61_B          255 ----LR--------------ALAPKYAADYSWFVGKLAEEIYSRVT---PQSIIRMYEIVGENNQYHGI  302 (324)
T ss_dssp             ----HH--------------HHHHHHSSCHHHHHHHHHHHHHHHSC---HHHHHHHHHHHHHHHHHTTT
T ss_pred             ----HH--------------HHHHHhccCHHHHHHHHHHHHHHhCC---HHHHHHHHHHHHHHHHHHHh
Confidence                00              01111111677788889999888665   46778889999999998864

>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=99.90  E-value=1.6e-22  Score=216.23  Aligned_cols=309  Identities=16%  Similarity=0.237  Sum_probs=181.2

Q ss_pred             CccccccCCCCccccccCHHHHHHHHHHH-HHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc-CCcE--EEEc--
Q 005987          137 QLWAEKYKPRSLEELAVQRKKVEEVRAWF-EERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL-GARL--YEWD--  210 (666)
Q Consensus       137 ~~W~eKY~P~sl~eLvg~~k~i~el~~wL-~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel-g~~v--iE~n--  210 (666)
                      .+|++||+|+++++++||+..++.++.|+ ..      ++.+ + ++|+||+|+||||+++++|+++ +...  +.++  
T Consensus         2 ~~w~~kyrP~~~~~~vg~~~~~~~l~~~~~~~------~~~~-~-~ll~Gp~G~GKTtl~~~la~~l~~~~~g~i~~~~~   73 (354)
T 1sxj_E            2 SLWVDKYRPKSLNALSHNEELTNFLKSLSDQP------RDLP-H-LLLYGPNGTGKKTRCMALLESIFGPGVYRLKIDVR   73 (354)
T ss_dssp             --CTTTTCCCSGGGCCSCHHHHHHHHTTTTCT------TCCC-C-EEEECSTTSSHHHHHHTHHHHHSCTTCCC------
T ss_pred             CcchhccCCCCHHHhcCCHHHHHHHHHHHhhC------CCCC-e-EEEECCCCCCHHHHHHHHHHHHcCCCCCeEEecce
Confidence            37999999999999999999998888877 43      4555 4 9999999999999999999975 2110  0000  


Q ss_pred             ---CCCch-hh-----h-hhh--hcccCCccccchhHHHHHHHHHHHhhcCCCCC--CCCCCCCceEEEEeCCCCCcchh
Q 005987          211 ---TPTPT-IW-----Q-EYM--HNCKTGLEYTSKLDEFENFVERIRRYGSTSPS--IPGESKSSAILLIDDLPVTNGRT  276 (666)
Q Consensus       211 ---asd~~-~~-----~-e~l--~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s--~~~~~~~~~IIlIDEid~l~~~~  276 (666)
                         .+... ..     . .++  .....+..   ....+++.++.+..+..+...  ..+-...++||||||++.+... 
T Consensus        74 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~i~~~~~~~~~~~~~~ls~l~~~~~vlilDE~~~L~~~-  149 (354)
T 1sxj_E           74 QFVTASNRKLELNVVSSPYHLEITPSDMGNN---DRIVIQELLKEVAQMEQVDFQDSKDGLAHRYKCVIINEANSLTKD-  149 (354)
T ss_dssp             ------------CCEECSSEEEECCC----C---CHHHHHHHHHHHTTTTC------------CCEEEEEECTTSSCHH-
T ss_pred             eecccccccceeeeecccceEEecHhhcCCc---chHHHHHHHHHHHHhccccccccccccCCCCeEEEEeCccccCHH-
Confidence               00000 00     0 000  00000000   001244455544332211000  0110224679999999997542 


Q ss_pred             HHHHHHHHHHHHHhcCCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCC
Q 005987          277 AFERLRQCLLLLVRSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSL  356 (666)
Q Consensus       277 ~~~~l~~~L~~l~~~~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v  356 (666)
                      ..+.+...|...   .....+|++++..        .+.++.++   +  ||..+.|++++.+++.++|..++.++++.+
T Consensus       150 ~~~~L~~~le~~---~~~~~~Il~t~~~--------~~l~~~l~---s--R~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  213 (354)
T 1sxj_E          150 AQAALRRTMEKY---SKNIRLIMVCDSM--------SPIIAPIK---S--QCLLIRCPAPSDSEISTILSDVVTNERIQL  213 (354)
T ss_dssp             HHHHHHHHHHHS---TTTEEEEEEESCS--------CSSCHHHH---T--TSEEEECCCCCHHHHHHHHHHHHHHHTCEE
T ss_pred             HHHHHHHHHHhh---cCCCEEEEEeCCH--------HHHHHHHH---h--hceEEecCCcCHHHHHHHHHHHHHHcCCCC
Confidence            334443333332   1222444444421        12233333   2  589999999999999999999999999999


Q ss_pred             C-HHHHHHHHHHcCCcHHHHHHHHHHHhcCCCCcccccccCCCCCCCccccCCCCCcccccCCccccchHHHHhHHhhCC
Q 005987          357 S-TEQIDLVAQASGGDIRQAITSLQFSSLKQDPMLNLSLSISKPNFPEEKADGHGGFSIQFGRDETLSLFHALGKFLHNK  435 (666)
Q Consensus       357 ~-~~~l~~Ia~~s~GDIR~AIn~LQf~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~~~~~RD~~l~lFhalGkil~~K  435 (666)
                      + +++++.|+..++||+|.|++.||.++.......                +...   .+...+..-.+|..+..++...
T Consensus       214 ~~~~~l~~i~~~~~G~~r~a~~~l~~~~~~~~~~i----------------~~~~---~~~~~~~~~~~~~l~~~i~~~~  274 (354)
T 1sxj_E          214 ETKDILKRIAQASNGNLRVSLLMLESMALNNELAL----------------KSSS---PIIKPDWIIVIHKLTRKIVKER  274 (354)
T ss_dssp             CCSHHHHHHHHHHTTCHHHHHHHHTHHHHTTTTEE----------------CSSC---CCCCCHHHHHHHHHHHHHHHCC
T ss_pred             CcHHHHHHHHHHcCCCHHHHHHHHHHHHHhCCCCc----------------CcCc---CCCCccHHHHHHHHHHHHHHhc
Confidence            9 999999999999999999999998876432100                0001   1233444456788888888653


Q ss_pred             CCCCccccccccchhhhhccccCCCCCCChHHHHHhcCCChhHHHHHHHhhcCC--CCCcchHHHHHHHHHHhhHhhhcc
Q 005987          436 RETDNLVKMDQDAFVVKDKFSRLPLKMDAPEKVLSQAHGQARPVLDFLHENFLD--FISEDAIDDAWAVASYLSDADLLL  513 (666)
Q Consensus       436 r~~~~~~~~~~~~~~~~~~~~r~pl~~~~pE~vl~~~~~~~~~~~~~LhENy~~--f~~d~~i~~~~~~~d~LS~aD~l~  513 (666)
                      ..  ....      ...+.+          .+++ ..+.++..++.-|+..+..  -++   .+...++++.++..|.-+
T Consensus       275 ~~--~~~~------~~~~~l----------~~l~-~~g~~~~~i~~~l~~~~~~~~~~~---~~~l~~~~~~l~~~d~~l  332 (354)
T 1sxj_E          275 SV--NSLI------ECRAVL----------YDLL-AHCIPANIILKELTFSLLDVETLN---TTNKSSIIEYSSVFDERL  332 (354)
T ss_dssp             SH--HHHH------HHHHHH----------HHHH-TTTCCHHHHHHHHHHTTTTCTTSC---HHHHHHHHHHHHHHHHHH
T ss_pred             ch--hHHH------HHHHHH----------HHHH-HcCCCHHHHHHHHHHHHHhccCCC---HHHHHHHHHHHHHHHHHH
Confidence            11  0000      011100          1122 2456677777778776655  344   456677889999999866


Q ss_pred             c
Q 005987          514 A  514 (666)
Q Consensus       514 ~  514 (666)
                      .
T Consensus       333 ~  333 (354)
T 1sxj_E          333 S  333 (354)
T ss_dssp             H
T ss_pred             h
Confidence            4

>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=99.88  E-value=8.9e-22  Score=209.94  Aligned_cols=203  Identities=21%  Similarity=0.367  Sum_probs=146.7

Q ss_pred             CCCCccccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcC-----CcEEE
Q 005987          134 STQQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLG-----ARLYE  208 (666)
Q Consensus       134 ~~~~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg-----~~viE  208 (666)
                      ....+|++||+|+++++++||+..++.|..+++.      |+.+  +++|+|||||||||+++++|+.+.     ..+++
T Consensus        10 ~~~~~~~~k~rp~~~~~~~g~~~~~~~L~~~i~~------g~~~--~~ll~Gp~G~GKTtla~~la~~l~~~~~~~~~~~   81 (340)
T 1sxj_C           10 KENLPWVEKYRPETLDEVYGQNEVITTVRKFVDE------GKLP--HLLFYGPPGTGKTSTIVALAREIYGKNYSNMVLE   81 (340)
T ss_dssp             --CCCHHHHTCCSSGGGCCSCHHHHHHHHHHHHT------TCCC--CEEEECSSSSSHHHHHHHHHHHHHTTSHHHHEEE
T ss_pred             ccCCchHHHhCCCcHHHhcCcHHHHHHHHHHHhc------CCCc--eEEEECCCCCCHHHHHHHHHHHHcCCCccceEEE
Confidence            3467999999999999999999999999999986      6655  399999999999999999999973     34777


Q ss_pred             EcCCCchhhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHH
Q 005987          209 WDTPTPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLL  288 (666)
Q Consensus       209 ~nasd~~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l  288 (666)
                      +++++.           .|      .+.+++.+.........   ..   ..++|++|||++.+... +.+    .|..+
T Consensus        82 ~~~~~~-----------~~------~~~ir~~i~~~~~~~~~---~~---~~~~viiiDe~~~l~~~-~~~----~L~~~  133 (340)
T 1sxj_C           82 LNASDD-----------RG------IDVVRNQIKDFASTRQI---FS---KGFKLIILDEADAMTNA-AQN----ALRRV  133 (340)
T ss_dssp             ECTTSC-----------CS------HHHHHTHHHHHHHBCCS---SS---CSCEEEEETTGGGSCHH-HHH----HHHHH
T ss_pred             EcCccc-----------cc------HHHHHHHHHHHHhhccc---CC---CCceEEEEeCCCCCCHH-HHH----HHHHH
Confidence            777651           11      22333333332211110   11   12579999999988643 223    34455


Q ss_pred             HhcCC-CceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHH
Q 005987          289 VRSTH-IPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQA  367 (666)
Q Consensus       289 ~~~~~-~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~  367 (666)
                      ++... ...++++++.        ..+.++.++   +  ||..+.|.+++..++.++|..++..+++.+++++++.|+..
T Consensus       134 le~~~~~~~~il~~n~--------~~~i~~~i~---s--R~~~~~~~~l~~~~~~~~l~~~~~~~~~~i~~~~~~~i~~~  200 (340)
T 1sxj_C          134 IERYTKNTRFCVLANY--------AHKLTPALL---S--QCTRFRFQPLPQEAIERRIANVLVHEKLKLSPNAEKALIEL  200 (340)
T ss_dssp             HHHTTTTEEEEEEESC--------GGGSCHHHH---T--TSEEEECCCCCHHHHHHHHHHHHHTTTCCBCHHHHHHHHHH
T ss_pred             HhcCCCCeEEEEEecC--------ccccchhHH---h--hceeEeccCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHH
Confidence            55432 2244444431        122333333   3  59999999999999999999999999999999999999999


Q ss_pred             cCCcHHHHHHHHHHHhcC
Q 005987          368 SGGDIRQAITSLQFSSLK  385 (666)
Q Consensus       368 s~GDIR~AIn~LQf~~~~  385 (666)
                      ++||+|.|++.||.++..
T Consensus       201 s~G~~r~~~~~l~~~~~~  218 (340)
T 1sxj_C          201 SNGDMRRVLNVLQSCKAT  218 (340)
T ss_dssp             HTTCHHHHHHHTTTTTTT
T ss_pred             cCCCHHHHHHHHHHHHHh
Confidence            999999999999887653

>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=99.87  E-value=1.3e-20  Score=198.28  Aligned_cols=287  Identities=18%  Similarity=0.276  Sum_probs=186.7

Q ss_pred             CCccccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcC-----CcEEEEc
Q 005987          136 QQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLG-----ARLYEWD  210 (666)
Q Consensus       136 ~~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg-----~~viE~n  210 (666)
                      +.+|++||+|.++++++|+++.++.+..|+..      ++.+  ++||+||||+|||++|+++|+++.     ..+++++
T Consensus        12 ~~~~~~k~~p~~~~~~~g~~~~~~~l~~~l~~------~~~~--~~ll~G~~G~GKT~la~~l~~~l~~~~~~~~~~~~~   83 (327)
T 1iqp_A           12 EKPWVEKYRPQRLDDIVGQEHIVKRLKHYVKT------GSMP--HLLFAGPPGVGKTTAALALARELFGENWRHNFLELN   83 (327)
T ss_dssp             TSCHHHHTCCCSTTTCCSCHHHHHHHHHHHHH------TCCC--EEEEESCTTSSHHHHHHHHHHHHHGGGHHHHEEEEE
T ss_pred             CCchhhccCCCCHHHhhCCHHHHHHHHHHHHc------CCCC--eEEEECcCCCCHHHHHHHHHHHhcCCcccCceEEee
Confidence            57899999999999999999999999999986      4444  599999999999999999999973     3467777


Q ss_pred             CCCchhhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHh
Q 005987          211 TPTPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVR  290 (666)
Q Consensus       211 asd~~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~  290 (666)
                      +++...                 .+.+...+........+    .  ...+.+|+|||++.+... .    ++.|..+++
T Consensus        84 ~~~~~~-----------------~~~~~~~~~~~~~~~~~----~--~~~~~vliiDe~~~l~~~-~----~~~L~~~le  135 (327)
T 1iqp_A           84 ASDERG-----------------INVIREKVKEFARTKPI----G--GASFKIIFLDEADALTQD-A----QQALRRTME  135 (327)
T ss_dssp             TTCHHH-----------------HHTTHHHHHHHHHSCCG----G--GCSCEEEEEETGGGSCHH-H----HHHHHHHHH
T ss_pred             ccccCc-----------------hHHHHHHHHHHHhhCCc----C--CCCCeEEEEeCCCcCCHH-H----HHHHHHHHH
Confidence            665211                 01111122221111110    0  023579999999988543 2    234555555


Q ss_pred             cCCCce-EEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcC
Q 005987          291 STHIPT-AVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASG  369 (666)
Q Consensus       291 ~~~~Pi-ViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~s~  369 (666)
                      .....+ ++++++.        ..+.++.+.+     ||..+.|.|++.+++.++|..++..+++.+++++++.|+..++
T Consensus       136 ~~~~~~~~i~~~~~--------~~~l~~~l~s-----r~~~~~~~~l~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~  202 (327)
T 1iqp_A          136 MFSSNVRFILSCNY--------SSKIIEPIQS-----RCAIFRFRPLRDEDIAKRLRYIAENEGLELTEEGLQAILYIAE  202 (327)
T ss_dssp             HTTTTEEEEEEESC--------GGGSCHHHHH-----TEEEEECCCCCHHHHHHHHHHHHHTTTCEECHHHHHHHHHHHT
T ss_pred             hcCCCCeEEEEeCC--------ccccCHHHHh-----hCcEEEecCCCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHCC
Confidence            433223 3333321        1122333332     5889999999999999999999999999999999999999999


Q ss_pred             CcHHHHHHHHHHHhcCCCCcccccccCCCCCCCccccCCCCCcccccCCccccchHHHHhHHhhCCCCCCccccccccch
Q 005987          370 GDIRQAITSLQFSSLKQDPMLNLSLSISKPNFPEEKADGHGGFSIQFGRDETLSLFHALGKFLHNKRETDNLVKMDQDAF  449 (666)
Q Consensus       370 GDIR~AIn~LQf~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~~~~~RD~~l~lFhalGkil~~Kr~~~~~~~~~~~~~  449 (666)
                      ||+|.+++.|+.++........                  +.+....+.-...++|..+..++.... ..          
T Consensus       203 g~~r~~~~~l~~~~~~~~~i~~------------------~~v~~~~~~~~~~~i~~l~~~~~~~~~-~~----------  253 (327)
T 1iqp_A          203 GDMRRAINILQAAAALDKKITD------------------ENVFMVASRARPEDIREMMLLALKGNF-LK----------  253 (327)
T ss_dssp             TCHHHHHHHHHHHHTTCSEECH------------------HHHHHHTTCCCHHHHHHHHHHHHHTCH-HH----------
T ss_pred             CCHHHHHHHHHHHHhcCCCCCH------------------HHHHHHHCCCCHHHHHHHHHHHHcCCH-HH----------
Confidence            9999999999988754321000                  000111122223456666665555321 00          


Q ss_pred             hhhhccccCCCCCCChHHHHHhcCCChhHHHHHHHhhcCC-CCCcchHHHHHHHHHHhhHhhhccc
Q 005987          450 VVKDKFSRLPLKMDAPEKVLSQAHGQARPVLDFLHENFLD-FISEDAIDDAWAVASYLSDADLLLA  514 (666)
Q Consensus       450 ~~~~~~~r~pl~~~~pE~vl~~~~~~~~~~~~~LhENy~~-f~~d~~i~~~~~~~d~LS~aD~l~~  514 (666)
                       ..+          .-.+++...+.++..++..|...+.. .++   .+....+++.+..+|.-+.
T Consensus       254 -~~~----------~~~~ll~~~g~~~~~i~~~l~~~~~~~~~~---~~~l~~~~~~l~~~~~~lk  305 (327)
T 1iqp_A          254 -ARE----------KLREILLKQGLSGEDVLVQMHKEVFNLPIE---EPKKVLLADKIGEYNFRLV  305 (327)
T ss_dssp             -HHH----------HHHHHHHHHCCCHHHHHHHHHHHGGGSSSC---HHHHHHHHHHHHHHHHHHH
T ss_pred             -HHH----------HHHHHHHHcCCCHHHHHHHHHHHHHhccCC---HHHHHHHHHHHHHHHHHHH
Confidence             000          01123323466777777777777665 233   5777888999999999775

>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=99.87  E-value=2.7e-21  Score=202.81  Aligned_cols=287  Identities=17%  Similarity=0.309  Sum_probs=185.2

Q ss_pred             CCccccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc-----CCcEEEEc
Q 005987          136 QQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL-----GARLYEWD  210 (666)
Q Consensus       136 ~~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel-----g~~viE~n  210 (666)
                      ..+|++||+|+++++++|++..++.+..++..      +..+  ++||+||||+|||++|+++|+++     +..+++++
T Consensus         4 ~~~~~~k~~p~~~~~~~g~~~~~~~l~~~l~~------~~~~--~~ll~G~~G~GKt~la~~l~~~l~~~~~~~~~~~~~   75 (319)
T 2chq_A            4 FEIWVEKYRPRTLDEVVGQDEVIQRLKGYVER------KNIP--HLLFSGPPGTGKTATAIALARDLFGENWRDNFIEMN   75 (319)
T ss_dssp             --CTTTTTSCSSGGGSCSCHHHHHHHHTTTTT------TCCC--CEEEESSSSSSHHHHHHHHHHHHHTTCHHHHCEEEE
T ss_pred             cccHHHhcCCCCHHHHhCCHHHHHHHHHHHhC------CCCC--eEEEECcCCcCHHHHHHHHHHHhcCCcccCCeEEEe
Confidence            46899999999999999999999999888764      4444  49999999999999999999997     34577888


Q ss_pred             CCCchhhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHh
Q 005987          211 TPTPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVR  290 (666)
Q Consensus       211 asd~~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~  290 (666)
                      +++.           .|..      .+...+........+    .  ...+.||+|||++.+...     .++.|..+++
T Consensus        76 ~~~~-----------~~~~------~~~~~~~~~~~~~~~----~--~~~~~vliiDe~~~l~~~-----~~~~L~~~le  127 (319)
T 2chq_A           76 ASDE-----------RGID------VVRHKIKEFARTAPI----G--GAPFKIIFLDEADALTAD-----AQAALRRTME  127 (319)
T ss_dssp             TTST-----------TCTT------TSSHHHHHHHHSCCS----S--SCCCEEEEEETGGGSCHH-----HHHTTGGGTS
T ss_pred             Cccc-----------cChH------HHHHHHHHHHhcCCC----C--CCCceEEEEeCCCcCCHH-----HHHHHHHHHH
Confidence            7652           1211      111112222111111    1  124679999999987542     2334555555


Q ss_pred             cCCCceEEE-EecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcC
Q 005987          291 STHIPTAVV-LTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASG  369 (666)
Q Consensus       291 ~~~~PiViI-it~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~s~  369 (666)
                      .....+++| +++.        ..+..+.+.   +  ||..|.|.+++.+++.++|..++..+++.+++++++.|+..++
T Consensus       128 ~~~~~~~~i~~~~~--------~~~l~~~l~---s--r~~~i~~~~~~~~~~~~~l~~~~~~~~~~i~~~~l~~l~~~~~  194 (319)
T 2chq_A          128 MYSKSCRFILSCNY--------VSRIIEPIQ---S--RCAVFRFKPVPKEAMKKRLLEICEKEGVKITEDGLEALIYISG  194 (319)
T ss_dssp             SSSSSEEEEEEESC--------GGGSCHHHH---T--TCEEEECCCCCHHHHHHHHHHHHHTTCCCBCHHHHHHHHHTTT
T ss_pred             hcCCCCeEEEEeCC--------hhhcchHHH---h--hCeEEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcC
Confidence            433223333 3331        112223332   2  5889999999999999999999999999999999999999999


Q ss_pred             CcHHHHHHHHHHHhcCCCCcccccccCCCCCCCccccCCCCCcccccCCccccchHHHHhHHhhCCCCCCccccccccch
Q 005987          370 GDIRQAITSLQFSSLKQDPMLNLSLSISKPNFPEEKADGHGGFSIQFGRDETLSLFHALGKFLHNKRETDNLVKMDQDAF  449 (666)
Q Consensus       370 GDIR~AIn~LQf~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~~~~~RD~~l~lFhalGkil~~Kr~~~~~~~~~~~~~  449 (666)
                      ||+|.+++.||.++........                  +.+..+.+.....++|+.+..++.....  .         
T Consensus       195 G~~r~~~~~l~~~~~~~~~i~~------------------~~v~~~~~~~~~~~~~~l~~~~~~~~~~--~---------  245 (319)
T 2chq_A          195 GDFRKAINALQGAAAIGEVVDA------------------DTIYQITATARPEEMTELIQTALKGNFM--E---------  245 (319)
T ss_dssp             TCHHHHHHHHHHHHHSSSCBCH------------------HHHHHHTTCCCHHHHHHHHHHHHHTCHH--H---------
T ss_pred             CCHHHHHHHHHHHHHcCCCCCH------------------HHHHHHHCCCCHHHHHHHHHHHHhCCHH--H---------
Confidence            9999999999998864221100                  0011222333344677777777753210  0         


Q ss_pred             hhhhccccCCCCCCChHHHHHhcCCChhHHHHHHHhhcCCC-CCcchHHHHHHHHHHhhHhhhccc
Q 005987          450 VVKDKFSRLPLKMDAPEKVLSQAHGQARPVLDFLHENFLDF-ISEDAIDDAWAVASYLSDADLLLA  514 (666)
Q Consensus       450 ~~~~~~~r~pl~~~~pE~vl~~~~~~~~~~~~~LhENy~~f-~~d~~i~~~~~~~d~LS~aD~l~~  514 (666)
                       ..+          .-.+++...+.++..++..|...+..+ ++   .+...++++.+..+|.-+.
T Consensus       246 -a~~----------~l~~l~~~~g~~~~~i~~~l~~~~~~l~~~---~~~l~~~~~~l~~~~~~lk  297 (319)
T 2chq_A          246 -ARE----------LLDRLMVEYGMSGEDIVAQLFREIISMPIK---DSLKVQLIDKLGEVDFRLT  297 (319)
T ss_dssp             -HHH----------HHHHHHHHSCCCHHHHHHHHHHHHHTSCSC---TTHHHHHHHHHHHHHHHHH
T ss_pred             -HHH----------HHHHHHHHcCCCHHHHHHHHHHHHHhccCC---HHHHHHHHHHHHHHHHHHH
Confidence             000          011233324556666766677666552 33   4566777889999998765

>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=99.86  E-value=3.5e-21  Score=205.29  Aligned_cols=207  Identities=21%  Similarity=0.330  Sum_probs=142.0

Q ss_pred             CCCCccccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcC------CcEE
Q 005987          134 STQQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLG------ARLY  207 (666)
Q Consensus       134 ~~~~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg------~~vi  207 (666)
                      ....+|++||+|+++++++|+++.++.+..++..      +..+  ++||+||||||||++++++|++++      ..++
T Consensus        22 ~~~~~~~~k~~p~~~~~i~g~~~~~~~l~~~l~~------~~~~--~~ll~G~~G~GKT~la~~la~~l~~~~~~~~~~~   93 (353)
T 1sxj_D           22 LAQQPWVEKYRPKNLDEVTAQDHAVTVLKKTLKS------ANLP--HMLFYGPPGTGKTSTILALTKELYGPDLMKSRIL   93 (353)
T ss_dssp             ----CHHHHTCCSSTTTCCSCCTTHHHHHHHTTC------TTCC--CEEEECSTTSSHHHHHHHHHHHHHHHHHHTTSEE
T ss_pred             ccCccHHHhcCCCCHHHhhCCHHHHHHHHHHHhc------CCCC--EEEEECCCCCCHHHHHHHHHHHhCCCcccccceE
Confidence            3467999999999999999999999999988865      4444  499999999999999999999974      4678


Q ss_pred             EEcCCCchhhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCC-----CCCCCCceEEEEeCCCCCcchhHHHHHH
Q 005987          208 EWDTPTPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSI-----PGESKSSAILLIDDLPVTNGRTAFERLR  282 (666)
Q Consensus       208 E~nasd~~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~-----~~~~~~~~IIlIDEid~l~~~~~~~~l~  282 (666)
                      ++++++..           +.      ..+.+.+....... .....     ......+.||+|||++.+... .    +
T Consensus        94 ~~~~~~~~-----------~~------~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~vliiDE~~~l~~~-~----~  150 (353)
T 1sxj_D           94 ELNASDER-----------GI------SIVREKVKNFARLT-VSKPSKHDLENYPCPPYKIIILDEADSMTAD-A----Q  150 (353)
T ss_dssp             EECSSSCC-----------CH------HHHTTHHHHHHHSC-CCCCCTTHHHHSCCCSCEEEEETTGGGSCHH-H----H
T ss_pred             EEcccccc-----------ch------HHHHHHHHHHhhhc-ccccchhhcccCCCCCceEEEEECCCccCHH-H----H
Confidence            88876521           11      11111111111110 00000     000123579999999988643 2    2


Q ss_pred             HHHHHHHhcCCC-ceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHH
Q 005987          283 QCLLLLVRSTHI-PTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQI  361 (666)
Q Consensus       283 ~~L~~l~~~~~~-PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l  361 (666)
                      +.|..+++.... ..++++++.        ..+.++.+++     ||..+.|.+++.+++.++|..++..+++.++++++
T Consensus       151 ~~Ll~~le~~~~~~~~il~~~~--------~~~l~~~l~s-----R~~~i~~~~~~~~~~~~~l~~~~~~~~~~i~~~~l  217 (353)
T 1sxj_D          151 SALRRTMETYSGVTRFCLICNY--------VTRIIDPLAS-----QCSKFRFKALDASNAIDRLRFISEQENVKCDDGVL  217 (353)
T ss_dssp             HHHHHHHHHTTTTEEEEEEESC--------GGGSCHHHHH-----HSEEEECCCCCHHHHHHHHHHHHHTTTCCCCHHHH
T ss_pred             HHHHHHHHhcCCCceEEEEeCc--------hhhCcchhhc-----cCceEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHH
Confidence            334445554332 234444431        1223333333     47899999999999999999999999999999999


Q ss_pred             HHHHHHcCCcHHHHHHHHHHHhc
Q 005987          362 DLVAQASGGDIRQAITSLQFSSL  384 (666)
Q Consensus       362 ~~Ia~~s~GDIR~AIn~LQf~~~  384 (666)
                      +.|+..++||+|.+++.|+.++.
T Consensus       218 ~~l~~~~~G~~r~~~~~l~~~~~  240 (353)
T 1sxj_D          218 ERILDISAGDLRRGITLLQSASK  240 (353)
T ss_dssp             HHHHHHTSSCHHHHHHHHHHTHH
T ss_pred             HHHHHHcCCCHHHHHHHHHHHHH
Confidence            99999999999999999998764

>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=99.85  E-value=3.5e-20  Score=194.73  Aligned_cols=201  Identities=19%  Similarity=0.364  Sum_probs=146.7

Q ss_pred             CCccccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc-----CCcEEEEc
Q 005987          136 QQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL-----GARLYEWD  210 (666)
Q Consensus       136 ~~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel-----g~~viE~n  210 (666)
                      ..+|++||+|.++++++|++..++.+..|++.      ++.+ + ++|+||||+|||++++.+|+++     +..+++++
T Consensus         8 ~~~~~~~~~p~~~~~~~g~~~~~~~l~~~l~~------~~~~-~-~ll~G~~G~GKt~la~~l~~~l~~~~~~~~~~~~~   79 (323)
T 1sxj_B            8 QLPWVEKYRPQVLSDIVGNKETIDRLQQIAKD------GNMP-H-MIISGMPGIGKTTSVHCLAHELLGRSYADGVLELN   79 (323)
T ss_dssp             CCCHHHHTCCSSGGGCCSCTHHHHHHHHHHHS------CCCC-C-EEEECSTTSSHHHHHHHHHHHHHGGGHHHHEEEEC
T ss_pred             cCcHHHhcCCCCHHHHHCCHHHHHHHHHHHHc------CCCC-e-EEEECcCCCCHHHHHHHHHHHhcCCcccCCEEEec
Confidence            57899999999999999999999999999875      5554 3 9999999999999999999997     34577877


Q ss_pred             CCCchhhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHh
Q 005987          211 TPTPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVR  290 (666)
Q Consensus       211 asd~~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~  290 (666)
                      +++..                 ..+.+++.+.........   ..  .++++||+|||++.+... .    .+.|..+++
T Consensus        80 ~~~~~-----------------~~~~i~~~~~~~~~~~~~---~~--~~~~~viiiDe~~~l~~~-~----~~~L~~~le  132 (323)
T 1sxj_B           80 ASDDR-----------------GIDVVRNQIKHFAQKKLH---LP--PGKHKIVILDEADSMTAG-A----QQALRRTME  132 (323)
T ss_dssp             TTSCC-----------------SHHHHHTHHHHHHHBCCC---CC--TTCCEEEEEESGGGSCHH-H----HHTTHHHHH
T ss_pred             Ccccc-----------------ChHHHHHHHHHHHhcccc---CC--CCCceEEEEECcccCCHH-H----HHHHHHHHh
Confidence            66411                 123344444443311100   00  123679999999987643 2    233455555


Q ss_pred             cCCC-ceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcC
Q 005987          291 STHI-PTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASG  369 (666)
Q Consensus       291 ~~~~-PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~s~  369 (666)
                      .... ..++++++.        ..+.++.+.   +  ||..+.|.+++.+++.++|..++..+++.+++++++.|+..++
T Consensus       133 ~~~~~~~~il~~~~--------~~~l~~~l~---s--r~~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~  199 (323)
T 1sxj_B          133 LYSNSTRFAFACNQ--------SNKIIEPLQ---S--QCAILRYSKLSDEDVLKRLLQIIKLEDVKYTNDGLEAIIFTAE  199 (323)
T ss_dssp             HTTTTEEEEEEESC--------GGGSCHHHH---T--TSEEEECCCCCHHHHHHHHHHHHHHHTCCBCHHHHHHHHHHHT
T ss_pred             ccCCCceEEEEeCC--------hhhchhHHH---h--hceEEeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcC
Confidence            4332 233334431        112223333   2  5889999999999999999999999999999999999999999


Q ss_pred             CcHHHHHHHHHHHhc
Q 005987          370 GDIRQAITSLQFSSL  384 (666)
Q Consensus       370 GDIR~AIn~LQf~~~  384 (666)
                      ||+|.|++.|+.++.
T Consensus       200 G~~r~a~~~l~~~~~  214 (323)
T 1sxj_B          200 GDMRQAINNLQSTVA  214 (323)
T ss_dssp             TCHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHh
Confidence            999999999998874

>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=99.84  E-value=1.7e-19  Score=177.74  Aligned_cols=201  Identities=21%  Similarity=0.406  Sum_probs=142.5

Q ss_pred             CCccccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc-----CCcEEEEc
Q 005987          136 QQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL-----GARLYEWD  210 (666)
Q Consensus       136 ~~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel-----g~~viE~n  210 (666)
                      ..+|.++|+|.++++++|++..++.+..|+..      +..+  .++|+||||||||++++.+++++     ...++.++
T Consensus         4 ~~~~~~~~~p~~~~~~~g~~~~~~~l~~~l~~------~~~~--~~ll~G~~G~GKT~l~~~l~~~~~~~~~~~~~~~~~   75 (226)
T 2chg_A            4 FEIWVEKYRPRTLDEVVGQDEVIQRLKGYVER------KNIP--HLLFSGPPGTGKTATAIALARDLFGENWRDNFIEMN   75 (226)
T ss_dssp             CCCHHHHTSCSSGGGCCSCHHHHHHHHHHHHT------TCCC--CEEEECSTTSSHHHHHHHHHHHHHGGGGGGGEEEEE
T ss_pred             hhhHHHhcCCCCHHHHcCcHHHHHHHHHHHhC------CCCC--eEEEECCCCCCHHHHHHHHHHHHhccccccceEEec
Confidence            46899999999999999999999999999985      3322  59999999999999999999986     34566776


Q ss_pred             CCCchhhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHh
Q 005987          211 TPTPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVR  290 (666)
Q Consensus       211 asd~~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~  290 (666)
                      ++...           +      ...+...+.........      ....+.+|+|||++.+...     ..+.|..+++
T Consensus        76 ~~~~~-----------~------~~~~~~~~~~~~~~~~~------~~~~~~vliiDe~~~l~~~-----~~~~l~~~l~  127 (226)
T 2chg_A           76 ASDER-----------G------IDVVRHKIKEFARTAPI------GGAPFKIIFLDEADALTAD-----AQAALRRTME  127 (226)
T ss_dssp             TTCTT-----------C------HHHHHHHHHHHHTSCCS------TTCSCEEEEEETGGGSCHH-----HHHHHHHHHH
T ss_pred             ccccc-----------C------hHHHHHHHHHHhcccCC------CccCceEEEEeChhhcCHH-----HHHHHHHHHH
Confidence            54311           1      11222222222211100      1124679999999987543     1223444454


Q ss_pred             cCCCc-eEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcC
Q 005987          291 STHIP-TAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASG  369 (666)
Q Consensus       291 ~~~~P-iViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~s~  369 (666)
                      ..... .++++++..        ....   ..+.+  |+..+.|.+++.+++.++|.+++..+++.+++++++.|+..++
T Consensus       128 ~~~~~~~~i~~~~~~--------~~~~---~~l~~--r~~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~  194 (226)
T 2chg_A          128 MYSKSCRFILSCNYV--------SRII---EPIQS--RCAVFRFKPVPKEAMKKRLLEICEKEGVKITEDGLEALIYISG  194 (226)
T ss_dssp             HTTTTEEEEEEESCG--------GGSC---HHHHT--TSEEEECCCCCHHHHHHHHHHHHHHHTCCBCHHHHHHHHHHHT
T ss_pred             hcCCCCeEEEEeCCh--------hhcC---HHHHH--hCceeecCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcC
Confidence            43322 333333311        1111   22222  4779999999999999999999999999999999999999999


Q ss_pred             CcHHHHHHHHHHHhcC
Q 005987          370 GDIRQAITSLQFSSLK  385 (666)
Q Consensus       370 GDIR~AIn~LQf~~~~  385 (666)
                      ||+|.+++.|+.++..
T Consensus       195 g~~r~l~~~l~~~~~~  210 (226)
T 2chg_A          195 GDFRKAINALQGAAAI  210 (226)
T ss_dssp             TCHHHHHHHHHHHHHT
T ss_pred             CCHHHHHHHHHHHHhc
Confidence            9999999999998864

>3pvs_A Replication-associated recombination protein A; maintenance of genome stability Pro recombination; 2.50A {Escherichia coli}

Probab=99.83  E-value=6.4e-20  Score=202.46  Aligned_cols=199  Identities=21%  Similarity=0.302  Sum_probs=146.0

Q ss_pred             CCccccccCCCCccccccCHHHH---HHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCC
Q 005987          136 QQLWAEKYKPRSLEELAVQRKKV---EEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTP  212 (666)
Q Consensus       136 ~~~W~eKY~P~sl~eLvg~~k~i---~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nas  212 (666)
                      ..+|.++|+|+++++++|++..+   ..+..+++.      ++.  +.+||+|||||||||+|+++|+.++..++++++.
T Consensus        13 ~~pla~r~rP~~l~~ivGq~~~~~~~~~L~~~i~~------~~~--~~vLL~GppGtGKTtlAr~ia~~~~~~f~~l~a~   84 (447)
T 3pvs_A           13 FQPLAARMRPENLAQYIGQQHLLAAGKPLPRAIEA------GHL--HSMILWGPPGTGKTTLAEVIARYANADVERISAV   84 (447)
T ss_dssp             -CCHHHHTCCCSTTTCCSCHHHHSTTSHHHHHHHH------TCC--CEEEEECSTTSSHHHHHHHHHHHTTCEEEEEETT
T ss_pred             cCChHHHhCCCCHHHhCCcHHHHhchHHHHHHHHc------CCC--cEEEEECCCCCcHHHHHHHHHHHhCCCeEEEEec
Confidence            36899999999999999999999   788888876      444  4799999999999999999999999999999875


Q ss_pred             CchhhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcC
Q 005987          213 TPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRST  292 (666)
Q Consensus       213 d~~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~  292 (666)
                      .            .|      .+.++..+..+.....        ...+.||||||++.+...     .++.|+..++.+
T Consensus        85 ~------------~~------~~~ir~~~~~a~~~~~--------~~~~~iLfIDEI~~l~~~-----~q~~LL~~le~~  133 (447)
T 3pvs_A           85 T------------SG------VKEIREAIERARQNRN--------AGRRTILFVDEVHRFNKS-----QQDAFLPHIEDG  133 (447)
T ss_dssp             T------------CC------HHHHHHHHHHHHHHHH--------TTCCEEEEEETTTCC-----------CCHHHHHTT
T ss_pred             c------------CC------HHHHHHHHHHHHHhhh--------cCCCcEEEEeChhhhCHH-----HHHHHHHHHhcC
Confidence            3            11      2344445554433221        013579999999988543     233456666665


Q ss_pred             CCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHH-------hCCCCCHHHHHHHH
Q 005987          293 HIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQ-------EQYSLSTEQIDLVA  365 (666)
Q Consensus       293 ~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~-------e~i~v~~~~l~~Ia  365 (666)
                      .. ++|.+++.+.      ....   ...+++  ||.++.|.+++.+++..+|.+++..       +++.+++++++.|+
T Consensus       134 ~v-~lI~att~n~------~~~l---~~aL~s--R~~v~~l~~l~~edi~~il~~~l~~~~~~~~~~~~~i~~~al~~L~  201 (447)
T 3pvs_A          134 TI-TFIGATTENP------SFEL---NSALLS--RARVYLLKSLSTEDIEQVLTQAMEDKTRGYGGQDIVLPDETRRAIA  201 (447)
T ss_dssp             SC-EEEEEESSCG------GGSS---CHHHHT--TEEEEECCCCCHHHHHHHHHHHHHCTTTSSTTSSEECCHHHHHHHH
T ss_pred             ce-EEEecCCCCc------cccc---CHHHhC--ceeEEeeCCcCHHHHHHHHHHHHHHHhhhhccccCcCCHHHHHHHH
Confidence            42 3333332221      1111   133333  5899999999999999999999987       55779999999999


Q ss_pred             HHcCCcHHHHHHHHHHHhcC
Q 005987          366 QASGGDIRQAITSLQFSSLK  385 (666)
Q Consensus       366 ~~s~GDIR~AIn~LQf~~~~  385 (666)
                      ..++||+|.++|.|+.++..
T Consensus       202 ~~~~Gd~R~lln~Le~a~~~  221 (447)
T 3pvs_A          202 ELVNGDARRALNTLEMMADM  221 (447)
T ss_dssp             HHHCSCHHHHHHHHHHHHHH
T ss_pred             HHCCCCHHHHHHHHHHHHHh
Confidence            99999999999999998754

>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=99.83  E-value=1.9e-19  Score=193.32  Aligned_cols=217  Identities=18%  Similarity=0.259  Sum_probs=145.1

Q ss_pred             CCccccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCC--C
Q 005987          136 QQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTP--T  213 (666)
Q Consensus       136 ~~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nas--d  213 (666)
                      -.+|++||+|+++++++|++..++.+..++..      ++.+ +.+||+||||+|||++++++|+.+++.......+  .
T Consensus         3 ~~~l~~k~rp~~~~~~vg~~~~~~~L~~~l~~------~~~~-~~~ll~G~~G~GKT~la~~la~~l~~~~~~~~~~~~~   75 (373)
T 1jr3_A            3 YQVLARKWRPQTFADVVGQEHVLTALANGLSL------GRIH-HAYLFSGTRGVGKTSIARLLAKGLNCETGITATPCGV   75 (373)
T ss_dssp             CCCHHHHTCCCSTTTSCSCHHHHHHHHHHHHH------TCCC-SEEEEESCTTSSHHHHHHHHHHHHSCTTCSCSSCCSS
T ss_pred             cHHHHHhhCCCchhhccCcHHHHHHHHHHHHh------CCCC-eEEEEECCCCCCHHHHHHHHHHHhCCCCCCCCCCCcc
Confidence            36799999999999999999999999999986      4544 5799999999999999999999986532110000  0


Q ss_pred             chhhhhhhhcccCCc---c--ccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHH
Q 005987          214 PTIWQEYMHNCKTGL---E--YTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLL  288 (666)
Q Consensus       214 ~~~~~e~l~~~~~g~---~--~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l  288 (666)
                      ...............   .  .....+.++.+++.+....        ....++||+|||++.+...     ..+.|..+
T Consensus        76 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~--------~~~~~~vliiDe~~~l~~~-----~~~~Ll~~  142 (373)
T 1jr3_A           76 CDNCREIEQGRFVDLIEIDAASRTKVEDTRDLLDNVQYAP--------ARGRFKVYLIDEVHMLSRH-----SFNALLKT  142 (373)
T ss_dssp             SHHHHHHHTSCCSSCEEEETTCSCCSSCHHHHHHHTTSCC--------SSSSSEEEEEECGGGSCHH-----HHHHHHHH
T ss_pred             cHHHHHHhccCCCceEEecccccCCHHHHHHHHHHHhhcc--------ccCCeEEEEEECcchhcHH-----HHHHHHHH
Confidence            000000000000000   0  0112234555555543211        1124679999999987542     22345566


Q ss_pred             HhcCCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHc
Q 005987          289 VRSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQAS  368 (666)
Q Consensus       289 ~~~~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~s  368 (666)
                      ++.....+++|++....       .+...   .+.+  ||..+.|.+++.+++.++|..++..+++.+++++++.|+..+
T Consensus       143 le~~~~~~~~Il~~~~~-------~~l~~---~l~s--r~~~i~~~~l~~~~~~~~l~~~~~~~~~~~~~~a~~~l~~~~  210 (373)
T 1jr3_A          143 LEEPPEHVKFLLATTDP-------QKLPV---TILS--RCLQFHLKALDVEQIRHQLEHILNEEHIAHEPRALQLLARAA  210 (373)
T ss_dssp             HHSCCSSEEEEEEESCG-------GGSCH---HHHT--TSEEEECCCCCHHHHHHHHHHHHHHHTCCBCHHHHHHHHHHS
T ss_pred             HhcCCCceEEEEEeCCh-------HhCcH---HHHh--heeEeeCCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHC
Confidence            66544344444443211       12222   2332  589999999999999999999999999999999999999999


Q ss_pred             CCcHHHHHHHHHHHhc
Q 005987          369 GGDIRQAITSLQFSSL  384 (666)
Q Consensus       369 ~GDIR~AIn~LQf~~~  384 (666)
                      +||+|.+++.|+.+..
T Consensus       211 ~G~~r~~~~~l~~~~~  226 (373)
T 1jr3_A          211 EGSLRDALSLTDQAIA  226 (373)
T ss_dssp             SSCHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHH
Confidence            9999999999977653

>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=99.83  E-value=3.2e-19  Score=177.82  Aligned_cols=217  Identities=17%  Similarity=0.246  Sum_probs=141.8

Q ss_pred             CCccccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCC--C
Q 005987          136 QQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTP--T  213 (666)
Q Consensus       136 ~~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nas--d  213 (666)
                      ..+|.++|+|..+++++|++..++.+..|+..      ++.+ +.++|+||||+|||++++.++++++........+  .
T Consensus        10 ~~~~~~~~~p~~~~~~~g~~~~~~~l~~~l~~------~~~~-~~~ll~G~~G~GKT~l~~~~~~~~~~~~~~~~~~~~~   82 (250)
T 1njg_A           10 YQVLARKWRPQTFADVVGQEHVLTALANGLSL------GRIH-HAYLFSGTRGVGKTSIARLLAKGLNCETGITATPCGV   82 (250)
T ss_dssp             -CCHHHHTCCCSGGGCCSCHHHHHHHHHHHHH------TCCC-SEEEEECSTTSCHHHHHHHHHHHHHCTTCSCSSCCSC
T ss_pred             HHHHhhccCCccHHHHhCcHHHHHHHHHHHHc------CCCC-eEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCcc
Confidence            57899999999999999999999999999986      4433 5899999999999999999999985432111100  0


Q ss_pred             chhhhhhhhcccCC---cc--ccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHH
Q 005987          214 PTIWQEYMHNCKTG---LE--YTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLL  288 (666)
Q Consensus       214 ~~~~~e~l~~~~~g---~~--~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l  288 (666)
                      ..............   ..  .......+..++..+...        .....+.+|+|||++.+...     ..+.|..+
T Consensus        83 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--------~~~~~~~vlviDe~~~l~~~-----~~~~l~~~  149 (250)
T 1njg_A           83 CDNCREIEQGRFVDLIEIDAASRTKVEDTRDLLDNVQYA--------PARGRFKVYLIDEVHMLSRH-----SFNALLKT  149 (250)
T ss_dssp             SHHHHHHHTTCCSSEEEEETTCGGGHHHHHHHHHSCCCS--------CSSSSSEEEEEETGGGSCHH-----HHHHHHHH
T ss_pred             cHHHHHHhccCCcceEEecCcccccHHHHHHHHHHhhhc--------hhcCCceEEEEECcccccHH-----HHHHHHHH
Confidence            00000000000000   00  011223344443322110        01234679999999987532     22334555


Q ss_pred             HhcCCCc-eEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHH
Q 005987          289 VRSTHIP-TAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQA  367 (666)
Q Consensus       289 ~~~~~~P-iViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~  367 (666)
                      ++..... .++++++..        ....   ..+++  ++..|.|++++.+++.+++..++..+++.+++++++.|++.
T Consensus       150 l~~~~~~~~~i~~t~~~--------~~~~---~~l~~--r~~~i~l~~l~~~e~~~~l~~~~~~~~~~~~~~~~~~l~~~  216 (250)
T 1njg_A          150 LEEPPEHVKFLLATTDP--------QKLP---VTILS--RCLQFHLKALDVEQIRHQLEHILNEEHIAHEPRALQLLARA  216 (250)
T ss_dssp             HHSCCTTEEEEEEESCG--------GGSC---HHHHT--TSEEEECCCCCHHHHHHHHHHHHHHTTCCBCHHHHHHHHHH
T ss_pred             HhcCCCceEEEEEeCCh--------HhCC---HHHHH--HhhhccCCCCCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHH
Confidence            5544333 334444311        1111   22222  48899999999999999999999999999999999999999


Q ss_pred             cCCcHHHHHHHHHHHhcC
Q 005987          368 SGGDIRQAITSLQFSSLK  385 (666)
Q Consensus       368 s~GDIR~AIn~LQf~~~~  385 (666)
                      ++|++|.+++.++.++..
T Consensus       217 ~~G~~~~~~~~~~~~~~~  234 (250)
T 1njg_A          217 AEGSLRDALSLTDQAIAS  234 (250)
T ss_dssp             HTTCHHHHHHHHHHHHTT
T ss_pred             cCCCHHHHHHHHHHHHhc
Confidence            999999999999887653

>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable holliday junction DNA helicase; HET: ADP; 2.69A {Campylobacter jejuni subsp}

Probab=99.81  E-value=4e-19  Score=188.79  Aligned_cols=199  Identities=14%  Similarity=0.198  Sum_probs=138.6

Q ss_pred             CCCCccccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCC
Q 005987          134 STQQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPT  213 (666)
Q Consensus       134 ~~~~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd  213 (666)
                      .....|.+||+|.++++++|++..++.+..|+......  +. +...+||+||||||||++|+++|++++..++.++++.
T Consensus        14 ~~~~~~~~~~~p~~~~~iiG~~~~~~~l~~~l~~~~~~--~~-~~~~vll~G~~GtGKT~la~~ia~~~~~~~~~~~~~~   90 (338)
T 3pfi_A           14 SFDETYETSLRPSNFDGYIGQESIKKNLNVFIAAAKKR--NE-CLDHILFSGPAGLGKTTLANIISYEMSANIKTTAAPM   90 (338)
T ss_dssp             ---------CCCCSGGGCCSCHHHHHHHHHHHHHHHHT--TS-CCCCEEEECSTTSSHHHHHHHHHHHTTCCEEEEEGGG
T ss_pred             chhhhhhhccCCCCHHHhCChHHHHHHHHHHHHHHHhc--CC-CCCeEEEECcCCCCHHHHHHHHHHHhCCCeEEecchh
Confidence            34678999999999999999999999999999876431  12 2257999999999999999999999999999988653


Q ss_pred             chhhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcCC
Q 005987          214 PTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTH  293 (666)
Q Consensus       214 ~~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~~  293 (666)
                      .                 .....+..++..   .           ..+.+|+|||++.+...     .+..|...++...
T Consensus        91 ~-----------------~~~~~~~~~~~~---~-----------~~~~vl~lDEi~~l~~~-----~~~~Ll~~l~~~~  134 (338)
T 3pfi_A           91 I-----------------EKSGDLAAILTN---L-----------SEGDILFIDEIHRLSPA-----IEEVLYPAMEDYR  134 (338)
T ss_dssp             C-----------------CSHHHHHHHHHT---C-----------CTTCEEEEETGGGCCHH-----HHHHHHHHHHTSC
T ss_pred             c-----------------cchhHHHHHHHh---c-----------cCCCEEEEechhhcCHH-----HHHHHHHHHHhcc
Confidence            1                 112233333322   1           13469999999987532     2333444444432


Q ss_pred             -----------------Cc-eEEEEecCCCCCCccchhhhhhHHHHHHhhcCe-eEEEeCCCCHHHHHHHHHHHHHHhCC
Q 005987          294 -----------------IP-TAVVLTECGKADSVDSTAQSFEELQSILVDAGA-RKVALNPITNGSIKRTLSKICRQEQY  354 (666)
Q Consensus       294 -----------------~P-iViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~-~~I~F~p~s~~~i~kiL~~I~~~e~i  354 (666)
                                       .| +++|++. +..      ....   .++++  |+ ..|.|.+++.+++..+|.+.+...++
T Consensus       135 ~~~~~~~~~~~~~~~~~~~~~~~i~at-n~~------~~l~---~~L~~--R~~~~i~l~~~~~~e~~~il~~~~~~~~~  202 (338)
T 3pfi_A          135 LDIIIGSGPAAQTIKIDLPKFTLIGAT-TRA------GMLS---NPLRD--RFGMQFRLEFYKDSELALILQKAALKLNK  202 (338)
T ss_dssp             C---------CCCCCCCCCCCEEEEEE-SCG------GGSC---HHHHT--TCSEEEECCCCCHHHHHHHHHHHHHHTTC
T ss_pred             chhhcccCccccceecCCCCeEEEEeC-CCc------cccC---HHHHh--hcCEEeeCCCcCHHHHHHHHHHHHHhcCC
Confidence                             12 3333332 221      1111   22333  35 78999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHcCCcHHHHHHHHHHHh
Q 005987          355 SLSTEQIDLVAQASGGDIRQAITSLQFSS  383 (666)
Q Consensus       355 ~v~~~~l~~Ia~~s~GDIR~AIn~LQf~~  383 (666)
                      .+++++++.|+..+.|++|.+++.|+.+.
T Consensus       203 ~~~~~~~~~l~~~~~G~~r~l~~~l~~~~  231 (338)
T 3pfi_A          203 TCEEKAALEIAKRSRSTPRIALRLLKRVR  231 (338)
T ss_dssp             EECHHHHHHHHHTTTTCHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHCcCHHHHHHHHHHHH
Confidence            99999999999999999999999998753

>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET: ADP; 2.95A {Homo sapiens} PDB: 2xsz_D*

Probab=99.77  E-value=6.4e-18  Score=181.39  Aligned_cols=228  Identities=18%  Similarity=0.181  Sum_probs=147.5

Q ss_pred             CCccccccCCCC-ccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCC--cEEEEcCC
Q 005987          136 QQLWAEKYKPRS-LEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGA--RLYEWDTP  212 (666)
Q Consensus       136 ~~~W~eKY~P~s-l~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~--~viE~nas  212 (666)
                      ...+.++|+|.. +++++|++..++.+..++.....   +..+++.+||+||||||||++|+++|++++.  .++.++++
T Consensus        30 ~l~l~~~~~p~~~~~~ivG~~~~~~~l~~l~~~~~~---~~~~~~~vLl~GppGtGKT~la~~la~~l~~~~~~~~~~~~  106 (368)
T 3uk6_A           30 GLGLDDALEPRQASQGMVGQLAARRAAGVVLEMIRE---GKIAGRAVLIAGQPGTGKTAIAMGMAQALGPDTPFTAIAGS  106 (368)
T ss_dssp             SCCBCTTSCBCSEETTEESCHHHHHHHHHHHHHHHT---TCCTTCEEEEEESTTSSHHHHHHHHHHHHCSSCCEEEEEGG
T ss_pred             ccCcccccCcCcchhhccChHHHHHHHHHHHHHHHc---CCCCCCEEEEECCCCCCHHHHHHHHHHHhcccCCcccccch
Confidence            456789999999 99999999998886665543322   4444478999999999999999999999975  44455432


Q ss_pred             Cch--------hhhhhhhc-------------------------------ccCCccccchhHHHHHHHHHHHh----hcC
Q 005987          213 TPT--------IWQEYMHN-------------------------------CKTGLEYTSKLDEFENFVERIRR----YGS  249 (666)
Q Consensus       213 d~~--------~~~e~l~~-------------------------------~~~g~~~~s~~~~f~~fl~~a~~----~~~  249 (666)
                      ...        ...+.+..                               ...|. .......++..+..+..    .+.
T Consensus       107 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ld~~~~~~~~~~~~~~~~-~g~~~~~~~~~~~~~~~~~~~~g~  185 (368)
T 3uk6_A          107 EIFSLEMSKTEALTQAFRRSIGVRIKAGAVHTVSLHEIDVINSRTQGFLALFSGD-TGEIKSEVREQINAKVAEWREEGK  185 (368)
T ss_dssp             GGSCSSSCHHHHHHHHHHHSBEECC------CEEHHHHHHHTC----CCSCC--------CHHHHHHHHHHHHHHHHHTC
T ss_pred             hhhhcccchhHHHHHHHHHHHHHHhhhhccccccHhhhhhhhcccccchhhccCc-ccccHHHHHHHHHHHHHHhhhhcc
Confidence            200        00000000                               00000 00112233333333221    110


Q ss_pred             CCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcCCCceEEEEecCCCCC----CccchhhhhhHHHHHHhh
Q 005987          250 TSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHIPTAVVLTECGKAD----SVDSTAQSFEELQSILVD  325 (666)
Q Consensus       250 l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~~~PiViIit~~~~~~----s~d~~~r~l~~L~s~L~r  325 (666)
                      .       ...+.||||||++.+...     ..+.|...++....|+++++++....-    ..+......   ..+++ 
T Consensus       186 ~-------~~~~~vl~IDEi~~l~~~-----~~~~L~~~le~~~~~~~ii~t~~~~~~i~~t~~~~~~~l~---~~l~s-  249 (368)
T 3uk6_A          186 A-------EIIPGVLFIDEVHMLDIE-----SFSFLNRALESDMAPVLIMATNRGITRIRGTSYQSPHGIP---IDLLD-  249 (368)
T ss_dssp             ----------CBCEEEEESGGGSBHH-----HHHHHHHHTTCTTCCEEEEEESCSEEECBTSSCEEETTCC---HHHHT-
T ss_pred             c-------cccCceEEEhhccccChH-----HHHHHHHHhhCcCCCeeeeecccceeeeeccCCCCcccCC---HHHHh-
Confidence            0       012469999999988532     334566777777778877766521100    000011111   23333 


Q ss_pred             cCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcC-CcHHHHHHHHHHHhc
Q 005987          326 AGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASG-GDIRQAITSLQFSSL  384 (666)
Q Consensus       326 ~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~s~-GDIR~AIn~LQf~~~  384 (666)
                       ||..|.|+|++.+++.++|.+.+..+++.+++++++.|+..+. ||+|.+++.|+.++.
T Consensus       250 -R~~~i~~~~~~~~e~~~il~~~~~~~~~~~~~~~l~~l~~~~~~G~~r~~~~ll~~a~~  308 (368)
T 3uk6_A          250 -RLLIVSTTPYSEKDTKQILRIRCEEEDVEMSEDAYTVLTRIGLETSLRYAIQLITAASL  308 (368)
T ss_dssp             -TEEEEEECCCCHHHHHHHHHHHHHHTTCCBCHHHHHHHHHHHHHSCHHHHHHHHHHHHH
T ss_pred             -hccEEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhcCCCHHHHHHHHHHHHH
Confidence             5888999999999999999999999999999999999999999 999999999988764

>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens}

Probab=99.75  E-value=3e-17  Score=178.18  Aligned_cols=213  Identities=14%  Similarity=0.143  Sum_probs=144.5

Q ss_pred             CCccccccCCCCccccccCHHHHHHHHHHHHHhhcCCC----CCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcC
Q 005987          136 QQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSK----DKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDT  211 (666)
Q Consensus       136 ~~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~----g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~na  211 (666)
                      ...|+++|+|.++++|+|++..++.|..++........    ...+.+.+||+||||||||++|+++|++++..++++++
T Consensus       102 ~~~~~~~~~~~~~~~iiG~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~vLL~GppGtGKT~la~aia~~~~~~~~~v~~  181 (389)
T 3vfd_A          102 MNEIVDNGTAVKFDDIAGQDLAKQALQEIVILPSLRPELFTGLRAPARGLLLFGPPGNGKTMLAKAVAAESNATFFNISA  181 (389)
T ss_dssp             GGTTBCCSCCCCGGGSCSCHHHHHHHHHHTHHHHHCTTTSCGGGCCCSEEEEESSTTSCHHHHHHHHHHHTTCEEEEECS
T ss_pred             HhhhhccCCCCChHHhCCHHHHHHHHHHHHHHhccCHHHhcccCCCCceEEEECCCCCCHHHHHHHHHHhhcCcEEEeeH
Confidence            34699999999999999999999999999864332110    11223789999999999999999999999999999998


Q ss_pred             CCchhhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchh------HHHHHHHHH
Q 005987          212 PTPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRT------AFERLRQCL  285 (666)
Q Consensus       212 sd~~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~------~~~~l~~~L  285 (666)
                      ++..           +.........+..++..+...            .+.||||||+|.+....      ...+++..|
T Consensus       182 ~~l~-----------~~~~g~~~~~~~~~~~~a~~~------------~~~il~iDEid~l~~~~~~~~~~~~~~~~~~l  238 (389)
T 3vfd_A          182 ASLT-----------SKYVGEGEKLVRALFAVAREL------------QPSIIFIDQVDSLLCERREGEHDASRRLKTEF  238 (389)
T ss_dssp             CCC------------------CHHHHHHHHHHHHHS------------SSEEEEEETGGGGC--------CTHHHHHHHH
T ss_pred             HHhh-----------ccccchHHHHHHHHHHHHHhc------------CCeEEEEECchhhcccCCCccchHHHHHHHHH
Confidence            7621           111111223344555555432            25699999999763211      122333333


Q ss_pred             HHHHhc----CCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCe-eEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHH
Q 005987          286 LLLVRS----THIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGA-RKVALNPITNGSIKRTLSKICRQEQYSLSTEQ  360 (666)
Q Consensus       286 ~~l~~~----~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~-~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~  360 (666)
                      ...+..    ....+++|++. +...          .+...+.+ |+ ..|.|..|+.++...+|..++...+..++++.
T Consensus       239 l~~l~~~~~~~~~~v~vI~at-n~~~----------~l~~~l~~-R~~~~i~i~~p~~~~r~~il~~~~~~~~~~l~~~~  306 (389)
T 3vfd_A          239 LIEFDGVQSAGDDRVLVMGAT-NRPQ----------ELDEAVLR-RFIKRVYVSLPNEETRLLLLKNLLCKQGSPLTQKE  306 (389)
T ss_dssp             HHHHHHHC-----CEEEEEEE-SCGG----------GCCHHHHT-TCCEEEECCCCCHHHHHHHHHHHHTTSCCCSCHHH
T ss_pred             HHHhhcccccCCCCEEEEEec-CCch----------hcCHHHHc-CcceEEEcCCcCHHHHHHHHHHHHHhcCCCCCHHH
Confidence            333332    12234444333 2211          12222223 45 57999999999999999999999999999999


Q ss_pred             HHHHHHHcCCcHHHHHHHHHHHh
Q 005987          361 IDLVAQASGGDIRQAITSLQFSS  383 (666)
Q Consensus       361 l~~Ia~~s~GDIR~AIn~LQf~~  383 (666)
                      +..|+..+.|+.+.+|+.|.-.+
T Consensus       307 ~~~la~~~~g~~~~~l~~L~~~a  329 (389)
T 3vfd_A          307 LAQLARMTDGYSGSDLTALAKDA  329 (389)
T ss_dssp             HHHHHHHTTTCCHHHHHHHHHHH
T ss_pred             HHHHHHHcCCCCHHHHHHHHHHH
Confidence            99999999999999888875544

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}

Probab=99.74  E-value=7.8e-17  Score=169.36  Aligned_cols=219  Identities=12%  Similarity=0.113  Sum_probs=139.3

Q ss_pred             cccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc----------CCcEEE
Q 005987          139 WAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL----------GARLYE  208 (666)
Q Consensus       139 W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel----------g~~viE  208 (666)
                      .-+-|.|..+  |.++++.++.|..+|...+..   ..+ +.++|+||||||||++++.+++++          .+.+++
T Consensus        12 l~~~~~~~~~--L~~Re~E~~~i~~~L~~~i~~---~~~-~~lli~GpPGTGKT~~v~~v~~~L~~~~~~~~~~~~~~v~   85 (318)
T 3te6_A           12 IRESLQKREL--LKSQVEDFTRIFLPIYDSLMS---SQN-KLFYITNADDSTKFQLVNDVMDELITSSARKELPIFDYIH   85 (318)
T ss_dssp             HHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHT---TCC-CEEEEECCCSHHHHHHHHHHHHHHHHTTTTTSSCCEEEEE
T ss_pred             hhhccCCccc--cCCHHHHHHHHHHHHHHHhcC---CCC-CeEEEECCCCCCHHHHHHHHHHHHHHHhhhccCCceEEEE
Confidence            4455656443  789999999999999988763   223 689999999999999999999999          467899


Q ss_pred             EcCCCchhh---hhhhhcccCCcc--ccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHH
Q 005987          209 WDTPTPTIW---QEYMHNCKTGLE--YTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQ  283 (666)
Q Consensus       209 ~nasd~~~~---~e~l~~~~~g~~--~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~  283 (666)
                      +|+......   ...+.....|..  .......+..++..+.+.          ...+.||+|||+|.+..+..   +..
T Consensus        86 INc~~~~t~~~~~~~I~~~L~g~~~~~~~~~~~L~~~f~~~~~~----------~~~~~ii~lDE~d~l~~q~~---L~~  152 (318)
T 3te6_A           86 IDALELAGMDALYEKIWFAISKENLCGDISLEALNFYITNVPKA----------KKRKTLILIQNPENLLSEKI---LQY  152 (318)
T ss_dssp             EETTCCC--HHHHHHHHHHHSCCC--CCCCHHHHHHHHHHSCGG----------GSCEEEEEEECCSSSCCTHH---HHH
T ss_pred             EeccccCCHHHHHHHHHHHhcCCCCCchHHHHHHHHHHHHhhhc----------cCCceEEEEecHHHhhcchH---HHH
Confidence            998653211   111111112221  122334455555443111          12467999999999873322   212


Q ss_pred             HHHHHHhcCCCceEEE-EecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhC---------
Q 005987          284 CLLLLVRSTHIPTAVV-LTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQ---------  353 (666)
Q Consensus       284 ~L~~l~~~~~~PiViI-it~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~---------  353 (666)
                       |..+.......+++| ++++..     ...+.+.  +.+.+|..+..|.|.|++.+++..+|++.+....         
T Consensus       153 -l~~~~~~~~s~~~vI~i~n~~d-----~~~~~L~--~~v~SR~~~~~i~F~pYt~~el~~Il~~Rl~~~~~~~f~~~~~  224 (318)
T 3te6_A          153 -FEKWISSKNSKLSIICVGGHNV-----TIREQIN--IMPSLKAHFTEIKLNKVDKNELQQMIITRLKSLLKPFHVKVND  224 (318)
T ss_dssp             -HHHHHHCSSCCEEEEEECCSSC-----CCHHHHH--TCHHHHTTEEEEECCCCCHHHHHHHHHHHHHHHCCCEEEEECT
T ss_pred             -HHhcccccCCcEEEEEEecCcc-----cchhhcc--hhhhccCCceEEEeCCCCHHHHHHHHHHHHHhhhccccccccc
Confidence             222222222233333 333211     1112221  1222344567899999999999999999987631         


Q ss_pred             --------------------------CCCCHHHHHHHHH---HcCCcHHHHHHHHHHHhc
Q 005987          354 --------------------------YSLSTEQIDLVAQ---ASGGDIRQAITSLQFSSL  384 (666)
Q Consensus       354 --------------------------i~v~~~~l~~Ia~---~s~GDIR~AIn~LQf~~~  384 (666)
                                                +.+++++|+.+|.   ...||+|.||+.|..+..
T Consensus       225 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~ai~~~A~~vA~~~GD~R~Al~ilr~A~~  284 (318)
T 3te6_A          225 KKEMTIYNNIREGQNQKIPDNVIVINHKINNKITQLIAKNVANVSGSTEKAFKICEAAVE  284 (318)
T ss_dssp             TCCEEECCCC--------CTTEEEECEECCHHHHHHHHHHHHHHHCSHHHHHHHHHHHHH
T ss_pred             cccccccccccccccccccccccccccccCHHHHHHHHHHHHhhCChHHHHHHHHHHHHH
Confidence                                      1379999999998   578999999999988764

>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=99.73  E-value=4.1e-17  Score=171.89  Aligned_cols=197  Identities=18%  Similarity=0.189  Sum_probs=136.4

Q ss_pred             ccccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCchhh
Q 005987          138 LWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTIW  217 (666)
Q Consensus       138 ~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~~~  217 (666)
                      +|.+||+|.++++++|++..++.+..++..+...  +.. .+.+||+||||||||++|++++++++..++.++++...  
T Consensus         1 ~~~~~~~p~~~~~~ig~~~~~~~l~~~l~~~~~~--~~~-~~~vll~G~~GtGKT~la~~i~~~~~~~~~~~~~~~~~--   75 (324)
T 1hqc_A            1 MEDLALRPKTLDEYIGQERLKQKLRVYLEAAKAR--KEP-LEHLLLFGPPGLGKTTLAHVIAHELGVNLRVTSGPAIE--   75 (324)
T ss_dssp             ----CCCCCSTTTCCSCHHHHHHHHHHHHHHHHH--CSC-CCCCEEECCTTCCCHHHHHHHHHHHTCCEEEECTTTCC--
T ss_pred             CCccccCcccHHHhhCHHHHHHHHHHHHHHHHcc--CCC-CCcEEEECCCCCCHHHHHHHHHHHhCCCEEEEeccccC--
Confidence            4678999999999999999999999999864321  122 25799999999999999999999999999888876411  


Q ss_pred             hhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcCC----
Q 005987          218 QEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTH----  293 (666)
Q Consensus       218 ~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~~----  293 (666)
                                     ....+...+.   ..          ...+.+|+|||++.+... ...    .|..+++...    
T Consensus        76 ---------------~~~~l~~~l~---~~----------~~~~~~l~lDEi~~l~~~-~~~----~L~~~l~~~~~~~v  122 (324)
T 1hqc_A           76 ---------------KPGDLAAILA---NS----------LEEGDILFIDEIHRLSRQ-AEE----HLYPAMEDFVMDIV  122 (324)
T ss_dssp             ---------------SHHHHHHHHT---TT----------CCTTCEEEETTTTSCCHH-HHH----HHHHHHHHSEEEEC
T ss_pred             ---------------ChHHHHHHHH---Hh----------ccCCCEEEEECCcccccc-hHH----HHHHHHHhhhhHHh
Confidence                           1112222221   10          013469999999988642 222    2333333321    


Q ss_pred             --------------CceEEEEecCCCCCCccchhhhhhHHHHHHhhcCe-eEEEeCCCCHHHHHHHHHHHHHHhCCCCCH
Q 005987          294 --------------IPTAVVLTECGKADSVDSTAQSFEELQSILVDAGA-RKVALNPITNGSIKRTLSKICRQEQYSLST  358 (666)
Q Consensus       294 --------------~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~-~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~  358 (666)
                                    .++++|++. +....      ..+.|   +.  |+ ..+.|.+++.+++..+|.+.+...++.+++
T Consensus       123 ~~~~~~~~~~~~~~~~~~~i~~t-~~~~~------~~~~l---~~--R~~~~i~l~~~~~~e~~~~l~~~~~~~~~~~~~  190 (324)
T 1hqc_A          123 IGQGPAARTIRLELPRFTLIGAT-TRPGL------ITAPL---LS--RFGIVEHLEYYTPEELAQGVMRDARLLGVRITE  190 (324)
T ss_dssp             CSSSSSCCCEEEECCCCEEEEEE-SCCSS------CSCST---TT--TCSCEEECCCCCHHHHHHHHHHHHHTTTCCCCH
T ss_pred             ccccccccccccCCCCEEEEEeC-CCccc------CCHHH---Hh--cccEEEecCCCCHHHHHHHHHHHHHhcCCCCCH
Confidence                          123333332 21111      11112   22  45 689999999999999999999998999999


Q ss_pred             HHHHHHHHHcCCcHHHHHHHHHHHhc
Q 005987          359 EQIDLVAQASGGDIRQAITSLQFSSL  384 (666)
Q Consensus       359 ~~l~~Ia~~s~GDIR~AIn~LQf~~~  384 (666)
                      ++++.|+..++|++|.+.+.++.+..
T Consensus       191 ~~~~~l~~~~~G~~r~l~~~l~~~~~  216 (324)
T 1hqc_A          191 EAALEIGRRSRGTMRVAKRLFRRVRD  216 (324)
T ss_dssp             HHHHHHHHHSCSCHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHccCCHHHHHHHHHHHHH
Confidence            99999999999999999999988764

>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=99.73  E-value=1.5e-16  Score=176.27  Aligned_cols=111  Identities=14%  Similarity=0.181  Sum_probs=82.7

Q ss_pred             eEEEEeCCCCCcchhHHHHHHHHHHHHHhcCCCceEEEEecCCC-----CCCccchhhhhhHHHHHHhhcCeeEEEeCCC
Q 005987          262 AILLIDDLPVTNGRTAFERLRQCLLLLVRSTHIPTAVVLTECGK-----ADSVDSTAQSFEELQSILVDAGARKVALNPI  336 (666)
Q Consensus       262 ~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~~~PiViIit~~~~-----~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~  336 (666)
                      +|++|||++.+..     ...++|+..++....+++|++++...     ...........+   .+++  ||..++|.++
T Consensus       297 ~VliIDEa~~l~~-----~a~~aLlk~lEe~~~~~~il~tn~~~~~i~~~~~~~~~~~l~~---~i~s--R~~~~~~~~~  366 (456)
T 2c9o_A          297 GVLFVDEVHMLDI-----ECFTYLHRALESSIAPIVIFASNRGNCVIRGTEDITSPHGIPL---DLLD--RVMIIRTMLY  366 (456)
T ss_dssp             CEEEEESGGGCBH-----HHHHHHHHHTTSTTCCEEEEEECCSEEECBTTSSCEEETTCCH---HHHT--TEEEEECCCC
T ss_pred             eEEEEechhhcCH-----HHHHHHHHHhhccCCCEEEEecCCccccccccccccccccCCh---hHHh--hcceeeCCCC
Confidence            5999999998853     23445677777777776555653210     000011122222   3333  5999999999


Q ss_pred             CHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHc-CCcHHHHHHHHHHH
Q 005987          337 TNGSIKRTLSKICRQEQYSLSTEQIDLVAQAS-GGDIRQAITSLQFS  382 (666)
Q Consensus       337 s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~s-~GDIR~AIn~LQf~  382 (666)
                      +.+++.++|++++..+++.++++++..|+..+ .|++|.|++.|+.+
T Consensus       367 ~~~e~~~iL~~~~~~~~~~~~~~~~~~i~~~a~~g~~r~a~~ll~~a  413 (456)
T 2c9o_A          367 TPQEMKQIIKIRAQTEGINISEEALNHLGEIGTKTTLRYSVQLLTPA  413 (456)
T ss_dssp             CHHHHHHHHHHHHHHHTCCBCHHHHHHHHHHHHHSCHHHHHHTHHHH
T ss_pred             CHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHccCCCHHHHHHHHHHH
Confidence            99999999999999999999999999999999 99999999999876

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster}

Probab=99.72  E-value=3e-16  Score=163.54  Aligned_cols=208  Identities=15%  Similarity=0.151  Sum_probs=139.5

Q ss_pred             ccccccCCCCccccccCHHHHHHHHHHHHHhhcCC----CCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCC
Q 005987          138 LWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDS----KDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPT  213 (666)
Q Consensus       138 ~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~----~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd  213 (666)
                      .|+++|+|.++++++|++..++.|..++.......    ....+.+.+||+||||||||++|+++|++++..++.+++++
T Consensus        10 ~~~~~~~~~~~~~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~vll~Gp~GtGKT~la~~la~~~~~~~~~i~~~~   89 (297)
T 3b9p_A           10 EIVEGGAKVEWTDIAGQDVAKQALQEMVILPSVRPELFTGLRAPAKGLLLFGPPGNGKTLLARAVATECSATFLNISAAS   89 (297)
T ss_dssp             TTBCCSSCCCGGGSCCCHHHHHHHHHHTHHHHHCGGGSCGGGCCCSEEEEESSSSSCHHHHHHHHHHHTTCEEEEEESTT
T ss_pred             HhccCCCCCCHHHhCChHHHHHHHHHHHHhhhhCHHHHhcCCCCCCeEEEECcCCCCHHHHHHHHHHHhCCCeEEeeHHH
Confidence            58999999999999999999999999886432210    01122378999999999999999999999999999999875


Q ss_pred             chhhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhH------HHHHHHHHHH
Q 005987          214 PTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTA------FERLRQCLLL  287 (666)
Q Consensus       214 ~~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~------~~~l~~~L~~  287 (666)
                      ..           +..........+.++..+...            .+.+|+|||++.+.....      ..++...|..
T Consensus        90 l~-----------~~~~~~~~~~~~~~~~~~~~~------------~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~ll~  146 (297)
T 3b9p_A           90 LT-----------SKYVGDGEKLVRALFAVARHM------------QPSIIFIDEVDSLLSERSSSEHEASRRLKTEFLV  146 (297)
T ss_dssp             TS-----------SSSCSCHHHHHHHHHHHHHHT------------CSEEEEEETGGGTSBCC-----CCSHHHHHHHHH
T ss_pred             Hh-----------hcccchHHHHHHHHHHHHHHc------------CCcEEEeccHHHhccccccCcchHHHHHHHHHHH
Confidence            21           111112223344455554322            357999999997643211      1223333333


Q ss_pred             HHhcCC-----CceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHH
Q 005987          288 LVRSTH-----IPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQID  362 (666)
Q Consensus       288 l~~~~~-----~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~  362 (666)
                      .++...     ..+++|++. +...       .+.  ..+++| ....+.|..|+.++...+|...+...+..++++.++
T Consensus       147 ~l~~~~~~~~~~~v~vi~~t-n~~~-------~l~--~~l~~R-~~~~i~~~~p~~~~r~~il~~~~~~~~~~~~~~~~~  215 (297)
T 3b9p_A          147 EFDGLPGNPDGDRIVVLAAT-NRPQ-------ELD--EAALRR-FTKRVYVSLPDEQTRELLLNRLLQKQGSPLDTEALR  215 (297)
T ss_dssp             HHHHCC------CEEEEEEE-SCGG-------GBC--HHHHHH-CCEEEECCCCCHHHHHHHHHHHHGGGSCCSCHHHHH
T ss_pred             HHhcccccCCCCcEEEEeec-CChh-------hCC--HHHHhh-CCeEEEeCCcCHHHHHHHHHHHHHhcCCCCCHHHHH
Confidence            333221     123343332 2211       111  222333 236789999999999999999999888889999999


Q ss_pred             HHHHHcCCcHHHHHHHH
Q 005987          363 LVAQASGGDIRQAITSL  379 (666)
Q Consensus       363 ~Ia~~s~GDIR~AIn~L  379 (666)
                      .|+..+.|..+.+|..|
T Consensus       216 ~la~~~~g~~~~~l~~l  232 (297)
T 3b9p_A          216 RLAKITDGYSGSDLTAL  232 (297)
T ss_dssp             HHHHHTTTCCHHHHHHH
T ss_pred             HHHHHcCCCCHHHHHHH
Confidence            99999999888777655

>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=99.72  E-value=1e-16  Score=169.57  Aligned_cols=212  Identities=13%  Similarity=0.130  Sum_probs=142.4

Q ss_pred             CccccccCCCCccccccCHHHHHHHHHHHHHhhcC----CCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCC
Q 005987          137 QLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGD----SKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTP  212 (666)
Q Consensus       137 ~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~----~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nas  212 (666)
                      ..|+++|.+.++++|+|++..++.|+.++......    ..+..+.+.+||+||||||||++|+++|++++..++.++++
T Consensus         6 ~~~~~~~~~~~~~di~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~vLl~GppGtGKT~la~aia~~~~~~~~~v~~~   85 (322)
T 3eie_A            6 TAILSEKPNVKWEDVAGLEGAKEALKEAVILPVKFPHLFKGNRKPTSGILLYGPPGTGKSYLAKAVATEANSTFFSVSSS   85 (322)
T ss_dssp             CCSEEECCCCCGGGSCSCHHHHHHHHHHTHHHHHCGGGCCTTCCCCCEEEEECSSSSCHHHHHHHHHHHHTCEEEEEEHH
T ss_pred             cceeecCCCCCHHHhcChHHHHHHHHHHHHHHHhCHHHHhcCCCCCCeEEEECCCCCcHHHHHHHHHHHHCCCEEEEchH
Confidence            46899999999999999999999999988532211    11233347899999999999999999999999999999865


Q ss_pred             CchhhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchh------HHHHHHHHHH
Q 005987          213 TPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRT------AFERLRQCLL  286 (666)
Q Consensus       213 d~~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~------~~~~l~~~L~  286 (666)
                      +.           .+.........+..++..+...            .+.||+|||+|.+....      ...++...+.
T Consensus        86 ~l-----------~~~~~g~~~~~~~~~f~~a~~~------------~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~ll  142 (322)
T 3eie_A           86 DL-----------VSKWMGESEKLVKQLFAMAREN------------KPSIIFIDQVDALTGTRGEGESEASRRIKTELL  142 (322)
T ss_dssp             HH-----------HTTTGGGHHHHHHHHHHHHHHT------------SSEEEEEECGGGGSCC------CCTHHHHHHHH
T ss_pred             HH-----------hhcccchHHHHHHHHHHHHHhc------------CCeEEEechhhhhhccCCCCcchHHHHHHHHHH
Confidence            31           0111122233455555555432            35799999999775421      1123343344


Q ss_pred             HHHhc---CCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHH
Q 005987          287 LLVRS---THIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDL  363 (666)
Q Consensus       287 ~l~~~---~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~  363 (666)
                      ..+..   ....+++|++. +...       .   |...+.++....|.|..|+.++..++|+..+...+..+++..++.
T Consensus       143 ~~l~~~~~~~~~v~vi~at-n~~~-------~---ld~al~~Rf~~~i~~~~p~~~~r~~il~~~~~~~~~~~~~~~l~~  211 (322)
T 3eie_A          143 VQMNGVGNDSQGVLVLGAT-NIPW-------Q---LDSAIRRRFERRIYIPLPDLAARTTMFEINVGDTPCVLTKEDYRT  211 (322)
T ss_dssp             HHHGGGGTSCCCEEEEEEE-SCGG-------G---SCHHHHHHCCEEEECCCCCHHHHHHHHHHHHTTCCCCCCHHHHHH
T ss_pred             HHhccccccCCceEEEEec-CChh-------h---CCHHHHcccCeEEEeCCCCHHHHHHHHHHHhccCCCCCCHHHHHH
Confidence            44432   22334444333 2221       1   222222212467899999999999999999988888889999999


Q ss_pred             HHHHcCC----cHHHHHHHHHHH
Q 005987          364 VAQASGG----DIRQAITSLQFS  382 (666)
Q Consensus       364 Ia~~s~G----DIR~AIn~LQf~  382 (666)
                      |+..+.|    ||+.+++...+.
T Consensus       212 la~~t~g~sg~di~~l~~~a~~~  234 (322)
T 3eie_A          212 LGAMTEGYSGSDIAVVVKDALMQ  234 (322)
T ss_dssp             HHHTTTTCCHHHHHHHHHHHTTH
T ss_pred             HHHHcCCCCHHHHHHHHHHHHHH
Confidence            9999887    777666544333

>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=99.70  E-value=2e-16  Score=169.63  Aligned_cols=214  Identities=13%  Similarity=0.134  Sum_probs=137.2

Q ss_pred             CCccccccCCCCccccccCHHHHHHHHHHHHHhhcCC----CCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcC
Q 005987          136 QQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDS----KDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDT  211 (666)
Q Consensus       136 ~~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~----~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~na  211 (666)
                      ...|+.++.|.++++|+|++..++.|+.++...+...    .+..+.+.+||+||||||||++|+++|++++..++.+++
T Consensus        38 ~~~~~~~~~~~~~~di~G~~~~~~~l~~~v~~~~~~~~~~~~~~~~~~~iLL~GppGtGKT~la~ala~~~~~~~~~v~~  117 (355)
T 2qp9_X           38 SSAILSEKPNVKWEDVAGLEGAKEALKEAVILPVKFPHLFKGNRKPTSGILLYGPPGTGKSYLAKAVATEANSTFFSVSS  117 (355)
T ss_dssp             ---------CCCGGGSCCGGGHHHHHHHHTHHHHHCGGGGCSSCCCCCCEEEECSTTSCHHHHHHHHHHHHTCEEEEEEH
T ss_pred             hhhhcccCCCCCHHHhCCHHHHHHHHHHHHHHHHhCHHHHhcCCCCCceEEEECCCCCcHHHHHHHHHHHhCCCEEEeeH
Confidence            4568899999999999999999999998875322110    122333689999999999999999999999999999886


Q ss_pred             CCchhhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcch------hHHHHHHHHH
Q 005987          212 PTPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGR------TAFERLRQCL  285 (666)
Q Consensus       212 sd~~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~------~~~~~l~~~L  285 (666)
                      ++.       .....    ......+..++..+...            .+.||||||+|.+...      ....++...|
T Consensus       118 ~~l-------~~~~~----g~~~~~~~~~f~~a~~~------------~~~vl~iDEid~l~~~r~~~~~~~~~~~~~~l  174 (355)
T 2qp9_X          118 SDL-------VSKWM----GESEKLVKQLFAMAREN------------KPSIIFIDQVDALTGTRGEGESEASRRIKTEL  174 (355)
T ss_dssp             HHH-------HSCC-------CHHHHHHHHHHHHHT------------SSEEEEEECGGGGTC------CTHHHHHHHHH
T ss_pred             HHH-------hhhhc----chHHHHHHHHHHHHHHc------------CCeEEEEechHhhcccCCCCcchHHHHHHHHH
Confidence            531       01011    11223445555555432            3579999999987532      1223344444


Q ss_pred             HHHHhcC---CCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCe-eEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHH
Q 005987          286 LLLVRST---HIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGA-RKVALNPITNGSIKRTLSKICRQEQYSLSTEQI  361 (666)
Q Consensus       286 ~~l~~~~---~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~-~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l  361 (666)
                      +..+...   ...+++|++. +...       .   |...+.+ |+ ..|.|.+|+.++...+|+..+...+..+++..+
T Consensus       175 l~~l~~~~~~~~~v~vI~at-n~~~-------~---ld~al~r-Rf~~~i~i~~P~~~~r~~il~~~l~~~~~~~~~~~l  242 (355)
T 2qp9_X          175 LVQMNGVGNDSQGVLVLGAT-NIPW-------Q---LDSAIRR-RFERRIYIPLPDLAARTTMFEINVGDTPSVLTKEDY  242 (355)
T ss_dssp             HHHHHHCC---CCEEEEEEE-SCGG-------G---SCHHHHH-TCCEEEECCCCCHHHHHHHHHHHHTTSCBCCCHHHH
T ss_pred             HHHhhcccccCCCeEEEeec-CCcc-------c---CCHHHHc-ccCEEEEeCCcCHHHHHHHHHHHHhhCCCCCCHHHH
Confidence            4444422   2234444332 2221       1   2222222 34 678999999999999999999888777899999


Q ss_pred             HHHHHHcCC----cHHHHHHHHHHHhc
Q 005987          362 DLVAQASGG----DIRQAITSLQFSSL  384 (666)
Q Consensus       362 ~~Ia~~s~G----DIR~AIn~LQf~~~  384 (666)
                      +.|+..+.|    ||+.+++...+.+.
T Consensus       243 ~~la~~t~G~sg~dl~~l~~~A~~~a~  269 (355)
T 2qp9_X          243 RTLGAMTEGYSGSDIAVVVKDALMQPI  269 (355)
T ss_dssp             HHHHHHTTTCCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHcCCCCHHHHHHHHHHHHHHHH
Confidence            999999988    88888877666654

>4b4t_J 26S protease regulatory subunit 8 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=99.69  E-value=7.3e-16  Score=165.91  Aligned_cols=213  Identities=16%  Similarity=0.211  Sum_probs=141.9

Q ss_pred             CccccccCCCCccccccCHHHHHHHHHHHHHhhcCC-----CCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcC
Q 005987          137 QLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDS-----KDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDT  211 (666)
Q Consensus       137 ~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~-----~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~na  211 (666)
                      .+-+++-...+++|+.|.++.+++|++.+.--+..+     -|..+++.+|||||||||||++|+++|++++..++.++.
T Consensus       136 ~~~~~~~p~v~~~dIgGl~~~k~~l~e~v~~Pl~~pe~f~~~gi~~prGvLL~GPPGTGKTllAkAiA~e~~~~f~~v~~  215 (405)
T 4b4t_J          136 LMMVEKVPDSTYDMVGGLTKQIKEIKEVIELPVKHPELFESLGIAQPKGVILYGPPGTGKTLLARAVAHHTDCKFIRVSG  215 (405)
T ss_dssp             SCEEECSCSCCGGGSCSCHHHHHHHHHHTHHHHHCHHHHHHHTCCCCCCEEEESCSSSSHHHHHHHHHHHHTCEEEEEEG
T ss_pred             hccccCCCCCCHHHhCCHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCceEEeCCCCCCHHHHHHHHHHhhCCCceEEEh
Confidence            445566666899999999999999998876322211     144455889999999999999999999999999999988


Q ss_pred             CCchhhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcch---------hHHHHHH
Q 005987          212 PTPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGR---------TAFERLR  282 (666)
Q Consensus       212 sd~~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~---------~~~~~l~  282 (666)
                      ++.           ....+......++.++..++..            .|+||+|||+|.+...         ....+..
T Consensus       216 s~l-----------~sk~vGese~~vr~lF~~Ar~~------------aP~IIFiDEiDai~~~R~~~~~~~~~~~~~~l  272 (405)
T 4b4t_J          216 AEL-----------VQKYIGEGSRMVRELFVMAREH------------APSIIFMDEIDSIGSTRVEGSGGGDSEVQRTM  272 (405)
T ss_dssp             GGG-----------SCSSTTHHHHHHHHHHHHHHHT------------CSEEEEEESSSCCTTSCSCSSSGGGGHHHHHH
T ss_pred             HHh-----------hccccchHHHHHHHHHHHHHHh------------CCceEeeecchhhccCCCCCCCCCcHHHHHHH
Confidence            751           1222234455677788877654            3789999999976321         1122233


Q ss_pred             HHHHHHHhc--CCCceEEEEecCCCCCCccchhhhhhHHHHHHhhc--CeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCH
Q 005987          283 QCLLLLVRS--THIPTAVVLTECGKADSVDSTAQSFEELQSILVDA--GARKVALNPITNGSIKRTLSKICRQEQYSLST  358 (666)
Q Consensus       283 ~~L~~l~~~--~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~--r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~  358 (666)
                      ..|+..++.  ....++ ++.+++.++..|          +.|.|+  .-..|.|..|+.....++|+..+....+. ++
T Consensus       273 ~~lL~~lDg~~~~~~V~-vIaATNrpd~LD----------pAllRpGRfD~~I~i~lPd~~~R~~Il~~~~~~~~l~-~d  340 (405)
T 4b4t_J          273 LELLNQLDGFETSKNIK-IIMATNRLDILD----------PALLRPGRIDRKIEFPPPSVAARAEILRIHSRKMNLT-RG  340 (405)
T ss_dssp             HHHHHHHHTTTCCCCEE-EEEEESCSSSSC----------HHHHSTTSSCCEEECCCCCHHHHHHHHHHHHTTSBCC-SS
T ss_pred             HHHHHhhhccCCCCCeE-EEeccCChhhCC----------HhHcCCCcCceEEEcCCcCHHHHHHHHHHHhcCCCCC-cc
Confidence            334433432  222343 444444444332          233332  24589999999999999998887665432 12


Q ss_pred             HHHHHHHHHcCC----cHHHHHHHHHHHhc
Q 005987          359 EQIDLVAQASGG----DIRQAITSLQFSSL  384 (666)
Q Consensus       359 ~~l~~Ia~~s~G----DIR~AIn~LQf~~~  384 (666)
                      -.++.||..+.|    ||+..++.--+.|.
T Consensus       341 vdl~~lA~~t~G~SGADi~~l~~eA~~~Ai  370 (405)
T 4b4t_J          341 INLRKVAEKMNGCSGADVKGVCTEAGMYAL  370 (405)
T ss_dssp             CCHHHHHHHCCSCCHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHCCCCCHHHHHHHHHHHHHHHH
Confidence            237888888665    99988876655554

>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=99.69  E-value=5.7e-16  Score=155.03  Aligned_cols=201  Identities=11%  Similarity=0.107  Sum_probs=136.5

Q ss_pred             CCccccccCC-CCcccccc---CHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcC---CcEEE
Q 005987          136 QQLWAEKYKP-RSLEELAV---QRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLG---ARLYE  208 (666)
Q Consensus       136 ~~~W~eKY~P-~sl~eLvg---~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg---~~viE  208 (666)
                      ..+|..+|+| .+++++++   ++..++.+..++..      +  ..+.++|+||||||||++++++|+++.   ..++.
T Consensus        14 q~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~------~--~~~~~ll~G~~G~GKT~la~~l~~~~~~~~~~~~~   85 (242)
T 3bos_A           14 QLSLPVHLPDDETFTSYYPAAGNDELIGALKSAASG------D--GVQAIYLWGPVKSGRTHLIHAACARANELERRSFY   85 (242)
T ss_dssp             CCEEECCCCTTCSTTTSCC--CCHHHHHHHHHHHHT------C--SCSEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEE
T ss_pred             hcCCCCCCCCCCChhhccCCCCCHHHHHHHHHHHhC------C--CCCeEEEECCCCCCHHHHHHHHHHHHHHcCCeEEE
Confidence            4579999999 89999996   35777777777653      2  126899999999999999999999874   66777


Q ss_pred             EcCCCchhhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchh-HHHHHHHHHHH
Q 005987          209 WDTPTPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRT-AFERLRQCLLL  287 (666)
Q Consensus       209 ~nasd~~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~-~~~~l~~~L~~  287 (666)
                      ++..+...          .         +...+.   .+           ..+.+|+|||++.+.... ....+...+..
T Consensus        86 ~~~~~~~~----------~---------~~~~~~---~~-----------~~~~vliiDe~~~~~~~~~~~~~l~~~l~~  132 (242)
T 3bos_A           86 IPLGIHAS----------I---------STALLE---GL-----------EQFDLICIDDVDAVAGHPLWEEAIFDLYNR  132 (242)
T ss_dssp             EEGGGGGG----------S---------CGGGGT---TG-----------GGSSEEEEETGGGGTTCHHHHHHHHHHHHH
T ss_pred             EEHHHHHH----------H---------HHHHHH---hc-----------cCCCEEEEeccccccCCHHHHHHHHHHHHH
Confidence            76543100          0         000010   11           124699999999875432 12334444444


Q ss_pred             HHhcCCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHH
Q 005987          288 LVRSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQA  367 (666)
Q Consensus       288 l~~~~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~  367 (666)
                      ....+. +.++++++..... .   ......+.+.+.  .+..+.|.+++.+++.++|...+...++.+++++++.|+..
T Consensus       133 ~~~~~~-~~ii~~~~~~~~~-~---~~~~~~l~~r~~--~~~~i~l~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~  205 (242)
T 3bos_A          133 VAEQKR-GSLIVSASASPME-A---GFVLPDLVSRMH--WGLTYQLQPMMDDEKLAALQRRAAMRGLQLPEDVGRFLLNR  205 (242)
T ss_dssp             HHHHCS-CEEEEEESSCTTT-T---TCCCHHHHHHHH--HSEEEECCCCCGGGHHHHHHHHHHHTTCCCCHHHHHHHHHH
T ss_pred             HHHcCC-CeEEEEcCCCHHH-H---HHhhhhhhhHhh--cCceEEeCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHH
Confidence            444432 3244444432211 0   111133333221  12789999999999999999999999999999999999999


Q ss_pred             cCCcHHHHHHHHHHHhc
Q 005987          368 SGGDIRQAITSLQFSSL  384 (666)
Q Consensus       368 s~GDIR~AIn~LQf~~~  384 (666)
                      ++||+|.+++.|+.++.
T Consensus       206 ~~g~~r~l~~~l~~~~~  222 (242)
T 3bos_A          206 MARDLRTLFDVLDRLDK  222 (242)
T ss_dssp             TTTCHHHHHHHHHHHHH
T ss_pred             ccCCHHHHHHHHHHHHH
Confidence            99999999999987764

>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=99.68  E-value=1.5e-15  Score=163.40  Aligned_cols=219  Identities=17%  Similarity=0.216  Sum_probs=139.0

Q ss_pred             CCccccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc----CCcEEEEcC
Q 005987          136 QQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL----GARLYEWDT  211 (666)
Q Consensus       136 ~~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel----g~~viE~na  211 (666)
                      ..+|..+|+|   ++++|+++.++.+..++..+.....+..  +.++|+||||+||||+++.+++++    ++.++++++
T Consensus         7 ~~~l~~~~~p---~~l~gr~~~~~~l~~~l~~~~~~~~~~~--~~~li~G~~G~GKTtl~~~l~~~~~~~~~~~~~~i~~   81 (389)
T 1fnn_A            7 DSVFSPSYVP---KRLPHREQQLQQLDILLGNWLRNPGHHY--PRATLLGRPGTGKTVTLRKLWELYKDKTTARFVYING   81 (389)
T ss_dssp             GGGGSTTCCC---SCCTTCHHHHHHHHHHHHHHHHSTTSSC--CEEEEECCTTSSHHHHHHHHHHHHTTSCCCEEEEEET
T ss_pred             HhhcCCccCC---CCCCChHHHHHHHHHHHHHHHcCCCCCC--CeEEEECCCCCCHHHHHHHHHHHHhhhcCeeEEEEeC
Confidence            4578999999   6789999999999999998765322111  389999999999999999999999    678899997


Q ss_pred             CCchhh----hhhhhcccCCcc--ccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHH
Q 005987          212 PTPTIW----QEYMHNCKTGLE--YTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCL  285 (666)
Q Consensus       212 sd~~~~----~e~l~~~~~g~~--~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L  285 (666)
                      +.....    ...+........  .......+..+...+...           +.+.||+|||++.+. .....    .|
T Consensus        82 ~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~-----------~~~~vlilDE~~~l~-~~~~~----~L  145 (389)
T 1fnn_A           82 FIYRNFTAIIGEIARSLNIPFPRRGLSRDEFLALLVEHLRER-----------DLYMFLVLDDAFNLA-PDILS----TF  145 (389)
T ss_dssp             TTCCSHHHHHHHHHHHTTCCCCSSCCCHHHHHHHHHHHHHHT-----------TCCEEEEEETGGGSC-HHHHH----HH
T ss_pred             ccCCCHHHHHHHHHHHhCccCCCCCCCHHHHHHHHHHHHhhc-----------CCeEEEEEECccccc-hHHHH----HH
Confidence            653321    111111100000  001111122222222111           236799999999883 22223    33


Q ss_pred             HHHHhc------CCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHh--CCCCC
Q 005987          286 LLLVRS------THIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQE--QYSLS  357 (666)
Q Consensus       286 ~~l~~~------~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e--~i~v~  357 (666)
                      ..++..      .+.++| ++++..     +........+.   ++.....|.|+|++.+++.++|...+...  ...++
T Consensus       146 ~~~~~~~~~~~~~~~~iI-~~~~~~-----~~~~~l~~~~~---~r~~~~~i~~~pl~~~~~~~~l~~~~~~~~~~~~~~  216 (389)
T 1fnn_A          146 IRLGQEADKLGAFRIALV-IVGHND-----AVLNNLDPSTR---GIMGKYVIRFSPYTKDQIFDILLDRAKAGLAEGSYS  216 (389)
T ss_dssp             HHHTTCHHHHSSCCEEEE-EEESST-----HHHHTSCHHHH---HHHTTCEEECCCCBHHHHHHHHHHHHHHHBCTTSSC
T ss_pred             HHHHHhCCCCCcCCEEEE-EEECCc-----hHHHHhCHHhh---hcCCCceEEeCCCCHHHHHHHHHHHHHhhcCCCCCC
Confidence            333322      233333 333211     01111222222   23233479999999999999999998762  24689


Q ss_pred             HHHHHHHHHHc---------CCcHHHHHHHHHHHhc
Q 005987          358 TEQIDLVAQAS---------GGDIRQAITSLQFSSL  384 (666)
Q Consensus       358 ~~~l~~Ia~~s---------~GDIR~AIn~LQf~~~  384 (666)
                      +++++.|+..+         .||+|.+++.|+.++.
T Consensus       217 ~~~~~~l~~~~~~~~~~~~~~G~~r~~~~~l~~a~~  252 (389)
T 1fnn_A          217 EDILQMIADITGAQTPLDTNRGDARLAIDILYRSAY  252 (389)
T ss_dssp             HHHHHHHHHHHSBSSTTCTTSCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhcccCCCCCCcHHHHHHHHHHHHH
Confidence            99999999999         8999999999988764

>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=99.68  E-value=7.6e-16  Score=165.31  Aligned_cols=208  Identities=16%  Similarity=0.166  Sum_probs=136.7

Q ss_pred             ccccccCCCCccccccCHHHHHHHHHHHHHhhcCCC----CCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCC
Q 005987          138 LWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSK----DKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPT  213 (666)
Q Consensus       138 ~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~----g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd  213 (666)
                      .++++|.|.++++|+|++..++.|+.++...+....    ...+.+.+||+||||||||++|+++|++++..++.+++++
T Consensus        73 ~i~~~~~~~~~~~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~vLl~GppGtGKT~la~aia~~~~~~~~~i~~~~  152 (357)
T 3d8b_A           73 EIMDHGPPVNWEDIAGVEFAKATIKEIVVWPMLRPDIFTGLRGPPKGILLFGPPGTGKTLIGKCIASQSGATFFSISASS  152 (357)
T ss_dssp             HTBCCSCCCCGGGSCSCHHHHHHHHHHTHHHHHCTTTSCGGGSCCSEEEEESSTTSSHHHHHHHHHHHTTCEEEEEEGGG
T ss_pred             hcccCCCCCCHHHhCChHHHHHHHHHHHHHHhhChHhHhhccCCCceEEEECCCCCCHHHHHHHHHHHcCCeEEEEehHH
Confidence            378899999999999999999999998874222110    1122378999999999999999999999999999998764


Q ss_pred             chhhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcch------hHHHHHHHHHHH
Q 005987          214 PTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGR------TAFERLRQCLLL  287 (666)
Q Consensus       214 ~~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~------~~~~~l~~~L~~  287 (666)
                      .           .+.........+..++..+...            .+.||||||+|.+...      ....+++..++.
T Consensus       153 l-----------~~~~~g~~~~~~~~~~~~a~~~------------~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~lL~  209 (357)
T 3d8b_A          153 L-----------TSKWVGEGEKMVRALFAVARCQ------------QPAVIFIDEIDSLLSQRGDGEHESSRRIKTEFLV  209 (357)
T ss_dssp             G-----------CCSSTTHHHHHHHHHHHHHHHT------------CSEEEEEETHHHHTBC------CHHHHHHHHHHH
T ss_pred             h-----------hccccchHHHHHHHHHHHHHhc------------CCeEEEEeCchhhhccCCCCcchHHHHHHHHHHH
Confidence            1           1111111223344445444322            3579999999865321      112233333444


Q ss_pred             HHhc----CCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHH
Q 005987          288 LVRS----THIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDL  363 (666)
Q Consensus       288 l~~~----~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~  363 (666)
                      .+..    ....+++|++. +...       .+.  ..+++| ....+.|..|+.++...+|..++...++.++++.++.
T Consensus       210 ~l~~~~~~~~~~v~vI~at-n~~~-------~l~--~~l~~R-f~~~i~i~~p~~~~r~~il~~~~~~~~~~l~~~~l~~  278 (357)
T 3d8b_A          210 QLDGATTSSEDRILVVGAT-NRPQ-------EID--EAARRR-LVKRLYIPLPEASARKQIVINLMSKEQCCLSEEEIEQ  278 (357)
T ss_dssp             HHHC----CCCCEEEEEEE-SCGG-------GBC--HHHHTT-CCEEEECCCCCHHHHHHHHHHHHHTSCBCCCHHHHHH
T ss_pred             HHhcccccCCCCEEEEEec-CChh-------hCC--HHHHhh-CceEEEeCCcCHHHHHHHHHHHHhhcCCCccHHHHHH
Confidence            4432    12234444333 2211       111  223332 2357899999999999999999998888899999999


Q ss_pred             HHHHcCCcHHHHHHHH
Q 005987          364 VAQASGGDIRQAITSL  379 (666)
Q Consensus       364 Ia~~s~GDIR~AIn~L  379 (666)
                      |+..+.|-....|+.|
T Consensus       279 la~~t~G~s~~dl~~l  294 (357)
T 3d8b_A          279 IVQQSDAFSGADMTQL  294 (357)
T ss_dssp             HHHHTTTCCHHHHHHH
T ss_pred             HHHHcCCCCHHHHHHH
Confidence            9999988444444443

>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=99.68  E-value=1.5e-15  Score=161.56  Aligned_cols=195  Identities=18%  Similarity=0.226  Sum_probs=131.2

Q ss_pred             CccccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCchh
Q 005987          137 QLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTI  216 (666)
Q Consensus       137 ~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~~  216 (666)
                      +.|+++++|+++++++|++..++.|..+++.....  +..+ .+++|+||||+||||+++++|++++..+...+.+..  
T Consensus        13 ~~~~~~lr~~~l~~~~g~~~~~~~l~~~i~~~~~~--~~~~-~~~ll~Gp~G~GKTTLa~~ia~~l~~~~~~~sg~~~--   87 (334)
T 1in4_A           13 DSGVQFLRPKSLDEFIGQENVKKKLSLALEAAKMR--GEVL-DHVLLAGPPGLGKTTLAHIIASELQTNIHVTSGPVL--   87 (334)
T ss_dssp             ----CTTSCSSGGGCCSCHHHHHHHHHHHHHHHHH--TCCC-CCEEEESSTTSSHHHHHHHHHHHHTCCEEEEETTTC--
T ss_pred             HHHHHHcCCccHHHccCcHHHHHHHHHHHHHHHhc--CCCC-CeEEEECCCCCcHHHHHHHHHHHhCCCEEEEechHh--
Confidence            46999999999999999999999999888753221  2222 579999999999999999999999987765554321  


Q ss_pred             hhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcCCC--
Q 005987          217 WQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHI--  294 (666)
Q Consensus       217 ~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~~~--  294 (666)
                                     .....+..++..   .           ....|++|||++.+...     ..+.|...++....  
T Consensus        88 ---------------~~~~~l~~~~~~---~-----------~~~~v~~iDE~~~l~~~-----~~e~L~~~~~~~~~~i  133 (334)
T 1in4_A           88 ---------------VKQGDMAAILTS---L-----------ERGDVLFIDEIHRLNKA-----VEELLYSAIEDFQIDI  133 (334)
T ss_dssp             ---------------CSHHHHHHHHHH---C-----------CTTCEEEEETGGGCCHH-----HHHHHHHHHHTSCCCC
T ss_pred             ---------------cCHHHHHHHHHH---c-----------cCCCEEEEcchhhcCHH-----HHHHHHHHHHhcccce
Confidence                           011122222221   1           12459999999987641     22233333332211  


Q ss_pred             ----------------ceEEEEecCCCCCCccchhhhhhHHHHHHhhcCe-eEEEeCCCCHHHHHHHHHHHHHHhCCCCC
Q 005987          295 ----------------PTAVVLTECGKADSVDSTAQSFEELQSILVDAGA-RKVALNPITNGSIKRTLSKICRQEQYSLS  357 (666)
Q Consensus       295 ----------------PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~-~~I~F~p~s~~~i~kiL~~I~~~e~i~v~  357 (666)
                                      ++.++. .++..      ......++   +  |+ ..+.|.+++.+++.++|++++...++.++
T Consensus       134 ~~~~~~~~~~i~~~l~~~~li~-at~~~------~~Ls~~l~---s--R~~l~~~Ld~~~~~~l~~iL~~~~~~~~~~~~  201 (334)
T 1in4_A          134 MIGKGPSAKSIRIDIQPFTLVG-ATTRS------GLLSSPLR---S--RFGIILELDFYTVKELKEIIKRAASLMDVEIE  201 (334)
T ss_dssp             ---------------CCCEEEE-EESCG------GGSCHHHH---T--TCSEEEECCCCCHHHHHHHHHHHHHHTTCCBC
T ss_pred             eeccCcccccccccCCCeEEEE-ecCCc------ccCCHHHH---H--hcCceeeCCCCCHHHHHHHHHHHHHHcCCCcC
Confidence                            122222 22111      11112222   2  34 46899999999999999999999999999


Q ss_pred             HHHHHHHHHHcCCcHHHHHHHHHHH
Q 005987          358 TEQIDLVAQASGGDIRQAITSLQFS  382 (666)
Q Consensus       358 ~~~l~~Ia~~s~GDIR~AIn~LQf~  382 (666)
                      ++++..|+..+.||+|.|++.|+.+
T Consensus       202 ~~~~~~ia~~~~G~~R~a~~ll~~~  226 (334)
T 1in4_A          202 DAAAEMIAKRSRGTPRIAIRLTKRV  226 (334)
T ss_dssp             HHHHHHHHHTSTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcCCChHHHHHHHHHH
Confidence            9999999999999999999999754

>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=99.68  E-value=1.9e-16  Score=170.43  Aligned_cols=215  Identities=16%  Similarity=0.159  Sum_probs=137.9

Q ss_pred             CCccccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc-----------CC
Q 005987          136 QQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL-----------GA  204 (666)
Q Consensus       136 ~~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel-----------g~  204 (666)
                      ...|..+|.|   ++++|+++.++++..++..+..   +..+ +.++|+||||||||++++.+++++           ++
T Consensus        10 ~~~l~~~~~p---~~l~gr~~~~~~l~~~l~~~~~---~~~~-~~vll~G~~G~GKT~la~~l~~~~~~~~~~~~~~~~~   82 (384)
T 2qby_B           10 KVFIDPLSVF---KEIPFREDILRDAAIAIRYFVK---NEVK-FSNLFLGLTGTGKTFVSKYIFNEIEEVKKEDEEYKDV   82 (384)
T ss_dssp             TTTTCHHHHC---SSCTTCHHHHHHHHHHHHHHHT---TCCC-CEEEEEECTTSSHHHHHHHHHHHHHHHHHHSSSSTTC
T ss_pred             HhhcCCccCC---CCCCChHHHHHHHHHHHHHHHc---CCCC-CcEEEECCCCCCHHHHHHHHHHHHHHHhhhhcCCCCc
Confidence            5679999999   6789999999999999998765   3333 689999999999999999999998           89


Q ss_pred             cEEEEcCCCch-h----hhhhhhcccCCccc----cchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcch
Q 005987          205 RLYEWDTPTPT-I----WQEYMHNCKTGLEY----TSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGR  275 (666)
Q Consensus       205 ~viE~nasd~~-~----~~e~l~~~~~g~~~----~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~  275 (666)
                      .++.+++.... .    +...+.. ..|...    ......+..+...+.             ..+.||+|||++.+...
T Consensus        83 ~~~~i~~~~~~~~~~~~~~~l~~~-l~~~~~~~~~~~~~~~~~~l~~~l~-------------~~~~vlilDEi~~l~~~  148 (384)
T 2qby_B           83 KQAYVNCREVGGTPQAVLSSLAGK-LTGFSVPKHGINLGEYIDKIKNGTR-------------NIRAIIYLDEVDTLVKR  148 (384)
T ss_dssp             EEEEEEHHHHCSCHHHHHHHHHHH-HHCSCCCSSSSCTHHHHHHHHHHHS-------------SSCEEEEEETTHHHHHS
T ss_pred             eEEEEECccCCCCHHHHHHHHHHH-hcCCCCCCCCCCHHHHHHHHHHHhc-------------cCCCEEEEECHHHhccC
Confidence            99999865321 1    1111111 001100    001111222222221             11239999999976432


Q ss_pred             hHHHHHHHH-HHHHHhcCCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHH--h
Q 005987          276 TAFERLRQC-LLLLVRSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQ--E  352 (666)
Q Consensus       276 ~~~~~l~~~-L~~l~~~~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~--e  352 (666)
                      ..    .+. +..+.... .++.+|++.... +   ........+   +++ .+..|.|+|++.+++.++|...+..  .
T Consensus       149 ~~----~~~~l~~l~~~~-~~~~iI~~t~~~-~---~~~~l~~~l---~sr-~~~~i~l~~l~~~~~~~il~~~~~~~~~  215 (384)
T 2qby_B          149 RG----GDIVLYQLLRSD-ANISVIMISNDI-N---VRDYMEPRV---LSS-LGPSVIFKPYDAEQLKFILSKYAEYGLI  215 (384)
T ss_dssp             TT----SHHHHHHHHTSS-SCEEEEEECSST-T---TTTTSCHHH---HHT-CCCEEEECCCCHHHHHHHHHHHHHHTSC
T ss_pred             CC----CceeHHHHhcCC-cceEEEEEECCC-c---hHhhhCHHH---Hhc-CCCeEEECCCCHHHHHHHHHHHHHhhcc
Confidence            10    122 33333332 223333332111 1   001111222   223 2459999999999999999999875  3


Q ss_pred             CCCCCHHHHHHHHHHcC---CcHHHHHHHHHHHhc
Q 005987          353 QYSLSTEQIDLVAQASG---GDIRQAITSLQFSSL  384 (666)
Q Consensus       353 ~i~v~~~~l~~Ia~~s~---GDIR~AIn~LQf~~~  384 (666)
                      +..+++++++.|+..++   ||+|.|++.|+.+..
T Consensus       216 ~~~~~~~~~~~i~~~~~~~~G~~r~a~~~l~~a~~  250 (384)
T 2qby_B          216 KGTYDDEILSYIAAISAKEHGDARKAVNLLFRAAQ  250 (384)
T ss_dssp             TTSCCSHHHHHHHHHHHTTCCCHHHHHHHHHHHHH
T ss_pred             cCCcCHHHHHHHHHHHHhccCCHHHHHHHHHHHHH
Confidence            46789999999999998   999999999998764

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens}

Probab=99.67  E-value=4.2e-15  Score=157.24  Aligned_cols=205  Identities=12%  Similarity=0.126  Sum_probs=136.8

Q ss_pred             ccccCCCCccccccCHHHHHHHHHHHHHhhcCC----CCCCCccEEEEECCCCchHHHHHHHHHHHc-CCcEEEEcCCCc
Q 005987          140 AEKYKPRSLEELAVQRKKVEEVRAWFEERLGDS----KDKFSTNVLVITGQAGVGKTATVRQIASHL-GARLYEWDTPTP  214 (666)
Q Consensus       140 ~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~----~g~~~~k~LLL~GPpG~GKTtla~~LAkel-g~~viE~nasd~  214 (666)
                      +..+.+.+++||+|.+..++.|++++...+...    .+..+++.+||+||||||||++|+++|+++ +..++.+++++.
T Consensus         3 ~~~~~~~~~~di~G~~~~k~~l~~~v~~p~~~~~~~~~~~~~~~~iLL~GppGtGKT~la~ala~~~~~~~~~~i~~~~l   82 (322)
T 1xwi_A            3 VIERPNVKWSDVAGLEGAKEALKEAVILPIKFPHLFTGKRTPWRGILLFGPPGTGKSYLAKAVATEANNSTFFSISSSDL   82 (322)
T ss_dssp             EEECCCCCGGGSCSCHHHHHHHHHHHHHHHHCGGGSCTTCCCCSEEEEESSSSSCHHHHHHHHHHHTTSCEEEEEECCSS
T ss_pred             eecCCCCCHHHhcCHHHHHHHHHHHHHHHHhCHHHHhCCCCCCceEEEECCCCccHHHHHHHHHHHcCCCcEEEEEhHHH
Confidence            456677899999999999999998886322211    123344789999999999999999999999 888999988752


Q ss_pred             hhhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcch------hHHHHHHHHHHHH
Q 005987          215 TIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGR------TAFERLRQCLLLL  288 (666)
Q Consensus       215 ~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~------~~~~~l~~~L~~l  288 (666)
                      .           +.........++.++..+...            .+.||+|||+|.+...      ....++...++..
T Consensus        83 ~-----------~~~~g~~~~~~~~lf~~a~~~------------~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~ll~~  139 (322)
T 1xwi_A           83 V-----------SKWLGESEKLVKNLFQLAREN------------KPSIIFIDEIDSLCGSRSENESEAARRIKTEFLVQ  139 (322)
T ss_dssp             C-----------CSSCCSCHHHHHHHHHHHHHT------------SSEEEEEETTTGGGCCSSSCCTTHHHHHHHHHHHH
T ss_pred             H-----------hhhhhHHHHHHHHHHHHHHhc------------CCcEEEeecHHHhccccccccchHHHHHHHHHHHH
Confidence            1           111122334455666665432            3679999999976321      2233444445444


Q ss_pred             HhcC---CCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCe-eEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHH
Q 005987          289 VRST---HIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGA-RKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLV  364 (666)
Q Consensus       289 ~~~~---~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~-~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~I  364 (666)
                      ++..   ...+++|++ ++....          +...+.+ |+ ..|.|.+|+.++..++|+..+...+..+++..++.|
T Consensus       140 ld~~~~~~~~v~vI~a-tn~~~~----------ld~al~r-Rf~~~i~i~~P~~~~r~~il~~~l~~~~~~l~~~~l~~l  207 (322)
T 1xwi_A          140 MQGVGVDNDGILVLGA-TNIPWV----------LDSAIRR-RFEKRIYIPLPEPHARAAMFKLHLGTTQNSLTEADFREL  207 (322)
T ss_dssp             HHCSSSCCTTEEEEEE-ESCTTT----------SCHHHHH-TCCEEEECCCCCHHHHHHHHHHHHTTCCBCCCHHHHHHH
T ss_pred             HhcccccCCCEEEEEe-cCCccc----------CCHHHHh-hcCeEEEeCCcCHHHHHHHHHHHHhcCCCCCCHHHHHHH
Confidence            4432   223444433 232221          1122222 35 689999999999999999999887777899999999


Q ss_pred             HHHcCC----cHHHHHHHH
Q 005987          365 AQASGG----DIRQAITSL  379 (666)
Q Consensus       365 a~~s~G----DIR~AIn~L  379 (666)
                      +..+.|    ||+..++..
T Consensus       208 a~~t~G~sgadl~~l~~~A  226 (322)
T 1xwi_A          208 GRKTDGYSGADISIIVRDA  226 (322)
T ss_dssp             HHTCTTCCHHHHHHHHHHH
T ss_pred             HHHcCCCCHHHHHHHHHHH
Confidence            999877    455544443

>4b4t_M 26S protease regulatory subunit 6A; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=99.67  E-value=1.1e-15  Score=166.90  Aligned_cols=214  Identities=14%  Similarity=0.176  Sum_probs=139.7

Q ss_pred             CCccccccCCCCccccccCHHHHHHHHHHHHHhhcCC-----CCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEc
Q 005987          136 QQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDS-----KDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWD  210 (666)
Q Consensus       136 ~~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~-----~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~n  210 (666)
                      ..+-+++-.+.+++|+.|.++.+++|++.+...+...     -|..+++.+|||||||||||++|+++|++++..++.++
T Consensus       168 ~~~~~~~~p~~t~~digGl~~~k~~l~e~v~~pl~~pe~f~~~g~~~prGvLLyGPPGTGKTllAkAiA~e~~~~f~~v~  247 (434)
T 4b4t_M          168 KAMEVDEKPTETYSDVGGLDKQIEELVEAIVLPMKRADKFKDMGIRAPKGALMYGPPGTGKTLLARACAAQTNATFLKLA  247 (434)
T ss_dssp             SCCEEESSCSCCGGGSCSCHHHHHHHHHHTHHHHHCSHHHHHHCCCCCCEEEEESCTTSSHHHHHHHHHHHHTCEEEEEE
T ss_pred             hhcccCCCCCCChHhcCcHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCeeEEECcCCCCHHHHHHHHHHHhCCCEEEEe
Confidence            3455666677899999999999999998866433321     14445589999999999999999999999999999998


Q ss_pred             CCCchhhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcch---------hHHHHH
Q 005987          211 TPTPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGR---------TAFERL  281 (666)
Q Consensus       211 asd~~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~---------~~~~~l  281 (666)
                      .++.           .+..+......++.++..++..            .|+||+|||+|.+...         ....+.
T Consensus       248 ~s~l-----------~~~~vGese~~ir~lF~~A~~~------------aP~IifiDEiDal~~~R~~~~~~~~~~~~~~  304 (434)
T 4b4t_M          248 APQL-----------VQMYIGEGAKLVRDAFALAKEK------------APTIIFIDELDAIGTKRFDSEKSGDREVQRT  304 (434)
T ss_dssp             GGGG-----------CSSCSSHHHHHHHHHHHHHHHH------------CSEEEEEECTHHHHCCCSSGGGGTTHHHHHH
T ss_pred             hhhh-----------hhcccchHHHHHHHHHHHHHhc------------CCeEEeecchhhhhhccCCCCCCCchHHHHH
Confidence            7651           1122233445667777777654            3789999999954211         111222


Q ss_pred             HHHHHHHHhcC--CCceEEEEecCCCCCCccchhhhhhHHHHHHhhc-C-eeEEEeCCCCHHHHHHHHHHHHHHhCCCCC
Q 005987          282 RQCLLLLVRST--HIPTAVVLTECGKADSVDSTAQSFEELQSILVDA-G-ARKVALNPITNGSIKRTLSKICRQEQYSLS  357 (666)
Q Consensus       282 ~~~L~~l~~~~--~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~-r-~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~  357 (666)
                      ...|+..++..  ...+++ +.+++.++..|          +.|.|+ | -..|.|+.|+.....++|+..+....+. +
T Consensus       305 ~~~lL~~ldg~~~~~~ViV-IaaTNrp~~LD----------~AllRpGRfD~~I~i~lPd~~~R~~Il~~~~~~~~~~-~  372 (434)
T 4b4t_M          305 MLELLNQLDGFSSDDRVKV-LAATNRVDVLD----------PALLRSGRLDRKIEFPLPSEDSRAQILQIHSRKMTTD-D  372 (434)
T ss_dssp             HHHHHHHHTTSCSSCSSEE-EEECSSCCCCC----------TTTCSTTSEEEEEECCCCCHHHHHHHHHHHHHHSCBC-S
T ss_pred             HHHHHHHhhccCCCCCEEE-EEeCCCchhcC----------HhHhcCCceeEEEEeCCcCHHHHHHHHHHHhcCCCCC-C
Confidence            22333333321  223333 34444444333          222221 2 4579999999999999999887765432 1


Q ss_pred             HHHHHHHHHHcCC----cHHHHHHHHHHHhc
Q 005987          358 TEQIDLVAQASGG----DIRQAITSLQFSSL  384 (666)
Q Consensus       358 ~~~l~~Ia~~s~G----DIR~AIn~LQf~~~  384 (666)
                      +-.++.||..+.|    ||+.+++.--+.|.
T Consensus       373 dvdl~~lA~~t~G~sGADi~~l~~eA~~~a~  403 (434)
T 4b4t_M          373 DINWQELARSTDEFNGAQLKAVTVEAGMIAL  403 (434)
T ss_dssp             CCCHHHHHHHCSSCCHHHHHHHHHHHHHHHH
T ss_pred             cCCHHHHHHhCCCCCHHHHHHHHHHHHHHHH
Confidence            1236788888665    99988876555554

>4b4t_I 26S protease regulatory subunit 4 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=99.66  E-value=1.9e-15  Score=163.24  Aligned_cols=215  Identities=14%  Similarity=0.178  Sum_probs=141.1

Q ss_pred             CCccccccCCCCccccccCHHHHHHHHHHHHHhhcCC-----CCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEc
Q 005987          136 QQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDS-----KDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWD  210 (666)
Q Consensus       136 ~~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~-----~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~n  210 (666)
                      ..+-+++-...+++||.|.++.+++|++.+.-.+...     -|..+++.+|||||||||||++|+++|.+++..++.++
T Consensus       169 ~~~~~~~~p~v~~~DIgGld~~k~~L~e~v~~Pl~~pe~f~~~Gi~~prGvLLyGPPGTGKTlLAkAiA~e~~~~fi~v~  248 (437)
T 4b4t_I          169 SVMKMDKSPTESYSDIGGLESQIQEIKESVELPLTHPELYEEMGIKPPKGVILYGAPGTGKTLLAKAVANQTSATFLRIV  248 (437)
T ss_dssp             CCCEEESSCCCCGGGTCSCHHHHHHHHHHHHHHHHCCHHHHHHTCCCCSEEEEESSTTTTHHHHHHHHHHHHTCEEEEEE
T ss_pred             eeeeeccCCCCcceecCcHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCCCceECCCCchHHHHHHHHHHHhCCCEEEEE
Confidence            4566777778899999999999999998876433221     14445589999999999999999999999999999999


Q ss_pred             CCCchhhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcch---------hHHHHH
Q 005987          211 TPTPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGR---------TAFERL  281 (666)
Q Consensus       211 asd~~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~---------~~~~~l  281 (666)
                      .++.           ....+......++.++..+...            .|+||+|||+|.+...         ....+.
T Consensus       249 ~s~l-----------~sk~vGesek~ir~lF~~Ar~~------------aP~IIfiDEiDai~~~R~~~~~~~~~~~~~~  305 (437)
T 4b4t_I          249 GSEL-----------IQKYLGDGPRLCRQIFKVAGEN------------APSIVFIDEIDAIGTKRYDSNSGGEREIQRT  305 (437)
T ss_dssp             SGGG-----------CCSSSSHHHHHHHHHHHHHHHT------------CSEEEEEEEESSSSCCCSCSSCSSCCHHHHH
T ss_pred             HHHh-----------hhccCchHHHHHHHHHHHHHhc------------CCcEEEEehhhhhcccCCCCCCCccHHHHHH
Confidence            8751           1222233445667777777654            3789999999975321         111222


Q ss_pred             HHHHHHHHhc-CCCceEEEEecCCCCCCccchhhhhhHHHHHHhhc-C-eeEEEeCCCCHHHHHHHHHHHHHHhCCCCCH
Q 005987          282 RQCLLLLVRS-THIPTAVVLTECGKADSVDSTAQSFEELQSILVDA-G-ARKVALNPITNGSIKRTLSKICRQEQYSLST  358 (666)
Q Consensus       282 ~~~L~~l~~~-~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~-r-~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~  358 (666)
                      ...|+..++. ....-|+++.+++..+..|          +.|.|+ | -..|.|..|+.+...++|+..+....+. ++
T Consensus       306 l~~LL~~lDg~~~~~~ViVIaATNrpd~LD----------pALlRpGRfD~~I~v~lPd~~~R~~Il~~~l~~~~l~-~d  374 (437)
T 4b4t_I          306 MLELLNQLDGFDDRGDVKVIMATNKIETLD----------PALIRPGRIDRKILFENPDLSTKKKILGIHTSKMNLS-ED  374 (437)
T ss_dssp             HHHHHHHHHHCCCSSSEEEEEEESCSTTCC----------TTSSCTTTEEEEECCCCCCHHHHHHHHHHHHTTSCBC-SC
T ss_pred             HHHHHHHhhCcCCCCCEEEEEeCCChhhcC----------HHHhcCCceeEEEEcCCcCHHHHHHHHHHHhcCCCCC-Cc
Confidence            2223333332 2222233344444444333          222221 2 3469999999999999998887654432 12


Q ss_pred             HHHHHHHHHcCC----cHHHHHHHHHHHhc
Q 005987          359 EQIDLVAQASGG----DIRQAITSLQFSSL  384 (666)
Q Consensus       359 ~~l~~Ia~~s~G----DIR~AIn~LQf~~~  384 (666)
                      -.++.||..+.|    ||+.+++..-+.|.
T Consensus       375 vdl~~LA~~T~GfSGADI~~l~~eA~~~Ai  404 (437)
T 4b4t_I          375 VNLETLVTTKDDLSGADIQAMCTEAGLLAL  404 (437)
T ss_dssp             CCHHHHHHHCCSCCHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHhCCCCCHHHHHHHHHHHHHHHH
Confidence            237888887654    99988877666554

>4b4t_H 26S protease regulatory subunit 7 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=99.66  E-value=2.4e-15  Score=163.84  Aligned_cols=212  Identities=14%  Similarity=0.154  Sum_probs=137.5

Q ss_pred             ccccccCCCCccccccCHHHHHHHHHHHHHhhcCC-----CCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCC
Q 005987          138 LWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDS-----KDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTP  212 (666)
Q Consensus       138 ~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~-----~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nas  212 (666)
                      +=++.-...+++|+.|.++.+++|++++.-.+...     -|-.+++.+|||||||||||++|+++|++++..++.++.+
T Consensus       198 m~v~e~P~vt~~DIgGl~~~k~~L~e~V~~pl~~pe~f~~~Gi~pprGILLyGPPGTGKTlLAkAiA~e~~~~fi~vs~s  277 (467)
T 4b4t_H          198 MTVEEKPDVTYSDVGGCKDQIEKLREVVELPLLSPERFATLGIDPPKGILLYGPPGTGKTLCARAVANRTDATFIRVIGS  277 (467)
T ss_dssp             CEEESSCSCCCSSCTTCHHHHHHHHHHTHHHHHCHHHHHHHTCCCCSEEEECSCTTSSHHHHHHHHHHHHTCEEEEEEGG
T ss_pred             eeecCCCCCCHHHhccHHHHHHHHHHHHHHHhcCHHHHHHCCCCCCCceEeeCCCCCcHHHHHHHHHhccCCCeEEEEhH
Confidence            34555455789999999999999998865322211     1434458999999999999999999999999999999876


Q ss_pred             CchhhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcch---------hHHHHHHH
Q 005987          213 TPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGR---------TAFERLRQ  283 (666)
Q Consensus       213 d~~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~---------~~~~~l~~  283 (666)
                      +.           .+..+......++.++..+...            .|+||||||+|.+...         ....+...
T Consensus       278 ~L-----------~sk~vGesek~ir~lF~~Ar~~------------aP~IIfiDEiDai~~~R~~~~~~~~~~~~~~l~  334 (467)
T 4b4t_H          278 EL-----------VQKYVGEGARMVRELFEMARTK------------KACIIFFDEIDAVGGARFDDGAGGDNEVQRTML  334 (467)
T ss_dssp             GG-----------CCCSSSHHHHHHHHHHHHHHHT------------CSEEEEEECCTTTSBCCSSSSCGGGGHHHHHHH
T ss_pred             Hh-----------hcccCCHHHHHHHHHHHHHHhc------------CCceEeecccccccccccCcCCCccHHHHHHHH
Confidence            51           1222233445677777777654            3789999999976321         11122222


Q ss_pred             HHHHHHhcC--CCceEEEEecCCCCCCccchhhhhhHHHHHHhhc--CeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHH
Q 005987          284 CLLLLVRST--HIPTAVVLTECGKADSVDSTAQSFEELQSILVDA--GARKVALNPITNGSIKRTLSKICRQEQYSLSTE  359 (666)
Q Consensus       284 ~L~~l~~~~--~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~--r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~  359 (666)
                      .++..++..  ..++++ +.+++..+..|          ..|.|+  .-..|.|..|+.+...++|+..+....+. .+-
T Consensus       335 ~lL~~lDg~~~~~~ViV-IaATNrpd~LD----------pALlRpGRFD~~I~i~lPd~~~R~~Ilk~~l~~~~l~-~dv  402 (467)
T 4b4t_H          335 ELITQLDGFDPRGNIKV-MFATNRPNTLD----------PALLRPGRIDRKVEFSLPDLEGRANIFRIHSKSMSVE-RGI  402 (467)
T ss_dssp             HHHHHHHSSCCTTTEEE-EEECSCTTSBC----------HHHHSTTTCCEEECCCCCCHHHHHHHHHHHHTTSCBC-SSC
T ss_pred             HHHHHhhccCCCCcEEE-EeCCCCcccCC----------hhhhccccccEEEEeCCcCHHHHHHHHHHHhcCCCCC-CCC
Confidence            233333321  223444 44444443322          223231  24679999999999999998877654432 112


Q ss_pred             HHHHHHHHcCC----cHHHHHHHHHHHhc
Q 005987          360 QIDLVAQASGG----DIRQAITSLQFSSL  384 (666)
Q Consensus       360 ~l~~Ia~~s~G----DIR~AIn~LQf~~~  384 (666)
                      .++.||..+.|    ||+.+++.--+.|.
T Consensus       403 dl~~LA~~T~GfSGADI~~l~~eAa~~Ai  431 (467)
T 4b4t_H          403 RWELISRLCPNSTGAELRSVCTEAGMFAI  431 (467)
T ss_dssp             CHHHHHHHCCSCCHHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHCCCCCHHHHHHHHHHHHHHHH
Confidence            36788888766    99988876555554

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A*

Probab=99.66  E-value=2.6e-15  Score=157.05  Aligned_cols=215  Identities=15%  Similarity=0.144  Sum_probs=138.4

Q ss_pred             CccccccCCCCc-------c-ccccCHHHHHHHHHHHHHhhc-------CCCCCCCccEEEEECCCCchHHHHHHHHHHH
Q 005987          137 QLWAEKYKPRSL-------E-ELAVQRKKVEEVRAWFEERLG-------DSKDKFSTNVLVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       137 ~~W~eKY~P~sl-------~-eLvg~~k~i~el~~wL~~~~~-------~~~g~~~~k~LLL~GPpG~GKTtla~~LAke  201 (666)
                      ..+.+.|.|..+       + +|+|++..++.|..++.....       ......+...+||+||||||||++|+++|+.
T Consensus        11 ~~~~~~~~~~~~~~~~~~l~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~g~~~~~~~~~vll~G~~GtGKT~la~~la~~   90 (309)
T 3syl_A           11 IDLRAEYEGSGAKEVLEELDRELIGLKPVKDRIRETAALLLVERARQKLGLAHETPTLHMSFTGNPGTGKTTVALKMAGL   90 (309)
T ss_dssp             CCHHHHHHHTTHHHHHHHHHHHSSSCHHHHHHHHHHHHHHHHHHHHHHHTCCSSCCCCEEEEEECTTSSHHHHHHHHHHH
T ss_pred             CCCChhhccccHHHHHHHHHHHccChHHHHHHHHHHHHHHHhHHHHHHcCCCCCCCCceEEEECCCCCCHHHHHHHHHHH
Confidence            345555555554       2 688999999999988764321       0011222357999999999999999999999


Q ss_pred             cC-------CcEEEEcCCCchhhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcc
Q 005987          202 LG-------ARLYEWDTPTPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNG  274 (666)
Q Consensus       202 lg-------~~viE~nasd~~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~  274 (666)
                      ++       ..++++++++.           .+..+..........+..+               .+.||+|||++.+..
T Consensus        91 l~~~~~~~~~~~~~~~~~~l-----------~~~~~g~~~~~~~~~~~~~---------------~~~vl~iDEid~l~~  144 (309)
T 3syl_A           91 LHRLGYVRKGHLVSVTRDDL-----------VGQYIGHTAPKTKEVLKRA---------------MGGVLFIDEAYYLYR  144 (309)
T ss_dssp             HHHTTSSSSCCEEEECGGGT-----------CCSSTTCHHHHHHHHHHHH---------------TTSEEEEETGGGSCC
T ss_pred             HHhcCCcCCCcEEEEcHHHh-----------hhhcccccHHHHHHHHHhc---------------CCCEEEEEChhhhcc
Confidence            83       36777775431           1111111222334444443               124999999997732


Q ss_pred             hh----HHHHHHHHHHHHHhcCCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCe-eEEEeCCCCHHHHHHHHHHHH
Q 005987          275 RT----AFERLRQCLLLLVRSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGA-RKVALNPITNGSIKRTLSKIC  349 (666)
Q Consensus       275 ~~----~~~~l~~~L~~l~~~~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~-~~I~F~p~s~~~i~kiL~~I~  349 (666)
                      ..    .-...+..|..+++..+..+++|++....  ..+...+..+.|++     |+ ..|.|.+++.+++..++..++
T Consensus       145 ~~~~~~~~~~~~~~Ll~~l~~~~~~~~~i~~~~~~--~~~~~~~~~~~l~~-----R~~~~i~~~~~~~~~~~~il~~~l  217 (309)
T 3syl_A          145 PDNERDYGQEAIEILLQVMENNRDDLVVILAGYAD--RMENFFQSNPGFRS-----RIAHHIEFPDYSDEELFEIAGHML  217 (309)
T ss_dssp             CC---CCTHHHHHHHHHHHHHCTTTCEEEEEECHH--HHHHHHHHSTTHHH-----HEEEEEEECCCCHHHHHHHHHHHH
T ss_pred             CCCcccccHHHHHHHHHHHhcCCCCEEEEEeCChH--HHHHHHhhCHHHHH-----hCCeEEEcCCcCHHHHHHHHHHHH
Confidence            11    01234445666666665445554443110  00000011122332     35 889999999999999999999


Q ss_pred             HHhCCCCCHHHHHHHHHHc--------CCcHHHHHHHHHHHhc
Q 005987          350 RQEQYSLSTEQIDLVAQAS--------GGDIRQAITSLQFSSL  384 (666)
Q Consensus       350 ~~e~i~v~~~~l~~Ia~~s--------~GDIR~AIn~LQf~~~  384 (666)
                      ...++.+++++++.|+..+        .|++|.+.+.|+.++.
T Consensus       218 ~~~~~~~~~~~~~~l~~~~~~~~~~~~~gn~r~l~~~l~~a~~  260 (309)
T 3syl_A          218 DDQNYQMTPEAETALRAYIGLRRNQPHFANARSIRNALDRARL  260 (309)
T ss_dssp             HHTTCEECHHHHHHHHHHHHHHTTSSSCCHHHHHHHHHHHHHH
T ss_pred             HHcCCCCCHHHHHHHHHHHHHhccCCCCCcHHHHHHHHHHHHH
Confidence            9999999999999999863        4999999999998874

>4b4t_L 26S protease subunit RPT4; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=99.65  E-value=1.9e-15  Score=165.05  Aligned_cols=212  Identities=16%  Similarity=0.212  Sum_probs=138.1

Q ss_pred             ccccccCCCCccccccCHHHHHHHHHHHHHhhcCC-----CCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCC
Q 005987          138 LWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDS-----KDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTP  212 (666)
Q Consensus       138 ~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~-----~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nas  212 (666)
                      +-+++-...+++||.|.+..+++|++++.-.+...     -|..+++.+|||||||||||++|+++|++++..++.++.+
T Consensus       170 ~~~~~~p~v~~~digGl~~~k~~l~e~v~~pl~~p~~f~~~g~~~prGvLL~GPPGtGKTllAkAiA~e~~~~~~~v~~s  249 (437)
T 4b4t_L          170 MTSFEQGEITFDGIGGLTEQIRELREVIELPLKNPEIFQRVGIKPPKGVLLYGPPGTGKTLLAKAVAATIGANFIFSPAS  249 (437)
T ss_dssp             CEEEESCSSCSGGGCSCHHHHHHHHHHHHHHHHCHHHHHHHCCCCCCEEEEESCTTSSHHHHHHHHHHHHTCEEEEEEGG
T ss_pred             eeeccCCCCChhHhCChHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCeEEEECCCCCcHHHHHHHHHHHhCCCEEEEehh
Confidence            34445555789999999999999999887433321     1444558999999999999999999999999999999876


Q ss_pred             CchhhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcch---------hHHHHHHH
Q 005987          213 TPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGR---------TAFERLRQ  283 (666)
Q Consensus       213 d~~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~---------~~~~~l~~  283 (666)
                      +.           .+..+......++.++..+...            .|+||||||+|.+...         ....+...
T Consensus       250 ~l-----------~sk~~Gese~~ir~~F~~A~~~------------~P~IifiDEiDai~~~R~~~~~~~~~~~~~~l~  306 (437)
T 4b4t_L          250 GI-----------VDKYIGESARIIREMFAYAKEH------------EPCIIFMDEVDAIGGRRFSEGTSADREIQRTLM  306 (437)
T ss_dssp             GT-----------CCSSSSHHHHHHHHHHHHHHHS------------CSEEEEEECCCSSSCCCSSSCCSSTTHHHHHHH
T ss_pred             hh-----------ccccchHHHHHHHHHHHHHHhc------------CCceeeeecccccccccccCCCCcchHHHHHHH
Confidence            51           1222233445566777777543            3789999999976321         11222333


Q ss_pred             HHHHHHhcC--CCceEEEEecCCCCCCccchhhhhhHHHHHHhhc-C-eeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHH
Q 005987          284 CLLLLVRST--HIPTAVVLTECGKADSVDSTAQSFEELQSILVDA-G-ARKVALNPITNGSIKRTLSKICRQEQYSLSTE  359 (666)
Q Consensus       284 ~L~~l~~~~--~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~-r-~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~  359 (666)
                      .|+..++..  ...+++|+ +++.++..|          +.|.|+ | -..|.|..|+.....++|+..+....+. ++.
T Consensus       307 ~lL~~lDg~~~~~~vivI~-ATNrp~~LD----------pAllRpGRfD~~I~i~lPd~~~R~~Il~~~~~~~~~~-~d~  374 (437)
T 4b4t_L          307 ELLTQMDGFDNLGQTKIIM-ATNRPDTLD----------PALLRPGRLDRKVEIPLPNEAGRLEIFKIHTAKVKKT-GEF  374 (437)
T ss_dssp             HHHHHHHSSSCTTSSEEEE-EESSTTSSC----------TTTTSTTSEEEEECCCCCCHHHHHHHHHHHHHTSCBC-SCC
T ss_pred             HHHHHhhcccCCCCeEEEE-ecCCchhhC----------HHHhCCCccceeeecCCcCHHHHHHHHHHHhcCCCCC-ccc
Confidence            344444322  12333333 333333222          223232 2 3579999999999999998887664432 222


Q ss_pred             HHHHHHHHcCC----cHHHHHHHHHHHhc
Q 005987          360 QIDLVAQASGG----DIRQAITSLQFSSL  384 (666)
Q Consensus       360 ~l~~Ia~~s~G----DIR~AIn~LQf~~~  384 (666)
                      .++.||..+.|    ||+.+++.--+.|.
T Consensus       375 dl~~lA~~t~G~sGADi~~l~~eA~~~ai  403 (437)
T 4b4t_L          375 DFEAAVKMSDGFNGADIRNCATEAGFFAI  403 (437)
T ss_dssp             CHHHHHHTCCSCCHHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHhCCCCCHHHHHHHHHHHHHHHH
Confidence            36788887665    99998876555554

>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix}

Probab=99.64  E-value=2.5e-15  Score=161.33  Aligned_cols=221  Identities=16%  Similarity=0.226  Sum_probs=138.7

Q ss_pred             CCccccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc---------CCcE
Q 005987          136 QQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL---------GARL  206 (666)
Q Consensus       136 ~~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel---------g~~v  206 (666)
                      ...|..+|.|   ++++|+++.++.+..|+..+..   +..+ +.++|+||||||||++++.+++++         ++.+
T Consensus         9 ~~~l~~~~~p---~~~~gr~~~~~~l~~~l~~~~~---~~~~-~~vll~G~~G~GKT~l~~~~~~~~~~~~~~~~~~~~~   81 (387)
T 2v1u_A            9 RWVLLPDYVP---DVLPHREAELRRLAEVLAPALR---GEKP-SNALLYGLTGTGKTAVARLVLRRLEARASSLGVLVKP   81 (387)
T ss_dssp             HHHHSTTCCC---SCCTTCHHHHHHHHHTTGGGTS---SCCC-CCEEECBCTTSSHHHHHHHHHHHHHHHHHHHTCCEEE
T ss_pred             HHhcCCccCC---CCCCCHHHHHHHHHHHHHHHHc---CCCC-CcEEEECCCCCCHHHHHHHHHHHHHHHHhccCCCeEE
Confidence            3567888988   6779999999999999987543   2222 589999999999999999999998         8889


Q ss_pred             EEEcCCCchhh----hhhhhcccCCccc-cchhHH-HHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHH
Q 005987          207 YEWDTPTPTIW----QEYMHNCKTGLEY-TSKLDE-FENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFER  280 (666)
Q Consensus       207 iE~nasd~~~~----~e~l~~~~~g~~~-~s~~~~-f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~  280 (666)
                      +.+++......    ...+......... ...... +..+...+..           .+.+.+|+|||++.+.....   
T Consensus        82 ~~i~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~-----------~~~~~vlilDEi~~l~~~~~---  147 (387)
T 2v1u_A           82 IYVNARHRETPYRVASAIAEAVGVRVPFTGLSVGEVYERLVKRLSR-----------LRGIYIIVLDEIDFLPKRPG---  147 (387)
T ss_dssp             EEEETTTSCSHHHHHHHHHHHHSCCCCSSCCCHHHHHHHHHHHHTT-----------SCSEEEEEEETTTHHHHSTT---
T ss_pred             EEEECCcCCCHHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHHhc-----------cCCeEEEEEccHhhhcccCC---
Confidence            99998753221    1111111100000 001122 2333332211           12467999999997643210   


Q ss_pred             HHHHHHHHHhcC-----CCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHH--hC
Q 005987          281 LRQCLLLLVRST-----HIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQ--EQ  353 (666)
Q Consensus       281 l~~~L~~l~~~~-----~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~--e~  353 (666)
                      .++.|..+++..     ..++++|++.... +.   .....   ..+.++.....|.|+|++.+++.++|...+..  .+
T Consensus       148 ~~~~l~~l~~~~~~~~~~~~~~~I~~t~~~-~~---~~~l~---~~l~~r~~~~~i~l~~l~~~~~~~il~~~~~~~~~~  220 (387)
T 2v1u_A          148 GQDLLYRITRINQELGDRVWVSLVGITNSL-GF---VENLE---PRVKSSLGEVELVFPPYTAPQLRDILETRAEEAFNP  220 (387)
T ss_dssp             HHHHHHHHHHGGGCC-----CEEEEECSCS-TT---SSSSC---HHHHTTTTSEECCBCCCCHHHHHHHHHHHHHHHBCT
T ss_pred             CChHHHhHhhchhhcCCCceEEEEEEECCC-ch---HhhhC---HHHHhcCCCeEEeeCCCCHHHHHHHHHHHHHhhccC
Confidence            122333333311     2233333332111 10   01111   22233322368999999999999999999876  45


Q ss_pred             CCCCHHHHHHHHHHcC---CcHHHHHHHHHHHhc
Q 005987          354 YSLSTEQIDLVAQASG---GDIRQAITSLQFSSL  384 (666)
Q Consensus       354 i~v~~~~l~~Ia~~s~---GDIR~AIn~LQf~~~  384 (666)
                      ..+++++++.|+..++   ||+|.+++.|+.+..
T Consensus       221 ~~~~~~~~~~l~~~~~~~~G~~r~~~~~l~~a~~  254 (387)
T 2v1u_A          221 GVLDPDVVPLCAALAAREHGDARRALDLLRVAGE  254 (387)
T ss_dssp             TTBCSSHHHHHHHHHHSSSCCHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHhccCHHHHHHHHHHHHH
Confidence            6789999999999998   999999999988753

>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=99.64  E-value=4.5e-15  Score=163.91  Aligned_cols=213  Identities=13%  Similarity=0.147  Sum_probs=137.9

Q ss_pred             CCccccccCCCCccccccCHHHHHHHHHHHHHhhcCC----CCCCCccEEEEECCCCchHHHHHHHHHHHc-CCcEEEEc
Q 005987          136 QQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDS----KDKFSTNVLVITGQAGVGKTATVRQIASHL-GARLYEWD  210 (666)
Q Consensus       136 ~~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~----~g~~~~k~LLL~GPpG~GKTtla~~LAkel-g~~viE~n  210 (666)
                      ...++.++.|.++++|+|++..++.|+.++...+...    .+..+.+.+||+||||||||++|+++|+++ +..++.++
T Consensus       121 ~~~i~~~~~~~~~~di~G~~~~k~~l~~~v~~p~~~~~~~~~~~~~~~~vLL~GppGtGKT~lA~aia~~~~~~~~~~v~  200 (444)
T 2zan_A          121 QGAIVIERPNVKWSDVAGLEGAKEALKEAVILPIKFPHLFTGKRTPWRGILLFGPPGTGKSYLAKAVATEANNSTFFSIS  200 (444)
T ss_dssp             ---CBCCCCCCCGGGSCSCHHHHHHHHHHHTHHHHCTTTTSGGGCCCSEEEEECSTTSSHHHHHHHHHHHCCSSEEEEEC
T ss_pred             hcceeccCCCCCHHHhcCHHHHHHHHHHHHHHHhhCHHHhhccCCCCceEEEECCCCCCHHHHHHHHHHHcCCCCEEEEe
Confidence            3457888999999999999999999998875322111    112334789999999999999999999999 88899998


Q ss_pred             CCCchhhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcch------hHHHHHHHH
Q 005987          211 TPTPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGR------TAFERLRQC  284 (666)
Q Consensus       211 asd~~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~------~~~~~l~~~  284 (666)
                      +++..  ...     .|.    ....+..++..+...            .+.||||||+|.+...      ....++...
T Consensus       201 ~~~l~--~~~-----~g~----~~~~~~~~f~~a~~~------------~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~  257 (444)
T 2zan_A          201 SSDLV--SKW-----LGE----SEKLVKNLFQLAREN------------KPSIIFIDEIDSLCGSRSENESEAARRIKTE  257 (444)
T ss_dssp             CC--------------------CCCTHHHHHHHHHHS------------CSEEEEESCTTTTCCCSSCCCCGGGHHHHHH
T ss_pred             HHHHH--hhh-----cch----HHHHHHHHHHHHHHc------------CCeEEEEechHhhccCCCCccccHHHHHHHH
Confidence            87521  111     111    112234455554322            3579999999987321      122344444


Q ss_pred             HHHHHhcC---CCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCe-eEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHH
Q 005987          285 LLLLVRST---HIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGA-RKVALNPITNGSIKRTLSKICRQEQYSLSTEQ  360 (666)
Q Consensus       285 L~~l~~~~---~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~-~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~  360 (666)
                      |+..+...   ...+++|++. +.+.       .   +...+.+ |+ ..|.|+.|+.++...+|+..+...+..+++..
T Consensus       258 lL~~l~~~~~~~~~v~vI~at-n~~~-------~---ld~al~r-Rf~~~i~i~~P~~~~r~~il~~~l~~~~~~l~~~~  325 (444)
T 2zan_A          258 FLVQMQGVGVDNDGILVLGAT-NIPW-------V---LDSAIRR-RFEKRIYIPLPEAHARAAMFRLHLGSTQNSLTEAD  325 (444)
T ss_dssp             HHTTTTCSSCCCSSCEEEEEE-SCGG-------G---SCHHHHT-TCCEEEECCCCCHHHHHHHHHHHHTTSCEECCHHH
T ss_pred             HHHHHhCcccCCCCEEEEecC-CCcc-------c---cCHHHHh-hcceEEEeCCcCHHHHHHHHHHHHhcCCCCCCHHH
Confidence            44444331   2234444333 2211       1   2222323 45 58899999999999999999887777789999


Q ss_pred             HHHHHHHcCC----cHHHHHHHHHHHh
Q 005987          361 IDLVAQASGG----DIRQAITSLQFSS  383 (666)
Q Consensus       361 l~~Ia~~s~G----DIR~AIn~LQf~~  383 (666)
                      ++.|+..+.|    ||+.+++..-+.+
T Consensus       326 l~~la~~t~G~sgadl~~l~~~a~~~a  352 (444)
T 2zan_A          326 FQELGRKTDGYSGADISIIVRDALMQP  352 (444)
T ss_dssp             HHHHHHHTTTCCHHHHHHHHHHHHTHH
T ss_pred             HHHHHHHcCCCCHHHHHHHHHHHHHHH
Confidence            9999999888    7777766554444

>4b4t_K 26S protease regulatory subunit 6B homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=99.64  E-value=1.2e-14  Score=158.37  Aligned_cols=213  Identities=14%  Similarity=0.155  Sum_probs=137.9

Q ss_pred             CccccccCCCCccccccCHHHHHHHHHHHHHhhcCC-----CCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcC
Q 005987          137 QLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDS-----KDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDT  211 (666)
Q Consensus       137 ~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~-----~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~na  211 (666)
                      .+.+++-...+++|+.|.++.+++|++.+.-.+...     -|..+++.+|||||||||||++|+++|++++..++.++.
T Consensus       160 ~~~~~~~p~v~~~digGl~~~k~~l~e~v~~pl~~p~~~~~~g~~~prGiLL~GPPGtGKT~lakAiA~~~~~~~~~v~~  239 (428)
T 4b4t_K          160 VMGENEKPDVTYADVGGLDMQKQEIREAVELPLVQADLYEQIGIDPPRGVLLYGPPGTGKTMLVKAVANSTKAAFIRVNG  239 (428)
T ss_dssp             CCEEESSCSCCGGGSCSCHHHHHHHHHHHHHHHHCHHHHHHHCCCCCCEEEEESCTTTTHHHHHHHHHHHHTCEEEEEEG
T ss_pred             hccCCCCCCCCHHHhccHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCceEEEECCCCCCHHHHHHHHHHHhCCCeEEEec
Confidence            344555555789999999999999998876433221     144455899999999999999999999999999999987


Q ss_pred             CCchhhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcc---------hhHHHHHH
Q 005987          212 PTPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNG---------RTAFERLR  282 (666)
Q Consensus       212 sd~~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~---------~~~~~~l~  282 (666)
                      ++.           .+..+......++.++..++..            .|+||+|||+|.+..         .....+..
T Consensus       240 ~~l-----------~~~~~Ge~e~~ir~lF~~A~~~------------aP~IifiDEiD~i~~~R~~~~~~~~~~~~r~l  296 (428)
T 4b4t_K          240 SEF-----------VHKYLGEGPRMVRDVFRLAREN------------APSIIFIDEVDSIATKRFDAQTGSDREVQRIL  296 (428)
T ss_dssp             GGT-----------CCSSCSHHHHHHHHHHHHHHHT------------CSEEEEEECTHHHHCSCSSSCSCCCCHHHHHH
T ss_pred             chh-----------hccccchhHHHHHHHHHHHHHc------------CCCeeechhhhhhhccccCCCCCCChHHHHHH
Confidence            651           1222233445677777777654            378999999984321         11223333


Q ss_pred             HHHHHHHhc--CCCceEEEEecCCCCCCccchhhhhhHHHHHHhhc-Ce-eEEEeC-CCCHHHHHHHHHHHHHHhCCCCC
Q 005987          283 QCLLLLVRS--THIPTAVVLTECGKADSVDSTAQSFEELQSILVDA-GA-RKVALN-PITNGSIKRTLSKICRQEQYSLS  357 (666)
Q Consensus       283 ~~L~~l~~~--~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~-r~-~~I~F~-p~s~~~i~kiL~~I~~~e~i~v~  357 (666)
                      ..|+..++.  ....+++| .+++.++.          |.+.|.|+ |+ ..|.|+ +|+......+|+..+....+. +
T Consensus       297 ~~lL~~ldg~~~~~~v~vI-~aTN~~~~----------LD~AllRpGRfd~~I~~p~lPd~~~R~~Il~~~~~~~~l~-~  364 (428)
T 4b4t_K          297 IELLTQMDGFDQSTNVKVI-MATNRADT----------LDPALLRPGRLDRKIEFPSLRDRRERRLIFGTIASKMSLA-P  364 (428)
T ss_dssp             HHHHHHHHHSCSSCSEEEE-EEESCSSS----------CCHHHHSSSSEEEEEECCSSCCHHHHHHHHHHHHHSSCBC-T
T ss_pred             HHHHHHhhCCCCCCCEEEE-EecCChhh----------cChhhhcCCcceEEEEcCCCCCHHHHHHHHHHHhcCCCCC-c
Confidence            334444442  22234444 33343332          22333332 33 468995 788999999998887655432 2


Q ss_pred             HHHHHHHHHHcCC----cHHHHHHHHHHHhc
Q 005987          358 TEQIDLVAQASGG----DIRQAITSLQFSSL  384 (666)
Q Consensus       358 ~~~l~~Ia~~s~G----DIR~AIn~LQf~~~  384 (666)
                      +..++.||..+.|    ||+.+++..-+.|.
T Consensus       365 ~~dl~~lA~~t~G~sgadi~~l~~eA~~~a~  395 (428)
T 4b4t_K          365 EADLDSLIIRNDSLSGAVIAAIMQEAGLRAV  395 (428)
T ss_dssp             TCCHHHHHHHTTTCCHHHHHHHHHHHHHHHH
T ss_pred             ccCHHHHHHHCCCCCHHHHHHHHHHHHHHHH
Confidence            2237888887665    99988876555554

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii}

Probab=99.63  E-value=8.8e-15  Score=151.30  Aligned_cols=212  Identities=14%  Similarity=0.173  Sum_probs=131.8

Q ss_pred             cccccCCCCccccccCHHHHHHHHHHHHHhhcCC-----CCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCC
Q 005987          139 WAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDS-----KDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPT  213 (666)
Q Consensus       139 W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~-----~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd  213 (666)
                      -++...+.++++|+|.+..+++|..++.......     .+..+++.+||+||||||||++|+++|++++..++.++.++
T Consensus         7 ~~~~~~~~~~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ll~G~~GtGKT~la~~la~~~~~~~~~v~~~~   86 (285)
T 3h4m_A            7 EVDERPNVRYEDIGGLEKQMQEIREVVELPLKHPELFEKVGIEPPKGILLYGPPGTGKTLLAKAVATETNATFIRVVGSE   86 (285)
T ss_dssp             EEESSCCCCGGGSCSCHHHHHHHHHHTHHHHHCHHHHHHHCCCCCSEEEEESSSSSSHHHHHHHHHHHTTCEEEEEEGGG
T ss_pred             cccCCCCCCHHHhcCHHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCeEEEECCCCCcHHHHHHHHHHHhCCCEEEEehHH
Confidence            4456667789999999999999999987543210     01223368999999999999999999999999999988654


Q ss_pred             chhhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCc----------chhHHHHHHH
Q 005987          214 PTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTN----------GRTAFERLRQ  283 (666)
Q Consensus       214 ~~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~----------~~~~~~~l~~  283 (666)
                      .           .+.........+...+..+...            .+.||+|||++.+.          .......+..
T Consensus        87 ~-----------~~~~~~~~~~~~~~~~~~~~~~------------~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~l~~  143 (285)
T 3h4m_A           87 L-----------VKKFIGEGASLVKDIFKLAKEK------------APSIIFIDEIDAIAAKRTDALTGGDREVQRTLMQ  143 (285)
T ss_dssp             G-----------CCCSTTHHHHHHHHHHHHHHHT------------CSEEEEEETTHHHHBCCSSSCCGGGGHHHHHHHH
T ss_pred             H-----------HHhccchHHHHHHHHHHHHHHc------------CCeEEEEECHHHhcccCccccCCccHHHHHHHHH
Confidence            1           1111122223344555555332            35799999998752          1111122222


Q ss_pred             HHHHHHh-cCCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCe-eEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHH
Q 005987          284 CLLLLVR-STHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGA-RKVALNPITNGSIKRTLSKICRQEQYSLSTEQI  361 (666)
Q Consensus       284 ~L~~l~~-~~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~-~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l  361 (666)
                      .+..+-. ....++++|++. +...       .+.  ..+++..|+ ..+.|.+|+.++..++|+..+...++. .+..+
T Consensus       144 ll~~~~~~~~~~~~~vI~tt-n~~~-------~l~--~~l~~~~Rf~~~i~~~~p~~~~r~~il~~~~~~~~~~-~~~~~  212 (285)
T 3h4m_A          144 LLAEMDGFDARGDVKIIGAT-NRPD-------ILD--PAILRPGRFDRIIEVPAPDEKGRLEILKIHTRKMNLA-EDVNL  212 (285)
T ss_dssp             HHHHHHTTCSSSSEEEEEEC-SCGG-------GBC--HHHHSTTSEEEEEECCCCCHHHHHHHHHHHHTTSCBC-TTCCH
T ss_pred             HHHHhhCCCCCCCEEEEEeC-CCch-------hcC--HHHcCCCcCCeEEEECCCCHHHHHHHHHHHHhcCCCC-CcCCH
Confidence            2222211 122234444443 2211       111  222221134 579999999999999999887765543 23346


Q ss_pred             HHHHHHcCC----cHHHHHHHHHHHhc
Q 005987          362 DLVAQASGG----DIRQAITSLQFSSL  384 (666)
Q Consensus       362 ~~Ia~~s~G----DIR~AIn~LQf~~~  384 (666)
                      ..|+..+.|    ||+.+++.....|.
T Consensus       213 ~~l~~~~~g~~~~~i~~l~~~a~~~a~  239 (285)
T 3h4m_A          213 EEIAKMTEGCVGAELKAICTEAGMNAI  239 (285)
T ss_dssp             HHHHHHCTTCCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHcCCCCHHHHHHHHHHHHHHHH
Confidence            778877766    88888887777765

>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=1.2e-14  Score=154.39  Aligned_cols=192  Identities=16%  Similarity=0.140  Sum_probs=121.3

Q ss_pred             cCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEE-EcCCCchhhhhhh--------hc
Q 005987          153 VQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYE-WDTPTPTIWQEYM--------HN  223 (666)
Q Consensus       153 g~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE-~nasd~~~~~e~l--------~~  223 (666)
                      .|+...+.+...++.      |+.+ +.+||+||||+|||++|+++|+.+.+.... ..+...+.....+        ..
T Consensus         6 w~~~~~~~l~~~i~~------~~~~-~a~L~~G~~G~GKt~~a~~la~~l~~~~~~~~~~c~~c~~c~~~~~~~~~d~~~   78 (334)
T 1a5t_A            6 WLRPDFEKLVASYQA------GRGH-HALLIQALPGMGDDALIYALSRYLLCQQPQGHKSCGHCRGCQLMQAGTHPDYYT   78 (334)
T ss_dssp             GGHHHHHHHHHHHHT------TCCC-SEEEEECCTTSCHHHHHHHHHHHHTCSSCBTTBCCSCSHHHHHHHHTCCTTEEE
T ss_pred             chHHHHHHHHHHHHc------CCcc-eeEEEECCCCchHHHHHHHHHHHHhCCCCCCCCCCCCCHHHHHHhcCCCCCEEE
Confidence            466777777777765      6665 689999999999999999999998653210 0000000000000        00


Q ss_pred             ccCC-ccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcCCCce-EEEEe
Q 005987          224 CKTG-LEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHIPT-AVVLT  301 (666)
Q Consensus       224 ~~~g-~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~~~Pi-ViIit  301 (666)
                      .... ..-....+.++++++.+...+        ....++|+||||+|.+...     ..+.|+.+++.....+ +|+++
T Consensus        79 ~~~~~~~~~~~i~~ir~l~~~~~~~~--------~~~~~kvviIdead~l~~~-----a~naLLk~lEep~~~~~~Il~t  145 (334)
T 1a5t_A           79 LAPEKGKNTLGVDAVREVTEKLNEHA--------RLGGAKVVWVTDAALLTDA-----AANALLKTLEEPPAETWFFLAT  145 (334)
T ss_dssp             ECCCTTCSSBCHHHHHHHHHHTTSCC--------TTSSCEEEEESCGGGBCHH-----HHHHHHHHHTSCCTTEEEEEEE
T ss_pred             EeccccCCCCCHHHHHHHHHHHhhcc--------ccCCcEEEEECchhhcCHH-----HHHHHHHHhcCCCCCeEEEEEe
Confidence            0000 000123455666665543221        1124679999999988643     2344666677654333 34444


Q ss_pred             cCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCcHHHHHHHHHH
Q 005987          302 ECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASGGDIRQAITSLQF  381 (666)
Q Consensus       302 ~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~s~GDIR~AIn~LQf  381 (666)
                      +.        ..+.++.+++     ||..+.|.+++.+++.++|..++     .+++++++.++..++||+|.|++.|+-
T Consensus       146 ~~--------~~~l~~ti~S-----Rc~~~~~~~~~~~~~~~~L~~~~-----~~~~~~~~~l~~~s~G~~r~a~~~l~~  207 (334)
T 1a5t_A          146 RE--------PERLLATLRS-----RCRLHYLAPPPEQYAVTWLSREV-----TMSQDALLAALRLSAGSPGAALALFQG  207 (334)
T ss_dssp             SC--------GGGSCHHHHT-----TSEEEECCCCCHHHHHHHHHHHC-----CCCHHHHHHHHHHTTTCHHHHHHTTSS
T ss_pred             CC--------hHhCcHHHhh-----cceeeeCCCCCHHHHHHHHHHhc-----CCCHHHHHHHHHHcCCCHHHHHHHhcc
Confidence            31        1233444443     59999999999999999998775     678999999999999999999998764


Q ss_pred             H
Q 005987          382 S  382 (666)
Q Consensus       382 ~  382 (666)
                      .
T Consensus       208 ~  208 (334)
T 1a5t_A          208 D  208 (334)
T ss_dssp             H
T ss_pred             c
Confidence            3

>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=99.61  E-value=4.7e-14  Score=143.61  Aligned_cols=202  Identities=16%  Similarity=0.182  Sum_probs=121.7

Q ss_pred             CCCccccccCHHHHHHHHHHHHHhhcCC----CCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCchhhhhh
Q 005987          145 PRSLEELAVQRKKVEEVRAWFEERLGDS----KDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTIWQEY  220 (666)
Q Consensus       145 P~sl~eLvg~~k~i~el~~wL~~~~~~~----~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~~~~e~  220 (666)
                      +.++++|+|++..++.|++++.......    .|...++.+||+||||||||++|+++|++++..++.+++++..     
T Consensus         2 ~~~~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~g~~~~~~vll~G~~GtGKT~la~~la~~~~~~~~~~~~~~~~-----   76 (262)
T 2qz4_A            2 GVSFKDVAGMHEAKLEVREFVDYLKSPERFLQLGAKVPKGALLLGPPGCGKTLLAKAVATEAQVPFLAMAGAEFV-----   76 (262)
T ss_dssp             CCCTTSSCSCHHHHHHHHHHHHHHHCCC------CCCCCEEEEESCTTSSHHHHHHHHHHHHTCCEEEEETTTTS-----
T ss_pred             CCCHHHhCCHHHHHHHHHHHHHHHHCHHHHHHcCCCCCceEEEECCCCCCHHHHHHHHHHHhCCCEEEechHHHH-----
Confidence            4678999999999999988876422111    0222346899999999999999999999999999999887521     


Q ss_pred             hhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchh-----------HHHHHHHHHHHHH
Q 005987          221 MHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRT-----------AFERLRQCLLLLV  289 (666)
Q Consensus       221 l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~-----------~~~~l~~~L~~l~  289 (666)
                        ....    ......+..++..+...            .+.||+|||++.+....           ....+.. +...+
T Consensus        77 --~~~~----~~~~~~~~~~~~~a~~~------------~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~l~~-ll~~~  137 (262)
T 2qz4_A           77 --EVIG----GLGAARVRSLFKEARAR------------APCIVYIDEIDAVGKKRSTTMSGFSNTEEEQTLNQ-LLVEM  137 (262)
T ss_dssp             --SSST----THHHHHHHHHHHHHHHT------------CSEEEEEECC-------------------CHHHHH-HHHHH
T ss_pred             --hhcc----ChhHHHHHHHHHHHHhc------------CCeEEEEeCcchhhccccccccCccchhHHHHHHH-HHHHh
Confidence              0011    11223445555555432            25799999999874321           0111222 22222


Q ss_pred             hc--CCCceEEEEecCCCCCCccchhhhhhHHHHHHhhc-Ce-eEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHH-HHHH
Q 005987          290 RS--THIPTAVVLTECGKADSVDSTAQSFEELQSILVDA-GA-RKVALNPITNGSIKRTLSKICRQEQYSLSTEQ-IDLV  364 (666)
Q Consensus       290 ~~--~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~-r~-~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~-l~~I  364 (666)
                      ..  ....+++|++. +...       .   +...+.++ |+ ..+.|.+|+.++..++++..+...++..+... +..|
T Consensus       138 ~~~~~~~~~~vi~~t-n~~~-------~---ld~~l~~~~R~~~~i~i~~p~~~~r~~il~~~~~~~~~~~~~~~~~~~l  206 (262)
T 2qz4_A          138 DGMGTTDHVIVLAST-NRAD-------I---LDGALMRPGRLDRHVFIDLPTLQERREIFEQHLKSLKLTQSSTFYSQRL  206 (262)
T ss_dssp             HTCCTTCCEEEEEEE-SCGG-------G---GGSGGGSTTSCCEEEECCSCCHHHHHHHHHHHHHHTTCCBTHHHHHHHH
T ss_pred             hCcCCCCCEEEEecC-CChh-------h---cCHHHhcCCcCCeEEEeCCcCHHHHHHHHHHHHHhCCCCcchhhHHHHH
Confidence            32  12234444433 2211       1   11222221 33 67899999999999999999998888777654 5788


Q ss_pred             HHHcCC----cHHHHHHHHHH
Q 005987          365 AQASGG----DIRQAITSLQF  381 (666)
Q Consensus       365 a~~s~G----DIR~AIn~LQf  381 (666)
                      +..+.|    ||+.+++....
T Consensus       207 ~~~~~g~~~~~l~~l~~~a~~  227 (262)
T 2qz4_A          207 AELTPGFSGADIANICNEAAL  227 (262)
T ss_dssp             HHTCTTCCHHHHHHHHHHHHT
T ss_pred             HHHCCCCCHHHHHHHHHHHHH
Confidence            887665    55555554433

>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=99.60  E-value=1.6e-14  Score=152.52  Aligned_cols=199  Identities=18%  Similarity=0.224  Sum_probs=126.9

Q ss_pred             CCccccc---cCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcCCCchhhhh
Q 005987          146 RSLEELA---VQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL---GARLYEWDTPTPTIWQE  219 (666)
Q Consensus       146 ~sl~eLv---g~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~nasd~~~~~e  219 (666)
                      .+|++++   .+......++.+++..     +. ..+.++|+|||||||||+++++++++   +..++.+++.+.  ..+
T Consensus         8 ~~f~~fv~g~~~~~a~~~~~~~~~~~-----~~-~~~~lll~G~~GtGKT~la~~i~~~~~~~~~~~~~i~~~~~--~~~   79 (324)
T 1l8q_A            8 YTLENFIVGEGNRLAYEVVKEALENL-----GS-LYNPIFIYGSVGTGKTHLLQAAGNEAKKRGYRVIYSSADDF--AQA   79 (324)
T ss_dssp             CCSSSCCCCTTTHHHHHHHHHHHHTT-----TT-SCSSEEEECSSSSSHHHHHHHHHHHHHHTTCCEEEEEHHHH--HHH
T ss_pred             CCcccCCCCCcHHHHHHHHHHHHhCc-----CC-CCCeEEEECCCCCcHHHHHHHHHHHHHHCCCEEEEEEHHHH--HHH
Confidence            3677776   3555666666666531     21 22579999999999999999999999   888998886431  111


Q ss_pred             hhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcch-hHHHHHHHHHHHHHhcCCCceEE
Q 005987          220 YMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGR-TAFERLRQCLLLLVRSTHIPTAV  298 (666)
Q Consensus       220 ~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~-~~~~~l~~~L~~l~~~~~~PiVi  298 (666)
                      .......     .   ....|.....              .+.+|+|||++.+... .....+...+..+.+.+.  .++
T Consensus        80 ~~~~~~~-----~---~~~~~~~~~~--------------~~~vL~iDEi~~l~~~~~~~~~l~~~l~~~~~~~~--~ii  135 (324)
T 1l8q_A           80 MVEHLKK-----G---TINEFRNMYK--------------SVDLLLLDDVQFLSGKERTQIEFFHIFNTLYLLEK--QII  135 (324)
T ss_dssp             HHHHHHH-----T---CHHHHHHHHH--------------TCSEEEEECGGGGTTCHHHHHHHHHHHHHHHHTTC--EEE
T ss_pred             HHHHHHc-----C---cHHHHHHHhc--------------CCCEEEEcCcccccCChHHHHHHHHHHHHHHHCCC--eEE
Confidence            1100000     0   1112222221              1359999999987652 222334444444444332  344


Q ss_pred             EEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCcHHHHHHH
Q 005987          299 VLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASGGDIRQAITS  378 (666)
Q Consensus       299 Iit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~s~GDIR~AIn~  378 (666)
                      ++++.. ...   .....+.|.+.+.  ....+.|.| +.+++..+|...+...++.+++++++.|+..+ ||+|.+.+.
T Consensus       136 i~~~~~-~~~---l~~l~~~L~sR~~--~~~~i~l~~-~~~e~~~il~~~~~~~~~~l~~~~l~~l~~~~-g~~r~l~~~  207 (324)
T 1l8q_A          136 LASDRH-PQK---LDGVSDRLVSRFE--GGILVEIEL-DNKTRFKIIKEKLKEFNLELRKEVIDYLLENT-KNVREIEGK  207 (324)
T ss_dssp             EEESSC-GGG---CTTSCHHHHHHHH--TSEEEECCC-CHHHHHHHHHHHHHHTTCCCCHHHHHHHHHHC-SSHHHHHHH
T ss_pred             EEecCC-hHH---HHHhhhHhhhccc--CceEEEeCC-CHHHHHHHHHHHHHhcCCCCCHHHHHHHHHhC-CCHHHHHHH
Confidence            444321 110   0112233443322  137899999 99999999999999999999999999999999 999999999


Q ss_pred             HHHHhc
Q 005987          379 LQFSSL  384 (666)
Q Consensus       379 LQf~~~  384 (666)
                      |+.++.
T Consensus       208 l~~~~~  213 (324)
T 1l8q_A          208 IKLIKL  213 (324)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            988764

>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A {Escherichia coli} SCOP: c.37.1.20

Probab=99.60  E-value=1.6e-14  Score=147.43  Aligned_cols=210  Identities=15%  Similarity=0.211  Sum_probs=127.2

Q ss_pred             ccccccCCCCccccccCHHHHHHHHHHHHHhhcCC-----CCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCC
Q 005987          138 LWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDS-----KDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTP  212 (666)
Q Consensus       138 ~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~-----~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nas  212 (666)
                      +|.++|.|.++++|+|++..++++...+.. +...     -+...++.++|+|||||||||+++++|++++..++.++.+
T Consensus         1 ~~~~~~~~~~~~~i~G~~~~~~~l~~~~~~-~~~~~~~~~~~~~~~~~vll~G~~GtGKT~la~~la~~~~~~~~~i~~~   79 (257)
T 1lv7_A            1 MLTEDQIKTTFADVAGCDEAKEEVAELVEY-LREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGEAKVPFFTISGS   79 (257)
T ss_dssp             CEEECSSCCCGGGSCSCHHHHHHTHHHHHH-HHCGGGC-----CCCCEEEEECCTTSCHHHHHHHHHHHHTCCEEEECSC
T ss_pred             CCCccCCCCCHHHhcCcHHHHHHHHHHHHH-HhCHHHHHHcCCCCCCeEEEECcCCCCHHHHHHHHHHHcCCCEEEEeHH
Confidence            599999999999999999999988877653 2210     0112236799999999999999999999999999999876


Q ss_pred             CchhhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcch---------hHHHHHHH
Q 005987          213 TPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGR---------TAFERLRQ  283 (666)
Q Consensus       213 d~~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~---------~~~~~l~~  283 (666)
                      +...       ...|    .....+..+++.+...            .+.+++|||+|.+...         ........
T Consensus        80 ~~~~-------~~~~----~~~~~~~~~~~~a~~~------------~~~il~iDeid~l~~~~~~~~~~~~~~~~~~~~  136 (257)
T 1lv7_A           80 DFVE-------MFVG----VGASRVRDMFEQAKKA------------APCIIFIDEIDAVGRQRGAGLGGGHDEREQTLN  136 (257)
T ss_dssp             SSTT-------SCCC----CCHHHHHHHHHHHHTT------------CSEEEEETTHHHHTCCCSTTSCCTTCHHHHHHH
T ss_pred             HHHH-------Hhhh----hhHHHHHHHHHHHHHc------------CCeeehhhhhhhhccCCCCCcCCCchHHHHHHH
Confidence            5211       0111    1223455556655321            3579999999754221         11122222


Q ss_pred             HHHHHHhc--CCCceEEEEecCCCCCCccchhhhhhHHHHHHhh--cCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHH
Q 005987          284 CLLLLVRS--THIPTAVVLTECGKADSVDSTAQSFEELQSILVD--AGARKVALNPITNGSIKRTLSKICRQEQYSLSTE  359 (666)
Q Consensus       284 ~L~~l~~~--~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r--~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~  359 (666)
                      .+...+..  ...++++|++. +.....+          ..+.+  +....|.|.+|+.++..++|+..+....+. ++.
T Consensus       137 ~ll~~l~~~~~~~~~~vI~~t-n~~~~l~----------~~l~r~~rf~~~i~i~~P~~~~r~~il~~~~~~~~l~-~~~  204 (257)
T 1lv7_A          137 QMLVEMDGFEGNEGIIVIAAT-NRPDVLD----------PALLRPGRFDRQVVVGLPDVRGREQILKVHMRRVPLA-PDI  204 (257)
T ss_dssp             HHHHHHHTCCSSSCEEEEEEE-SCTTTSC----------GGGGSTTSSCEEEECCCCCHHHHHHHHHHHHTTSCBC-TTC
T ss_pred             HHHHHhhCcccCCCEEEEEee-CCchhCC----------HHHcCCCcCCeEEEeCCCCHHHHHHHHHHHHhcCCCC-ccc
Confidence            23333332  22334444433 2222111          11111  123578999999999999998877654322 223


Q ss_pred             HHHHHHHHcCC----cHHHHHHHHHHHh
Q 005987          360 QIDLVAQASGG----DIRQAITSLQFSS  383 (666)
Q Consensus       360 ~l~~Ia~~s~G----DIR~AIn~LQf~~  383 (666)
                      .+..++..+.|    |++.+++.....|
T Consensus       205 ~~~~la~~~~G~~~~dl~~l~~~a~~~a  232 (257)
T 1lv7_A          205 DAAIIARGTPGFSGADLANLVNEAALFA  232 (257)
T ss_dssp             CHHHHHHTCTTCCHHHHHHHHHHHHHHH
T ss_pred             cHHHHHHHcCCCCHHHHHHHHHHHHHHH
Confidence            36778888888    4555544444433

>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=99.58  E-value=1.3e-14  Score=155.37  Aligned_cols=223  Identities=16%  Similarity=0.245  Sum_probs=135.9

Q ss_pred             CCccccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc------CCcEEEE
Q 005987          136 QQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL------GARLYEW  209 (666)
Q Consensus       136 ~~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel------g~~viE~  209 (666)
                      ..+|..+|.|   ++++|+++.++.+..++..+...   .. .+.++|+|||||||||+++.+++++      +..++.+
T Consensus        10 ~~~l~~~~~p---~~~~gr~~e~~~l~~~l~~~~~~---~~-~~~vli~G~~G~GKTtl~~~l~~~~~~~~~~~~~~~~i   82 (386)
T 2qby_A           10 REYLLPDYIP---DELPHREDQIRKIASILAPLYRE---EK-PNNIFIYGLTGTGKTAVVKFVLSKLHKKFLGKFKHVYI   82 (386)
T ss_dssp             GGGGSSSCCC---SCCTTCHHHHHHHHHSSGGGGGT---CC-CCCEEEEECTTSSHHHHHHHHHHHHHHHTCSSCEEEEE
T ss_pred             hhhCCCccCC---CCCCChHHHHHHHHHHHHHHHcC---CC-CCeEEEECCCCCCHHHHHHHHHHHHHHHhcCCceEEEE
Confidence            4567788988   56799999999999999865432   22 2589999999999999999999998      8888888


Q ss_pred             cCCCchh----hhhhhhcccCCccc-c-chhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHH
Q 005987          210 DTPTPTI----WQEYMHNCKTGLEY-T-SKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQ  283 (666)
Q Consensus       210 nasd~~~----~~e~l~~~~~g~~~-~-s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~  283 (666)
                      ++.....    +...+......... . +..+.+..+...+...           +.+.||+|||++.+..... ..+..
T Consensus        83 ~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~~-----------~~~~vlilDE~~~l~~~~~-~~~l~  150 (386)
T 2qby_A           83 NTRQIDTPYRVLADLLESLDVKVPFTGLSIAELYRRLVKAVRDY-----------GSQVVIVLDEIDAFVKKYN-DDILY  150 (386)
T ss_dssp             EHHHHCSHHHHHHHHTTTTSCCCCSSSCCHHHHHHHHHHHHHTC-----------CSCEEEEEETHHHHHHSSC-STHHH
T ss_pred             ECCCCCCHHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHHhcc-----------CCeEEEEEcChhhhhccCc-CHHHH
Confidence            8643211    11111111000000 0 1111233333332211           2367999999987542100 01122


Q ss_pred             HHHHHHhc-CCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHh--CCCCCHHH
Q 005987          284 CLLLLVRS-THIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQE--QYSLSTEQ  360 (666)
Q Consensus       284 ~L~~l~~~-~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e--~i~v~~~~  360 (666)
                      .|...+.. ...++.+|++.... .   ........+.   ++.....|.|+|++.+++.++|...+...  ...+++++
T Consensus       151 ~l~~~~~~~~~~~~~~I~~~~~~-~---~~~~~~~~~~---~r~~~~~i~l~~l~~~~~~~il~~~~~~~~~~~~~~~~~  223 (386)
T 2qby_A          151 KLSRINSEVNKSKISFIGITNDV-K---FVDLLDPRVK---SSLSEEEIIFPPYNAEELEDILTKRAQMAFKPGVLPDNV  223 (386)
T ss_dssp             HHHHHHHSCCC--EEEEEEESCG-G---GGGGCTTHHH---HTTTTEEEEECCCCHHHHHHHHHHHHHHHBCSSCSCHHH
T ss_pred             HHhhchhhcCCCeEEEEEEECCC-C---hHhhhCHHHh---ccCCCeeEEeCCCCHHHHHHHHHHHHHhhccCCCCCHHH
Confidence            23333332 22234333333211 0   1111112222   23223689999999999999999988653  36789999


Q ss_pred             HHHHHHHcC---CcHHHHHHHHHHHhc
Q 005987          361 IDLVAQASG---GDIRQAITSLQFSSL  384 (666)
Q Consensus       361 l~~Ia~~s~---GDIR~AIn~LQf~~~  384 (666)
                      ++.|+..++   ||+|.+++.|+.++.
T Consensus       224 ~~~l~~~~~~~~G~~r~~~~ll~~a~~  250 (386)
T 2qby_A          224 IKLCAALAAREHGDARRALDLLRVSGE  250 (386)
T ss_dssp             HHHHHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHH
Confidence            999999988   999999998887653

>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=99.57  E-value=2.6e-14  Score=147.13  Aligned_cols=196  Identities=16%  Similarity=0.198  Sum_probs=120.9

Q ss_pred             ccccCHHHHHHHHHH---HHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCchhhhhhhhcccC
Q 005987          150 ELAVQRKKVEEVRAW---FEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTIWQEYMHNCKT  226 (666)
Q Consensus       150 eLvg~~k~i~el~~w---L~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~~~~e~l~~~~~  226 (666)
                      .++++...++.+...   +...+... +..+.+.+||+||||||||++|+++|++++..++.+++++.          ..
T Consensus        34 ~~i~~~~~~~~i~~~~~~l~~~l~~~-~~~~~~~vLl~G~~GtGKT~la~~ia~~~~~~~~~i~~~~~----------~~  102 (272)
T 1d2n_A           34 GIIKWGDPVTRVLDDGELLVQQTKNS-DRTPLVSVLLEGPPHSGKTALAAKIAEESNFPFIKICSPDK----------MI  102 (272)
T ss_dssp             CCCCCSHHHHHHHHHHHHHHHHHHHC-SSCSEEEEEEECSTTSSHHHHHHHHHHHHTCSEEEEECGGG----------CT
T ss_pred             CCCCccHHHHHHHHHHHHHHHHHhcc-CCCCCeEEEEECCCCCcHHHHHHHHHHHhCCCEEEEeCHHH----------hc
Confidence            356766666666553   22222211 22333789999999999999999999999999999987641          11


Q ss_pred             CccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcc-----hhHHHHHHHHHHHHHhcC---CCceEE
Q 005987          227 GLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNG-----RTAFERLRQCLLLLVRST---HIPTAV  298 (666)
Q Consensus       227 g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~-----~~~~~~l~~~L~~l~~~~---~~PiVi  298 (666)
                      |.........+...+..+..            ..+.+|+|||++.+.+     ......+.+.|..++...   ..++++
T Consensus       103 g~~~~~~~~~~~~~~~~~~~------------~~~~vl~iDEid~l~~~~~~~~~~~~~~l~~L~~~~~~~~~~~~~~~i  170 (272)
T 1d2n_A          103 GFSETAKCQAMKKIFDDAYK------------SQLSCVVVDDIERLLDYVPIGPRFSNLVLQALLVLLKKAPPQGRKLLI  170 (272)
T ss_dssp             TCCHHHHHHHHHHHHHHHHT------------SSEEEEEECCHHHHTTCBTTTTBCCHHHHHHHHHHTTCCCSTTCEEEE
T ss_pred             CCchHHHHHHHHHHHHHHHh------------cCCcEEEEEChhhhhccCCCChhHHHHHHHHHHHHhcCccCCCCCEEE
Confidence            21111222344445554422            1357999999986521     111234555566666542   234444


Q ss_pred             EEecCCCCCCccchhhhhhHHHH-HHhhcCeeEEEeCCCCH-HHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCC-----c
Q 005987          299 VLTECGKADSVDSTAQSFEELQS-ILVDAGARKVALNPITN-GSIKRTLSKICRQEQYSLSTEQIDLVAQASGG-----D  371 (666)
Q Consensus       299 Iit~~~~~~s~d~~~r~l~~L~s-~L~r~r~~~I~F~p~s~-~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~s~G-----D  371 (666)
                      |++. +..       .   .+.. .+.++.+..|.|++++. .++.+++.+    . ..++++.+..|+..+.|     |
T Consensus       171 i~tt-n~~-------~---~l~~~~l~~rf~~~i~~p~l~~r~~i~~i~~~----~-~~~~~~~~~~l~~~~~g~~~~g~  234 (272)
T 1d2n_A          171 IGTT-SRK-------D---VLQEMEMLNAFSTTIHVPNIATGEQLLEALEL----L-GNFKDKERTTIAQQVKGKKVWIG  234 (272)
T ss_dssp             EEEE-SCH-------H---HHHHTTCTTTSSEEEECCCEEEHHHHHHHHHH----H-TCSCHHHHHHHHHHHTTSEEEEC
T ss_pred             EEec-CCh-------h---hcchhhhhcccceEEcCCCccHHHHHHHHHHh----c-CCCCHHHHHHHHHHhcCCCcccc
Confidence            4443 211       1   1222 22222378899998887 666655543    2 25789999999999988     9


Q ss_pred             HHHHHHHHHHHhc
Q 005987          372 IRQAITSLQFSSL  384 (666)
Q Consensus       372 IR~AIn~LQf~~~  384 (666)
                      +|.++|.++.+..
T Consensus       235 ir~l~~~l~~a~~  247 (272)
T 1d2n_A          235 IKKLLMLIEMSLQ  247 (272)
T ss_dssp             HHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHhh
Confidence            9999999999864

>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=99.56  E-value=3e-14  Score=157.08  Aligned_cols=200  Identities=20%  Similarity=0.237  Sum_probs=127.2

Q ss_pred             Cccccc-c--CHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc-----CCcEEEEcCCCchhhh
Q 005987          147 SLEELA-V--QRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL-----GARLYEWDTPTPTIWQ  218 (666)
Q Consensus       147 sl~eLv-g--~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel-----g~~viE~nasd~~~~~  218 (666)
                      +|++++ |  +......+..+.+.     ++.  .+.++|+|||||||||+++++|+++     +..++.+++.+.  ..
T Consensus       103 tfd~fv~g~~n~~a~~~~~~~a~~-----~~~--~~~lll~Gp~G~GKTtLa~aia~~l~~~~~~~~v~~v~~~~~--~~  173 (440)
T 2z4s_A          103 TFENFVVGPGNSFAYHAALEVAKH-----PGR--YNPLFIYGGVGLGKTHLLQSIGNYVVQNEPDLRVMYITSEKF--LN  173 (440)
T ss_dssp             SGGGCCCCTTTHHHHHHHHHHHHS-----TTS--SCCEEEECSSSSSHHHHHHHHHHHHHHHCCSSCEEEEEHHHH--HH
T ss_pred             ChhhcCCCCchHHHHHHHHHHHhC-----CCC--CCeEEEECCCCCCHHHHHHHHHHHHHHhCCCCeEEEeeHHHH--HH
Confidence            788887 4  44445555554443     122  3689999999999999999999998     788888775431  11


Q ss_pred             hhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcch-hHHHHHHHHHHHHHhcCCCceE
Q 005987          219 EYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGR-TAFERLRQCLLLLVRSTHIPTA  297 (666)
Q Consensus       219 e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~-~~~~~l~~~L~~l~~~~~~PiV  297 (666)
                      +.......+        ....|...   +.          ..+.||||||++.+... .....+...+..+.+.+ . .|
T Consensus       174 ~~~~~~~~~--------~~~~~~~~---~~----------~~~~vL~IDEi~~l~~~~~~q~~l~~~l~~l~~~~-~-~i  230 (440)
T 2z4s_A          174 DLVDSMKEG--------KLNEFREK---YR----------KKVDILLIDDVQFLIGKTGVQTELFHTFNELHDSG-K-QI  230 (440)
T ss_dssp             HHHHHHHTT--------CHHHHHHH---HT----------TTCSEEEEECGGGGSSCHHHHHHHHHHHHHHHTTT-C-EE
T ss_pred             HHHHHHHcc--------cHHHHHHH---hc----------CCCCEEEEeCcccccCChHHHHHHHHHHHHHHHCC-C-eE
Confidence            111000000        01112221   11          02459999999987653 23344444455544433 2 34


Q ss_pred             EEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCcHHHHHH
Q 005987          298 VVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASGGDIRQAIT  377 (666)
Q Consensus       298 iIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~s~GDIR~AIn  377 (666)
                      +++++... ..   .....+.|.+.+..  ...+.|.+|+.+++..+|.+.+..+++.+++++++.|+..+.||+|.+.+
T Consensus       231 Iitt~~~~-~~---l~~l~~~L~sR~~~--g~~i~l~~p~~e~r~~iL~~~~~~~~~~i~~e~l~~la~~~~gn~R~l~~  304 (440)
T 2z4s_A          231 VICSDREP-QK---LSEFQDRLVSRFQM--GLVAKLEPPDEETRKSIARKMLEIEHGELPEEVLNFVAENVDDNLRRLRG  304 (440)
T ss_dssp             EEEESSCG-GG---CSSCCHHHHHHHHS--SBCCBCCCCCHHHHHHHHHHHHHHHTCCCCTTHHHHHHHHCCSCHHHHHH
T ss_pred             EEEECCCH-HH---HHHHHHHHHhhccC--CeEEEeCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHH
Confidence            44444211 10   01122334443321  26789999999999999999999999999999999999999999999999


Q ss_pred             HHHHHhc
Q 005987          378 SLQFSSL  384 (666)
Q Consensus       378 ~LQf~~~  384 (666)
                      .|+.++.
T Consensus       305 ~L~~~~~  311 (440)
T 2z4s_A          305 AIIKLLV  311 (440)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            9987764

>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=99.56  E-value=4.5e-14  Score=148.11  Aligned_cols=168  Identities=9%  Similarity=0.092  Sum_probs=114.9

Q ss_pred             cCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc------CCcEEEEcCCCchhhhhhhhcccC
Q 005987          153 VQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL------GARLYEWDTPTPTIWQEYMHNCKT  226 (666)
Q Consensus       153 g~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel------g~~viE~nasd~~~~~e~l~~~~~  226 (666)
                      ||++.++.++..++.      ++ . +++||+||||+|||++++++|+.+      ..+++++++.+.            
T Consensus         1 g~~~~~~~L~~~i~~------~~-~-~~~Lf~Gp~G~GKtt~a~~la~~~~~~~~~~~d~~~l~~~~~------------   60 (305)
T 2gno_A            1 GAKDQLETLKRIIEK------SE-G-ISILINGEDLSYPREVSLELPEYVEKFPPKASDVLEIDPEGE------------   60 (305)
T ss_dssp             ---CHHHHHHHHHHT------CS-S-EEEEEECSSSSHHHHHHHHHHHHHHTSCCCTTTEEEECCSSS------------
T ss_pred             ChHHHHHHHHHHHHC------CC-C-cEEEEECCCCCCHHHHHHHHHHhCchhhccCCCEEEEcCCcC------------
Confidence            577888888888876      55 2 589999999999999999999974      346677765420            


Q ss_pred             CccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcCCCce-EEEEecCCC
Q 005987          227 GLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHIPT-AVVLTECGK  305 (666)
Q Consensus       227 g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~~~Pi-ViIit~~~~  305 (666)
                          ....+.++++++.+...+.     .   ...+|+||||++.+...     .+++|+.+++.....+ +|++++ + 
T Consensus        61 ----~~~id~ir~li~~~~~~p~-----~---~~~kvviIdead~lt~~-----a~naLLk~LEep~~~t~fIl~t~-~-  121 (305)
T 2gno_A           61 ----NIGIDDIRTIKDFLNYSPE-----L---YTRKYVIVHDCERMTQQ-----AANAFLKALEEPPEYAVIVLNTR-R-  121 (305)
T ss_dssp             ----CBCHHHHHHHHHHHTSCCS-----S---SSSEEEEETTGGGBCHH-----HHHHTHHHHHSCCTTEEEEEEES-C-
T ss_pred             ----CCCHHHHHHHHHHHhhccc-----c---CCceEEEeccHHHhCHH-----HHHHHHHHHhCCCCCeEEEEEEC-C-
Confidence                1234566777776643221     1   23579999999988643     2345777777654333 344443 1 


Q ss_pred             CCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCcHHHHHHHHHH
Q 005987          306 ADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASGGDIRQAITSLQF  381 (666)
Q Consensus       306 ~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~s~GDIR~AIn~LQf  381 (666)
                            ..+.++.+++     |  .+.|.+++.+++.+.|.+++     .++++++    ..+.||+|.|+|.||-
T Consensus       122 ------~~kl~~tI~S-----R--~~~f~~l~~~~i~~~L~~~~-----~i~~~~~----~~~~g~~~~al~~l~~  175 (305)
T 2gno_A          122 ------WHYLLPTIKS-----R--VFRVVVNVPKEFRDLVKEKI-----GDLWEEL----PLLERDFKTALEAYKL  175 (305)
T ss_dssp             ------GGGSCHHHHT-----T--SEEEECCCCHHHHHHHHHHH-----TTHHHHC----GGGGTCHHHHHHHHHH
T ss_pred             ------hHhChHHHHc-----e--eEeCCCCCHHHHHHHHHHHh-----CCCHHHH----HHHCCCHHHHHHHHHH
Confidence                  2244444443     4  89999999999999999988     2566665    4468999999999873

>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=99.55  E-value=1.8e-13  Score=142.56  Aligned_cols=209  Identities=15%  Similarity=0.193  Sum_probs=127.9

Q ss_pred             ccccCHHHHHHHHHHHHHhhcCC-------CCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCchhhhhhhh
Q 005987          150 ELAVQRKKVEEVRAWFEERLGDS-------KDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTIWQEYMH  222 (666)
Q Consensus       150 eLvg~~k~i~el~~wL~~~~~~~-------~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~~~~e~l~  222 (666)
                      +++|++..++.|...+.......       .+.. ++.+||+||||||||++|+++|+.++..++.+++++...      
T Consensus        16 ~i~G~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~-~~~vll~G~~GtGKT~la~~la~~l~~~~~~i~~~~~~~------   88 (310)
T 1ofh_A           16 HIIGQADAKRAVAIALRNRWRRMQLQEPLRHEVT-PKNILMIGPTGVGKTEIARRLAKLANAPFIKVEATKFTE------   88 (310)
T ss_dssp             TCCSCHHHHHHHHHHHHHHHHTTSSCHHHHHHCC-CCCEEEECCTTSSHHHHHHHHHHHHTCCEEEEEGGGGSS------
T ss_pred             hcCChHHHHHHHHHHHHHHHhhhhhcccccccCC-CceEEEECCCCCCHHHHHHHHHHHhCCCEEEEcchhccc------
Confidence            47999999999998887532110       0112 267999999999999999999999999999998764210      


Q ss_pred             cccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchh-------HHHHHHHHHHHHHhcCC--
Q 005987          223 NCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRT-------AFERLRQCLLLLVRSTH--  293 (666)
Q Consensus       223 ~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~-------~~~~l~~~L~~l~~~~~--  293 (666)
                         .+..-......+..++..+..  .+    . ....+.||+|||++.+....       ....+++.|..+++...  
T Consensus        89 ---~~~~~~~~~~~~~~~~~~~~~--~~----~-~~~~~~vl~iDEi~~l~~~~~~~~~~~~~~~~~~~Ll~~le~~~~~  158 (310)
T 1ofh_A           89 ---VGYVGKEVDSIIRDLTDSAGG--AI----D-AVEQNGIVFIDEIDKICKKGEYSGADVSREGVQRDLLPLVEGSTVS  158 (310)
T ss_dssp             ---CCSGGGSTTHHHHHHHHTTTT--CH----H-HHHHHCEEEEECGGGGSCCSSCCSSHHHHHHHHHHHHHHHHCCEEE
T ss_pred             ---CCccCccHHHHHHHHHHHhhH--HH----h-hccCCCEEEEEChhhcCccccccccchhHHHHHHHHHHHhcCCeEe
Confidence               010000111123333321100  00    0 00124599999999875321       11223455666666531  


Q ss_pred             --------CceEEEEecCCCCCCccchhhhhhHHHHHHhhcCe-eEEEeCCCCHHHHHHHHHH-----------HHHHhC
Q 005987          294 --------IPTAVVLTECGKADSVDSTAQSFEELQSILVDAGA-RKVALNPITNGSIKRTLSK-----------ICRQEQ  353 (666)
Q Consensus       294 --------~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~-~~I~F~p~s~~~i~kiL~~-----------I~~~e~  353 (666)
                              ..+++|++......   ......   ..+++|  + ..|.|++++.+++.++|++           .+..++
T Consensus       159 ~~~~~~~~~~~~~i~~~~~~~~---~~~~l~---~~l~~R--~~~~i~~~~~~~~~~~~il~~~~~~~~~~~~~~~~~~~  230 (310)
T 1ofh_A          159 TKHGMVKTDHILFIASGAFQVA---RPSDLI---PELQGR--LPIRVELTALSAADFERILTEPHASLTEQYKALMATEG  230 (310)
T ss_dssp             ETTEEEECTTCEEEEEECCSSS---CGGGSC---HHHHHT--CCEEEECCCCCHHHHHHHHHSSTTCHHHHHHHHHHHTT
T ss_pred             cccccccCCcEEEEEcCCcccC---CcccCC---HHHHhh--CCceEEcCCcCHHHHHHHHHhhHHHHHHHHHHHHHhcC
Confidence                    23455554311000   011111   233333  5 5699999999999999882           333344


Q ss_pred             --CCCCHHHHHHHHHHc--------CCcHHHHHHHHHHHh
Q 005987          354 --YSLSTEQIDLVAQAS--------GGDIRQAITSLQFSS  383 (666)
Q Consensus       354 --i~v~~~~l~~Ia~~s--------~GDIR~AIn~LQf~~  383 (666)
                        +.+++++++.|+..+        .||+|.+.+.|+.+.
T Consensus       231 ~~~~~~~~a~~~l~~~~~~~~~~~~~g~~R~l~~~l~~~~  270 (310)
T 1ofh_A          231 VNIAFTTDAVKKIAEAAFRVNEKTENIGARRLHTVMERLM  270 (310)
T ss_dssp             CEEEECHHHHHHHHHHHHHHHHHSCCCTTHHHHHHHHHHS
T ss_pred             CeeccCHHHHHHHHHHhhhhcccccccCcHHHHHHHHHHH
Confidence              368999999999998        899999999998865

>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=99.53  E-value=2.9e-14  Score=149.27  Aligned_cols=211  Identities=14%  Similarity=0.193  Sum_probs=128.9

Q ss_pred             ccccCCCCccccccCHHHHHHHHHHHHHhhcCC-----CCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCc
Q 005987          140 AEKYKPRSLEELAVQRKKVEEVRAWFEERLGDS-----KDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTP  214 (666)
Q Consensus       140 ~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~-----~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~  214 (666)
                      +.++.+.++++|+|.+..+++|+.++...+...     -+..+++.+||+||||||||++|+++|++++..++.+++++.
T Consensus         6 ~~~~~~~~~~di~G~~~~~~~l~~~v~~~~~~~~~~~~~~~~~~~~vLL~Gp~GtGKT~la~ala~~~~~~~i~v~~~~l   85 (301)
T 3cf0_A            6 VVEVPQVTWEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANECQANFISIKGPEL   85 (301)
T ss_dssp             CEECCCCCGGGSCSCHHHHHHHHHHHHHHHHCHHHHHHHCCCCCSEEEEECSSSSSHHHHHHHHHHHTTCEEEEECHHHH
T ss_pred             cccCCCCCHHHhCCHHHHHHHHHHHHHHHhhCHHHHHHcCCCCCceEEEECCCCcCHHHHHHHHHHHhCCCEEEEEhHHH
Confidence            345677899999999999999999987422110     022334789999999999999999999999999999886531


Q ss_pred             hhhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchh---------HHHHHHHHH
Q 005987          215 TIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRT---------AFERLRQCL  285 (666)
Q Consensus       215 ~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~---------~~~~l~~~L  285 (666)
                        .....     |.    ....+..++..+...            .+.||+|||+|.+....         ...++...|
T Consensus        86 --~~~~~-----g~----~~~~~~~~f~~a~~~------------~p~il~iDEid~l~~~~~~~~~~~~~~~~~~~~~l  142 (301)
T 3cf0_A           86 --LTMWF-----GE----SEANVREIFDKARQA------------APCVLFFDELDSIAKARGGNIGDGGGAADRVINQI  142 (301)
T ss_dssp             --HHHHH-----TT----CTTHHHHHHHHHHHT------------CSEEEEECSTTHHHHHHTTTTCCSSCSCCHHHHHH
T ss_pred             --Hhhhc-----Cc----hHHHHHHHHHHHHhc------------CCeEEEEEChHHHhhccCCCcCCcchHHHHHHHHH
Confidence              11111     11    112345556655432            35799999999653210         011223334


Q ss_pred             HHHHhcC--CCceEEEEecCCCCCCccchhhhhhHHHHHHhhcC-eeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHH
Q 005987          286 LLLVRST--HIPTAVVLTECGKADSVDSTAQSFEELQSILVDAG-ARKVALNPITNGSIKRTLSKICRQEQYSLSTEQID  362 (666)
Q Consensus       286 ~~l~~~~--~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r-~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~  362 (666)
                      +..++..  ...+++|++. +.....|         ..+++..| ...|.|.+|+..+..++|+..+...++. .+..++
T Consensus       143 L~~l~~~~~~~~v~vi~at-n~~~~ld---------~al~r~gRf~~~i~i~~p~~~~r~~il~~~l~~~~~~-~~~~~~  211 (301)
T 3cf0_A          143 LTEMDGMSTKKNVFIIGAT-NRPDIID---------PAILRPGRLDQLIYIPLPDEKSRVAILKANLRKSPVA-KDVDLE  211 (301)
T ss_dssp             HHHHHSSCTTSSEEEEEEE-SCGGGSC---------GGGGSTTSSCEEEECCCCCHHHHHHHHHHHHTTSCBC-SSCCHH
T ss_pred             HHHhhcccCCCCEEEEEec-CCccccC---------hHHhcCCccceEEecCCcCHHHHHHHHHHHHccCCCC-ccchHH
Confidence            4444421  2234444333 2221111         11222112 3579999999999999999988776543 122345


Q ss_pred             HHHHHc----CCcHHHHHHHHHHHhc
Q 005987          363 LVAQAS----GGDIRQAITSLQFSSL  384 (666)
Q Consensus       363 ~Ia~~s----~GDIR~AIn~LQf~~~  384 (666)
                      .|+..+    ++||+.+++...+.+.
T Consensus       212 ~la~~~~g~sg~dl~~l~~~a~~~a~  237 (301)
T 3cf0_A          212 FLAKMTNGFSGADLTEICQRACKLAI  237 (301)
T ss_dssp             HHHHTCSSCCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHcCCCCHHHHHHHHHHHHHHHH
Confidence            566553    4588888877666654

>3pxg_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 3.65A {Bacillus subtilis}

Probab=99.53  E-value=1.3e-14  Score=161.21  Aligned_cols=199  Identities=19%  Similarity=0.210  Sum_probs=130.9

Q ss_pred             CCCCccccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc----------C
Q 005987          134 STQQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL----------G  203 (666)
Q Consensus       134 ~~~~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel----------g  203 (666)
                      .....|+++|+|.++++++|+++.++.+..++..      ..  .+.+||+||||||||++|+++|+.+          +
T Consensus       165 ~~~~~l~~~~r~~~ld~iiGr~~~i~~l~~~l~r------~~--~~~~LL~G~pG~GKT~la~~la~~l~~~~~p~~l~~  236 (468)
T 3pxg_A          165 SLARDLTAIAKEDSLDPVIGRSKEIQRVIEVLSR------RT--KNNPVLIGEPGVGKTAIAEGLAQQIINNEVPEILRD  236 (468)
T ss_dssp             SSCCBHHHHTTSSCSCCCCCCHHHHHHHHHHHHC------SS--SCEEEEESCTTTTTHHHHHHHHHHHHSSCSCTTTSS
T ss_pred             HHHHHHHHHHhcCCCCCccCcHHHHHHHHHHHhc------cC--CCCeEEECCCCCCHHHHHHHHHHHHHhCCCChhhcC
Confidence            3567899999999999999999999999998875      11  2578999999999999999999997          6


Q ss_pred             CcEEEEcCCCchhhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHH
Q 005987          204 ARLYEWDTPTPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQ  283 (666)
Q Consensus       204 ~~viE~nasd~~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~  283 (666)
                      ..++.+++..          ...|.    ....+..++..+...            .+.|||||   .  ..    ...+
T Consensus       237 ~~~~~l~~~~----------~~~g~----~e~~~~~~~~~~~~~------------~~~iLfiD---~--~~----~a~~  281 (468)
T 3pxg_A          237 KRVMTLDMGT----------KYRGE----FEDRLKKVMDEIRQA------------GNIILFID---A--AI----DASN  281 (468)
T ss_dssp             CCEECC------------------------CTTHHHHHHHHHTC------------CCCEEEEC---C------------
T ss_pred             CeEEEeeCCc----------cccch----HHHHHHHHHHHHHhc------------CCeEEEEe---C--ch----hHHH
Confidence            6677666541          00111    112345566665432            24699999   1  11    1223


Q ss_pred             HHHHHHhcCCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHH----hCCCCCHH
Q 005987          284 CLLLLVRSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQ----EQYSLSTE  359 (666)
Q Consensus       284 ~L~~l~~~~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~----e~i~v~~~  359 (666)
                      .|...+..+.  +.+|++. +...    +.+.+. +...+.+ ||..|.|.+|+.+++..+|+.++..    .++.++++
T Consensus       282 ~L~~~L~~g~--v~vI~at-~~~e----~~~~~~-~~~al~~-Rf~~i~v~~p~~e~~~~iL~~~~~~~~~~~~~~i~~~  352 (468)
T 3pxg_A          282 ILKPSLARGE--LQCIGAT-TLDE----YRKYIE-KDAALER-RFQPIQVDQPSVDESIQILQGLRDRYEAHHRVSITDD  352 (468)
T ss_dssp             --CCCTTSSS--CEEEEEC-CTTT----THHHHT-TCSHHHH-SEEEEECCCCCHHHHHHHHHHTTTTSGGGSSCSCCHH
T ss_pred             HHHHhhcCCC--EEEEecC-CHHH----HHHHhh-cCHHHHH-hCccceeCCCCHHHHHHHHHHHHHHHHHhcCCCCCHH
Confidence            3444445443  3333332 2211    111121 2222333 6889999999999999999998876    67889999


Q ss_pred             HHHHHHHHcCCcH------HHHHHHHHHHhc
Q 005987          360 QIDLVAQASGGDI------RQAITSLQFSSL  384 (666)
Q Consensus       360 ~l~~Ia~~s~GDI------R~AIn~LQf~~~  384 (666)
                      ++..++..+.+.+      +.||+.|.-++.
T Consensus       353 al~~l~~~s~~~~~~~~lp~~ai~ll~~a~~  383 (468)
T 3pxg_A          353 AIEAAVKLSDRYISDRFLPDKAIDLIDEAGS  383 (468)
T ss_dssp             HHHHHHHHHHHSSCCSCTTHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhccCcCCcHHHHHHHHHHH
Confidence            9999999877655      468888877663

>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=99.51  E-value=8.1e-14  Score=165.89  Aligned_cols=211  Identities=17%  Similarity=0.155  Sum_probs=134.6

Q ss_pred             CCCccccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc----------CC
Q 005987          135 TQQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL----------GA  204 (666)
Q Consensus       135 ~~~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel----------g~  204 (666)
                      ....|+++|+|.++++++|+++.++.+..++..      +.  .+.+||+||||||||++|+.+|+.+          +.
T Consensus       156 ~~~~l~~~~r~~~ld~viGr~~~i~~l~~~l~~------~~--~~~vlL~G~pG~GKT~la~~la~~l~~~~~p~~l~~~  227 (854)
T 1qvr_A          156 YGIDLTRLAAEGKLDPVIGRDEEIRRVIQILLR------RT--KNNPVLIGEPGVGKTAIVEGLAQRIVKGDVPEGLKGK  227 (854)
T ss_dssp             HEEEHHHHHHTTCSCCCCSCHHHHHHHHHHHHC------SS--CCCCEEEECTTSCHHHHHHHHHHHHHHTCSCTTSTTC
T ss_pred             HHHhHHHHHhcCCCcccCCcHHHHHHHHHHHhc------CC--CCceEEEcCCCCCHHHHHHHHHHHHhcCCCchhhcCC
Confidence            346799999999999999999999999998864      22  1468999999999999999999998          78


Q ss_pred             cEEEEcCCCchhhhhhhhcccCCccc-cchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHH---HH
Q 005987          205 RLYEWDTPTPTIWQEYMHNCKTGLEY-TSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAF---ER  280 (666)
Q Consensus       205 ~viE~nasd~~~~~e~l~~~~~g~~~-~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~---~~  280 (666)
                      .++.++.+..          ..|..+ ......+..++..+...           ..+.||+|||++.+.+....   ..
T Consensus       228 ~~~~l~~~~l----------~~g~~~~g~~~~~l~~~~~~~~~~-----------~~~~iL~IDEi~~l~~~~~~~g~~~  286 (854)
T 1qvr_A          228 RIVSLQMGSL----------LAGAKYRGEFEERLKAVIQEVVQS-----------QGEVILFIDELHTVVGAGKAEGAVD  286 (854)
T ss_dssp             EEEEECC---------------------CHHHHHHHHHHHHHTT-----------CSSEEEEECCC--------------
T ss_pred             eEEEeehHHh----------hccCccchHHHHHHHHHHHHHHhc-----------CCCeEEEEecHHHHhccCCccchHH
Confidence            8888876541          112222 12233456666666432           13579999999987532111   12


Q ss_pred             HHHHHHHHHhcCCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHH----hCCCC
Q 005987          281 LRQCLLLLVRSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQ----EQYSL  356 (666)
Q Consensus       281 l~~~L~~l~~~~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~----e~i~v  356 (666)
                      +.+.|..++..+...+|..++. .      ...+ +. +...|.+ |+..|.|.+|+.+++..+|+.++..    .++.+
T Consensus       287 ~~~~L~~~l~~~~i~~I~at~~-~------~~~~-~~-~d~aL~r-Rf~~i~l~~p~~~e~~~iL~~~~~~~~~~~~~~i  356 (854)
T 1qvr_A          287 AGNMLKPALARGELRLIGATTL-D------EYRE-IE-KDPALER-RFQPVYVDEPTVEETISILRGLKEKYEVHHGVRI  356 (854)
T ss_dssp             -----HHHHHTTCCCEEEEECH-H------HHHH-HT-TCTTTCS-CCCCEEECCCCHHHHHHHHHHHHHHHHHHTTCEE
T ss_pred             HHHHHHHHHhCCCeEEEEecCc-h------HHhh-hc-cCHHHHh-CCceEEeCCCCHHHHHHHHHhhhhhhhhhcCCCC
Confidence            3345666676665543332221 0      0111 11 1223333 5778999999999999999887764    47889


Q ss_pred             CHHHHHHHHHHcCCc------HHHHHHHHHHHhc
Q 005987          357 STEQIDLVAQASGGD------IRQAITSLQFSSL  384 (666)
Q Consensus       357 ~~~~l~~Ia~~s~GD------IR~AIn~LQf~~~  384 (666)
                      +++++..++..+.|.      .+.|+..+.-++.
T Consensus       357 ~~~al~~~~~ls~r~i~~~~lp~kai~lldea~a  390 (854)
T 1qvr_A          357 SDSAIIAAATLSHRYITERRLPDKAIDLIDEAAA  390 (854)
T ss_dssp             CHHHHHHHHHHHHHHCCSSCTHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHhhhcccccChHHHHHHHHHHHH
Confidence            999999999987654      5677777765543

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20

Probab=99.50  E-value=4.1e-14  Score=135.68  Aligned_cols=172  Identities=19%  Similarity=0.208  Sum_probs=105.6

Q ss_pred             CCccccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc----------CCc
Q 005987          136 QQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL----------GAR  205 (666)
Q Consensus       136 ~~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel----------g~~  205 (666)
                      ..+|.++|+|.++++++|+++.++.+..++..      +.  .+.++|+||||||||++++.+|+++          +..
T Consensus         9 ~~~l~~~~~~~~~~~~~g~~~~~~~l~~~l~~------~~--~~~~ll~G~~G~GKT~l~~~~~~~~~~~~~~~~~~~~~   80 (195)
T 1jbk_A            9 TIDLTERAEQGKLDPVIGRDEEIRRTIQVLQR------RT--KNNPVLIGEPGVGKTAIVEGLAQRIINGEVPEGLKGRR   80 (195)
T ss_dssp             EEEHHHHHHTTCSCCCCSCHHHHHHHHHHHTS------SS--SCEEEEECCTTSCHHHHHHHHHHHHHHTCSCGGGTTCE
T ss_pred             hHHHHHHHhhccccccccchHHHHHHHHHHhc------CC--CCceEEECCCCCCHHHHHHHHHHHHHhCCCchhhcCCc
Confidence            35799999999999999999999999988764      22  2579999999999999999999997          566


Q ss_pred             EEEEcCCCchhhhhhhhcccCCccc-cchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHH---HHH
Q 005987          206 LYEWDTPTPTIWQEYMHNCKTGLEY-TSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAF---ERL  281 (666)
Q Consensus       206 viE~nasd~~~~~e~l~~~~~g~~~-~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~---~~l  281 (666)
                      ++.++....          ..+..+ ......+..++..+...           ..+.||+|||++.+......   ..+
T Consensus        81 ~~~~~~~~~----------~~~~~~~~~~~~~~~~~~~~~~~~-----------~~~~vl~iDe~~~l~~~~~~~~~~~~  139 (195)
T 1jbk_A           81 VLALDMGAL----------VAGAKYRGEFEERLKGVLNDLAKQ-----------EGNVILFIDELHTMVGAGKADGAMDA  139 (195)
T ss_dssp             EEEECHHHH----------HTTTCSHHHHHHHHHHHHHHHHHS-----------TTTEEEEEETGGGGTT------CCCC
T ss_pred             EEEeeHHHH----------hccCCccccHHHHHHHHHHHHhhc-----------CCCeEEEEeCHHHHhccCcccchHHH
Confidence            666654220          011111 11122344455444322           13579999999987532100   112


Q ss_pred             HHHHHHHHhcCCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHH
Q 005987          282 RQCLLLLVRSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTL  345 (666)
Q Consensus       282 ~~~L~~l~~~~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL  345 (666)
                      .+.|..+++..+..+|++++..       .....+ .+...+.+ |+..|.|.+|+.+++.++|
T Consensus       140 ~~~l~~~~~~~~~~~i~~~~~~-------~~~~~~-~~~~~l~~-r~~~i~~~~p~~~~~~~il  194 (195)
T 1jbk_A          140 GNMLKPALARGELHCVGATTLD-------EYRQYI-EKDAALER-RFQKVFVAEPSVEDTIAIL  194 (195)
T ss_dssp             HHHHHHHHHTTSCCEEEEECHH-------HHHHHT-TTCHHHHT-TEEEEECCCCCHHHHHTTC
T ss_pred             HHHHHHhhccCCeEEEEeCCHH-------HHHHHH-hcCHHHHH-HhceeecCCCCHHHHHHHh
Confidence            3345555665554443333220       001111 11222323 5778999999999887654

>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=99.49  E-value=6e-13  Score=147.31  Aligned_cols=211  Identities=14%  Similarity=0.251  Sum_probs=128.0

Q ss_pred             ccccc-cCCCCccccccCHHHHHHHHHHHHHhhc-----CCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcC
Q 005987          138 LWAEK-YKPRSLEELAVQRKKVEEVRAWFEERLG-----DSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDT  211 (666)
Q Consensus       138 ~W~eK-Y~P~sl~eLvg~~k~i~el~~wL~~~~~-----~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~na  211 (666)
                      +|.+. ..+.+|+||+|.+..++++++.+.....     ......+ +.+||+||||||||++++++|.+++..++.++.
T Consensus         4 ~~~~~~~~~~~f~di~G~~~~~~~l~e~v~~l~~~~~~~~~g~~~p-~gvLL~GppGtGKT~Laraia~~~~~~f~~is~   82 (476)
T 2ce7_A            4 MYKPSGNKRVTFKDVGGAEEAIEELKEVVEFLKDPSKFNRIGARMP-KGILLVGPPGTGKTLLARAVAGEANVPFFHISG   82 (476)
T ss_dssp             -CCCCCSCCCCGGGCCSCHHHHHHHHHHHHHHHCTHHHHTTTCCCC-SEEEEECCTTSSHHHHHHHHHHHHTCCEEEEEG
T ss_pred             eeccCCCCCCCHHHhCCcHHHHHHHHHHHHHhhChHHHhhcCCCCC-CeEEEECCCCCCHHHHHHHHHHHcCCCeeeCCH
Confidence            35555 4556899999999999999888764211     1112333 679999999999999999999999999999887


Q ss_pred             CCchhhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchh---------HHHHHH
Q 005987          212 PTPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRT---------AFERLR  282 (666)
Q Consensus       212 sd~~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~---------~~~~l~  282 (666)
                      ++...       ...|    .....++..+.++...            .+.||||||+|.+....         ......
T Consensus        83 ~~~~~-------~~~g----~~~~~~r~lf~~A~~~------------~p~ILfIDEid~l~~~r~~~~~g~~~~~~~~l  139 (476)
T 2ce7_A           83 SDFVE-------LFVG----VGAARVRDLFAQAKAH------------APCIVFIDEIDAVGRHRGAGLGGGHDEREQTL  139 (476)
T ss_dssp             GGTTT-------CCTT----HHHHHHHHHHHHHHHT------------CSEEEEEETGGGTCCC---------CHHHHHH
T ss_pred             HHHHH-------HHhc----ccHHHHHHHHHHHHhc------------CCCEEEEechhhhhhhcccccCcCcHHHHHHH
Confidence            64210       1111    1233456666666432            36799999999764321         111222


Q ss_pred             HHHHHHHhc--CCCceEEEEecCCCCCCccchhhhhhHHHHHHhh-cC-eeEEEeCCCCHHHHHHHHHHHHHHhCCCCCH
Q 005987          283 QCLLLLVRS--THIPTAVVLTECGKADSVDSTAQSFEELQSILVD-AG-ARKVALNPITNGSIKRTLSKICRQEQYSLST  358 (666)
Q Consensus       283 ~~L~~l~~~--~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r-~r-~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~  358 (666)
                      ..|+..++.  ....+++|+++ +..+.          +...+.+ -| -..|.|.+|+..+..++|+..+....+. ++
T Consensus       140 ~~LL~~ld~~~~~~~viVIaaT-n~~~~----------Ld~allR~gRFd~~i~i~~Pd~~~R~~Il~~~~~~~~l~-~~  207 (476)
T 2ce7_A          140 NQLLVEMDGFDSKEGIIVMAAT-NRPDI----------LDPALLRPGRFDKKIVVDPPDMLGRKKILEIHTRNKPLA-ED  207 (476)
T ss_dssp             HHHHHHHHHSCGGGTEEEEEEE-SCGGG----------SCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHHTTSCBC-TT
T ss_pred             HHHHHHHhccCCCCCEEEEEec-CChhh----------hchhhcccCcceeEeecCCCCHHHHHHHHHHHHHhCCCc-ch
Confidence            223333331  12234444433 22211          1111211 12 3478999999999999998777654332 22


Q ss_pred             HHHHHHHHHcCC----cHHHHHHHHHHHhc
Q 005987          359 EQIDLVAQASGG----DIRQAITSLQFSSL  384 (666)
Q Consensus       359 ~~l~~Ia~~s~G----DIR~AIn~LQf~~~  384 (666)
                      ..+..|+..+.|    ||+.+++..-..+.
T Consensus       208 v~l~~la~~t~G~sgadL~~lv~~Aal~A~  237 (476)
T 2ce7_A          208 VNLEIIAKRTPGFVGADLENLVNEAALLAA  237 (476)
T ss_dssp             CCHHHHHHTCTTCCHHHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHhcCCCcHHHHHHHHHHHHHHHH
Confidence            237778888777    56666665555443

>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=99.46  E-value=2.3e-13  Score=151.52  Aligned_cols=204  Identities=17%  Similarity=0.236  Sum_probs=129.4

Q ss_pred             cccCCCCccccccCHHHHHHHHHHHHHhhcCC-----CCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCch
Q 005987          141 EKYKPRSLEELAVQRKKVEEVRAWFEERLGDS-----KDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPT  215 (666)
Q Consensus       141 eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~-----~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~  215 (666)
                      +.+.+.++++|+|.+..+++|++++...+...     -|..+++.+||+||||||||++|+++|++++..++.+++++..
T Consensus       196 ~~~~~~~~~~i~G~~~~~~~l~~~i~~~l~~~~~~~~~g~~~~~~vLL~GppGtGKT~lAraia~~~~~~fv~vn~~~l~  275 (489)
T 3hu3_A          196 ESLNEVGYDDIGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGAFFFLINGPEIM  275 (489)
T ss_dssp             HHHTCCCGGGCCSCHHHHHHHHHHTHHHHHCHHHHHHHTCCCCCEEEEECSTTSSHHHHHHHHHHHCSSEEEEEEHHHHH
T ss_pred             cccCCCCHHHcCCHHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCcEEEECcCCCCHHHHHHHHHHHhCCCEEEEEchHhh
Confidence            45678899999999999999999987532210     0122336899999999999999999999999999999875411


Q ss_pred             hhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcc------hhHHHHHHHHHHHHH
Q 005987          216 IWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNG------RTAFERLRQCLLLLV  289 (666)
Q Consensus       216 ~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~------~~~~~~l~~~L~~l~  289 (666)
                             .    ..+......+...+..+...            .+.+|||||+|.+..      .....+++..|+.++
T Consensus       276 -------~----~~~g~~~~~~~~~f~~A~~~------------~p~iLfLDEId~l~~~~~~~~~~~~~~~~~~LL~~l  332 (489)
T 3hu3_A          276 -------S----KLAGESESNLRKAFEEAEKN------------APAIIFIDELDAIAPKREKTHGEVERRIVSQLLTLM  332 (489)
T ss_dssp             -------T----SCTTHHHHHHHHHHHHHHHT------------CSEEEEEESHHHHCBCTTSCCCHHHHHHHHHHHHHH
T ss_pred             -------h----hhcchhHHHHHHHHHHHHhc------------CCcEEEecchhhhccccccccchHHHHHHHHHHHHh
Confidence                   1    11122233455666666432            357999999976533      112234455565555


Q ss_pred             hcC--CCceEEEEecCCCCCCccchhhhhhHHHHHHhh--cCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHH
Q 005987          290 RST--HIPTAVVLTECGKADSVDSTAQSFEELQSILVD--AGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVA  365 (666)
Q Consensus       290 ~~~--~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r--~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia  365 (666)
                      +..  ...+++|+++ +....          |...+.+  .....|.|.+|+..+..++|+..+....+. .+..+..++
T Consensus       333 d~~~~~~~v~vIaaT-n~~~~----------Ld~al~r~gRf~~~i~i~~P~~~eR~~IL~~~~~~~~l~-~~~~l~~la  400 (489)
T 3hu3_A          333 DGLKQRAHVIVMAAT-NRPNS----------IDPALRRFGRFDREVDIGIPDATGRLEILQIHTKNMKLA-DDVDLEQVA  400 (489)
T ss_dssp             HHSCTTSCEEEEEEE-SCGGG----------BCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHTTTSCBC-TTCCHHHHH
T ss_pred             hccccCCceEEEEec-CCccc----------cCHHHhCCCcCceEEEeCCCCHHHHHHHHHHHHhcCCCc-chhhHHHHH
Confidence            532  2234444333 32211          1122222  123569999999999999999887654433 233467888


Q ss_pred             HHcCCcHHHHHHHH
Q 005987          366 QASGGDIRQAITSL  379 (666)
Q Consensus       366 ~~s~GDIR~AIn~L  379 (666)
                      ..+.|.....|..|
T Consensus       401 ~~t~g~s~~dL~~L  414 (489)
T 3hu3_A          401 NETHGHVGADLAAL  414 (489)
T ss_dssp             HTCTTCCHHHHHHH
T ss_pred             HHccCCcHHHHHHH
Confidence            88877555444444

>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=99.45  E-value=3.2e-13  Score=157.40  Aligned_cols=200  Identities=18%  Similarity=0.238  Sum_probs=129.1

Q ss_pred             CCCccccccCHHHHHHHHHHHHHhhcC-----CCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCchhhhh
Q 005987          145 PRSLEELAVQRKKVEEVRAWFEERLGD-----SKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTIWQE  219 (666)
Q Consensus       145 P~sl~eLvg~~k~i~el~~wL~~~~~~-----~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~~~~e  219 (666)
                      ..+++||.|.++.+++|++++.-.+..     .-|..+++.+|||||||||||++|+++|+++|..++++++++.     
T Consensus       200 ~v~~~dIgGl~~~~~~l~e~v~~pl~~p~~f~~~g~~~p~GILL~GPPGTGKT~LAraiA~elg~~~~~v~~~~l-----  274 (806)
T 3cf2_A          200 EVGYDDIGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGAFFFLINGPEI-----  274 (806)
T ss_dssp             SCCGGGCCSCCTTHHHHHHHHHHHHHCCGGGTSCCCCCCCEEEEECCTTSCHHHHHHHHHTTTTCEEEEEEHHHH-----
T ss_pred             CCChhhhcCHHHHHHHHHHHHHHHccCHHHHhhcCCCCCCeEEEECCCCCCHHHHHHHHHHHhCCeEEEEEhHHh-----
Confidence            467899999999999999887643322     1133445899999999999999999999999999999987641     


Q ss_pred             hhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcch------hHHHHHHHHHHHHHhcC-
Q 005987          220 YMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGR------TAFERLRQCLLLLVRST-  292 (666)
Q Consensus       220 ~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~------~~~~~l~~~L~~l~~~~-  292 (666)
                            .+..+......++..++.+...            .|.||+|||+|.+...      ..-.++...|+..+..- 
T Consensus       275 ------~sk~~gese~~lr~lF~~A~~~------------~PsIIfIDEiDal~~~r~~~~~~~~~riv~~LL~~mdg~~  336 (806)
T 3cf2_A          275 ------MSKLAGESESNLRKAFEEAEKN------------APAIIFIDELDAIAPKREKTHGEVERRIVSQLLTLMDGLK  336 (806)
T ss_dssp             ------HSSCTTHHHHHHHHHHHHHTTS------------CSEEEEEESGGGTCCTTTTCCCTTHHHHHHHHHTHHHHCC
T ss_pred             ------hcccchHHHHHHHHHHHHHHHc------------CCeEEEEehhcccccccCCCCChHHHHHHHHHHHHHhccc
Confidence                  1122233445667777777543            4789999999976431      11233434444444332 


Q ss_pred             -CCceEEEEecCCCCCCccchhhhhhHHHHHHhhc--CeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcC
Q 005987          293 -HIPTAVVLTECGKADSVDSTAQSFEELQSILVDA--GARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASG  369 (666)
Q Consensus       293 -~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~--r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~s~  369 (666)
                       ..+++ ++..++..+..|          ..|.|+  .-..|.|..|+.....++|+..+....+. ++..+..||..+.
T Consensus       337 ~~~~V~-VIaaTN~~d~LD----------~ALrR~GRFd~~I~i~~Pd~~~R~~IL~~~l~~~~~~-~dvdl~~lA~~T~  404 (806)
T 3cf2_A          337 QRAHVI-VMAATNRPNSID----------PALRRFGRFDREVDIGIPDATGRLEILQIHTKNMKLA-DDVDLEQVANETH  404 (806)
T ss_dssp             GGGCEE-EEEECSSTTTSC----------TTTTSTTSSCEEEECCCCCHHHHHHHHHHTCSSSEEC-TTCCHHHHHHHCC
T ss_pred             ccCCEE-EEEecCChhhcC----------HHHhCCcccceEEecCCCCHHHHHHHHHHHhcCCCCC-cccCHHHHHHhcC
Confidence             22343 444444443333          222221  24579999999999999998766543322 2234678888765


Q ss_pred             C----cHHHHHHHH
Q 005987          370 G----DIRQAITSL  379 (666)
Q Consensus       370 G----DIR~AIn~L  379 (666)
                      |    ||...++..
T Consensus       405 GfsgaDL~~Lv~eA  418 (806)
T 3cf2_A          405 GHVGADLAALCSEA  418 (806)
T ss_dssp             SCCHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHH
Confidence            4    676655543

>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=99.43  E-value=5e-13  Score=157.19  Aligned_cols=212  Identities=16%  Similarity=0.225  Sum_probs=135.0

Q ss_pred             CCCCCccccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc----------
Q 005987          133 SSTQQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL----------  202 (666)
Q Consensus       133 ~~~~~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel----------  202 (666)
                      ......|+++|+|.++++++|++..++.+..+|...        ..+.+||+||||||||++|+.+|+.+          
T Consensus       170 ~~~~~~l~~~~~~~~~d~~iGr~~~i~~l~~~l~~~--------~~~~vlL~G~~GtGKT~la~~la~~l~~~~v~~~~~  241 (758)
T 1r6b_X          170 ENFTTNLNQLARVGGIDPLIGREKELERAIQVLCRR--------RKNNPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMA  241 (758)
T ss_dssp             CSSSCBHHHHHHTTCSCCCCSCHHHHHHHHHHHTSS--------SSCEEEEECCTTSSHHHHHHHHHHHHHHTCSCGGGT
T ss_pred             HHHhHhHHHHHhcCCCCCccCCHHHHHHHHHHHhcc--------CCCCeEEEcCCCCCHHHHHHHHHHHHHhCCCChhhc
Confidence            345678999999999999999999999998887642        12579999999999999999999987          


Q ss_pred             CCcEEEEcCCCchhhhhhhhcccCCcccc-chhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchh----H
Q 005987          203 GARLYEWDTPTPTIWQEYMHNCKTGLEYT-SKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRT----A  277 (666)
Q Consensus       203 g~~viE~nasd~~~~~e~l~~~~~g~~~~-s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~----~  277 (666)
                      +..++.++....          ..|..+. .....+..+++.+...            .+.||+|||++.+.+..    .
T Consensus       242 ~~~~~~~~~~~l----------~~~~~~~g~~e~~l~~~~~~~~~~------------~~~iL~IDEi~~l~~~~~~~~~  299 (758)
T 1r6b_X          242 DCTIYSLDIGSL----------LAGTKYRGDFEKRFKALLKQLEQD------------TNSILFIDEIHTIIGAGAASGG  299 (758)
T ss_dssp             TCEEEECCCC-------------CCCCCSSCHHHHHHHHHHHHSSS------------SCEEEEETTTTTTTTSCCSSSC
T ss_pred             CCEEEEEcHHHH----------hccccccchHHHHHHHHHHHHHhc------------CCeEEEEechHHHhhcCCCCcc
Confidence            455555543321          1122222 2223455555554321            25799999999873210    0


Q ss_pred             HHHHHHHHHHHHhcCCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHH----hC
Q 005987          278 FERLRQCLLLLVRSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQ----EQ  353 (666)
Q Consensus       278 ~~~l~~~L~~l~~~~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~----e~  353 (666)
                      ...+.+.|..+++.+.. .+|.+++..      .....+. +...|.+ |+..|.|.+|+.++...+|..++..    .+
T Consensus       300 ~~~~~~~L~~~l~~~~~-~~I~at~~~------~~~~~~~-~d~aL~~-Rf~~i~v~~p~~~e~~~il~~l~~~~~~~~~  370 (758)
T 1r6b_X          300 QVDAANLIKPLLSSGKI-RVIGSTTYQ------EFSNIFE-KDRALAR-RFQKIDITEPSIEETVQIINGLKPKYEAHHD  370 (758)
T ss_dssp             HHHHHHHHSSCSSSCCC-EEEEEECHH------HHHCCCC-CTTSSGG-GEEEEECCCCCHHHHHHHHHHHHHHHHHHHT
T ss_pred             hHHHHHHHHHHHhCCCe-EEEEEeCch------HHhhhhh-cCHHHHh-CceEEEcCCCCHHHHHHHHHHHHHHHHHhcC
Confidence            12233344444444433 222233210      0001111 1122223 5789999999999999999988865    67


Q ss_pred             CCCCHHHHHHHHHHcCCcH------HHHHHHHHHHh
Q 005987          354 YSLSTEQIDLVAQASGGDI------RQAITSLQFSS  383 (666)
Q Consensus       354 i~v~~~~l~~Ia~~s~GDI------R~AIn~LQf~~  383 (666)
                      +.+++++++.++..+.|.+      ..++..+.-++
T Consensus       371 v~~~~~al~~~~~~s~~~i~~~~lp~~~i~lld~a~  406 (758)
T 1r6b_X          371 VRYTAKAVRAAVELAVKYINDRHLPDKAIDVIDEAG  406 (758)
T ss_dssp             CCCCHHHHHHHHHHHHHHCTTSCTTHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHhhhhcccccCchHHHHHHHHHH
Confidence            8899999999998876632      35666554443

>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural genomics, structural genomics consortium, SGC, unknown function; 1.70A {Plasmodium falciparum}

Probab=99.42  E-value=2.2e-13  Score=130.35  Aligned_cols=132  Identities=14%  Similarity=0.267  Sum_probs=85.8

Q ss_pred             CCCccccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc----------CC
Q 005987          135 TQQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL----------GA  204 (666)
Q Consensus       135 ~~~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel----------g~  204 (666)
                      ....|.++|+|.++++++|++..++.+..++..      +.  .+.+||+||||||||++++.+|+++          +.
T Consensus         8 ~~~~l~~~~~~~~~~~~~g~~~~~~~l~~~l~~------~~--~~~vll~G~~G~GKT~la~~~~~~~~~~~~~~~~~~~   79 (187)
T 2p65_A            8 YSRDLTALARAGKLDPVIGRDTEIRRAIQILSR------RT--KNNPILLGDPGVGKTAIVEGLAIKIVQGDVPDSLKGR   79 (187)
T ss_dssp             TEEEHHHHHHTTCSCCCCSCHHHHHHHHHHHTS------SS--SCEEEEESCGGGCHHHHHHHHHHHHHTTCSCTTTTTC
T ss_pred             HHHHHHHHHhccccchhhcchHHHHHHHHHHhC------CC--CCceEEECCCCCCHHHHHHHHHHHHHhcCCcchhcCC
Confidence            356799999999999999999999999888864      21  2578999999999999999999997          66


Q ss_pred             cEEEEcCCCchhhhhhhhcccCCccc-cchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCc-----chhHH
Q 005987          205 RLYEWDTPTPTIWQEYMHNCKTGLEY-TSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTN-----GRTAF  278 (666)
Q Consensus       205 ~viE~nasd~~~~~e~l~~~~~g~~~-~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~-----~~~~~  278 (666)
                      .++.++...      ..    .+..+ ......+..++..+...           +.+.+|+|||++.+.     ... .
T Consensus        80 ~~~~~~~~~------~~----~~~~~~~~~~~~~~~~~~~~~~~-----------~~~~vl~iDe~~~l~~~~~~~~~-~  137 (187)
T 2p65_A           80 KLVSLDLSS------LI----AGAKYRGDFEERLKSILKEVQDA-----------EGQVVMFIDEIHTVVGAGAVAEG-A  137 (187)
T ss_dssp             EEEEECHHH------HH----HHCCSHHHHHHHHHHHHHHHHHT-----------TTSEEEEETTGGGGSSSSSSCTT-S
T ss_pred             eEEEEeHHH------hh----cCCCchhHHHHHHHHHHHHHHhc-----------CCceEEEEeCHHHhccccccccc-c
Confidence            666655321      00    00001 11122344455554332           135699999999875     210 0


Q ss_pred             HHHHHHHHHHHhcCCCce
Q 005987          279 ERLRQCLLLLVRSTHIPT  296 (666)
Q Consensus       279 ~~l~~~L~~l~~~~~~Pi  296 (666)
                      ..+.+.|..+++.....+
T Consensus       138 ~~~~~~l~~~~~~~~~~i  155 (187)
T 2p65_A          138 LDAGNILKPMLARGELRC  155 (187)
T ss_dssp             CCTHHHHHHHHHTTCSCE
T ss_pred             hHHHHHHHHHHhcCCeeE
Confidence            123344555556555433

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=99.41  E-value=4.1e-13  Score=157.94  Aligned_cols=197  Identities=19%  Similarity=0.238  Sum_probs=128.1

Q ss_pred             CCCCccccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc----------C
Q 005987          134 STQQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL----------G  203 (666)
Q Consensus       134 ~~~~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel----------g  203 (666)
                      .....|+++|+|..+++++|+++.++.+..+|..      ..  .+.+||+||||||||++|+++|+.+          +
T Consensus       165 ~~~~~l~~~~~~~~ld~iiG~~~~i~~l~~~l~~------~~--~~~vLL~G~pGtGKT~la~~la~~l~~~~~p~~l~~  236 (758)
T 3pxi_A          165 SLARDLTAIAKEDSLDPVIGRSKEIQRVIEVLSR------RT--KNNPVLIGEPGVGKTAIAEGLAQQIINNEVPEILRD  236 (758)
T ss_dssp             SSCCBHHHHTTSSCSCCCCCCHHHHHHHHHHHHC------SS--SCEEEEESCTTTTTHHHHHHHHHHHHSSCSCTTTSS
T ss_pred             HHHHHHHHHHhhCCCCCccCchHHHHHHHHHHhC------CC--CCCeEEECCCCCCHHHHHHHHHHHHhcCCCChhhcC
Confidence            3567899999999999999999999999999875      11  2579999999999999999999997          6


Q ss_pred             CcEEEEcCCCchhhhhhhhcccCCccc-cchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHH
Q 005987          204 ARLYEWDTPTPTIWQEYMHNCKTGLEY-TSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLR  282 (666)
Q Consensus       204 ~~viE~nasd~~~~~e~l~~~~~g~~~-~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~  282 (666)
                      ..++.++.               |..| ......+..++..+...            .+.|||||   .  .    ....
T Consensus       237 ~~~~~~~~---------------g~~~~G~~e~~l~~~~~~~~~~------------~~~iLfiD---~--~----~~~~  280 (758)
T 3pxi_A          237 KRVMTLDM---------------GTKYRGEFEDRLKKVMDEIRQA------------GNIILFID---A--A----IDAS  280 (758)
T ss_dssp             CCEECC-------------------------CTTHHHHHHHHHTC------------CCCEEEEC---C-----------
T ss_pred             CeEEEecc---------------cccccchHHHHHHHHHHHHHhc------------CCEEEEEc---C--c----hhHH
Confidence            66666554               1111 11122455566665432            25699999   1  1    1123


Q ss_pred             HHHHHHHhcCCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHH----hCCCCCH
Q 005987          283 QCLLLLVRSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQ----EQYSLST  358 (666)
Q Consensus       283 ~~L~~l~~~~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~----e~i~v~~  358 (666)
                      +.|...++.+.  +.+|.+. +...    +...+. +...+.+ |+..|.|.+|+.+++.++|+.++..    .++.+++
T Consensus       281 ~~L~~~l~~~~--v~~I~at-~~~~----~~~~~~-~d~al~r-Rf~~i~v~~p~~~~~~~il~~~~~~~~~~~~~~i~~  351 (758)
T 3pxi_A          281 NILKPSLARGE--LQCIGAT-TLDE----YRKYIE-KDAALER-RFQPIQVDQPSVDESIQILQGLRDRYEAHHRVSITD  351 (758)
T ss_dssp             ---CCCTTSSS--CEEEEEC-CTTT----THHHHT-TCSHHHH-SEEEEECCCCCHHHHHHHHHHTTTTSGGGSSCSCCH
T ss_pred             HHHHHHHhcCC--EEEEeCC-ChHH----HHHHhh-ccHHHHh-hCcEEEeCCCCHHHHHHHHHHHHHHHHHhcCCCCCH
Confidence            33444455443  3333332 2211    111111 2223333 6889999999999999999988766    6788999


Q ss_pred             HHHHHHHHHcCCcH------HHHHHHHHHHh
Q 005987          359 EQIDLVAQASGGDI------RQAITSLQFSS  383 (666)
Q Consensus       359 ~~l~~Ia~~s~GDI------R~AIn~LQf~~  383 (666)
                      +++..++..+.+.+      +.||..|.-++
T Consensus       352 ~al~~~~~~s~~~i~~~~~p~~ai~ll~~a~  382 (758)
T 3pxi_A          352 DAIEAAVKLSDRYISDRFLPDKAIDLIDEAG  382 (758)
T ss_dssp             HHHHHHHHHHHHSSCCSCTTHHHHHHHHHHH
T ss_pred             HHHHHHHHHhhcccccCcCCcHHHHHHHHHH
Confidence            99999998865443      56777666554

>2r44_A Uncharacterized protein; putative ATPase, structural genomics, joint center for struc genomics, JCSG; HET: MSE PG4; 2.00A {Cytophaga hutchinsonii atcc 33406}

Probab=99.41  E-value=1.3e-12  Score=138.07  Aligned_cols=207  Identities=12%  Similarity=0.150  Sum_probs=130.2

Q ss_pred             CccccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCchh
Q 005987          137 QLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTI  216 (666)
Q Consensus       137 ~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~~  216 (666)
                      ..|+++|+|..+.+++|++..++.+..++..      +    +.+||+||||||||++|+++|+.++..+..++......
T Consensus        15 ~~~~~~~~~~~~~~i~g~~~~~~~l~~~l~~------~----~~vll~G~pGtGKT~la~~la~~~~~~~~~i~~~~~~~   84 (331)
T 2r44_A           15 RNKIKEVIDEVGKVVVGQKYMINRLLIGICT------G----GHILLEGVPGLAKTLSVNTLAKTMDLDFHRIQFTPDLL   84 (331)
T ss_dssp             HHHHHHHHHHHTTTCCSCHHHHHHHHHHHHH------T----CCEEEESCCCHHHHHHHHHHHHHTTCCEEEEECCTTCC
T ss_pred             HHHHHHHHHHhccceeCcHHHHHHHHHHHHc------C----CeEEEECCCCCcHHHHHHHHHHHhCCCeEEEecCCCCC
Confidence            3599999999999999999999999888775      2    47999999999999999999999999888877632111


Q ss_pred             hhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcC----
Q 005987          217 WQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRST----  292 (666)
Q Consensus       217 ~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~----  292 (666)
                      ..+.+....    +...          ...+...    .+.- ...||+|||++.+...     .+..|...++..    
T Consensus        85 ~~~l~g~~~----~~~~----------~~~~~~~----~g~l-~~~vl~iDEi~~~~~~-----~~~~Ll~~l~~~~~~~  140 (331)
T 2r44_A           85 PSDLIGTMI----YNQH----------KGNFEVK----KGPV-FSNFILADEVNRSPAK-----VQSALLECMQEKQVTI  140 (331)
T ss_dssp             HHHHHEEEE----EETT----------TTEEEEE----ECTT-CSSEEEEETGGGSCHH-----HHHHHHHHHHHSEEEE
T ss_pred             hhhcCCcee----ecCC----------CCceEec----cCcc-cccEEEEEccccCCHH-----HHHHHHHHHhcCceee
Confidence            111111000    0000          0000000    0000 1259999999987543     233344444432    


Q ss_pred             -------CCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHh-------------
Q 005987          293 -------HIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQE-------------  352 (666)
Q Consensus       293 -------~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e-------------  352 (666)
                             ..+.+++++. +.....+ ... +  ...+++|+ ...+.|.+|+.++..++|++.+..+             
T Consensus       141 ~g~~~~~~~~~~viat~-np~~~~~-~~~-l--~~~l~~Rf-~~~i~i~~p~~~~~~~il~~~~~~~~~~~~~~~~~~~~  214 (331)
T 2r44_A          141 GDTTYPLDNPFLVLATQ-NPVEQEG-TYP-L--PEAQVDRF-MMKIHLTYLDKESELEVMRRVSNMNFNYQVQKIVSKND  214 (331)
T ss_dssp             TTEEEECCSSCEEEEEE-CTTCCSC-CCC-C--CHHHHTTS-SEEEECCCCCHHHHHHHHHHHHCTTCCCCCCCCSCHHH
T ss_pred             CCEEEECCCCEEEEEec-CCCcccC-ccc-C--CHHHHhhe-eEEEEcCCCCHHHHHHHHHhccccCcchhccccCCHHH
Confidence                   2234444433 2111100 000 1  12333431 3369999999999999999887642             


Q ss_pred             ---------CCCCCHHHHHHHHHHc-----CC---------------cHHHHHHHHHHHh
Q 005987          353 ---------QYSLSTEQIDLVAQAS-----GG---------------DIRQAITSLQFSS  383 (666)
Q Consensus       353 ---------~i~v~~~~l~~Ia~~s-----~G---------------DIR~AIn~LQf~~  383 (666)
                               ++.+++++++.|+..+     .|               +.|.+++.++.+.
T Consensus       215 i~~~~~~~~~v~~~~~~~~~i~~~~~~~r~~~~~~~~~~~~~~~~~~s~R~~~~ll~~a~  274 (331)
T 2r44_A          215 VLEIRNEINKVTISESLEKYIIELVFATRFPAEYGLEAEASYILYGASTRAAINLNRVAK  274 (331)
T ss_dssp             HHHHHHHHHTCBCCHHHHHHHHHHHHHHHSGGGGTCHHHHHHEEECCCHHHHHHHHHHHH
T ss_pred             HHHHHHHhccCCCCHHHHHHHHHHHHHHhccccccccccccccccCcChhHHHHHHHHHH
Confidence                     6778999999998754     23               5999998887764

>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=99.41  E-value=4.8e-15  Score=152.02  Aligned_cols=209  Identities=15%  Similarity=0.210  Sum_probs=121.8

Q ss_pred             cccCCCCccccccCHHHHHHHHHHHHHhhcCCC-----CCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCch
Q 005987          141 EKYKPRSLEELAVQRKKVEEVRAWFEERLGDSK-----DKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPT  215 (666)
Q Consensus       141 eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~-----g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~  215 (666)
                      .++.+.++++|+|++..++.+..++.. +....     +...++.+||+||||||||++|+++|++++..++.+++++..
T Consensus         3 ~~~~~~~~~~i~G~~~~~~~l~~~~~~-~~~~~~~~~~~~~~~~~vll~G~~GtGKT~la~~la~~~~~~~~~v~~~~~~   81 (268)
T 2r62_A            3 AEKPNVRFKDMAGNEEAKEEVVEIVDF-LKYPERYANLGAKIPKGVLLVGPPGTGKTLLAKAVAGEAHVPFFSMGGSSFI   81 (268)
T ss_dssp             CCCCCCCSTTSSSCTTTHHHHHHHHHH-HHCHHHHHHHSCCCCSCCCCBCSSCSSHHHHHHHHHHHHTCCCCCCCSCTTT
T ss_pred             ccCCCCCHHHhCCcHHHHHHHHHHHHH-HHChHHHHHCCCCCCceEEEECCCCCcHHHHHHHHHHHhCCCEEEechHHHH
Confidence            456788999999999998888887763 21100     111225699999999999999999999999888887766421


Q ss_pred             hhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHH----------HHHHHH
Q 005987          216 IWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFE----------RLRQCL  285 (666)
Q Consensus       216 ~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~----------~l~~~L  285 (666)
                      .       ...|....    .+..+++.+...            .+.||+|||+|.+.......          .....|
T Consensus        82 ~-------~~~~~~~~----~~~~~~~~a~~~------------~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~~~~~l  138 (268)
T 2r62_A           82 E-------MFVGLGAS----RVRDLFETAKKQ------------APSIIFIDEIDAIGKSRAAGGVVSGNDEREQTLNQL  138 (268)
T ss_dssp             T-------SCSSSCSS----SSSTTHHHHHHS------------CSCEEEESCGGGTTC----------CCCSCSSTTTT
T ss_pred             H-------hhcchHHH----HHHHHHHHHHhc------------CCeEEEEeChhhhcccccccccCCCchhHHHHHHHH
Confidence            0       11111111    112233333321            24699999999875431100          011112


Q ss_pred             HHHHhc---CCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcC-eeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHH
Q 005987          286 LLLVRS---THIPTAVVLTECGKADSVDSTAQSFEELQSILVDAG-ARKVALNPITNGSIKRTLSKICRQEQYSLSTEQI  361 (666)
Q Consensus       286 ~~l~~~---~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r-~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l  361 (666)
                      ...+..   ...++++|++. +.....+         ..++++.| ...|.|.+|+.++..++|+..+....+. ++..+
T Consensus       139 l~~l~~~~~~~~~v~vi~tt-n~~~~ld---------~~l~r~~Rf~~~i~i~~p~~~~r~~il~~~~~~~~~~-~~~~~  207 (268)
T 2r62_A          139 LAEMDGFGSENAPVIVLAAT-NRPEILD---------PALMRPGRFDRQVLVDKPDFNGRVEILKVHIKGVKLA-NDVNL  207 (268)
T ss_dssp             TTTTTCSSCSCSCCEEEECB-SCCTTSC---------GGGGSSSSSCCCCBCCCCCTTTHHHHHHHHTSSSCCC-SSCCT
T ss_pred             HHHhhCcccCCCCEEEEEec-CCchhcC---------HhHcCCCCCCeEEEecCcCHHHHHHHHHHHHhcCCCC-CccCH
Confidence            222221   12234554443 3222111         11122112 3578999999999999998887543322 22235


Q ss_pred             HHHHHHcCC----cHHHHHHHHHHHhc
Q 005987          362 DLVAQASGG----DIRQAITSLQFSSL  384 (666)
Q Consensus       362 ~~Ia~~s~G----DIR~AIn~LQf~~~  384 (666)
                      +.|+..+.|    ||+.+++...+.+.
T Consensus       208 ~~la~~~~g~~g~dl~~l~~~a~~~a~  234 (268)
T 2r62_A          208 QEVAKLTAGLAGADLANIINEAALLAG  234 (268)
T ss_dssp             TTTTSSSCSSCHHHHHHHHHHHHHTTS
T ss_pred             HHHHHHcCCCCHHHHHHHHHHHHHHHH
Confidence            667766665    88888888777665

>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=99.40  E-value=7.4e-12  Score=135.66  Aligned_cols=217  Identities=15%  Similarity=0.243  Sum_probs=128.4

Q ss_pred             ccccccCCCCccccccCHHHHHHHHHHH-HHhhcCCCCCCCccEEEE--ECCCCchHHHHHHHHHHHc---------CCc
Q 005987          138 LWAEKYKPRSLEELAVQRKKVEEVRAWF-EERLGDSKDKFSTNVLVI--TGQAGVGKTATVRQIASHL---------GAR  205 (666)
Q Consensus       138 ~W~eKY~P~sl~eLvg~~k~i~el~~wL-~~~~~~~~g~~~~k~LLL--~GPpG~GKTtla~~LAkel---------g~~  205 (666)
                      ++..+|.|   ++++|+++.++.|..++ ....... +.. ++.++|  +||||+|||++++.+++++         ++.
T Consensus        14 ~~~~~~~p---~~l~gR~~el~~l~~~l~~~~~~~~-~~~-~~~~li~i~G~~G~GKT~L~~~~~~~~~~~~~~~~~~~~   88 (412)
T 1w5s_A           14 VFDENYIP---PELRVRRGEAEALARIYLNRLLSGA-GLS-DVNMIYGSIGRVGIGKTTLAKFTVKRVSEAAAKEGLTVK   88 (412)
T ss_dssp             GGSTTCCC---SSCSSSCHHHHHHHHHHHHHHHTSS-CBC-CEEEEEECTTCCSSSHHHHHHHHHHHHHHHHHHTTCCEE
T ss_pred             hcCCccCC---CCCCChHHHHHHHHHHHhHHHhcCC-CCC-CCEEEEeCcCcCCCCHHHHHHHHHHHHHHHHhccCCcee
Confidence            34556777   56799999999999999 7655310 022 258999  9999999999999999887         556


Q ss_pred             EEEEcCCCch----hhhhhhhcccCCcc--ccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcc-----
Q 005987          206 LYEWDTPTPT----IWQEYMHNCKTGLE--YTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNG-----  274 (666)
Q Consensus       206 viE~nasd~~----~~~e~l~~~~~g~~--~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~-----  274 (666)
                      ++.+++....    .+...+........  ..+....+..+...+...           +.+.||+|||++.+..     
T Consensus        89 ~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~-----------~~~~llvlDe~~~l~~~~~~~  157 (412)
T 1w5s_A           89 QAYVNAFNAPNLYTILSLIVRQTGYPIQVRGAPALDILKALVDNLYVE-----------NHYLLVILDEFQSMLSSPRIA  157 (412)
T ss_dssp             EEEEEGGGCCSHHHHHHHHHHHHTCCCCCTTCCHHHHHHHHHHHHHHH-----------TCEEEEEEESTHHHHSCTTSC
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHHHhc-----------CCeEEEEEeCHHHHhhccCcc
Confidence            7777753211    11111111100000  001111122222222111           2367999999997643     


Q ss_pred             hhHHHHHHHHHHHHHhcC---C--CceEEEEecCCCCCCccchhhhhhHHH----HHHhhcCeeEEEeCCCCHHHHHHHH
Q 005987          275 RTAFERLRQCLLLLVRST---H--IPTAVVLTECGKADSVDSTAQSFEELQ----SILVDAGARKVALNPITNGSIKRTL  345 (666)
Q Consensus       275 ~~~~~~l~~~L~~l~~~~---~--~PiViIit~~~~~~s~d~~~r~l~~L~----s~L~r~r~~~I~F~p~s~~~i~kiL  345 (666)
                      ...+..    |...+...   .  .++.+|++....        .....+.    ...++. ...|.|.|++.+++.++|
T Consensus       158 ~~~l~~----l~~~~~~~~~~~~~~~v~lI~~~~~~--------~~~~~l~~~~~~~~~~~-~~~i~l~~l~~~e~~~ll  224 (412)
T 1w5s_A          158 AEDLYT----LLRVHEEIPSRDGVNRIGFLLVASDV--------RALSYMREKIPQVESQI-GFKLHLPAYKSRELYTIL  224 (412)
T ss_dssp             HHHHHH----HHTHHHHSCCTTSCCBEEEEEEEEET--------HHHHHHHHHCHHHHTTC-SEEEECCCCCHHHHHHHH
T ss_pred             hHHHHH----HHHHHHhcccCCCCceEEEEEEeccc--------cHHHHHhhhcchhhhhc-CCeeeeCCCCHHHHHHHH
Confidence            122222    22222221   2  444444332110        1111121    222232 334999999999999999


Q ss_pred             HHHHHHhC--CCCCHHHHHHHHHHcC------CcHHHHHHHHHHHh
Q 005987          346 SKICRQEQ--YSLSTEQIDLVAQASG------GDIRQAITSLQFSS  383 (666)
Q Consensus       346 ~~I~~~e~--i~v~~~~l~~Ia~~s~------GDIR~AIn~LQf~~  383 (666)
                      ...+...+  ..++++++..|+..++      |++|.+++.++.++
T Consensus       225 ~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~G~p~~~~~l~~~a~  270 (412)
T 1w5s_A          225 EQRAELGLRDTVWEPRHLELISDVYGEDKGGDGSARRAIVALKMAC  270 (412)
T ss_dssp             HHHHHHHBCTTSCCHHHHHHHHHHHCGGGTSCCCHHHHHHHHHHHH
T ss_pred             HHHHHhcCCCCCCChHHHHHHHHHHHHhccCCCcHHHHHHHHHHHH
Confidence            88876543  3578999999999999      99999998887654

>4fcw_A Chaperone protein CLPB; AAA domain; HET: ADP; 2.35A {Thermus thermophilus} PDB: 4fcv_A* 4fd2_A* 4fct_A*

Probab=99.40  E-value=6.2e-12  Score=131.29  Aligned_cols=211  Identities=14%  Similarity=0.174  Sum_probs=125.6

Q ss_pred             ccccCHHHHHHHHHHHHHhhcC--CCCCCCccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcCCCchh---hhhhh
Q 005987          150 ELAVQRKKVEEVRAWFEERLGD--SKDKFSTNVLVITGQAGVGKTATVRQIASHL---GARLYEWDTPTPTI---WQEYM  221 (666)
Q Consensus       150 eLvg~~k~i~el~~wL~~~~~~--~~g~~~~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~nasd~~~---~~e~l  221 (666)
                      +++|++..++.|...+......  .+.+ +..++||+||||||||++|+++|+.+   +..++.++++....   ....+
T Consensus        18 ~i~G~~~~~~~l~~~i~~~~~~~~~~~~-~~~~~ll~G~~GtGKt~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~l~   96 (311)
T 4fcw_A           18 RVVGQDEAIRAVADAIRRARAGLKDPNR-PIGSFLFLGPTGVGKTELAKTLAATLFDTEEAMIRIDMTEYMEKHAVSRLI   96 (311)
T ss_dssp             TCCSCHHHHHHHHHHHHHHHHTCSCTTS-CSEEEEEESCSSSSHHHHHHHHHHHHHSCGGGEEEEEGGGCCSTTHHHHHH
T ss_pred             hcCCHHHHHHHHHHHHHHHhcCCCCCCC-CceEEEEECCCCcCHHHHHHHHHHHHcCCCcceEEeecccccccccHHHhc
Confidence            5789999999999999875421  1122 22579999999999999999999998   45577777653211   11111


Q ss_pred             hcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcCC--------
Q 005987          222 HNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTH--------  293 (666)
Q Consensus       222 ~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~~--------  293 (666)
                      ........+. ....+...+..   .            ...+|+|||++.+...     .++.|..+++...        
T Consensus        97 g~~~~~~~~~-~~~~~~~~~~~---~------------~~~vl~lDEi~~l~~~-----~~~~Ll~~le~~~~~~~~~~~  155 (311)
T 4fcw_A           97 GAPPGYVGYE-EGGQLTEAVRR---R------------PYSVILFDAIEKAHPD-----VFNILLQMLDDGRLTDSHGRT  155 (311)
T ss_dssp             CCCTTSTTTT-TCCHHHHHHHH---C------------SSEEEEEETGGGSCHH-----HHHHHHHHHHHSEEECTTSCE
T ss_pred             CCCCcccccc-ccchHHHHHHh---C------------CCeEEEEeChhhcCHH-----HHHHHHHHHhcCEEEcCCCCE
Confidence            1110000110 01122222211   1            2369999999987532     3334555555432        


Q ss_pred             ----CceEEEEecCCC---------CCCccchhhhh-----hHH-HHHHhhcCe-eEEEeCCCCHHHHHHHHHHHHHHh-
Q 005987          294 ----IPTAVVLTECGK---------ADSVDSTAQSF-----EEL-QSILVDAGA-RKVALNPITNGSIKRTLSKICRQE-  352 (666)
Q Consensus       294 ----~PiViIit~~~~---------~~s~d~~~r~l-----~~L-~s~L~r~r~-~~I~F~p~s~~~i~kiL~~I~~~e-  352 (666)
                          ..++|++++...         ....+.....+     ..+ ..++.|  + ..+.|.|++.+++..++...+... 
T Consensus       156 ~~~~~~iiI~ttn~~~~~i~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~R--~~~~~~~~p~~~~~~~~i~~~~l~~~~  233 (311)
T 4fcw_A          156 VDFRNTVIIMTSNLGSPLILEGLQKGWPYERIRDEVFKVLQQHFRPEFLNR--LDEIVVFRPLTKEQIRQIVEIQMSYLR  233 (311)
T ss_dssp             EECTTEEEEEEESTTHHHHHTTTTSCCCSSTHHHHTHHHHHHHSCHHHHTT--CSEEEECCCCCHHHHHHHHHHHTHHHH
T ss_pred             EECCCcEEEEecccCHHHHHhhhcccccHHHHHHHHHHHHHHhCCHHHHhc--CCeEEEeCCCCHHHHHHHHHHHHHHHH
Confidence                223444444310         00000000000     111 233333  5 789999999999999998877652 


Q ss_pred             --------CCCCCHHHHHHHHHHcC---CcHHHHHHHHHHHhc
Q 005987          353 --------QYSLSTEQIDLVAQASG---GDIRQAITSLQFSSL  384 (666)
Q Consensus       353 --------~i~v~~~~l~~Ia~~s~---GDIR~AIn~LQf~~~  384 (666)
                              .+.+++++++.|+..+-   |++|...+.++-++.
T Consensus       234 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~gn~R~L~~~i~~~~~  276 (311)
T 4fcw_A          234 ARLAEKRISLELTEAAKDFLAERGYDPVFGARPLRRVIQRELE  276 (311)
T ss_dssp             HHHHTTTCEEEECHHHHHHHHHHSCBTTTBTTTHHHHHHHHTH
T ss_pred             HHHHhCCcEEEeCHHHHHHHHHhCCCccCCchhHHHHHHHHHH
Confidence                    35689999999999764   999988888887664

>3t15_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic; photosynthesis, rubisco activase, AAA+ protein; 2.95A {Nicotiana tabacum} PDB: 3zw6_A

Probab=99.36  E-value=8e-12  Score=130.26  Aligned_cols=164  Identities=14%  Similarity=0.150  Sum_probs=90.3

Q ss_pred             CccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCchhhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCC
Q 005987          177 STNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPG  256 (666)
Q Consensus       177 ~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~  256 (666)
                      +++.+||+||||||||++|+++|++++..++.+++++.       .....    ......+...+..+.....       
T Consensus        35 ~p~~lLl~GppGtGKT~la~aiA~~l~~~~i~v~~~~l-------~~~~~----g~~~~~i~~~f~~a~~~~~-------   96 (293)
T 3t15_A           35 VPLILGIWGGKGQGKSFQCELVFRKMGINPIMMSAGEL-------ESGNA----GEPAKLIRQRYREAAEIIR-------   96 (293)
T ss_dssp             CCSEEEEEECTTSCHHHHHHHHHHHHTCCCEEEEHHHH-------HCC-------HHHHHHHHHHHHHHHHHT-------
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHhCCCEEEEeHHHh-------hhccC----chhHHHHHHHHHHHHHHHh-------
Confidence            34789999999999999999999999999999986531       01011    1122334455555421110       


Q ss_pred             CCCCceEEEEeCCCCCcchhH--------HHHHHHHHHHHHhc--------------CCCceEEEEecCCCCCCccchhh
Q 005987          257 ESKSSAILLIDDLPVTNGRTA--------FERLRQCLLLLVRS--------------THIPTAVVLTECGKADSVDSTAQ  314 (666)
Q Consensus       257 ~~~~~~IIlIDEid~l~~~~~--------~~~l~~~L~~l~~~--------------~~~PiViIit~~~~~~s~d~~~r  314 (666)
                       ...+.||+|||+|.+..+..        -..+...|..+++.              ....+||++++  .....+    
T Consensus        97 -~~~~~vl~iDEiD~~~~~~~~~~~~~~~~~~v~~~Ll~~ld~~~~~~~~~~~~~~~~~~v~vI~ttN--~~~~ld----  169 (293)
T 3t15_A           97 -KGNMCCLFINDLDAGAGRMGGTTQYTVNNQMVNATLMNIADNPTNVQLPGMYNKQENARVPIIVTGN--DFSTLY----  169 (293)
T ss_dssp             -TSSCCCEEEECCC--------------CHHHHHHHHHHHHHCCC-----------CCCCCCEEEECS--SCCC------
T ss_pred             -cCCCeEEEEechhhhcCCCCCCccccchHHHHHHHHHHHhccccccccccccccccCCCcEEEEecC--CcccCC----
Confidence             12467999999997654211        11344556666541              11223333333  221111    


Q ss_pred             hhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHH-cCCcHH
Q 005987          315 SFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQA-SGGDIR  373 (666)
Q Consensus       315 ~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~-s~GDIR  373 (666)
                           .++++..|+..+-+ .|+.++..++++.++...+  ++.+.+..++.. ++.||.
T Consensus       170 -----~al~R~~R~d~~i~-~P~~~~r~~Il~~~~~~~~--~~~~~l~~~~~~~~~~~l~  221 (293)
T 3t15_A          170 -----APLIRDGRMEKFYW-APTREDRIGVCTGIFRTDN--VPAEDVVKIVDNFPGQSID  221 (293)
T ss_dssp             -----CHHHHHHHEEEEEE-CCCHHHHHHHHHHHHGGGC--CCHHHHHHHHHHSCSCCHH
T ss_pred             -----HHHhCCCCCceeEe-CcCHHHHHHHHHHhccCCC--CCHHHHHHHhCCCCcccHH
Confidence                 11222123444334 4599999999998887665  456666666655 445554

>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=99.35  E-value=9.9e-13  Score=153.27  Aligned_cols=207  Identities=14%  Similarity=0.199  Sum_probs=120.0

Q ss_pred             CCCccccccCHHHHHHHHHHHHHhhcC-----CCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCchhhhh
Q 005987          145 PRSLEELAVQRKKVEEVRAWFEERLGD-----SKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTIWQE  219 (666)
Q Consensus       145 P~sl~eLvg~~k~i~el~~wL~~~~~~-----~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~~~~e  219 (666)
                      +.+++++.|.+...++|.+.+.-.+..     .-|..+++.+|||||||||||.+|+++|.+++..++.+..++  ..  
T Consensus       473 ~v~w~diggl~~~k~~l~e~v~~p~~~p~~f~~~g~~~~~gvLl~GPPGtGKT~lAkaiA~e~~~~f~~v~~~~--l~--  548 (806)
T 3cf2_A          473 QVTWEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANECQANFISIKGPE--LL--  548 (806)
T ss_dssp             CCCSTTCCSCHHHHHHHTTTTTTTTTCSGGGSSSCCCCCSCCEEESSTTSSHHHHHHHHHHTTTCEEEECCHHH--HH--
T ss_pred             CCCHHHhCCHHHHHHHHHHHHHhhhhCHHHHHhcCCCCCceEEEecCCCCCchHHHHHHHHHhCCceEEeccch--hh--
Confidence            356788999999888888776532221     113344578999999999999999999999999999887654  11  


Q ss_pred             hhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchh---------HHHHHHHHHHHHHh
Q 005987          220 YMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRT---------AFERLRQCLLLLVR  290 (666)
Q Consensus       220 ~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~---------~~~~l~~~L~~l~~  290 (666)
                             +..+......+++++..++..            .|+||+|||+|.+....         ...++...|+..++
T Consensus       549 -------s~~vGese~~vr~lF~~Ar~~------------~P~IifiDEiDsl~~~R~~~~~~~~~~~~rv~~~lL~~md  609 (806)
T 3cf2_A          549 -------TMWFGESEANVREIFDKARQA------------APCVLFFDELDSIAKARGGNIGDGGGAADRVINQILTEMD  609 (806)
T ss_dssp             -------TTTCSSCHHHHHHHHHHHHTT------------CSEEEECSCGGGCC--------------CHHHHHHHHHHH
T ss_pred             -------ccccchHHHHHHHHHHHHHHc------------CCceeechhhhHHhhccCCCCCCCchHHHHHHHHHHHHHh
Confidence                   111223345678888888654            37899999999764321         12234444555555


Q ss_pred             cC-CCceEEEEecCCCCCCccchhhhhhHHHHHHhh-cCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHH-
Q 005987          291 ST-HIPTAVVLTECGKADSVDSTAQSFEELQSILVD-AGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQA-  367 (666)
Q Consensus       291 ~~-~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r-~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~-  367 (666)
                      .- ...-|++++.++.++..|         .++++. +.-..|.|..|+.+...++|+..+.+..+. ++-.++.||+. 
T Consensus       610 g~~~~~~V~vi~aTN~p~~lD---------~AllRpgRfd~~i~v~lPd~~~R~~il~~~l~~~~~~-~~~dl~~la~~t  679 (806)
T 3cf2_A          610 GMSTKKNVFIIGATNRPDIID---------PAILRPGRLDQLIYIPLPDEKSRVAILKANLRKSPVA-KDVDLEFLAKMT  679 (806)
T ss_dssp             SSCSSSSEEEECC-CCSSSSC---------HHHHSTTTSCCEEEC-----CHHHHTTTTTSSCC--C-CC----------
T ss_pred             CCCCCCCEEEEEeCCCchhCC---------HhHcCCCcceEEEEECCcCHHHHHHHHHHHhcCCCCC-CCCCHHHHHHhC
Confidence            32 122355566666554333         222320 124579999999999999888776544332 22235666654 


Q ss_pred             ---cCCcHHHHHHHHHHHhc
Q 005987          368 ---SGGDIRQAITSLQFSSL  384 (666)
Q Consensus       368 ---s~GDIR~AIn~LQf~~~  384 (666)
                         |+.||..+++.-.+.+.
T Consensus       680 ~g~SGadi~~l~~~A~~~a~  699 (806)
T 3cf2_A          680 NGFSGADLTEICQRACKLAI  699 (806)
T ss_dssp             ------CHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHHH
Confidence               66799998887666664

>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=99.34  E-value=1.3e-11  Score=126.35  Aligned_cols=206  Identities=15%  Similarity=0.203  Sum_probs=114.1

Q ss_pred             CccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcC---CcEEEEcCCCchh--hhhhh
Q 005987          147 SLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLG---ARLYEWDTPTPTI--WQEYM  221 (666)
Q Consensus       147 sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg---~~viE~nasd~~~--~~e~l  221 (666)
                      +|++++|+...++.+...++....     .+ ..+||+||||||||++|+++++.+.   ..++.++++....  ....+
T Consensus         4 ~f~~~ig~~~~~~~~~~~~~~~~~-----~~-~~vll~G~~GtGKt~la~~i~~~~~~~~~~~~~v~~~~~~~~~~~~~l   77 (265)
T 2bjv_A            4 YKDNLLGEANSFLEVLEQVSHLAP-----LD-KPVLIIGERGTGKELIASRLHYLSSRWQGPFISLNCAALNENLLDSEL   77 (265)
T ss_dssp             ------CCCHHHHHHHHHHHHHTT-----SC-SCEEEECCTTSCHHHHHHHHHHTSTTTTSCEEEEEGGGSCHHHHHHHH
T ss_pred             ccccceeCCHHHHHHHHHHHHHhC-----CC-CCEEEECCCCCcHHHHHHHHHHhcCccCCCeEEEecCCCChhHHHHHh
Confidence            678899999999999988886532     11 4799999999999999999999874   5688888764210  00000


Q ss_pred             hcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcCC--------
Q 005987          222 HNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTH--------  293 (666)
Q Consensus       222 ~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~~--------  293 (666)
                      .....|. +..........++.+               .+.+|+|||++.+...     .+..|..+++...        
T Consensus        78 ~g~~~~~-~~g~~~~~~~~l~~a---------------~~~~l~lDEi~~l~~~-----~q~~Ll~~l~~~~~~~~g~~~  136 (265)
T 2bjv_A           78 FGHEAGA-FTGAQKRHPGRFERA---------------DGGTLFLDELATAPMM-----VQEKLLRVIEYGELERVGGSQ  136 (265)
T ss_dssp             HCCC----------CCCCHHHHT---------------TTSEEEEESGGGSCHH-----HHHHHHHHHHHCEECCCCC--
T ss_pred             cCCcccc-cccccccccchhhhc---------------CCcEEEEechHhcCHH-----HHHHHHHHHHhCCeecCCCcc
Confidence            0000000 000000000001110               1349999999988642     2333445554321        


Q ss_pred             ----CceEEEEecCCCCCCccch-hhhhhHHHHHHhhcCeeEEEeCCCCH--HHHHHHH----HHHHHHhCC----CCCH
Q 005987          294 ----IPTAVVLTECGKADSVDST-AQSFEELQSILVDAGARKVALNPITN--GSIKRTL----SKICRQEQY----SLST  358 (666)
Q Consensus       294 ----~PiViIit~~~~~~s~d~~-~r~l~~L~s~L~r~r~~~I~F~p~s~--~~i~kiL----~~I~~~e~i----~v~~  358 (666)
                          ...||++++....   +.. ...+.  ..++.|.....|.++|+..  +++..++    .+.+...+.    .+++
T Consensus       137 ~~~~~~~iI~atn~~~~---~~~~~~~~~--~~L~~Rl~~~~i~lp~L~~R~~di~~l~~~~l~~~~~~~~~~~~~~~~~  211 (265)
T 2bjv_A          137 PLQVNVRLVCATNADLP---AMVNEGTFR--ADLLDALAFDVVQLPPLRERESDIMLMAEYFAIQMCREIKLPLFPGFTE  211 (265)
T ss_dssp             CEECCCEEEEEESSCHH---HHHHHTSSC--HHHHHHHCSEEEECCCGGGCHHHHHHHHHHHHHHHHHHTTCSSCCCBCH
T ss_pred             cccCCeEEEEecCcCHH---HHHHcCCcc--HHHHHhhcCcEEeCCChhhhhHHHHHHHHHHHHHHHHHhCCCcccCcCH
Confidence                1234444442110   000 00010  2333343345788999876  5665554    444444554    6899


Q ss_pred             HHHHHHHHHc-CCcHHHHHHHHHHHhc
Q 005987          359 EQIDLVAQAS-GGDIRQAITSLQFSSL  384 (666)
Q Consensus       359 ~~l~~Ia~~s-~GDIR~AIn~LQf~~~  384 (666)
                      ++++.|.... .|++|...+.++.++.
T Consensus       212 ~a~~~L~~~~~~gn~reL~~~l~~~~~  238 (265)
T 2bjv_A          212 RARETLLNYRWPGNIRELKNVVERSVY  238 (265)
T ss_dssp             HHHHHHHHSCCTTHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhCCCCCCHHHHHHHHHHHHH
Confidence            9999998775 8999999999988764

>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=99.33  E-value=1.2e-11  Score=125.82  Aligned_cols=208  Identities=16%  Similarity=0.247  Sum_probs=119.9

Q ss_pred             ccccCCCCccccccCHHHHHHHHHHHHHhhc-----CCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCc
Q 005987          140 AEKYKPRSLEELAVQRKKVEEVRAWFEERLG-----DSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTP  214 (666)
Q Consensus       140 ~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~-----~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~  214 (666)
                      +..+.+.++++++|.+....++++.......     ...-..+ +.++|+|||||||||+++++|..++...+.++..+.
T Consensus         7 ~~~~~~~~~~~i~g~~~~~~~l~~l~~~~~~~~~~~~~~~~~~-~g~ll~G~~G~GKTtl~~~i~~~~~~~~i~~~~~~~   85 (254)
T 1ixz_A            7 LTEAPKVTFKDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIP-KGVLLVGPPGVGKTHLARAVAGEARVPFITASGSDF   85 (254)
T ss_dssp             -CCCCSCCGGGCCSCHHHHHHHHHHHHHHHCHHHHHHTTCCCC-SEEEEECCTTSSHHHHHHHHHHHTTCCEEEEEHHHH
T ss_pred             ccCCCCCCHHHhCCcHHHHHHHHHHHHHHHCHHHHHHcCCCCC-CeEEEECCCCCCHHHHHHHHHHHhCCCEEEeeHHHH
Confidence            4566778999999999888888776553211     0011223 469999999999999999999999877777764321


Q ss_pred             hhhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcch---------hHHHHHHHHH
Q 005987          215 TIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGR---------TAFERLRQCL  285 (666)
Q Consensus       215 ~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~---------~~~~~l~~~L  285 (666)
                             .....+    .....+..+++.+..            ..+.++++||++.+...         .........+
T Consensus        86 -------~~~~~~----~~~~~i~~~~~~~~~------------~~~~i~~~Deid~l~~~~~~~~~~~~~~~~~~~~~l  142 (254)
T 1ixz_A           86 -------VEMFVG----VGAARVRDLFETAKR------------HAPCIVFIDEIDAVGRKRGSGVGGGNDEREQTLNQL  142 (254)
T ss_dssp             -------HHSCTT----HHHHHHHHHHHHHTT------------SSSEEEEEETHHHHHC---------CHHHHHHHHHH
T ss_pred             -------HHHHhh----HHHHHHHHHHHHHHh------------cCCeEEEehhhhhhhcccCccccccchHHHHHHHHH
Confidence                   000111    112233444444421            12569999999754211         1111222223


Q ss_pred             HHHHhcCC--CceEEEEecCCCCCCccchhhhhhHHHHHHhhc-CeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHH-HH
Q 005987          286 LLLVRSTH--IPTAVVLTECGKADSVDSTAQSFEELQSILVDA-GARKVALNPITNGSIKRTLSKICRQEQYSLSTE-QI  361 (666)
Q Consensus       286 ~~l~~~~~--~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~-r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~-~l  361 (666)
                      ...+....  ..++++++ ++.+...|         ..++++. ....|.|.+|+.++..++|+..+.  +..++++ .+
T Consensus       143 l~~l~g~~~~~~~i~~a~-t~~p~~ld---------~~l~r~~rf~~~i~i~~p~~~~r~~il~~~~~--~~~~~~~~~~  210 (254)
T 1ixz_A          143 LVEMDGFEKDTAIVVMAA-TNRPDILD---------PALLRPGRFDRQIAIDAPDVKGREQILRIHAR--GKPLAEDVDL  210 (254)
T ss_dssp             HHHHHTCCTTCCEEEEEE-ESCGGGSC---------GGGGSTTSSCEEEECCSCCHHHHHHHHHHHHT--TSCBCTTCCH
T ss_pred             HHHHhCCCCCCCEEEEEc-cCCchhCC---------HHHcCCCcCCeEEeeCCcCHHHHHHHHHHHHc--CCCCCcccCH
Confidence            33333332  23343333 33222111         1122211 245799999999999999987764  3444443 37


Q ss_pred             HHHHHHcCC----cHHHHHHHHHHHh
Q 005987          362 DLVAQASGG----DIRQAITSLQFSS  383 (666)
Q Consensus       362 ~~Ia~~s~G----DIR~AIn~LQf~~  383 (666)
                      ..|+..+.|    |++.+++..-..+
T Consensus       211 ~~la~~~~G~~~~dl~~~~~~a~~~a  236 (254)
T 1ixz_A          211 ALLAKRTPGFVGADLENLLNEAALLA  236 (254)
T ss_dssp             HHHHHTCTTCCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHcCCCCHHHHHHHHHHHHHHH
Confidence            889988877    5666666554444

>2dhr_A FTSH; AAA+ protein, hexameric Zn metalloprotease, hydrolase; HET: ADP; 3.90A {Thermus thermophilus}

Probab=99.32  E-value=1.2e-11  Score=137.59  Aligned_cols=211  Identities=16%  Similarity=0.249  Sum_probs=124.3

Q ss_pred             CccccccCCCCccccccCHHHHHHHHHHHHHhhc-----CCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcC
Q 005987          137 QLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLG-----DSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDT  211 (666)
Q Consensus       137 ~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~-----~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~na  211 (666)
                      .+|.+. .+.+|+|++|.+..+.++++.+.....     ......+ +.++|+||||||||++++++|.+++..++.++.
T Consensus        20 ~~~~~~-~~~~f~dv~G~~~~k~~l~~lv~~l~~~~~~~~lg~~ip-~GvLL~GppGtGKTtLaraIa~~~~~~~i~i~g   97 (499)
T 2dhr_A           20 RVLTEA-PKVTFKDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIP-KGVLLVGPPGVGKTHLARAVAGEARVPFITASG   97 (499)
T ss_dssp             EEECSC-CCCCTTSSCSCHHHHHHHHHHHHHHHCGGGTTTTSCCCC-SEEEEECSSSSSHHHHHHHHHHHTTCCEEEEEG
T ss_pred             eeeccC-CCCCHHHcCCcHHHHHHHHHHHHHhhchhhhhhccCCCC-ceEEEECCCCCCHHHHHHHHHHHhCCCEEEEeh
Confidence            456666 788999999999998888887663211     1112233 579999999999999999999999988888887


Q ss_pred             CCchhhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcc---------hhHHHHHH
Q 005987          212 PTPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNG---------RTAFERLR  282 (666)
Q Consensus       212 sd~~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~---------~~~~~~l~  282 (666)
                      ++..       ....|    .....+..+++.+.            ...+.+++|||++.+..         ........
T Consensus        98 ~~~~-------~~~~g----~~~~~v~~lfq~a~------------~~~p~il~IDEId~l~~~r~~~~~~~~~e~~~~l  154 (499)
T 2dhr_A           98 SDFV-------EMFVG----VGAARVRDLFETAK------------RHAPCIVFIDEIDAVGRKRGSGVGGGNDEREQTL  154 (499)
T ss_dssp             GGGT-------SSCTT----HHHHHHHHHTTTSS------------SSSSCEEEEECGGGTCCCSSSSTTTSSHHHHHHH
T ss_pred             hHHH-------Hhhhh----hHHHHHHHHHHHHH------------hcCCCEEEEehHHHHHHhhccCcCCCcHHHHHHH
Confidence            5411       00011    11112222222111            12357999999986532         11112222


Q ss_pred             HHHHHHHhcCC--CceEEEEecCCCCCCccchhhhhhHHHHHHhhc-CeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHH
Q 005987          283 QCLLLLVRSTH--IPTAVVLTECGKADSVDSTAQSFEELQSILVDA-GARKVALNPITNGSIKRTLSKICRQEQYSLSTE  359 (666)
Q Consensus       283 ~~L~~l~~~~~--~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~-r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~  359 (666)
                      ..|...+....  ..++++ +.++.+...|         ..++++. ....|.|.+|+..+..++|+..+.  ++.++++
T Consensus       155 ~~LL~~Ldg~~~~~~vivi-Aatn~p~~LD---------~aLlr~gRfdr~i~i~~Pd~~~R~~IL~~~~~--~~~l~~d  222 (499)
T 2dhr_A          155 NQLLVEMDGFEKDTAIVVM-AATNRPDILD---------PALLRPGRFDRQIAIDAPDVKGREQILRIHAR--GKPLAED  222 (499)
T ss_dssp             HHHHHHGGGCCSSCCCEEE-ECCSCGGGSC---------TTTSSTTSSCCEEECCCCCHHHHHHHHHHTTS--SSCCCCS
T ss_pred             HHHHHHhcccccCccEEEE-EecCChhhcC---------cccccccccceEEecCCCCHHHHHHHHHHHHh--cCCCChH
Confidence            22333333322  234444 3333322111         1112211 235799999999999998876653  3455544


Q ss_pred             -HHHHHHHHcCC----cHHHHHHHHHHHhc
Q 005987          360 -QIDLVAQASGG----DIRQAITSLQFSSL  384 (666)
Q Consensus       360 -~l~~Ia~~s~G----DIR~AIn~LQf~~~  384 (666)
                       .+..|+..+.|    |++.+++..-..+.
T Consensus       223 v~l~~lA~~t~G~~gadL~~lv~~Aa~~A~  252 (499)
T 2dhr_A          223 VDLALLAKRTPGFVGADLENLLNEAALLAA  252 (499)
T ss_dssp             STTHHHHTTSCSCCHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHhcCCCCHHHHHHHHHHHHHHHH
Confidence             37888988877    56667766555554

>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=99.32  E-value=9.9e-12  Score=133.93  Aligned_cols=217  Identities=14%  Similarity=0.137  Sum_probs=122.0

Q ss_pred             ccccCHHHHHHHHHHHHHhhcCC----------------------CCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEE
Q 005987          150 ELAVQRKKVEEVRAWFEERLGDS----------------------KDKFSTNVLVITGQAGVGKTATVRQIASHLGARLY  207 (666)
Q Consensus       150 eLvg~~k~i~el~~wL~~~~~~~----------------------~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~vi  207 (666)
                      .++|++..++.|..++..+....                      ....+...+||+||||||||++|+++|+.++..++
T Consensus        22 ~viGq~~ak~~l~~~~~~~~~~~~~g~~~~~~~~~~~~~p~~~~~~~~~~~~~ill~Gp~GtGKT~la~~la~~l~~~~~  101 (376)
T 1um8_A           22 YVIGQEQAKKVFSVAVYNHYKRLSFKEKLKKQDNQDSNVELEHLEEVELSKSNILLIGPTGSGKTLMAQTLAKHLDIPIA  101 (376)
T ss_dssp             TCCSCHHHHHHHHHHHHHHHHHHHHHHHHHHHCSHHHHHHHHHHHHTTCCCCCEEEECCTTSSHHHHHHHHHHHTTCCEE
T ss_pred             HccCcHHHHHHHHHHHHHHHHHHHhhhhhhhccccccccccccccccccCCCCEEEECCCCCCHHHHHHHHHHHhCCCEE
Confidence            47899999999998883211100                      00112357999999999999999999999999999


Q ss_pred             EEcCCCchhhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhH---------H
Q 005987          208 EWDTPTPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTA---------F  278 (666)
Q Consensus       208 E~nasd~~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~---------~  278 (666)
                      .+++.....      ....|..   ....+..++......  +      ....+.||+|||++.+.....         .
T Consensus       102 ~~~~~~~~~------~~~~g~~---~~~~~~~~~~~~~~~--~------~~~~~~vl~iDEi~~l~~~~~~~~~~~~~~~  164 (376)
T 1um8_A          102 ISDATSLTE------AGYVGED---VENILTRLLQASDWN--V------QKAQKGIVFIDEIDKISRLSENRSITRDVSG  164 (376)
T ss_dssp             EEEGGGCC-----------------CTHHHHHHHHHTTTC--H------HHHTTSEEEEETGGGC--------------C
T ss_pred             Eecchhhhh------cCcCCcc---HHHHHHHHHhhccch--h------hhcCCeEEEEcCHHHHhhhcCCCceecccch
Confidence            887653110      0001111   112233333221100  0      001245999999998754300         0


Q ss_pred             HHHHHHHHHHHhcC----------------------CCceEEEEecCCC----------------CCCcc------chhh
Q 005987          279 ERLRQCLLLLVRST----------------------HIPTAVVLTECGK----------------ADSVD------STAQ  314 (666)
Q Consensus       279 ~~l~~~L~~l~~~~----------------------~~PiViIit~~~~----------------~~s~d------~~~r  314 (666)
                      ..+++.|+.+++..                      ..++++++++...                .....      ...+
T Consensus       165 ~~~~~~Ll~~le~~~~~~~~~~~~~~~~~~~~~i~t~n~~~I~~~~~~~l~~~l~~R~~~~~~g~~~~~~~~~~~~~~~~  244 (376)
T 1um8_A          165 EGVQQALLKIVEGSLVNIPPKGGRKHPEGNFIQIDTSDILFICAGAFDGLAEIIKKRTTQNVLGFTQEKMSKKEQEAILH  244 (376)
T ss_dssp             HHHHHHHHHHHHCCEEC---------------CEECTTCEEEEEECCTTHHHHTTTSCSSCCCSCCCSSCCTTTTTTSGG
T ss_pred             HHHHHHHHHHhhccceecccccccccCCcceEEEecCCeEEEecCCHHHHHHHHHHHhcccccCCCchhhhccchhHHHh
Confidence            11455566666633                      1123333332100                00000      0000


Q ss_pred             --------hhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHH----HHH----H-----hCCCCCHHHHHHHHHHcC---C
Q 005987          315 --------SFEELQSILVDAGARKVALNPITNGSIKRTLSK----ICR----Q-----EQYSLSTEQIDLVAQASG---G  370 (666)
Q Consensus       315 --------~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~----I~~----~-----e~i~v~~~~l~~Ia~~s~---G  370 (666)
                              ...-..+++.|. ...|.|+|++.+++..++..    ++.    .     .++.+++++++.|+..+.   |
T Consensus       245 ~~~~~~l~~~~~~p~l~~R~-~~~i~~~~l~~~~l~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~l~~~~~~~~~  323 (376)
T 1um8_A          245 LVQTHDLVTYGLIPELIGRL-PVLSTLDSISLEAMVDILQKPKNALIKQYQQLFKMDEVDLIFEEEAIKEIAQLALERKT  323 (376)
T ss_dssp             GCCHHHHHHTTCCHHHHTTC-CEEEECCCCCHHHHHHHHHSSTTCHHHHHHHHHHTTTCEEEECHHHHHHHHHHHHHTTC
T ss_pred             hcCHHHHhhcCCChHHhcCC-CceeeccCCCHHHHHHHHhhhHHHHHHHHHHHHhhcCceEEECHHHHHHHHHHhccccc
Confidence                    000113444442 26799999999999998862    222    1     135689999999999866   9


Q ss_pred             cHHHHHHHHHHHhc
Q 005987          371 DIRQAITSLQFSSL  384 (666)
Q Consensus       371 DIR~AIn~LQf~~~  384 (666)
                      ++|.+.+.|+-++.
T Consensus       324 ~~R~L~~~le~~~~  337 (376)
T 1um8_A          324 GARGLRAIIEDFCL  337 (376)
T ss_dssp             TGGGHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHHH
Confidence            99999999988765

>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=99.30  E-value=1.2e-11  Score=139.90  Aligned_cols=215  Identities=13%  Similarity=0.074  Sum_probs=119.3

Q ss_pred             ccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCchhhhh
Q 005987          140 AEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTIWQE  219 (666)
Q Consensus       140 ~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~~~~e  219 (666)
                      ..+.+..-.++++|.++....+..++.-....  ...+..+++|+|||||||||+++++|..++.....++........+
T Consensus        72 ~~~~~~~l~~di~G~~~vk~~i~~~~~l~~~~--~~~~g~~vll~Gp~GtGKTtlar~ia~~l~~~~~~i~~~~~~~~~~  149 (543)
T 3m6a_A           72 LKEAGRLLDEEHHGLEKVKERILEYLAVQKLT--KSLKGPILCLAGPPGVGKTSLAKSIAKSLGRKFVRISLGGVRDESE  149 (543)
T ss_dssp             TTTGGGTHHHHCSSCHHHHHHHHHHHHHHHHS--SSCCSCEEEEESSSSSSHHHHHHHHHHHHTCEEEEECCCC------
T ss_pred             HHHHHHHHHHHhccHHHHHHHHHHHHHHHHhc--ccCCCCEEEEECCCCCCHHHHHHHHHHhcCCCeEEEEecccchhhh
Confidence            33333333466899999988887776532211  1223468999999999999999999999999999888765221111


Q ss_pred             hhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcCC------
Q 005987          220 YMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTH------  293 (666)
Q Consensus       220 ~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~~------  293 (666)
                      ........+  ......+...+..+.             ....||+|||++.+.... .+..++.|+..++..+      
T Consensus       150 ~~g~~~~~i--g~~~~~~~~~~~~a~-------------~~~~vl~lDEid~l~~~~-~~~~~~~LL~~ld~~~~~~~~~  213 (543)
T 3m6a_A          150 IRGHRRTYV--GAMPGRIIQGMKKAG-------------KLNPVFLLDEIDKMSSDF-RGDPSSAMLEVLDPEQNSSFSD  213 (543)
T ss_dssp             ----------------CHHHHHHTTC-------------SSSEEEEEEESSSCC----------CCGGGTCTTTTTBCCC
T ss_pred             hhhHHHHHh--ccCchHHHHHHHHhh-------------ccCCEEEEhhhhhhhhhh-ccCHHHHHHHHHhhhhcceeec
Confidence            100000000  000011111111110             122399999999886431 1112333444443211      


Q ss_pred             ---------CceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHH-----h-----CC
Q 005987          294 ---------IPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQ-----E-----QY  354 (666)
Q Consensus       294 ---------~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~-----e-----~i  354 (666)
                               ..+++|++ ++...      ...   .++++  |+..|.|.+|+.++...++.+.+..     .     ++
T Consensus       214 ~~~~~~~~~~~v~iI~t-tN~~~------~l~---~aL~~--R~~vi~~~~~~~~e~~~Il~~~l~~~~~~~~~~~~~~i  281 (543)
T 3m6a_A          214 HYIEETFDLSKVLFIAT-ANNLA------TIP---GPLRD--RMEIINIAGYTEIEKLEIVKDHLLPKQIKEHGLKKSNL  281 (543)
T ss_dssp             SSSCCCCBCSSCEEEEE-CSSTT------TSC---HHHHH--HEEEEECCCCCHHHHHHHHHHTHHHHHHHHTTCCGGGC
T ss_pred             ccCCeeecccceEEEec-cCccc------cCC---HHHHh--hcceeeeCCCCHHHHHHHHHHHHHHHHHHHcCCCcccc
Confidence                     11334433 22211      111   23333  4789999999999999998886532     2     45


Q ss_pred             CCCHHHHHHHHHHcC--CcHHHHHHHHHHHhc
Q 005987          355 SLSTEQIDLVAQASG--GDIRQAITSLQFSSL  384 (666)
Q Consensus       355 ~v~~~~l~~Ia~~s~--GDIR~AIn~LQf~~~  384 (666)
                      .++++++..|+....  |.+|..-+.++-+|.
T Consensus       282 ~i~~~~l~~l~~~~~~~~~vR~L~~~i~~~~~  313 (543)
T 3m6a_A          282 QLRDQAILDIIRYYTREAGVRSLERQLAAICR  313 (543)
T ss_dssp             EECHHHHHHHHHHHCCCSSSHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHhCChhhchhHHHHHHHHHHH
Confidence            678999999988654  677777666665553

>1iy2_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 3.20A {Thermus thermophilus} SCOP: c.37.1.20

Probab=99.29  E-value=5.3e-11  Score=122.79  Aligned_cols=208  Identities=16%  Similarity=0.230  Sum_probs=118.4

Q ss_pred             ccccCCCCccccccCHHHHHHHHHHHHHhhc-----CCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCc
Q 005987          140 AEKYKPRSLEELAVQRKKVEEVRAWFEERLG-----DSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTP  214 (666)
Q Consensus       140 ~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~-----~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~  214 (666)
                      +....+.++++++|.+....++++.......     ...-..+ +.++|+|||||||||+++++|..++..++.++..+.
T Consensus        31 ~~~~~~~~~~~i~g~~~~~~~l~~l~~~~~~~~~l~~~~~~~~-~gvll~Gp~GtGKTtl~~~i~~~~~~~~i~~~~~~~  109 (278)
T 1iy2_A           31 LTEAPKVTFKDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIP-KGVLLVGPPGVGKTHLARAVAGEARVPFITASGSDF  109 (278)
T ss_dssp             BCCCCCCCGGGSSSCHHHHHHHHHHHHHHHCHHHHHHTTCCCC-CEEEEECCTTSSHHHHHHHHHHHTTCCEEEEEHHHH
T ss_pred             ccCCCCCCHHHhCChHHHHHHHHHHHHHHHCHHHHHHcCCCCC-CeEEEECCCcChHHHHHHHHHHHcCCCEEEecHHHH
Confidence            3344678999999999988888876653211     0011223 459999999999999999999999877777764321


Q ss_pred             hhhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcch---------hHHHHHHHHH
Q 005987          215 TIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGR---------TAFERLRQCL  285 (666)
Q Consensus       215 ~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~---------~~~~~l~~~L  285 (666)
                             .....+    .....+..+++.+...            .+.++++||++.+...         .........+
T Consensus       110 -------~~~~~~----~~~~~i~~~~~~~~~~------------~~~i~~iDeid~l~~~~~~~~~~~~~~~~~~~~~l  166 (278)
T 1iy2_A          110 -------VEMFVG----VGAARVRDLFETAKRH------------APCIVFIDEIDAVGRKRGSGVGGGNDEREQTLNQL  166 (278)
T ss_dssp             -------HHSTTT----HHHHHHHHHHHHHHTS------------CSEEEEEETHHHHHCC--------CHHHHHHHHHH
T ss_pred             -------HHHHhh----HHHHHHHHHHHHHHhc------------CCcEEehhhhHhhhcccccccCCcchHHHHHHHHH
Confidence                   000011    1122344444444321            2569999999754211         1111121222


Q ss_pred             HHHHhcCC--CceEEEEecCCCCCCccchhhhhhHHHHHHhhc-CeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHH-HH
Q 005987          286 LLLVRSTH--IPTAVVLTECGKADSVDSTAQSFEELQSILVDA-GARKVALNPITNGSIKRTLSKICRQEQYSLSTE-QI  361 (666)
Q Consensus       286 ~~l~~~~~--~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~-r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~-~l  361 (666)
                      ...+..+.  ..++++ +.++.+...|         ..++++. ....|.|.+|+.++..++|+..+.  +..++++ .+
T Consensus       167 l~~lsgg~~~~~~i~~-a~t~~p~~ld---------~~l~r~~rf~~~i~i~~p~~~~r~~il~~~~~--~~~~~~~~~~  234 (278)
T 1iy2_A          167 LVEMDGFEKDTAIVVM-AATNRPDILD---------PALLRPGRFDRQIAIDAPDVKGREQILRIHAR--GKPLAEDVDL  234 (278)
T ss_dssp             HHHHTTCCTTCCEEEE-EEESCTTSSC---------HHHHSTTSSCCEEECCCCCHHHHHHHHHHHHT--TSCBCTTCCH
T ss_pred             HHHHhCCCCCCCEEEE-EecCCchhCC---------HhHcCCCcCCeEEEeCCcCHHHHHHHHHHHHc--cCCCCcccCH
Confidence            22233222  233333 3333322211         2222211 245799999999999999987764  3444443 37


Q ss_pred             HHHHHHcCCc----HHHHHHHHHHHh
Q 005987          362 DLVAQASGGD----IRQAITSLQFSS  383 (666)
Q Consensus       362 ~~Ia~~s~GD----IR~AIn~LQf~~  383 (666)
                      ..|+..+.|.    |+.+++..-..+
T Consensus       235 ~~la~~~~G~~~~dl~~l~~~a~~~a  260 (278)
T 1iy2_A          235 ALLAKRTPGFVGADLENLLNEAALLA  260 (278)
T ss_dssp             HHHHHTCTTCCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHcCCCCHHHHHHHHHHHHHHH
Confidence            8899888874    555555444433

>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=99.26  E-value=8e-11  Score=138.38  Aligned_cols=211  Identities=16%  Similarity=0.185  Sum_probs=127.4

Q ss_pred             ccccCHHHHHHHHHHHHHhhcCCC-CCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCchhhhhhhhcccCCc
Q 005987          150 ELAVQRKKVEEVRAWFEERLGDSK-DKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTIWQEYMHNCKTGL  228 (666)
Q Consensus       150 eLvg~~k~i~el~~wL~~~~~~~~-g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~~~~e~l~~~~~g~  228 (666)
                      +++|++..++.|...+........ .+.+...+||+||||||||++|+++|+.++..++.++++....  .+......|.
T Consensus       459 ~v~g~~~~~~~l~~~i~~~~~g~~~~~~p~~~~ll~G~~GtGKT~la~~la~~l~~~~~~i~~s~~~~--~~~~~~l~g~  536 (758)
T 1r6b_X          459 LVFGQDKAIEALTEAIKMARAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSKALGIELLRFDMSEYME--RHTVSRLIGA  536 (758)
T ss_dssp             TSCSCHHHHHHHHHHHHHHHTTCSCTTSCSEEEEEECSTTSSHHHHHHHHHHHHTCEEEEEEGGGCSS--SSCCSSSCCC
T ss_pred             hccCHHHHHHHHHHHHHHHhcccCCCCCCceEEEEECCCCCcHHHHHHHHHHHhcCCEEEEechhhcc--hhhHhhhcCC
Confidence            478999999999998886543210 1112247999999999999999999999999999998765211  0000001111


Q ss_pred             c--ccc--hhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcCC-----------
Q 005987          229 E--YTS--KLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTH-----------  293 (666)
Q Consensus       229 ~--~~s--~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~~-----------  293 (666)
                      .  |..  ....+...   +...            ++.||||||++.+..     .+++.|+.+++.++           
T Consensus       537 ~~g~~g~~~~~~l~~~---~~~~------------~~~vl~lDEi~~~~~-----~~~~~Ll~~le~~~~~~~~g~~~~~  596 (758)
T 1r6b_X          537 PPGYVGFDQGGLLTDA---VIKH------------PHAVLLLDEIEKAHP-----DVFNILLQVMDNGTLTDNNGRKADF  596 (758)
T ss_dssp             CSCSHHHHHTTHHHHH---HHHC------------SSEEEEEETGGGSCH-----HHHHHHHHHHHHSEEEETTTEEEEC
T ss_pred             CCCCcCccccchHHHH---HHhC------------CCcEEEEeCccccCH-----HHHHHHHHHhcCcEEEcCCCCEEec
Confidence            1  110  01112222   2211            246999999997753     24445666666542           


Q ss_pred             -CceEEEEecCCCCCCcc----ch-----hhhhh----HH-HHHHhhcCe-eEEEeCCCCHHHHHHHHHHHHHHh-----
Q 005987          294 -IPTAVVLTECGKADSVD----ST-----AQSFE----EL-QSILVDAGA-RKVALNPITNGSIKRTLSKICRQE-----  352 (666)
Q Consensus       294 -~PiViIit~~~~~~s~d----~~-----~r~l~----~L-~s~L~r~r~-~~I~F~p~s~~~i~kiL~~I~~~e-----  352 (666)
                       ..+||++++........    +.     .....    .+ .++++|  + ..|.|+|++.+++..++...+.+.     
T Consensus       597 ~~~~iI~tsN~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~l~~R--~~~~i~~~~l~~~~~~~i~~~~l~~~~~~~~  674 (758)
T 1r6b_X          597 RNVVLVMTTNAGVRETERKSIGLIHQDNSTDAMEEIKKIFTPEFRNR--LDNIIWFDHLSTDVIHQVVDKFIVELQVQLD  674 (758)
T ss_dssp             TTEEEEEEECSSCC-----------------CHHHHHHHSCHHHHTT--CSEEEECCCCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCeEEEEecCcchhhhhhcccCccccchHHHHHHHHHHhcCHHHHhh--CCcceeeCCCCHHHHHHHHHHHHHHHHHHHH
Confidence             12344444432111000    00     00000    11 234444  4 679999999999999999887642     


Q ss_pred             ----CCCCCHHHHHHHHHHc---CCcHHHHHHHHHHHhc
Q 005987          353 ----QYSLSTEQIDLVAQAS---GGDIRQAITSLQFSSL  384 (666)
Q Consensus       353 ----~i~v~~~~l~~Ia~~s---~GDIR~AIn~LQf~~~  384 (666)
                          .+.+++++++.|+..+   ++++|...+.|+-.+.
T Consensus       675 ~~~~~~~~~~~a~~~l~~~~~~~~~g~R~l~~~i~~~~~  713 (758)
T 1r6b_X          675 QKGVSLEVSQEARNWLAEKGYDRAMGARPMARVIQDNLK  713 (758)
T ss_dssp             HTTEEEEECHHHHHHHHHHHCBTTTBTTTHHHHHHHHHT
T ss_pred             HCCcEEEeCHHHHHHHHHhCCCcCCCchHHHHHHHHHHH
Confidence                3568999999999886   6668887777776654

>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=99.24  E-value=9.7e-11  Score=124.48  Aligned_cols=165  Identities=13%  Similarity=0.122  Sum_probs=112.4

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc---CCc---EEEEcCCCchhhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL---GAR---LYEWDTPTPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSP  252 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel---g~~---viE~nasd~~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~  252 (666)
                      +++||+||+|.||++++..+++.+   ++.   +++++..                      ..++++++.+...+..  
T Consensus        19 ~~yl~~G~e~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~----------------------~~~~~l~~~~~~~plf--   74 (343)
T 1jr3_D           19 AAYLLLGNDPLLLQESQDAVRQVAAAQGFEEHHTFSIDPN----------------------TDWNAIFSLCQAMSLF--   74 (343)
T ss_dssp             SEEEEEESCHHHHHHHHHHHHHHHHHHTCCEEEEEECCTT----------------------CCHHHHHHHHHHHHHC--
T ss_pred             cEEEEECCcHHHHHHHHHHHHHHHHhCCCCeeEEEEecCC----------------------CCHHHHHHHhcCcCCc--
Confidence            689999999999999999999976   331   2222210                      1334555555433311  


Q ss_pred             CCCCCCCCceEEEEeCCCC-CcchhHHHHHHHHHHHHHhcCCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEE
Q 005987          253 SIPGESKSSAILLIDDLPV-TNGRTAFERLRQCLLLLVRSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKV  331 (666)
Q Consensus       253 s~~~~~~~~~IIlIDEid~-l~~~~~~~~l~~~L~~l~~~~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I  331 (666)
                         +   .++|++|||++. +... .    .+.|..+++....-+++|+...... ..+...+.+   +.+.+  +|..+
T Consensus        75 ---~---~~kvvii~~~~~kl~~~-~----~~aLl~~le~p~~~~~~il~~~~~~-~~~~~~k~~---~~i~s--r~~~~  137 (343)
T 1jr3_D           75 ---A---SRQTLLLLLPENGPNAA-I----NEQLLTLTGLLHDDLLLIVRGNKLS-KAQENAAWF---TALAN--RSVQV  137 (343)
T ss_dssp             ---C---SCEEEEEECCSSCCCTT-H----HHHHHHHHTTCBTTEEEEEEESCCC-TTTTTSHHH---HHHTT--TCEEE
T ss_pred             ---c---CCeEEEEECCCCCCChH-H----HHHHHHHHhcCCCCeEEEEEcCCCC-hhhHhhHHH---HHHHh--CceEE
Confidence               1   357999999998 6532 2    2345666665432233333322111 011112222   23322  59999


Q ss_pred             EeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCcHHHHHHHHHHHhc
Q 005987          332 ALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASGGDIRQAITSLQFSSL  384 (666)
Q Consensus       332 ~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~s~GDIR~AIn~LQf~~~  384 (666)
                      .|.+++..++.+.|.+++..+|+.+++++++.|++.++||+|.+++.|+-++.
T Consensus       138 ~~~~l~~~~l~~~l~~~~~~~g~~i~~~a~~~l~~~~~gdl~~~~~elekl~l  190 (343)
T 1jr3_D          138 TCQTPEQAQLPRWVAARAKQLNLELDDAANQVLCYCYEGNLLALAQALERLSL  190 (343)
T ss_dssp             EECCCCTTHHHHHHHHHHHHTTCEECHHHHHHHHHSSTTCHHHHHHHHHHHHH
T ss_pred             EeeCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhchHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999997775

>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=99.23  E-value=3.8e-11  Score=128.77  Aligned_cols=62  Identities=15%  Similarity=0.163  Sum_probs=48.9

Q ss_pred             cccCHHHHHHHHHHHHHhhcC-------CCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCC
Q 005987          151 LAVQRKKVEEVRAWFEERLGD-------SKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTP  212 (666)
Q Consensus       151 Lvg~~k~i~el~~wL~~~~~~-------~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nas  212 (666)
                      ++|++..++.|..++......       .....+.+.+||+||||||||++|+++|+.++..++.++++
T Consensus        17 i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~~~~vll~GppGtGKT~la~~ia~~~~~~~~~~~~~   85 (363)
T 3hws_A           17 VIGQEQAKKVLAVAVYNHYKRLRNGDTSNGVELGKSNILLIGPTGSGKTLLAETLARLLDVPFTMADAT   85 (363)
T ss_dssp             CCSCHHHHHHHHHHHHHHHHHHHTTSCSSSCCCCCCCEEEECCTTSSHHHHHHHHHHHTTCCEEEEEHH
T ss_pred             ccCHHHHHHHHHHHHHHHHhhhccccccccccCCCCeEEEECCCCCCHHHHHHHHHHHcCCCEEEechH
Confidence            689999999999888533211       01112346899999999999999999999999999999865

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=99.23  E-value=9.6e-11  Score=137.74  Aligned_cols=199  Identities=16%  Similarity=0.190  Sum_probs=119.3

Q ss_pred             cccccCHHHHHHHHHHHHHhhcCCC-CCCCccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcCCCchhhhhhhhcc
Q 005987          149 EELAVQRKKVEEVRAWFEERLGDSK-DKFSTNVLVITGQAGVGKTATVRQIASHL---GARLYEWDTPTPTIWQEYMHNC  224 (666)
Q Consensus       149 ~eLvg~~k~i~el~~wL~~~~~~~~-g~~~~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~nasd~~~~~e~l~~~  224 (666)
                      .+++|++..++.|...+........ ...+...+||+||||||||++|+++|+.+   +..++.++++....        
T Consensus       491 ~~viGq~~a~~~l~~~i~~~~~~~~~~~~p~~~~Ll~Gp~GtGKT~lA~ala~~l~~~~~~~i~i~~s~~~~--------  562 (758)
T 3pxi_A          491 SRVIGQDEAVVAVAKAVRRARAGLKDPKRPIGSFIFLGPTGVGKTELARALAESIFGDEESMIRIDMSEYME--------  562 (758)
T ss_dssp             TTSCSCHHHHHHHHHHHHHHTTTCSCTTSCSEEEEEESCTTSSHHHHHHHHHHHHHSCTTCEEEEEGGGGCS--------
T ss_pred             CcCcChHHHHHHHHHHHHHHHcccCCCCCCceEEEEECCCCCCHHHHHHHHHHHhcCCCcceEEEechhccc--------
Confidence            4588999999999999987543211 11122369999999999999999999998   67788888764110        


Q ss_pred             cCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcCC-----------
Q 005987          225 KTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTH-----------  293 (666)
Q Consensus       225 ~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~~-----------  293 (666)
                         ....+ ...+...   +...            +..||||||++.+..     .+++.|+.+++.+.           
T Consensus       563 ---~~~~~-~~~l~~~---~~~~------------~~~vl~lDEi~~~~~-----~~~~~Ll~~le~g~~~~~~g~~~~~  618 (758)
T 3pxi_A          563 ---KHSTS-GGQLTEK---VRRK------------PYSVVLLDAIEKAHP-----DVFNILLQVLEDGRLTDSKGRTVDF  618 (758)
T ss_dssp             ---SCCCC----CHHH---HHHC------------SSSEEEEECGGGSCH-----HHHHHHHHHHHHSBCC-----CCBC
T ss_pred             ---ccccc-cchhhHH---HHhC------------CCeEEEEeCccccCH-----HHHHHHHHHhccCeEEcCCCCEecc
Confidence               00000 1112111   2111            235999999997753     23344555555532           


Q ss_pred             -CceEEEEecCCCCCCccchhhhh-hHH-HHHHhhcCe-eEEEeCCCCHHHHHHHHHHHHHHh---------CCCCCHHH
Q 005987          294 -IPTAVVLTECGKADSVDSTAQSF-EEL-QSILVDAGA-RKVALNPITNGSIKRTLSKICRQE---------QYSLSTEQ  360 (666)
Q Consensus       294 -~PiViIit~~~~~~s~d~~~r~l-~~L-~s~L~r~r~-~~I~F~p~s~~~i~kiL~~I~~~e---------~i~v~~~~  360 (666)
                       ..+||++++..... .+.....+ ..+ ..++.|  + ..|.|+|++.+++.+++...+...         .+.+++++
T Consensus       619 ~~~~iI~ttn~~~~~-~~~~~~~~~~~f~p~l~~R--l~~~i~~~~l~~~~~~~i~~~~l~~~~~~~~~~~~~~~~~~~a  695 (758)
T 3pxi_A          619 RNTILIMTSNVGASE-KDKVMGELKRAFRPEFINR--IDEIIVFHSLEKKHLTEIVSLMSDQLTKRLKEQDLSIELTDAA  695 (758)
T ss_dssp             TTCEEEEEESSSTTC-CHHHHHHHHHHSCHHHHTT--SSEEEECC--CHHHHHHHHHHHHHHHHHHHHTTTCEEEECHHH
T ss_pred             CCeEEEEeCCCChhh-HHHHHHHHHhhCCHHHHhh--CCeEEecCCCCHHHHHHHHHHHHHHHHHHHHhCCCeEEECHHH
Confidence             12445555432211 00000000 011 234443  5 799999999999999998887652         35689999


Q ss_pred             HHHHHHH---cCCcHHHHHHHHHHH
Q 005987          361 IDLVAQA---SGGDIRQAITSLQFS  382 (666)
Q Consensus       361 l~~Ia~~---s~GDIR~AIn~LQf~  382 (666)
                      ++.|+..   -.|.+|..-+.++-.
T Consensus       696 ~~~l~~~~~~~~~~~R~L~~~i~~~  720 (758)
T 3pxi_A          696 KAKVAEEGVDLEYGARPLRRAIQKH  720 (758)
T ss_dssp             HHHHHGGGCCTTTTTTTHHHHHHHH
T ss_pred             HHHHHHhCCCCCCCChHHHHHHHHH
Confidence            9999875   346666665655543

>2x8a_A Nuclear valosin-containing protein-like; nuclear protein; 2.60A {Homo sapiens}

Probab=99.22  E-value=1e-10  Score=120.65  Aligned_cols=207  Identities=12%  Similarity=0.176  Sum_probs=114.3

Q ss_pred             CCCCccccccCHHHHHHHHHHHHHhhcC------CCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCchhh
Q 005987          144 KPRSLEELAVQRKKVEEVRAWFEERLGD------SKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTIW  217 (666)
Q Consensus       144 ~P~sl~eLvg~~k~i~el~~wL~~~~~~------~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~~~  217 (666)
                      ...+++|+.|.+...++|++.+...+..      -.-..+ +.++|+|||||||||+++++|.+++...+.++.++..  
T Consensus         5 ~~~~~~di~g~~~~~~~l~~~i~~~~~~~~~l~~~~l~~~-~GvlL~Gp~GtGKTtLakala~~~~~~~i~i~g~~l~--   81 (274)
T 2x8a_A            5 PNVTWADIGALEDIREELTMAILAPVRNPDQFKALGLVTP-AGVLLAGPPGCGKTLLAKAVANESGLNFISVKGPELL--   81 (274)
T ss_dssp             -------CCHHHHHHHHHHHHHTHHHHSHHHHHHTTCCCC-SEEEEESSTTSCHHHHHHHHHHHTTCEEEEEETTTTC--
T ss_pred             CCCCHHHhCCHHHHHHHHHHHHHHHhhCHHHHHHcCCCCC-CeEEEECCCCCcHHHHHHHHHHHcCCCEEEEEcHHHH--
Confidence            3467899999999888888765422211      111223 5699999999999999999999999988888876411  


Q ss_pred             hhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhH------HHHHHHHHHHHHhc
Q 005987          218 QEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTA------FERLRQCLLLLVRS  291 (666)
Q Consensus       218 ~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~------~~~l~~~L~~l~~~  291 (666)
                               ..........+..+++.+...            .+.++++||++.+.....      ..++...+...+..
T Consensus        82 ---------~~~~~~~~~~i~~vf~~a~~~------------~p~i~~~Deid~~~~~r~~~~~~~~~~~~~~~l~~Lsg  140 (274)
T 2x8a_A           82 ---------NMYVGESERAVRQVFQRAKNS------------APCVIFFDEVDALCPRRSDRETGASVRVVNQLLTEMDG  140 (274)
T ss_dssp             ---------SSTTHHHHHHHHHHHHHHHHT------------CSEEEEEETCTTTCC---------CTTHHHHHHHHHHT
T ss_pred             ---------hhhhhHHHHHHHHHHHHHHhc------------CCCeEeeehhhhhhcccCCCcchHHHHHHHHHHHhhhc
Confidence                     111111122344445544322            257999999997543210      01122223333333


Q ss_pred             CC-CceEEEEecCCCCCCccchhhhhhHHHHHHhh--cCeeEEEeCCCCHHHHHHHHHHHHHHhC-CCCC-HHHHHHHHH
Q 005987          292 TH-IPTAVVLTECGKADSVDSTAQSFEELQSILVD--AGARKVALNPITNGSIKRTLSKICRQEQ-YSLS-TEQIDLVAQ  366 (666)
Q Consensus       292 ~~-~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r--~r~~~I~F~p~s~~~i~kiL~~I~~~e~-i~v~-~~~l~~Ia~  366 (666)
                      +. ...+++++.++.+.       .   |.+.+.|  +.-..|.|..|+..+..++|+.++.... ..+. +..++.|+.
T Consensus       141 g~~~~~~i~ia~tn~p~-------~---LD~al~r~gRfd~~i~~~~P~~~~r~~il~~~~~~~~~~~~~~~~~~~~la~  210 (274)
T 2x8a_A          141 LEARQQVFIMAATNRPD-------I---IDPAILRPGRLDKTLFVGLPPPADRLAILKTITKNGTKPPLDADVNLEAIAG  210 (274)
T ss_dssp             CCSTTCEEEEEEESCGG-------G---SCHHHHSTTSSCEEEECCSCCHHHHHHHHHHHTTTTBTTBBCTTCCHHHHHT
T ss_pred             ccccCCEEEEeecCChh-------h---CCHhhcCcccCCeEEEeCCcCHHHHHHHHHHHHhcccCCCCccccCHHHHHH
Confidence            22 22333333333322       1   2223332  1356789999999999999998775422 2222 223556664


Q ss_pred             ------HcCCcHHHHHHHHHHHhc
Q 005987          367 ------ASGGDIRQAITSLQFSSL  384 (666)
Q Consensus       367 ------~s~GDIR~AIn~LQf~~~  384 (666)
                            .+++||...++..-+.+.
T Consensus       211 ~~~~~g~sgadl~~l~~~a~~~a~  234 (274)
T 2x8a_A          211 DLRCDCYTGADLSALVREASICAL  234 (274)
T ss_dssp             CSGGGSCCHHHHHHHHHHHHHHHH
T ss_pred             hhccCCcCHHHHHHHHHHHHHHHH
Confidence                  345688877765554443

>1ojl_A Transcriptional regulatory protein ZRAR; response regulator, two component system, AAA domain, NTRC family, DNA-binding; HET: ATP; 3.0A {Salmonella typhimurium}

Probab=99.22  E-value=1.4e-10  Score=121.40  Aligned_cols=204  Identities=12%  Similarity=0.186  Sum_probs=118.8

Q ss_pred             cccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcCCCchh--hhhhhhc
Q 005987          149 EELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL---GARLYEWDTPTPTI--WQEYMHN  223 (666)
Q Consensus       149 ~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~nasd~~~--~~e~l~~  223 (666)
                      ++++|+...++++...+.....     .. ..+||+||||||||++|+++++..   +..++.+|++....  ....+..
T Consensus         2 ~~iig~s~~~~~~~~~~~~~a~-----~~-~~vLi~Ge~GtGKt~lAr~i~~~~~~~~~~~v~v~~~~~~~~l~~~~lfg   75 (304)
T 1ojl_A            2 SHMIGSSPAMQHLLNEIAMVAP-----SD-ATVLIHGDSGTGKELVARALHACSARSDRPLVTLNCAALNESLLESELFG   75 (304)
T ss_dssp             -CCCCCSHHHHHHHHHHHHHCS-----TT-SCEEEESCTTSCHHHHHHHHHHHSSCSSSCCCEEECSSCCHHHHHHHHTC
T ss_pred             CCcEECCHHHHHHHHHHHHHhC-----CC-CcEEEECCCCchHHHHHHHHHHhCcccCCCeEEEeCCCCChHHHHHHhcC
Confidence            3578999999999999887532     11 469999999999999999999976   56778888765211  0000100


Q ss_pred             ccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcCC----------
Q 005987          224 CKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTH----------  293 (666)
Q Consensus       224 ~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~~----------  293 (666)
                      ...|. ++.........++.+               .+.+|||||++.+...     .+..|..+++...          
T Consensus        76 ~~~g~-~tg~~~~~~g~~~~a---------------~~g~L~LDEi~~l~~~-----~q~~Ll~~l~~~~~~~~g~~~~~  134 (304)
T 1ojl_A           76 HEKGA-FTGADKRREGRFVEA---------------DGGTLFLDEIGDISPL-----MQVRLLRAIQEREVQRVGSNQTI  134 (304)
T ss_dssp             CCSSC-CC---CCCCCHHHHH---------------TTSEEEEESCTTCCHH-----HHHHHHHHHHSSBCCBTTBCCCC
T ss_pred             ccccc-cCchhhhhcCHHHhc---------------CCCEEEEeccccCCHH-----HHHHHHHHHhcCEeeecCCcccc
Confidence            00110 000000000111111               1248999999988643     2333445555432          


Q ss_pred             -C-ceEEEEecCCCCCCccch-hhhhhHHHHHHhhcCeeEEEeCCCC--HHHHHHHHHHHH----HHhC---CCCCHHHH
Q 005987          294 -I-PTAVVLTECGKADSVDST-AQSFEELQSILVDAGARKVALNPIT--NGSIKRTLSKIC----RQEQ---YSLSTEQI  361 (666)
Q Consensus       294 -~-PiViIit~~~~~~s~d~~-~r~l~~L~s~L~r~r~~~I~F~p~s--~~~i~kiL~~I~----~~e~---i~v~~~~l  361 (666)
                       . ..||++++....   +.. ...+.  ..+..|.....|.++|+.  .+++..++...+    ...+   ..++++++
T Consensus       135 ~~~~riI~atn~~l~---~~v~~g~fr--~~L~~Rl~~~~i~lPpL~eR~edi~~l~~~~l~~~~~~~~~~~~~~s~~a~  209 (304)
T 1ojl_A          135 SVDVRLIAATHRDLA---EEVSAGRFR--QDLYYRLNVVAIEMPSLRQRREDIPLLADHFLRRFAERNRKVVKGFTPQAM  209 (304)
T ss_dssp             BCCCEEEEEESSCHH---HHHHHTSSC--HHHHHHHSSEEEECCCSGGGGGGHHHHHHHHHHHHHHHTTCCCCCBCHHHH
T ss_pred             cCCeEEEEecCccHH---HHHHhCCcH--HHHHhhcCeeEEeccCHHHhHhhHHHHHHHHHHHHHHHhccCccCCCHHHH
Confidence             1 233444432100   000 00110  223334346678899988  566665555444    3333   56899999


Q ss_pred             HHHHHHc-CCcHHHHHHHHHHHhc
Q 005987          362 DLVAQAS-GGDIRQAITSLQFSSL  384 (666)
Q Consensus       362 ~~Ia~~s-~GDIR~AIn~LQf~~~  384 (666)
                      +.|...+ .|++|...|.++.++.
T Consensus       210 ~~L~~~~wpGnvReL~~~l~~~~~  233 (304)
T 1ojl_A          210 DLLIHYDWPGNIRELENAIERAVV  233 (304)
T ss_dssp             HHHHHCCCSSHHHHHHHHHHHHHH
T ss_pred             HHHHcCCCCCCHHHHHHHHHHHHH
Confidence            9999987 8999999999998775

>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=99.18  E-value=4.5e-10  Score=119.03  Aligned_cols=56  Identities=16%  Similarity=0.163  Sum_probs=41.0

Q ss_pred             cccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCC
Q 005987          141 EKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGA  204 (666)
Q Consensus       141 eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~  204 (666)
                      ..-+|.+|++++|++..++.+...+..      +.  ...+||+||||||||++|+++|+.++.
T Consensus        16 ~~~~~~~f~~i~G~~~~~~~l~~~~~~------~~--~~~vLl~G~~GtGKT~la~~la~~~~~   71 (350)
T 1g8p_A           16 KTRPVFPFSAIVGQEDMKLALLLTAVD------PG--IGGVLVFGDRGTGKSTAVRALAALLPE   71 (350)
T ss_dssp             --CCCCCGGGSCSCHHHHHHHHHHHHC------GG--GCCEEEECCGGGCTTHHHHHHHHHSCC
T ss_pred             CCCCCCCchhccChHHHHHHHHHHhhC------CC--CceEEEECCCCccHHHHHHHHHHhCcc
Confidence            344678999999999866654333221      11  135999999999999999999999863

>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=99.13  E-value=2.1e-10  Score=136.51  Aligned_cols=213  Identities=15%  Similarity=0.195  Sum_probs=127.4

Q ss_pred             cccccCHHHHHHHHHHHHHhhcC--CCCCCCccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcCCCchhhhhhhhc
Q 005987          149 EELAVQRKKVEEVRAWFEERLGD--SKDKFSTNVLVITGQAGVGKTATVRQIASHL---GARLYEWDTPTPTIWQEYMHN  223 (666)
Q Consensus       149 ~eLvg~~k~i~el~~wL~~~~~~--~~g~~~~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~nasd~~~~~e~l~~  223 (666)
                      .+++|++..++.|...+......  .+++ +...+||+||||||||++|++||+.+   +..++.++++.....  +...
T Consensus       558 ~~viG~~~a~~~l~~~i~~~~~g~~~~~~-p~~~vLl~Gp~GtGKT~lA~~la~~~~~~~~~~i~i~~~~~~~~--~~~s  634 (854)
T 1qvr_A          558 KRVVGQDEAIRAVADAIRRARAGLKDPNR-PIGSFLFLGPTGVGKTELAKTLAATLFDTEEAMIRIDMTEYMEK--HAVS  634 (854)
T ss_dssp             HHSCSCHHHHHHHHHHHHHHGGGCSCSSS-CSEEEEEBSCSSSSHHHHHHHHHHHHHSSGGGEEEECTTTCCSS--GGGG
T ss_pred             cccCCcHHHHHHHHHHHHHHhcccCCCCC-CceEEEEECCCCCCHHHHHHHHHHHhcCCCCcEEEEechhccch--hHHH
Confidence            46799999999999999875431  1122 22479999999999999999999999   778999998753210  0000


Q ss_pred             ccCCc--cccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcCC--------
Q 005987          224 CKTGL--EYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTH--------  293 (666)
Q Consensus       224 ~~~g~--~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~~--------  293 (666)
                      ...|.  .|... +....+.+.+...            +..+|||||++.+..     .+++.|+.+++.+.        
T Consensus       635 ~l~g~~~~~~G~-~~~g~l~~~~~~~------------~~~vl~lDEi~~l~~-----~~~~~Ll~~l~~~~~~~~~g~~  696 (854)
T 1qvr_A          635 RLIGAPPGYVGY-EEGGQLTEAVRRR------------PYSVILFDEIEKAHP-----DVFNILLQILDDGRLTDSHGRT  696 (854)
T ss_dssp             GC---------------CHHHHHHHC------------SSEEEEESSGGGSCH-----HHHHHHHHHHTTTEECCSSSCC
T ss_pred             HHcCCCCCCcCc-cccchHHHHHHhC------------CCeEEEEecccccCH-----HHHHHHHHHhccCceECCCCCE
Confidence            00110  00000 0001122222211            246999999997753     24455666666542        


Q ss_pred             ----CceEEEEecCCCCCCcc-------c--hhhhh-----hHH-HHHHhhcCe-eEEEeCCCCHHHHHHHHHHHHHHh-
Q 005987          294 ----IPTAVVLTECGKADSVD-------S--TAQSF-----EEL-QSILVDAGA-RKVALNPITNGSIKRTLSKICRQE-  352 (666)
Q Consensus       294 ----~PiViIit~~~~~~s~d-------~--~~r~l-----~~L-~s~L~r~r~-~~I~F~p~s~~~i~kiL~~I~~~e-  352 (666)
                          ..+||++++.......+       .  ....+     ..+ ..++.|  + ..+.|.|++.+++..++...+... 
T Consensus       697 vd~~~~iiI~tsn~~~~~~~~~~~~~~~~~~l~~~v~~~~~~~f~~~l~~R--l~~~i~~~pl~~edi~~i~~~~l~~~~  774 (854)
T 1qvr_A          697 VDFRNTVIILTSNLGSPLILEGLQKGWPYERIRDEVFKVLQQHFRPEFLNR--LDEIVVFRPLTKEQIRQIVEIQLSYLR  774 (854)
T ss_dssp             EECTTEEEEEECCTTHHHHHHHHHTTCCHHHHHHHHHHHHHTTSCHHHHHT--CSBCCBCCCCCHHHHHHHHHHHHHHHH
T ss_pred             eccCCeEEEEecCcChHHHhhhcccccchHHHHHHHHHHHHhhCCHHHHHh--cCeEEeCCCCCHHHHHHHHHHHHHHHH
Confidence                22344444421100000       0  00000     001 223333  4 678999999999999988776531 


Q ss_pred             --------CCCCCHHHHHHHHHHcC---CcHHHHHHHHHHHhc
Q 005987          353 --------QYSLSTEQIDLVAQASG---GDIRQAITSLQFSSL  384 (666)
Q Consensus       353 --------~i~v~~~~l~~Ia~~s~---GDIR~AIn~LQf~~~  384 (666)
                              .+.+++++++.|+..+.   |++|...+.++-+..
T Consensus       775 ~~~~~~~~~~~~~~~a~~~L~~~~~~~~gn~R~L~~~i~~~~~  817 (854)
T 1qvr_A          775 ARLAEKRISLELTEAAKDFLAERGYDPVFGARPLRRVIQRELE  817 (854)
T ss_dssp             HHHHTTTCEEEECHHHHHHHHHHHCBTTTBTSTHHHHHHHHTH
T ss_pred             HHHHhCCceEEECHHHHHHHHHcCCCCCCChHHHHHHHHHHHH
Confidence                    24689999999999865   999988888877654

>2qen_A Walker-type ATPase; unknown function; HET: ADP; 2.25A {Pyrococcus abyssi}

Probab=99.07  E-value=6.8e-09  Score=109.35  Aligned_cols=202  Identities=12%  Similarity=0.094  Sum_probs=117.9

Q ss_pred             CCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCch--------
Q 005987          144 KPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPT--------  215 (666)
Q Consensus       144 ~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~--------  215 (666)
                      .|.....++|+++.++.|..++..      +    +.++|+||+|+|||++++.++++.+  ++.++.....        
T Consensus         7 ~~~~~~~~~gR~~el~~L~~~l~~------~----~~v~i~G~~G~GKT~Ll~~~~~~~~--~~~~~~~~~~~~~~~~~~   74 (350)
T 2qen_A            7 PKTRREDIFDREEESRKLEESLEN------Y----PLTLLLGIRRVGKSSLLRAFLNERP--GILIDCRELYAERGHITR   74 (350)
T ss_dssp             CCCSGGGSCSCHHHHHHHHHHHHH------C----SEEEEECCTTSSHHHHHHHHHHHSS--EEEEEHHHHHHTTTCBCH
T ss_pred             CCCChHhcCChHHHHHHHHHHHhc------C----CeEEEECCCcCCHHHHHHHHHHHcC--cEEEEeecccccccCCCH
Confidence            344567789999999999999875      3    4899999999999999999999986  4555432210        


Q ss_pred             -hhhhhhhcccC----------------CccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcch--h
Q 005987          216 -IWQEYMHNCKT----------------GLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGR--T  276 (666)
Q Consensus       216 -~~~e~l~~~~~----------------g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~--~  276 (666)
                       .....+.....                |.........+..++..+.....        .+.+.+|+|||++.+...  .
T Consensus        75 ~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~--------~~~~~vlvlDe~~~~~~~~~~  146 (350)
T 2qen_A           75 EELIKELQSTISPFQKFQSKFKISLNLKFLTLEPRKLSLREVFRELNDLGE--------ELGEFIVAFDEAQYLRFYGSR  146 (350)
T ss_dssp             HHHHHHHHHHSCSHHHHHHHHTCCCCCGGGTSCGGGCCHHHHHHHHHHHHH--------HHSCEEEEEETGGGGGGBTTT
T ss_pred             HHHHHHHHHHHHHHHhHhhhceeEEEecceeeccccchHHHHHHHHHHHHh--------ccCCEEEEEeCHHHHhccCcc
Confidence             00011110000                10000000112222222211100        002579999999987530  0


Q ss_pred             HHHHHHHHHHHHHhcCCCceEEEEecCCCCCCccchhhhhhHH------HHHHhhcCeeEEEeCCCCHHHHHHHHHHHHH
Q 005987          277 AFERLRQCLLLLVRSTHIPTAVVLTECGKADSVDSTAQSFEEL------QSILVDAGARKVALNPITNGSIKRTLSKICR  350 (666)
Q Consensus       277 ~~~~l~~~L~~l~~~~~~PiViIit~~~~~~s~d~~~r~l~~L------~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~  350 (666)
                      ....+...|..+.+... ++.+|++....        ..+..+      ...+.......+.+.|++.+++.+++...+.
T Consensus       147 ~~~~~~~~L~~~~~~~~-~~~~il~g~~~--------~~l~~~l~~~~~~~~l~~~~~~~i~l~pl~~~e~~~~l~~~~~  217 (350)
T 2qen_A          147 GGKELLALFAYAYDSLP-NLKIILTGSEV--------GLLHDFLKITDYESPLYGRIAGEVLVKPFDKDTSVEFLKRGFR  217 (350)
T ss_dssp             TTHHHHHHHHHHHHHCT-TEEEEEEESSH--------HHHHHHHCTTCTTSTTTTCCCEEEECCCCCHHHHHHHHHHHHH
T ss_pred             chhhHHHHHHHHHHhcC-CeEEEEECCcH--------HHHHHHHhhcCCCCccccCccceeeCCCCCHHHHHHHHHHHHH
Confidence            00123333444444432 34444443210        001111      0111111246899999999999999998887


Q ss_pred             HhCCCCCHHHHHHHHHHcCCcHHH
Q 005987          351 QEQYSLSTEQIDLVAQASGGDIRQ  374 (666)
Q Consensus       351 ~e~i~v~~~~l~~Ia~~s~GDIR~  374 (666)
                      ..+..++++.+..|+..++|..+.
T Consensus       218 ~~~~~~~~~~~~~i~~~tgG~P~~  241 (350)
T 2qen_A          218 EVNLDVPENEIEEAVELLDGIPGW  241 (350)
T ss_dssp             TTTCCCCHHHHHHHHHHHTTCHHH
T ss_pred             HcCCCCCHHHHHHHHHHhCCCHHH
Confidence            778888999999999999999974

>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=99.06  E-value=5.9e-09  Score=113.95  Aligned_cols=64  Identities=19%  Similarity=0.291  Sum_probs=49.8

Q ss_pred             ccccCHHHHHHHHHHHHHhhc------CCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCC
Q 005987          150 ELAVQRKKVEEVRAWFEERLG------DSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPT  213 (666)
Q Consensus       150 eLvg~~k~i~el~~wL~~~~~------~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd  213 (666)
                      +++|+++.++.|..++.....      ......+++.+||+||||||||++|+++|+.++..++.++++.
T Consensus        16 ~IvGqe~ak~~l~~av~~~~~r~~~~~~~~~~~~~~~iLl~GppGtGKT~lar~lA~~l~~~~~~v~~~~   85 (444)
T 1g41_A           16 HIIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAKLANAPFIKVEATK   85 (444)
T ss_dssp             TCCSCHHHHHHHHHHHHHHHHHHHSCTTTTTTCCCCCEEEECCTTSSHHHHHHHHHHHTTCCEEEEEGGG
T ss_pred             HhCCHHHHHHHHHHHHHHHHhhhccccccccccCCceEEEEcCCCCCHHHHHHHHHHHcCCCceeecchh
Confidence            579999999999888854211      0111223467999999999999999999999999999887643

>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=99.05  E-value=1.3e-09  Score=104.56  Aligned_cols=66  Identities=23%  Similarity=0.323  Sum_probs=48.0

Q ss_pred             ccccCCCCccccccC----HHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc----CCcEEEEc
Q 005987          140 AEKYKPRSLEELAVQ----RKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL----GARLYEWD  210 (666)
Q Consensus       140 ~eKY~P~sl~eLvg~----~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel----g~~viE~n  210 (666)
                      .++|+|.+|++++..    ++.++.++.|+++...     .+++.++|+||||+||||+++++|..+    |..++.++
T Consensus         1 ~~r~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~g~~~~l~G~~G~GKTtL~~~i~~~~~~~~g~~~~~~~   74 (180)
T 3ec2_A            1 AKRYWNANLDTYHPKNVSQNRALLTIRVFVHNFNP-----EEGKGLTFVGSPGVGKTHLAVATLKAIYEKKGIRGYFFD   74 (180)
T ss_dssp             CCSCTTCCSSSCCCCSHHHHHHHHHHHHHHHSCCG-----GGCCEEEECCSSSSSHHHHHHHHHHHHHHHSCCCCCEEE
T ss_pred             CchhhhCccccccCCCHHHHHHHHHHHHHHHhccc-----cCCCEEEEECCCCCCHHHHHHHHHHHHHHHcCCeEEEEE
Confidence            368999999999873    4455555555554211     123689999999999999999999987    55555544

>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural genomics, center for structural genomics; 2.80A {Escherichia coli}

Probab=98.94  E-value=2.3e-09  Score=99.51  Aligned_cols=57  Identities=14%  Similarity=0.205  Sum_probs=45.2

Q ss_pred             ccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcCCC
Q 005987          150 ELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL---GARLYEWDTPT  213 (666)
Q Consensus       150 eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~nasd  213 (666)
                      +++|+...++++...++.+..   .  . ..+||+||||||||++|+++++..   +..++ +++..
T Consensus         2 ~iiG~s~~~~~~~~~~~~~a~---~--~-~~vll~G~~GtGKt~lA~~i~~~~~~~~~~~v-~~~~~   61 (145)
T 3n70_A            2 ELIGRSEWINQYRRRLQQLSE---T--D-IAVWLYGAPGTGRMTGARYLHQFGRNAQGEFV-YRELT   61 (145)
T ss_dssp             --CCSSHHHHHHHHHHHHHTT---C--C-SCEEEESSTTSSHHHHHHHHHHSSTTTTSCCE-EEECC
T ss_pred             CceeCCHHHHHHHHHHHHHhC---C--C-CCEEEECCCCCCHHHHHHHHHHhCCccCCCEE-EECCC
Confidence            678999999999999987532   1  1 469999999999999999999986   56677 77654

>3k1j_A LON protease, ATP-dependent protease LON; ATP-binding, nucleotide-binding, Pro hydrolase; HET: ADP PE8; 2.00A {Thermococcus onnurineus}

Probab=98.92  E-value=4.9e-09  Score=119.96  Aligned_cols=56  Identities=16%  Similarity=0.242  Sum_probs=50.0

Q ss_pred             ccccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcC
Q 005987          138 LWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLG  203 (666)
Q Consensus       138 ~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg  203 (666)
                      ....+|+|+++++++|++..++.+...+..      +    ..++|+|||||||||+++++|+.+.
T Consensus        30 ~~~~~~rp~~l~~i~G~~~~l~~l~~~i~~------g----~~vll~Gp~GtGKTtlar~ia~~l~   85 (604)
T 3k1j_A           30 TEEIEVPEKLIDQVIGQEHAVEVIKTAANQ------K----RHVLLIGEPGTGKSMLGQAMAELLP   85 (604)
T ss_dssp             GGGSCCCSSHHHHCCSCHHHHHHHHHHHHT------T----CCEEEECCTTSSHHHHHHHHHHTSC
T ss_pred             cCcccccccccceEECchhhHhhccccccC------C----CEEEEEeCCCCCHHHHHHHHhccCC
Confidence            456799999999999999999999888875      3    4799999999999999999999884

>3nbx_X ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structure, rossman fold, hydro; HET: ADP; 2.91A {Escherichia coli}

Probab=98.89  E-value=1.5e-08  Score=112.88  Aligned_cols=193  Identities=11%  Similarity=0.110  Sum_probs=106.6

Q ss_pred             ccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCC--cEEEEcCCCchhhhhhhhcccCC
Q 005987          150 ELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGA--RLYEWDTPTPTIWQEYMHNCKTG  227 (666)
Q Consensus       150 eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~--~viE~nasd~~~~~e~l~~~~~g  227 (666)
                      .++|++..++.+...+..      +    .++||+||||||||++|+++|+.++.  .+...+..- ....+.+.. ..+
T Consensus        23 ~ivGq~~~i~~l~~al~~------~----~~VLL~GpPGtGKT~LAraLa~~l~~~~~f~~~~~~~-~t~~dL~G~-~~~   90 (500)
T 3nbx_X           23 GLYERSHAIRLCLLAALS------G----ESVFLLGPPGIAKSLIARRLKFAFQNARAFEYLMTRF-STPEEVFGP-LSI   90 (500)
T ss_dssp             TCSSCHHHHHHHHHHHHH------T----CEEEEECCSSSSHHHHHHHGGGGBSSCCEEEEECCTT-CCHHHHHCC-BC-
T ss_pred             hhHHHHHHHHHHHHHHhc------C----CeeEeecCchHHHHHHHHHHHHHHhhhhHHHHHHHhc-CCHHHhcCc-ccH
Confidence            468999999888877765      2    47999999999999999999999843  223333211 000111100 000


Q ss_pred             ccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcC-----------CCce
Q 005987          228 LEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRST-----------HIPT  296 (666)
Q Consensus       228 ~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~-----------~~Pi  296 (666)
                      ..          . .....+...   ..|....+.||+|||++.+..     ..+..|...++..           ..++
T Consensus        91 ~~----------~-~~~g~~~~~---~~g~l~~~~IL~IDEI~r~~~-----~~q~~LL~~lee~~v~i~G~~~~~~~~~  151 (500)
T 3nbx_X           91 QA----------L-KDEGRYERL---TSGYLPEAEIVFLDEIWKAGP-----AILNTLLTAINERQFRNGAHVEKIPMRL  151 (500)
T ss_dssp             --------------------CBC---CTTSGGGCSEEEEESGGGCCH-----HHHHHHHHHHHSSEEECSSSEEECCCCE
T ss_pred             HH----------H-hhchhHHhh---hccCCCcceeeeHHhHhhhcH-----HHHHHHHHHHHHHhccCCCCcCCcchhh
Confidence            00          0 000011000   011100245899999987643     2334455555432           2244


Q ss_pred             EEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCH-HHHHHHHHHHH-----------------------HHh
Q 005987          297 AVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITN-GSIKRTLSKIC-----------------------RQE  352 (666)
Q Consensus       297 ViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~-~~i~kiL~~I~-----------------------~~e  352 (666)
                      ++++++. .+. .   ..   .+.+++.|+ ...|.+.+|+. ++...+|.+.+                       ...
T Consensus       152 iI~ATN~-lpe-~---~~---~~~aLldRF-~~~i~v~~p~~~ee~~~IL~~~~~~~~~~~~~~~~~~~e~l~~~~~~~~  222 (500)
T 3nbx_X          152 LVAASNE-LPE-A---DS---SLEALYDRM-LIRLWLDKVQDKANFRSMLTSQQDENDNPVPDALQVTDEEYERWQKEIG  222 (500)
T ss_dssp             EEEEESS-CCC-T---TC---TTHHHHTTC-CEEEECCSCCCHHHHHHHHTCCCCTTSCCSCTTTSBCHHHHHHHHHHHT
T ss_pred             hhhcccc-CCC-c---cc---cHHHHHHHH-HHHHHHHHhhhhhhHHHHHhcccccCCCCCCccceecHHHHHHHHhcCC
Confidence            4555541 111 0   01   124555553 67789999987 55666665433                       123


Q ss_pred             CCCCCHHHHHHHHHHc----------CCcHHHHHHHHHHH
Q 005987          353 QYSLSTEQIDLVAQAS----------GGDIRQAITSLQFS  382 (666)
Q Consensus       353 ~i~v~~~~l~~Ia~~s----------~GDIR~AIn~LQf~  382 (666)
                      ++.++++++++|+...          +...|.++..+..+
T Consensus       223 ~v~v~d~v~e~i~~l~~~lr~~r~~~~iS~R~~~~llr~A  262 (500)
T 3nbx_X          223 EITLPDHVFELIFMLRQQLDKLPDAPYVSDRRWKKAIRLL  262 (500)
T ss_dssp             TCBCCHHHHHHHHHHHHHHHHCSSSCCCCHHHHHHHHHHH
T ss_pred             cccCchHHHHHHHHHHHHhhcCCCCCccchhHHHHHHHHH
Confidence            6778999999998776          55778876666543

>3co5_A Putative two-component system transcriptional RES regulator; structural genomics, APC89341.1; 2.40A {Neisseria gonorrhoeae}

Probab=98.86  E-value=6.5e-09  Score=96.22  Aligned_cols=57  Identities=12%  Similarity=0.056  Sum_probs=45.0

Q ss_pred             ccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCC
Q 005987          150 ELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPT  213 (666)
Q Consensus       150 eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd  213 (666)
                      +++|+...++++...++.+..   ..   ..+||+||||||||++|+++++..+ .++.+++.+
T Consensus         5 ~~iG~s~~~~~l~~~~~~~~~---~~---~~vll~G~~GtGKt~lA~~i~~~~~-~~~~~~~~~   61 (143)
T 3co5_A            5 DKLGNSAAIQEMNREVEAAAK---RT---SPVFLTGEAGSPFETVARYFHKNGT-PWVSPARVE   61 (143)
T ss_dssp             ---CCCHHHHHHHHHHHHHHT---CS---SCEEEEEETTCCHHHHHGGGCCTTS-CEECCSSTT
T ss_pred             CceeCCHHHHHHHHHHHHHhC---CC---CcEEEECCCCccHHHHHHHHHHhCC-CeEEechhh
Confidence            578999999999999987543   11   4699999999999999999999887 777777654

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426}

Probab=98.84  E-value=1.7e-08  Score=98.37  Aligned_cols=70  Identities=23%  Similarity=0.250  Sum_probs=51.3

Q ss_pred             cccccCCCCccccccCH----HHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcC
Q 005987          139 WAEKYKPRSLEELAVQR----KKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL---GARLYEWDT  211 (666)
Q Consensus       139 W~eKY~P~sl~eLvg~~----k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~na  211 (666)
                      +..+|++.+++++++..    ..++.+..|+..+..   +. .++.++|+||||||||++++++++++   +..++.+++
T Consensus        15 ~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~---~~-~~~~~~l~G~~GtGKT~la~~i~~~~~~~~~~~~~~~~   90 (202)
T 2w58_A           15 MPREILRASLSDVDLNDDGRIKAIRFAERFVAEYEP---GK-KMKGLYLHGSFGVGKTYLLAAIANELAKRNVSSLIVYV   90 (202)
T ss_dssp             SCGGGGCCCTTSSCCSSHHHHHHHHHHHHHHHHCCS---SC-CCCEEEEECSTTSSHHHHHHHHHHHHHTTTCCEEEEEH
T ss_pred             CCHHHHcCCHhhccCCChhHHHHHHHHHHHHHHhhh---cc-CCCeEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEEh
Confidence            45678899999999754    355566666665321   11 12589999999999999999999988   667776665


Q ss_pred             C
Q 005987          212 P  212 (666)
Q Consensus       212 s  212 (666)
                      +
T Consensus        91 ~   91 (202)
T 2w58_A           91 P   91 (202)
T ss_dssp             H
T ss_pred             H
Confidence            4

>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=98.82  E-value=3.2e-08  Score=100.83  Aligned_cols=42  Identities=24%  Similarity=0.169  Sum_probs=33.4

Q ss_pred             HHHHHHHHhhcCCCCC-CCccEEEEECCCCchHHHHHHHHHHHcCC
Q 005987          160 EVRAWFEERLGDSKDK-FSTNVLVITGQAGVGKTATVRQIASHLGA  204 (666)
Q Consensus       160 el~~wL~~~~~~~~g~-~~~k~LLL~GPpG~GKTtla~~LAkelg~  204 (666)
                      .+..|+..|+.   +. ++.+.++|+||||||||.++.+||+.++.
T Consensus        88 ~~~~~l~~~l~---~~~~~~n~~~l~GppgtGKt~~a~ala~~~~l  130 (267)
T 1u0j_A           88 YAASVFLGWAT---KKFGKRNTIWLFGPATTGKTNIAEAIAHTVPF  130 (267)
T ss_dssp             HHHHHHHHHHT---TCSTTCCEEEEECSTTSSHHHHHHHHHHHSSC
T ss_pred             HHHHHHHHHHh---CCCCCCcEEEEECCCCCCHHHHHHHHHhhhcc
Confidence            56667777776   44 33468999999999999999999998654

>2fna_A Conserved hypothetical protein; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2; HET: MSE ADP; 2.00A {Sulfolobus solfataricus} SCOP: a.4.5.11 c.37.1.20

Probab=98.79  E-value=8.5e-08  Score=101.05  Aligned_cols=203  Identities=12%  Similarity=0.162  Sum_probs=112.9

Q ss_pred             CCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCc--------hh
Q 005987          145 PRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTP--------TI  216 (666)
Q Consensus       145 P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~--------~~  216 (666)
                      |.....++|+++.++.|.. +..           +.++|+||+|+|||++++.++++++..++.++....        ..
T Consensus         9 ~~~~~~~~gR~~el~~L~~-l~~-----------~~v~i~G~~G~GKT~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   76 (357)
T 2fna_A            9 KDNRKDFFDREKEIEKLKG-LRA-----------PITLVLGLRRTGKSSIIKIGINELNLPYIYLDLRKFEERNYISYKD   76 (357)
T ss_dssp             CCSGGGSCCCHHHHHHHHH-TCS-----------SEEEEEESTTSSHHHHHHHHHHHHTCCEEEEEGGGGTTCSCCCHHH
T ss_pred             CCCHHHhcChHHHHHHHHH-hcC-----------CcEEEECCCCCCHHHHHHHHHHhcCCCEEEEEchhhccccCCCHHH
Confidence            3455678999999988877 542           389999999999999999999998776666664321        11


Q ss_pred             hhhhhhc-----------------ccCCc-------cccc---hhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCC
Q 005987          217 WQEYMHN-----------------CKTGL-------EYTS---KLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDL  269 (666)
Q Consensus       217 ~~e~l~~-----------------~~~g~-------~~~s---~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEi  269 (666)
                      ....+..                 ...|+       ....   ....+..++..+....        .  .+.+|+|||+
T Consensus        77 ~~~~l~~~l~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~--------~--~~~vlvlDe~  146 (357)
T 2fna_A           77 FLLELQKEINKLVKRLPSLLKALKNIQGIVIMGNEIKFNWNRKDRLSFANLLESFEQAS--------K--DNVIIVLDEA  146 (357)
T ss_dssp             HHHHHHHHHHHHHHHCTTHHHHTTTSTTEEECSSSEEEC-----CCCHHHHHHHHHHTC--------S--SCEEEEEETG
T ss_pred             HHHHHHHHHHHHhhhhhHHHHHhcccceEEecceEEEeccCCcchhhHHHHHHHHHhcC--------C--CCeEEEEECH
Confidence            0000000                 00010       0000   0112334444443221        0  2679999999


Q ss_pred             CCCcchhHHHHHHHHHHHHHhcCCCceEEEEecCCCCCCccchhhhh--hHHHHHHhhcCeeEEEeCCCCHHHHHHHHHH
Q 005987          270 PVTNGRTAFERLRQCLLLLVRSTHIPTAVVLTECGKADSVDSTAQSF--EELQSILVDAGARKVALNPITNGSIKRTLSK  347 (666)
Q Consensus       270 d~l~~~~~~~~l~~~L~~l~~~~~~PiViIit~~~~~~s~d~~~r~l--~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~  347 (666)
                      +.+..... ..+...|..+..... ++.+|++.....    ...+.+  ......+.......|.+.|++.+++.+++..
T Consensus       147 ~~~~~~~~-~~~~~~l~~~~~~~~-~~~~i~~g~~~~----~l~~~l~~~~~~~~l~~r~~~~i~l~~l~~~e~~~~l~~  220 (357)
T 2fna_A          147 QELVKLRG-VNLLPALAYAYDNLK-RIKFIMSGSEMG----LLYDYLRVEDPESPLFGRAFSTVELKPFSREEAIEFLRR  220 (357)
T ss_dssp             GGGGGCTT-CCCHHHHHHHHHHCT-TEEEEEEESSHH----HHHHHTTTTCTTSTTTTCCCEEEEECCCCHHHHHHHHHH
T ss_pred             HHhhccCc-hhHHHHHHHHHHcCC-CeEEEEEcCchH----HHHHHHhccCCCCccccCccceeecCCCCHHHHHHHHHH
Confidence            98643100 012222333443322 343444432100    000000  0000111111246899999999999999998


Q ss_pred             HHHHhCCCCCHHHHHHHHHHcCCcHHHHHH
Q 005987          348 ICRQEQYSLSTEQIDLVAQASGGDIRQAIT  377 (666)
Q Consensus       348 I~~~e~i~v~~~~l~~Ia~~s~GDIR~AIn  377 (666)
                      .+...+...++.  ..|+..++|.......
T Consensus       221 ~~~~~~~~~~~~--~~i~~~t~G~P~~l~~  248 (357)
T 2fna_A          221 GFQEADIDFKDY--EVVYEKIGGIPGWLTY  248 (357)
T ss_dssp             HHHHHTCCCCCH--HHHHHHHCSCHHHHHH
T ss_pred             HHHHcCCCCCcH--HHHHHHhCCCHHHHHH
Confidence            877666666544  8899999999885433

>1tue_A Replication protein E1; helicase, replication, E1E2 complex, AAA+ protein; 2.10A {Human papillomavirus type 18} SCOP: c.37.1.20

Probab=98.78  E-value=2.6e-08  Score=97.23  Aligned_cols=47  Identities=15%  Similarity=0.253  Sum_probs=35.1

Q ss_pred             HHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEE
Q 005987          156 KKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEW  209 (666)
Q Consensus       156 k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~  209 (666)
                      ..+..++.|++.       .+..+.+||+||||||||++|.++|+.++..++.+
T Consensus        43 ~f~~~l~~~~~~-------iPkkn~ili~GPPGtGKTt~a~ala~~l~g~i~~f   89 (212)
T 1tue_A           43 TFLGALKSFLKG-------TPKKNCLVFCGPANTGKSYFGMSFIHFIQGAVISF   89 (212)
T ss_dssp             HHHHHHHHHHHT-------CTTCSEEEEESCGGGCHHHHHHHHHHHHTCEECCC
T ss_pred             HHHHHHHHHHhc-------CCcccEEEEECCCCCCHHHHHHHHHHHhCCCeeeE
Confidence            345566666652       22235799999999999999999999997766543

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3}

Probab=98.54  E-value=9e-08  Score=100.23  Aligned_cols=69  Identities=17%  Similarity=0.308  Sum_probs=50.4

Q ss_pred             cccccCCCCccccccCH----HHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcC----CcEEEEc
Q 005987          139 WAEKYKPRSLEELAVQR----KKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLG----ARLYEWD  210 (666)
Q Consensus       139 W~eKY~P~sl~eLvg~~----k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg----~~viE~n  210 (666)
                      ....|++.+|+++.+..    ..+..+..|+..+-    .. ..+.++|+||||||||+++.++|+++.    ..++.++
T Consensus       114 l~~~~~~~tfd~f~~~~~~~~~~~~~~~~~i~~~~----~~-~~~~lll~G~~GtGKT~La~aia~~~~~~~g~~v~~~~  188 (308)
T 2qgz_A          114 LPKSYRHIHLSDIDVNNASRMEAFSAILDFVEQYP----SA-EQKGLYLYGDMGIGKSYLLAAMAHELSEKKGVSTTLLH  188 (308)
T ss_dssp             SCGGGGSCCGGGSCCCSHHHHHHHHHHHHHHHHCS----CS-SCCEEEEECSTTSSHHHHHHHHHHHHHHHSCCCEEEEE
T ss_pred             CCHHHHhCCHhhCcCCChHHHHHHHHHHHHHHhcc----cc-CCceEEEECCCCCCHHHHHHHHHHHHHHhcCCcEEEEE
Confidence            45677889999998643    34556667776532    11 136899999999999999999998764    6777666


Q ss_pred             CC
Q 005987          211 TP  212 (666)
Q Consensus       211 as  212 (666)
                      ++
T Consensus       189 ~~  190 (308)
T 2qgz_A          189 FP  190 (308)
T ss_dssp             HH
T ss_pred             HH
Confidence            54

>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=98.52  E-value=1.2e-07  Score=104.80  Aligned_cols=60  Identities=22%  Similarity=0.266  Sum_probs=41.2

Q ss_pred             CCCCccccccCCCCccccc-cCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc
Q 005987          134 STQQLWAEKYKPRSLEELA-VQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       134 ~~~~~W~eKY~P~sl~eLv-g~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      ..+.+|++||+|.++++|- .|...+..+..++..      +.   +.++|.||||||||+++..+++.+
T Consensus         9 ~~~~~~~~~~~p~~~~~Ln~~Q~~av~~~~~~i~~------~~---~~~li~G~aGTGKT~ll~~~~~~l   69 (459)
T 3upu_A            9 HHSSGLVPRGSHMTFDDLTEGQKNAFNIVMKAIKE------KK---HHVTINGPAGTGATTLTKFIIEAL   69 (459)
T ss_dssp             ------------CCSSCCCHHHHHHHHHHHHHHHS------SS---CEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CccCCCccccCCCccccCCHHHHHHHHHHHHHHhc------CC---CEEEEEeCCCCCHHHHHHHHHHHH
Confidence            3467899999999999997 688888888888775      22   379999999999999999999887

>2kjq_A DNAA-related protein; solution structure, NESG, structural genomics, PSI-2, protei structure initiative; NMR {Neisseria meningitidis serogroup B}

Probab=98.51  E-value=6.3e-07  Score=83.55  Aligned_cols=85  Identities=13%  Similarity=0.114  Sum_probs=56.0

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcCCCchhhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL---GARLYEWDTPTPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIP  255 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel---g~~viE~nasd~~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~  255 (666)
                      ..++|+||+|+||||++++++..+   |..++.++..+..                ..     .++              
T Consensus        37 ~~~~l~G~~G~GKTtL~~~i~~~~~~~g~~~~~~~~~~~~----------------~~-----~~~--------------   81 (149)
T 2kjq_A           37 QFIYVWGEEGAGKSHLLQAWVAQALEAGKNAAYIDAASMP----------------LT-----DAA--------------   81 (149)
T ss_dssp             SEEEEESSSTTTTCHHHHHHHHHHHTTTCCEEEEETTTSC----------------CC-----GGG--------------
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHhcCCcEEEEcHHHhh----------------HH-----HHH--------------
Confidence            589999999999999999999988   7777777765410                00     010              


Q ss_pred             CCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcCCCceEEEEecC
Q 005987          256 GESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHIPTAVVLTEC  303 (666)
Q Consensus       256 ~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~~~PiViIit~~  303 (666)
                         ..+.+|+|||++.+.... ...+...+..+.+.+ .++++++++.
T Consensus        82 ---~~~~lLilDE~~~~~~~~-~~~l~~li~~~~~~g-~~~iiits~~  124 (149)
T 2kjq_A           82 ---FEAEYLAVDQVEKLGNEE-QALLFSIFNRFRNSG-KGFLLLGSEY  124 (149)
T ss_dssp             ---GGCSEEEEESTTCCCSHH-HHHHHHHHHHHHHHT-CCEEEEEESS
T ss_pred             ---hCCCEEEEeCccccChHH-HHHHHHHHHHHHHcC-CcEEEEECCC
Confidence               124599999999876543 344555555555544 3435556653

>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=98.41  E-value=2.4e-06  Score=91.57  Aligned_cols=202  Identities=16%  Similarity=0.252  Sum_probs=118.3

Q ss_pred             cccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCc--EEEEcCCCch--hh-hhhhhc
Q 005987          149 EELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGAR--LYEWDTPTPT--IW-QEYMHN  223 (666)
Q Consensus       149 ~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~--viE~nasd~~--~~-~e~l~~  223 (666)
                      .+++++.....++...+.....   ..   ..++++|++|+||+++++++.+..+-.  ++.+|+....  .. .+.+..
T Consensus       129 ~~~ig~s~~~~~~~~~~~~~a~---~~---~~vli~GesGtGKe~lAr~ih~~s~r~~~fv~vnc~~~~~~~~~~~lfg~  202 (368)
T 3dzd_A          129 IEFVGEHPKILEIKRLIPKIAK---SK---APVLITGESGTGKEIVARLIHRYSGRKGAFVDLNCASIPQELAESELFGH  202 (368)
T ss_dssp             CCCCCCSHHHHHHHHHHHHHHT---SC---SCEEEECCTTSSHHHHHHHHHHHHCCCSCEEEEESSSSCTTTHHHHHHEE
T ss_pred             ccccccchHHHHHHhhhhhhhc---cc---hhheEEeCCCchHHHHHHHHHHhccccCCcEEEEcccCChHHHHHHhcCc
Confidence            4578888888888887775432   22   359999999999999999998876433  8888886521  11 111110


Q ss_pred             ---ccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcCCC------
Q 005987          224 ---CKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHI------  294 (666)
Q Consensus       224 ---~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~~~------  294 (666)
                         ..+|.. .....    .++.+               ....|+|||++.+...     .+..|+.+++.+..      
T Consensus       203 ~~g~~tga~-~~~~g----~~~~a---------------~~gtlfldei~~l~~~-----~Q~~Ll~~l~~~~~~~~g~~  257 (368)
T 3dzd_A          203 EKGAFTGAL-TRKKG----KLELA---------------DQGTLFLDEVGELDQR-----VQAKLLRVLETGSFTRLGGN  257 (368)
T ss_dssp             CSCSSSSCC-CCEEC----HHHHT---------------TTSEEEEETGGGSCHH-----HHHHHHHHHHHSEECCBTCC
T ss_pred             cccccCCcc-cccCC----hHhhc---------------CCCeEEecChhhCCHH-----HHHHHHHHHHhCCcccCCCC
Confidence               001100 00000    11111               1237999999988643     33345555554321      


Q ss_pred             ------ceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCH--HHHHHHHHHHHHH----hC---CCCCHH
Q 005987          295 ------PTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITN--GSIKRTLSKICRQ----EQ---YSLSTE  359 (666)
Q Consensus       295 ------PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~--~~i~kiL~~I~~~----e~---i~v~~~  359 (666)
                            -.+|.+|+.+....  .....+.  ..++.|..+..|.++|+..  +++..++...+.+    .+   ..++++
T Consensus       258 ~~~~~~~rii~at~~~l~~~--v~~g~fr--~dL~~rl~~~~i~lPpLreR~~Di~~l~~~~l~~~~~~~~~~~~~~~~~  333 (368)
T 3dzd_A          258 QKIEVDIRVISATNKNLEEE--IKKGNFR--EDLYYRLSVFQIYLPPLRERGKDVILLAEYFLKKFAKEYKKNCFELSEE  333 (368)
T ss_dssp             CBEECCCEEEEEESSCHHHH--HHTTSSC--HHHHHHHTSEEEECCCGGGSTTHHHHHHHHHHHHHHHHTTCCCCCBCHH
T ss_pred             cceeeeeEEEEecCCCHHHH--HHcCCcc--HHHHHHhCCeEEeCCChhhchhhHHHHHHHHHHHHHHHcCCCCCCcCHH
Confidence                  12333343211000  0000110  1233444567889999987  6766655555433    33   458999


Q ss_pred             HHHHHHHHc-CCcHHHHHHHHHHHhcC
Q 005987          360 QIDLVAQAS-GGDIRQAITSLQFSSLK  385 (666)
Q Consensus       360 ~l~~Ia~~s-~GDIR~AIn~LQf~~~~  385 (666)
                      +++.|.... .|++|...|.++.++..
T Consensus       334 a~~~L~~~~wpGNvreL~n~i~~~~~~  360 (368)
T 3dzd_A          334 TKEYLMKQEWKGNVRELKNLIERAVIL  360 (368)
T ss_dssp             HHHHHHTCCCTTHHHHHHHHHHHHHHT
T ss_pred             HHHHHHhCCCCcHHHHHHHHHHHHHHh
Confidence            999999887 89999999999988764

>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=98.38  E-value=1e-06  Score=114.26  Aligned_cols=186  Identities=11%  Similarity=0.143  Sum_probs=101.1

Q ss_pred             CccccccCCC-------CccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHH-HHHHHHcCCcEEE
Q 005987          137 QLWAEKYKPR-------SLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATV-RQIASHLGARLYE  208 (666)
Q Consensus       137 ~~W~eKY~P~-------sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla-~~LAkelg~~viE  208 (666)
                      .+|.++..+-       .+.+++++.--......++..++..      .+.+||+||||||||++| +++++..++.++.
T Consensus      1225 ~~W~~~v~~~~~~~~~~~~~~iiVpT~DT~R~~~ll~~~l~~------~~~vLL~GPpGtGKT~la~~~l~~~~~~~~~~ 1298 (2695)
T 4akg_A         1225 SSFCSEIPSVSLEAHEVMRPDIVIPTIDTIKHEKIFYDLLNS------KRGIILCGPPGSGKTMIMNNALRNSSLYDVVG 1298 (2695)
T ss_dssp             BCCCCCCCCCCCCSGGGSCSSCCCCCHHHHHHHHHHHHHHHH------TCEEEEECSTTSSHHHHHHHHHHSCSSCEEEE
T ss_pred             eechhcCCCcccCccccCccceeEeccchHHHHHHHHHHHHC------CCeEEEECCCCCCHHHHHHHHHhcCCCCceEE
Confidence            4677765332       3455666555445555555554431      158999999999999999 5555555788888


Q ss_pred             EcCCCchhhhhhhhcccCCccccchhHHHHHHHHHHHhhcCC-CCCC--CCCCCCceEEEEeCCCCCcchh-HHHHHHHH
Q 005987          209 WDTPTPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGST-SPSI--PGESKSSAILLIDDLPVTNGRT-AFERLRQC  284 (666)
Q Consensus       209 ~nasd~~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l-~~s~--~~~~~~~~IIlIDEid~l~~~~-~~~~l~~~  284 (666)
                      ++.+..+                 ....+...++..-..... .+..  ....+++.||+|||++...... .-+...+.
T Consensus      1299 infsa~t-----------------s~~~~~~~i~~~~~~~~~~~g~~~~P~~~gk~~VlFiDEinmp~~d~yg~q~~lel 1361 (2695)
T 4akg_A         1299 INFSKDT-----------------TTEHILSALHRHTNYVTTSKGLTLLPKSDIKNLVLFCDEINLPKLDKYGSQNVVLF 1361 (2695)
T ss_dssp             EECCTTC-----------------CHHHHHHHHHHHBCCEEETTTEEEEEBSSSSCEEEEEETTTCSCCCSSSCCHHHHH
T ss_pred             EEeecCC-----------------CHHHHHHHHHHHhhhccccCCccccCCCCCceEEEEecccccccccccCchhHHHH
Confidence            8876521                 112344444432111000 0000  0012346799999976532110 00123445


Q ss_pred             HHHHHhcCCC-----------ceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHH
Q 005987          285 LLLLVRSTHI-----------PTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQ  351 (666)
Q Consensus       285 L~~l~~~~~~-----------PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~  351 (666)
                      |+.+++.+..           .-+.++++++..+...   |.  .|.+++.| ++..|.++.|+.+.+.+++..++..
T Consensus      1362 LRq~le~gg~yd~~~~~~~~~~~i~lIaA~Npp~~gG---R~--~l~~rllR-rf~vi~i~~P~~~~l~~I~~~il~~ 1433 (2695)
T 4akg_A         1362 LRQLMEKQGFWKTPENKWVTIERIHIVGACNPPTDPG---RI--PMSERFTR-HAAILYLGYPSGKSLSQIYEIYYKA 1433 (2695)
T ss_dssp             HHHHHHTSSEECTTTCCEEEEESEEEEEEECCTTSTT---CC--CCCHHHHT-TEEEEECCCCTTTHHHHHHHHHHHH
T ss_pred             HHHHHhcCCEEEcCCCcEEEecCEEEEEecCCCccCC---Cc--cCChhhhh-eeeEEEeCCCCHHHHHHHHHHHHHH
Confidence            6666664321           1123334444332111   10  12223333 5889999999999999999998864

>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=98.26  E-value=3.9e-05  Score=82.73  Aligned_cols=207  Identities=16%  Similarity=0.232  Sum_probs=114.4

Q ss_pred             ccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcC---CcEEEEcCCCchh--hhhhhh
Q 005987          148 LEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLG---ARLYEWDTPTPTI--WQEYMH  222 (666)
Q Consensus       148 l~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg---~~viE~nasd~~~--~~e~l~  222 (666)
                      +.+++++...++++...++....   ..   ..++|+|++|+||+++|+++.....   ..++.+|+.....  ....+.
T Consensus       136 ~~~~ig~s~~m~~l~~~i~~~a~---~~---~~vli~Ge~GtGK~~lAr~ih~~s~r~~~~fv~v~~~~~~~~~~~~elf  209 (387)
T 1ny5_A          136 EEEYVFESPKMKEILEKIKKISC---AE---CPVLITGESGVGKEVVARLIHKLSDRSKEPFVALNVASIPRDIFEAELF  209 (387)
T ss_dssp             CCCCCCCSHHHHHHHHHHHHHTT---CC---SCEEEECSTTSSHHHHHHHHHHHSTTTTSCEEEEETTTSCHHHHHHHHH
T ss_pred             chhhhhccHHhhHHHHHHHHhcC---CC---CCeEEecCCCcCHHHHHHHHHHhcCCCCCCeEEEecCCCCHHHHHHHhc
Confidence            34678888888888888876432   22   3589999999999999999988763   5688888765210  000000


Q ss_pred             cccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcCC-------C-
Q 005987          223 NCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTH-------I-  294 (666)
Q Consensus       223 ~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~~-------~-  294 (666)
                      ....|.. +.....-...++.+               ...+|+|||++.+...     .+..|..+++...       . 
T Consensus       210 g~~~g~~-tga~~~~~g~~~~a---------------~~gtlfldei~~l~~~-----~q~~Ll~~l~~~~~~~~g~~~~  268 (387)
T 1ny5_A          210 GYEKGAF-TGAVSSKEGFFELA---------------DGGTLFLDEIGELSLE-----AQAKLLRVIESGKFYRLGGRKE  268 (387)
T ss_dssp             CBCTTSS-TTCCSCBCCHHHHT---------------TTSEEEEESGGGCCHH-----HHHHHHHHHHHSEECCBTCCSB
T ss_pred             CCCCCCC-CCcccccCCceeeC---------------CCcEEEEcChhhCCHH-----HHHHHHHHHhcCcEEeCCCCce
Confidence            0001100 00000000011111               1248999999988643     2333444444321       1 


Q ss_pred             ---c-eEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCH--HHHHHHHHHH----HHHhCC---CCCHHHH
Q 005987          295 ---P-TAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITN--GSIKRTLSKI----CRQEQY---SLSTEQI  361 (666)
Q Consensus       295 ---P-iViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~--~~i~kiL~~I----~~~e~i---~v~~~~l  361 (666)
                         . .||.+++.......  ....+.  ..++.|..+..|.++|+..  +++..++...    +.+.+.   .++++++
T Consensus       269 ~~~~~rii~at~~~l~~~~--~~g~fr--~dl~~rl~~~~i~lPpLreR~~Di~~l~~~~l~~~~~~~~~~~~~~~~~a~  344 (387)
T 1ny5_A          269 IEVNVRILAATNRNIKELV--KEGKFR--EDLYYRLGVIEIEIPPLRERKEDIIPLANHFLKKFSRKYAKEVEGFTKSAQ  344 (387)
T ss_dssp             EECCCEEEEEESSCHHHHH--HTTSSC--HHHHHHHTTEEEECCCGGGCHHHHHHHHHHHHHHHHHHTTCCCCEECHHHH
T ss_pred             eeccEEEEEeCCCCHHHHH--HcCCcc--HHHHHhhcCCeecCCcchhccccHHHHHHHHHHHHHHHcCCCCCCCCHHHH
Confidence               1 23334432110000  000010  2223333466788888865  5555554444    333332   3789999


Q ss_pred             HHHHHHc-CCcHHHHHHHHHHHhcC
Q 005987          362 DLVAQAS-GGDIRQAITSLQFSSLK  385 (666)
Q Consensus       362 ~~Ia~~s-~GDIR~AIn~LQf~~~~  385 (666)
                      +.|.... .|++|..-|.++.++..
T Consensus       345 ~~l~~~~wpGNvreL~~~i~~~~~~  369 (387)
T 1ny5_A          345 ELLLSYPWYGNVRELKNVIERAVLF  369 (387)
T ss_dssp             HHHHHSCCTTHHHHHHHHHHHHHHH
T ss_pred             HHHHhCCCCcHHHHHHHHHHHHHHh
Confidence            9999775 79999999999988753

>3f9v_A Minichromosome maintenance protein MCM; replicative helicase, DNA replication, MCM complex, AAA+ Pro ATP-binding, DNA-binding, helicase; 4.35A {Sulfolobus solfataricus}

Probab=98.18  E-value=7.4e-07  Score=101.58  Aligned_cols=27  Identities=19%  Similarity=0.325  Sum_probs=24.3

Q ss_pred             EEEEECCCCchHHHHHHHHHHHcCCcE
Q 005987          180 VLVITGQAGVGKTATVRQIASHLGARL  206 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkelg~~v  206 (666)
                      ++||+||||||||++|+++|+.++..+
T Consensus       329 ~vLL~GppGtGKT~LAr~la~~~~r~~  355 (595)
T 3f9v_A          329 HILIIGDPGTAKSQMLQFISRVAPRAV  355 (595)
T ss_dssp             CEEEEESSCCTHHHHHHSSSTTCSCEE
T ss_pred             ceEEECCCchHHHHHHHHHHHhCCCce
Confidence            699999999999999999999986543

>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=98.11  E-value=2e-05  Score=75.52  Aligned_cols=28  Identities=46%  Similarity=0.790  Sum_probs=24.3

Q ss_pred             EEEEECCCCchHHHHHHHHHHHcCCcEE
Q 005987          180 VLVITGQAGVGKTATVRQIASHLGARLY  207 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkelg~~vi  207 (666)
                      .+.|.||+|+||||++++++..++..+.
T Consensus         2 ~i~l~G~nGsGKTTLl~~l~g~l~i~~~   29 (178)
T 1ye8_A            2 KIIITGEPGVGKTTLVKKIVERLGKRAI   29 (178)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHGGGEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCcCC
Confidence            4789999999999999999999865443

>1z6t_A APAF-1, apoptotic protease activating factor 1; caspase activation, ADP, nucleotide binding, CARD, apoptosis; HET: ADP; 2.21A {Homo sapiens}

Probab=97.91  E-value=0.00013  Score=82.77  Aligned_cols=51  Identities=20%  Similarity=0.314  Sum_probs=41.5

Q ss_pred             CCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHH
Q 005987          144 KPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIAS  200 (666)
Q Consensus       144 ~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAk  200 (666)
                      -|.....++|++..+++|..+|...    .+.  .+.++|+||+|+||||+|..+++
T Consensus       119 ~P~~~~~~vGR~~~l~~L~~~L~~~----~~~--~~~v~I~G~~GiGKTtLa~~~~~  169 (591)
T 1z6t_A          119 VPQRPVVFVTRKKLVNAIQQKLSKL----KGE--PGWVTIHGMAGCGKSVLAAEAVR  169 (591)
T ss_dssp             CCCCCSSCCCCHHHHHHHHHHHTTS----TTS--CEEEEEECCTTSSHHHHHHHHHC
T ss_pred             CCCCCCeecccHHHHHHHHHHHhcc----cCC--CceEEEEcCCCCCHHHHHHHHHh
Confidence            4666677899999999999998742    022  36899999999999999999874

>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=97.82  E-value=4e-05  Score=79.92  Aligned_cols=31  Identities=26%  Similarity=0.523  Sum_probs=25.4

Q ss_pred             CccEEEEECCCCchHHHHHHHHHHHcCCcEE
Q 005987          177 STNVLVITGQAGVGKTATVRQIASHLGARLY  207 (666)
Q Consensus       177 ~~k~LLL~GPpG~GKTtla~~LAkelg~~vi  207 (666)
                      +.+.++|+||||||||+++..+|.+.|..++
T Consensus       122 ~gsviLI~GpPGsGKTtLAlqlA~~~G~~Vl  152 (331)
T 2vhj_A          122 ASGMVIVTGKGNSGKTPLVHALGEALGGKDK  152 (331)
T ss_dssp             ESEEEEEECSCSSSHHHHHHHHHHHHHTTSC
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHhCCCCEE
Confidence            3467899999999999999999987655543

>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=97.79  E-value=0.00022  Score=69.59  Aligned_cols=37  Identities=22%  Similarity=0.144  Sum_probs=30.8

Q ss_pred             CccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCC
Q 005987          177 STNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPT  213 (666)
Q Consensus       177 ~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd  213 (666)
                      +..+++|+||||+||||++..+|...+..++.+....
T Consensus        19 ~G~~~~i~G~~GsGKTtl~~~l~~~~~~~v~~i~~~~   55 (220)
T 2cvh_A           19 PGVLTQVYGPYASGKTTLALQTGLLSGKKVAYVDTEG   55 (220)
T ss_dssp             TTSEEEEECSTTSSHHHHHHHHHHHHCSEEEEEESSC
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHcCCcEEEEECCC
Confidence            3468999999999999999999986677787776543

>3vkg_A Dynein heavy chain, cytoplasmic; AAA+ protein, molecular motor, microtubles, motor protein; HET: ADP SPM; 2.81A {Dictyostelium discoideum} PDB: 3vkh_A*

Probab=97.77  E-value=6.8e-05  Score=98.16  Aligned_cols=186  Identities=12%  Similarity=0.209  Sum_probs=96.7

Q ss_pred             Ccccccc-----CCC--CccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc-CCcEEE
Q 005987          137 QLWAEKY-----KPR--SLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL-GARLYE  208 (666)
Q Consensus       137 ~~W~eKY-----~P~--sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel-g~~viE  208 (666)
                      .+|.++.     .|.  .+.+++++---..+...++..++..   +   +++||+||||||||+++..+.+.+ ++.++.
T Consensus      1262 ~~W~~~v~~~~~~~~~~~~~~ilVPT~DTvR~~~ll~~ll~~---~---~pvLL~GptGtGKT~li~~~L~~l~~~~~~~ 1335 (3245)
T 3vkg_A         1262 SLWKNKVPSVEVETHKVASPDVVIPTVDTTRHVDVLHAWLSE---H---RPLILCGPPGSGKTMTLTSTLRAFPDFEVVS 1335 (3245)
T ss_dssp             EETTCCC---CCCSTTTTCTTCCCCCHHHHHHHHHHHHHHHT---T---CCCEEESSTTSSHHHHHHHHGGGCTTEEEEE
T ss_pred             eehhhcCCccccCCccCCcccceecchHHHHHHHHHHHHHHC---C---CcEEEECCCCCCHHHHHHHHHHhCCCCceEE
Confidence            4576653     232  3556777655544555556655542   1   469999999999998875544444 677788


Q ss_pred             EcCCCchhhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCC--CCCCC--CCCCceEEEEeCCCCCcch-hHHHHHHH
Q 005987          209 WDTPTPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTS--PSIPG--ESKSSAILLIDDLPVTNGR-TAFERLRQ  283 (666)
Q Consensus       209 ~nasd~~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~--~s~~~--~~~~~~IIlIDEid~l~~~-~~~~~l~~  283 (666)
                      +|.+..+.                 ...+...++..-.+....  +...+  ..+++.|++|||++.-... -..+...+
T Consensus      1336 infS~~Tt-----------------a~~l~~~~e~~~e~~~~~~~G~~~~p~~~Gk~~VlFiDDiNmp~~D~yGtQ~~ie 1398 (3245)
T 3vkg_A         1336 LNFSSATT-----------------PELLLKTFDHHCEYKRTPSGETVLRPTQLGKWLVVFCDEINLPSTDKYGTQRVIT 1398 (3245)
T ss_dssp             ECCCTTCC-----------------HHHHHHHHHHHEEEEECTTSCEEEEESSTTCEEEEEETTTTCCCCCTTSCCHHHH
T ss_pred             EEeeCCCC-----------------HHHHHHHHhhcceEEeccCCCcccCCCcCCceEEEEecccCCCCccccccccHHH
Confidence            88765321                 123333333211111100  00001  1134679999999753211 00012334


Q ss_pred             HHHHHHhcCC-----------CceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHH
Q 005987          284 CLLLLVRSTH-----------IPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQ  351 (666)
Q Consensus       284 ~L~~l~~~~~-----------~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~  351 (666)
                      .|+.+++.+.           .+-+.++++.+.+....   |  .++..++.| ++..|.+..|+.+.+..+...++..
T Consensus      1399 lLrqlld~~g~yd~~~~~~~~i~d~~~vaamnPp~~gG---r--~~l~~Rf~r-~F~vi~i~~ps~esL~~If~til~~ 1471 (3245)
T 3vkg_A         1399 FIRQMVEKGGFWRTSDHTWIKLDKIQFVGACNPPTDAG---R--VQLTHRFLR-HAPILLVDFPSTSSLTQIYGTFNRA 1471 (3245)
T ss_dssp             HHHHHHHHSEEEETTTTEEEEESSEEEEEEECCTTSTT---C--CCCCHHHHT-TCCEEECCCCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCeEECCCCeEEEecCeEEEEEcCCCCCCC---C--ccCCHHHHh-hceEEEeCCCCHHHHHHHHHHHHHH
Confidence            4555555321           01122233333321111   1  012233333 5888999999999999998877653

>2w0m_A SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus solfataricus P2}

Probab=97.63  E-value=0.00039  Score=68.10  Aligned_cols=35  Identities=23%  Similarity=0.230  Sum_probs=28.1

Q ss_pred             ccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcCC
Q 005987          178 TNVLVITGQAGVGKTATVRQIASHL---GARLYEWDTP  212 (666)
Q Consensus       178 ~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~nas  212 (666)
                      ...++|.||||+||||+++.+|..+   +..++.+...
T Consensus        23 G~~~~i~G~~GsGKTtl~~~l~~~~~~~~~~v~~~~~~   60 (235)
T 2w0m_A           23 GFFIALTGEPGTGKTIFSLHFIAKGLRDGDPCIYVTTE   60 (235)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHHHHHHHHTCCEEEEESS
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHHHHHCCCeEEEEEcc
Confidence            3689999999999999999999665   5666666543

>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=97.62  E-value=0.00045  Score=89.92  Aligned_cols=128  Identities=19%  Similarity=0.256  Sum_probs=77.6

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCchhhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGES  258 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~  258 (666)
                      ...++.||||||||++++.+|+.+|..++.+|+++..             .+    ..+..++..+...+          
T Consensus       646 ~~~~l~GpaGtGKTe~vk~LA~~lg~~~v~~nc~e~l-------------d~----~~lg~~~~g~~~~G----------  698 (2695)
T 4akg_A          646 YGGCFFGPAGTGKTETVKAFGQNLGRVVVVFNCDDSF-------------DY----QVLSRLLVGITQIG----------  698 (2695)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHTTTCCCEEEETTSSC-------------CH----HHHHHHHHHHHHHT----------
T ss_pred             CCCcccCCCCCCcHHHHHHHHHHhCCcEEEEECCCCC-------------Ch----hHhhHHHHHHHhcC----------
Confidence            4688999999999999999999999999999987632             21    23344444443332          


Q ss_pred             CCceEEEEeCCCCCcchhHHHHHH---HHHHHHHhcC--------------CCceEEEEecCCCCCCccchhhhhhHHHH
Q 005987          259 KSSAILLIDDLPVTNGRTAFERLR---QCLLLLVRST--------------HIPTAVVLTECGKADSVDSTAQSFEELQS  321 (666)
Q Consensus       259 ~~~~IIlIDEid~l~~~~~~~~l~---~~L~~l~~~~--------------~~PiViIit~~~~~~s~d~~~r~l~~L~s  321 (666)
                         ..+++||++.+... ....+.   ..+...+...              ....||++.+.+..      .+.  .|+.
T Consensus       699 ---aw~~~DE~nr~~~e-vLs~l~~~l~~i~~al~~~~~~i~~~g~~i~l~~~~~vfiT~NPgy~------g~~--eLP~  766 (2695)
T 4akg_A          699 ---AWGCFDEFNRLDEK-VLSAVSANIQQIQNGLQVGKSHITLLEEETPLSPHTAVFITLNPGYN------GRS--ELPE  766 (2695)
T ss_dssp             ---CEEEEETTTSSCHH-HHHHHHHHHHHHHHHHHHTCSEEECSSSEEECCTTCEEEEEECCCSS------SSC--CCCH
T ss_pred             ---CEeeehhhhhcChH-HHHHHHHHHHHHHHHHHcCCcEEeeCCcEEecCCCceEEEEeCCCcc------Ccc--cccH
Confidence               48999999987543 222221   1122222211              11234444442111      110  1233


Q ss_pred             HHhhcCeeEEEeCCCCHHHHHHHHH
Q 005987          322 ILVDAGARKVALNPITNGSIKRTLS  346 (666)
Q Consensus       322 ~L~r~r~~~I~F~p~s~~~i~kiL~  346 (666)
                      .|.+ ++..|.+..|+.+.+.+++.
T Consensus       767 ~Lk~-~Fr~v~m~~Pd~~~i~ei~l  790 (2695)
T 4akg_A          767 NLKK-SFREFSMKSPQSGTIAEMIL  790 (2695)
T ss_dssp             HHHT-TEEEEECCCCCHHHHHHHHH
T ss_pred             HHHh-heEEEEeeCCCHHHHHHHHH
Confidence            3333 58889999999988887753

>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=97.62  E-value=0.00078  Score=75.82  Aligned_cols=44  Identities=25%  Similarity=0.363  Sum_probs=36.7

Q ss_pred             ccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHH
Q 005987          152 AVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIAS  200 (666)
Q Consensus       152 vg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAk  200 (666)
                      +|++..+++|..||...-     ....+++.|+|++|+||||+|+.+++
T Consensus       131 ~GR~~~~~~l~~~L~~~~-----~~~~~vv~I~G~gGvGKTtLA~~v~~  174 (549)
T 2a5y_B          131 YIREYHVDRVIKKLDEMC-----DLDSFFLFLHGRAGSGKSVIASQALS  174 (549)
T ss_dssp             CCCHHHHHHHHHHHHHHT-----TSSSEEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCchHHHHHHHHHHhccc-----CCCceEEEEEcCCCCCHHHHHHHHHH
Confidence            499999999999997521     11226899999999999999999997

>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=97.60  E-value=0.00016  Score=75.04  Aligned_cols=158  Identities=13%  Similarity=0.171  Sum_probs=85.4

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCchhhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGES  258 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~  258 (666)
                      +.++|.||+|+|||+++..||+.++.+++..+.-.  .        ..|.........-    ++....           
T Consensus        11 ~~i~i~GptgsGKt~la~~La~~~~~~iis~Ds~q--v--------Y~~~~igTakp~~----~E~~~v-----------   65 (316)
T 3foz_A           11 KAIFLMGPTASGKTALAIELRKILPVELISVDSAL--I--------YKGMDIGTAKPNA----EELLAA-----------   65 (316)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHHSCEEEEECCTTT--T--------BTTCCTTTTCCCH----HHHHHS-----------
T ss_pred             cEEEEECCCccCHHHHHHHHHHhCCCcEEeccccc--c--------cccccccCCCCCH----HHHcCC-----------
Confidence            68999999999999999999999997776544321  1        1122111000000    001111           


Q ss_pred             CCceEEEEeCCC--CCcchhHHH-HHHHHHHHHHhcCCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCC
Q 005987          259 KSSAILLIDDLP--VTNGRTAFE-RLRQCLLLLVRSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNP  335 (666)
Q Consensus       259 ~~~~IIlIDEid--~l~~~~~~~-~l~~~L~~l~~~~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p  335 (666)
                        + --+||.++  .......|. .....+..+...++.|+  +++.++      .      -+++++..     +..-|
T Consensus        66 --~-hhlid~~~~~e~~s~~~f~~~a~~~i~~i~~~g~~pi--lVGGTg------l------Yi~all~g-----l~~~p  123 (316)
T 3foz_A           66 --P-HRLLDIRDPSQAYSAADFRRDALAEMADITAAGRIPL--LVGGTM------L------YFKALLEG-----LSPLP  123 (316)
T ss_dssp             --C-EETSSCBCTTSCCCHHHHHHHHHHHHHHHHHTTCEEE--EEESCH------H------HHHHHHSC-----CCCCC
T ss_pred             --C-EEEeccCCccccccHHHHHHHHHHHHHHHHhCCCcEE--EEcCcH------H------HHHHHHcC-----cCCCC
Confidence              1 12344332  222223333 33355677777777664  455532      1      14555432     22334


Q ss_pred             CCHHHHHHHHHHHHHHhCCC--------CCHHHHHHHHHHcCCcHHHHHHHHHHHhcCC
Q 005987          336 ITNGSIKRTLSKICRQEQYS--------LSTEQIDLVAQASGGDIRQAITSLQFSSLKQ  386 (666)
Q Consensus       336 ~s~~~i~kiL~~I~~~e~i~--------v~~~~l~~Ia~~s~GDIR~AIn~LQf~~~~~  386 (666)
                      ..+.++++.|...+..+|..        +++....   .....|.|+.+..|+.+...+
T Consensus       124 ~~~~~~R~~l~~~~~~~g~~~l~~~L~~~DP~~A~---ri~pnd~~Ri~RALEV~~~TG  179 (316)
T 3foz_A          124 SADPEVRARIEQQAAEQGWESLHRQLQEVDPVAAA---RIHPNDPQRLSRALEVFFISG  179 (316)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHH---HSCTTCHHHHHHHHHHHHHHS
T ss_pred             CCCHHHHHHHHHHHHhcCHHHHHHHHHHhCHHHHh---hCCCccHHHHHHHHHHHHHHC
Confidence            45556777777777665521        2222211   124689999999999876543

>3crm_A TRNA delta(2)-isopentenylpyrophosphate transferase; ATP-binding, nucleotide-binding, nucleotidyltransferase, tRNA processing; 1.90A {Pseudomonas aeruginosa} PDB: 3crq_A 3crr_A

Probab=97.54  E-value=0.00014  Score=76.06  Aligned_cols=155  Identities=15%  Similarity=0.216  Sum_probs=53.5

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCchhhhhhhhcccCCcccc---chhHHHHHHHHHHHhhcCCCCCCC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTIWQEYMHNCKTGLEYT---SKLDEFENFVERIRRYGSTSPSIP  255 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~~~~e~l~~~~~g~~~~---s~~~~f~~fl~~a~~~~~l~~s~~  255 (666)
                      +.++|+||+|+||||+++.||++++..++..+...  .        ..|....   ...++       ....        
T Consensus         6 ~~i~i~GptGsGKTtla~~La~~l~~~iis~Ds~q--v--------y~~~~igTakp~~~e-------~~gv--------   60 (323)
T 3crm_A            6 PAIFLMGPTAAGKTDLAMALADALPCELISVDSAL--I--------YRGMDIGTAKPSREL-------LARY--------   60 (323)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHHSCEEEEEECTTT--T--------BTTCCTTTTCCCHHH-------HHHS--------
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHcCCcEEeccchh--h--------hcCCCcccCCCCHHH-------HcCC--------
Confidence            58999999999999999999999998888765432  0        1121110   00111       0111        


Q ss_pred             CCCCCceEEEEeCCCC--CcchhHHHH-HHHHHHHHHhcCCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEE
Q 005987          256 GESKSSAILLIDDLPV--TNGRTAFER-LRQCLLLLVRSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVA  332 (666)
Q Consensus       256 ~~~~~~~IIlIDEid~--l~~~~~~~~-l~~~L~~l~~~~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~  332 (666)
                           + -.+||.++-  ..+...|.. ...++..+...++.  +|+++.+.            .-+++++..  .  ..
T Consensus        61 -----p-h~lid~~~~~~~~~~~~F~~~a~~~i~~i~~~g~~--~IlvGGt~------------~y~~all~g--~--~~  116 (323)
T 3crm_A           61 -----P-HRLIDIRDPAESYSAAEFRADALAAMAKATARGRI--PLLVGGTM------------LYYKALLEG--L--AD  116 (323)
T ss_dssp             -----C-EETSSCBCTTSCCCHHHHHHHHHHHHHHHHHTTCE--EEEEESCH------------HHHHHHHCC--C----
T ss_pred             -----C-EEEeeccCcccccCHHHHHHHHHHHHHHHHHcCCe--EEEECCch------------hhHHHHHcC--C--CC
Confidence                 1 245554432  222333332 33456666666654  44455422            113444421  1  12


Q ss_pred             eCCCCHHHHHHHHHHHHHHhCC--------CCCHHHHHHHHHHcCCcHHHHHHHHHHHhcCC
Q 005987          333 LNPITNGSIKRTLSKICRQEQY--------SLSTEQIDLVAQASGGDIRQAITSLQFSSLKQ  386 (666)
Q Consensus       333 F~p~s~~~i~kiL~~I~~~e~i--------~v~~~~l~~Ia~~s~GDIR~AIn~LQf~~~~~  386 (666)
                      +++ ...++++.|...+..+|.        .+++.....|   ...|.|+.+..|+.+...+
T Consensus       117 ~p~-~~~~~R~~l~~~~~~~g~~~l~~~L~~~Dp~~a~~i---~~nd~~Ri~RALEv~~~tG  174 (323)
T 3crm_A          117 MPG-ADPEVRAAIEAEAQAEGWEALHRQLAEVDPESAARI---HPNDPQRLMRALEVYRLGG  174 (323)
T ss_dssp             --------------------------------------------------------------
T ss_pred             CCC-CCHHHHHHHHHHHHHcCHHHHHHHHHHhCHHHHhhc---CCCCHHHHHHHHHHHHHHC
Confidence            333 445577777776665552        2344443333   3579999999999887644

>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=97.49  E-value=0.0013  Score=80.70  Aligned_cols=52  Identities=17%  Similarity=0.208  Sum_probs=42.7

Q ss_pred             CCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHH
Q 005987          144 KPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       144 ~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAke  201 (666)
                      -|.....++|+++.+++|..+|...      ....+.+.|+|++|+||||+|..+++.
T Consensus       119 ~p~~~~~~vgR~~~~~~l~~~l~~~------~~~~~~v~i~G~gG~GKTtLa~~~~~~  170 (1249)
T 3sfz_A          119 VPQRPVIFVTRKKLVHAIQQKLWKL------NGEPGWVTIYGMAGCGKSVLAAEAVRD  170 (1249)
T ss_dssp             CCCCCSSCCCCHHHHHHHHHHHHTT------TTSCEEEEEECSTTSSHHHHHHHHTCC
T ss_pred             CCCCCceeccHHHHHHHHHHHHhhc------cCCCCEEEEEeCCCCCHHHHHHHHhcC
Confidence            5667778999999999999999642      112268999999999999999988775

>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=97.43  E-value=0.00026  Score=73.56  Aligned_cols=158  Identities=16%  Similarity=0.241  Sum_probs=86.5

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCchhhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGES  258 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~  258 (666)
                      ++++|.||+|+|||+++..||+.++..++....-  ..+        .++.....-..    .++...            
T Consensus         4 ~~i~i~GptgsGKt~la~~La~~~~~~iis~Ds~--QvY--------r~~~igTakp~----~~E~~g------------   57 (322)
T 3exa_A            4 KLVAIVGPTAVGKTKTSVMLAKRLNGEVISGDSM--QVY--------RGMDIGTAKIT----AEEMDG------------   57 (322)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHTTTEEEEECCGG--GGB--------TTCCTTTTCCC----HHHHTT------------
T ss_pred             cEEEEECCCcCCHHHHHHHHHHhCccceeecCcc--cce--------eeeeecCCCCC----HHHHcC------------
Confidence            5789999999999999999999998766543321  111        12111100000    001100            


Q ss_pred             CCceEEEEeCCC--CCcchhHH-HHHHHHHHHHHhcCCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCC
Q 005987          259 KSSAILLIDDLP--VTNGRTAF-ERLRQCLLLLVRSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNP  335 (666)
Q Consensus       259 ~~~~IIlIDEid--~l~~~~~~-~~l~~~L~~l~~~~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p  335 (666)
                       -+ --+||.++  .......| +.....+..+...++.|+  +++.++      .      -+++++..     +.|.|
T Consensus        58 -vp-hhlid~~~~~e~~s~~~F~~~a~~~i~~i~~~gk~pI--lVGGTg------l------Yi~aLl~g-----~~~~~  116 (322)
T 3exa_A           58 -VP-HHLIDIKDPSESFSVADFQDLATPLITEIHERGRLPF--LVGGTG------L------YVNAVIHQ-----FNLGD  116 (322)
T ss_dssp             -CC-EESSSCBCTTSCCCHHHHHHHHHHHHHHHHHTTCEEE--EESCCH------H------HHHHHHHT-----CCCCC
T ss_pred             -CC-EEEeccCChhhhccHHHHHHHHHHHHHHHHhCCCcEE--EEcCcH------H------HHHHHHcC-----CcCCC
Confidence             11 23455433  22222233 333456667777777654  456532      1      14555432     35666


Q ss_pred             C-CHHHHHHHHHHHHHHhCC--------CCCHHHHHHHHHHcCCcHHHHHHHHHHHhcCC
Q 005987          336 I-TNGSIKRTLSKICRQEQY--------SLSTEQIDLVAQASGGDIRQAITSLQFSSLKQ  386 (666)
Q Consensus       336 ~-s~~~i~kiL~~I~~~e~i--------~v~~~~l~~Ia~~s~GDIR~AIn~LQf~~~~~  386 (666)
                      . ...++++.|...+..+|.        .+++.....   ....|.|+.+..|+.+...+
T Consensus       117 ~~~~~~~R~~l~~~~~~~g~~~L~~~L~~~DP~~A~~---i~pnd~~Ri~RALEV~~~TG  173 (322)
T 3exa_A          117 IRADEDYRHELEAFVNSYGVQALHDKLSKIDPKAAAA---IHPNNYRRVIRALEIIKLTG  173 (322)
T ss_dssp             CBCCHHHHHHHHHHHHHSCHHHHHHHHHTTCHHHHTT---SCTTCHHHHHHHHHHHHHTC
T ss_pred             CCCCHHHHHHHHHHHHhcCHHHHHHHHHhhCHHHHhh---cCcccHHHHHHHHHHHHHHC
Confidence            5 345788888877776652        123322111   14589999999999986544

>2orw_A Thymidine kinase; TMTK, TP4A, transferase; HET: 4TA; 1.50A {Thermotoga maritima} PDB: 2qpo_A 2qq0_A* 2qqe_A*

Probab=97.38  E-value=0.00016  Score=69.62  Aligned_cols=32  Identities=22%  Similarity=0.279  Sum_probs=25.1

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc---CCcEEEEc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL---GARLYEWD  210 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel---g~~viE~n  210 (666)
                      ++.+++||+|+||||++..++..+   |.+++-+.
T Consensus         4 ~i~vi~G~~gsGKTT~ll~~~~~~~~~g~~v~~~~   38 (184)
T 2orw_A            4 KLTVITGPMYSGKTTELLSFVEIYKLGKKKVAVFK   38 (184)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHHHHHHTTCEEEEEE
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEe
Confidence            589999999999999997666654   66666553

>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=97.38  E-value=0.00052  Score=68.08  Aligned_cols=33  Identities=24%  Similarity=0.258  Sum_probs=27.4

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL---GARLYEWDT  211 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel---g~~viE~na  211 (666)
                      .+.+++||+|+||||++..++..+   |..++-+..
T Consensus        13 ~i~litG~mGsGKTT~ll~~~~r~~~~g~kVli~~~   48 (223)
T 2b8t_A           13 WIEFITGPMFAGKTAELIRRLHRLEYADVKYLVFKP   48 (223)
T ss_dssp             EEEEEECSTTSCHHHHHHHHHHHHHHTTCCEEEEEE
T ss_pred             EEEEEECCCCCcHHHHHHHHHHHHHhcCCEEEEEEe
Confidence            689999999999999998888776   667776653

>3trf_A Shikimate kinase, SK; amino acid biosynthesis, transferase; 2.60A {Coxiella burnetii}

Probab=97.37  E-value=0.00012  Score=69.68  Aligned_cols=31  Identities=29%  Similarity=0.378  Sum_probs=28.3

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEEEE
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLYEW  209 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~viE~  209 (666)
                      +.++|+|||||||||+++.||+.+|+.++..
T Consensus         6 ~~i~l~G~~GsGKst~a~~La~~l~~~~i~~   36 (185)
T 3trf_A            6 TNIYLIGLMGAGKTSVGSQLAKLTKRILYDS   36 (185)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHHCCCEEEH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHhCCCEEEC
Confidence            5799999999999999999999999988754

>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=97.37  E-value=0.00076  Score=66.73  Aligned_cols=37  Identities=22%  Similarity=0.259  Sum_probs=29.5

Q ss_pred             CccEEEEECCCCchHHHHHHHHHHH--c-------CCcEEEEcCCC
Q 005987          177 STNVLVITGQAGVGKTATVRQIASH--L-------GARLYEWDTPT  213 (666)
Q Consensus       177 ~~k~LLL~GPpG~GKTtla~~LAke--l-------g~~viE~nasd  213 (666)
                      +..+++|+||||+||||+++.+|..  +       +..++.++...
T Consensus        23 ~G~~~~i~G~~GsGKTtl~~~l~~~~~~~~~~g~~~~~~~~i~~~~   68 (243)
T 1n0w_A           23 TGSITEMFGEFRTGKTQICHTLAVTCQLPIDRGGGEGKAMYIDTEG   68 (243)
T ss_dssp             TTSEEEEECCTTSSHHHHHHHHHHHTTSCGGGTCCSSEEEEEESSS
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHHHhCchhcCCCCCeEEEEECCC
Confidence            3468999999999999999999985  3       45677776544

>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=97.35  E-value=0.014  Score=63.60  Aligned_cols=182  Identities=13%  Similarity=0.132  Sum_probs=91.9

Q ss_pred             ccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcCCCchhh-hhhh--hcccCCccc------cchhHHHHHHHHHHH
Q 005987          178 TNVLVITGQAGVGKTATVRQIASHL---GARLYEWDTPTPTIW-QEYM--HNCKTGLEY------TSKLDEFENFVERIR  245 (666)
Q Consensus       178 ~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~nasd~~~~-~e~l--~~~~~g~~~------~s~~~~f~~fl~~a~  245 (666)
                      +.+++++||+|+||||++..||..+   |.++.-+.+...+.- .+.+  .....|+.+      ....+...+.+..+.
T Consensus       100 p~vIlivG~~G~GKTTt~~kLA~~l~~~G~kVllv~~D~~R~aa~eqL~~~~~~~gvpv~~~~~~~dp~~i~~~al~~a~  179 (443)
T 3dm5_A          100 PTILLMVGIQGSGKTTTVAKLARYFQKRGYKVGVVCSDTWRPGAYHQLRQLLDRYHIEVFGNPQEKDAIKLAKEGVDYFK  179 (443)
T ss_dssp             SEEEEEECCTTSSHHHHHHHHHHHHHTTTCCEEEEECCCSSTHHHHHHHHHHGGGTCEEECCTTCCCHHHHHHHHHHHHH
T ss_pred             CeEEEEECcCCCCHHHHHHHHHHHHHHCCCeEEEEeCCCcchhHHHHHHHHHHhcCCcEEecCCCCCHHHHHHHHHHHHH
Confidence            4799999999999999999999876   778777665432210 0000  001112111      112223344555554


Q ss_pred             hhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcCC-CceEEEEecCCCCCCccchhhhhhHHHHHHh
Q 005987          246 RYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTH-IPTAVVLTECGKADSVDSTAQSFEELQSILV  324 (666)
Q Consensus       246 ~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~~-~PiViIit~~~~~~s~d~~~r~l~~L~s~L~  324 (666)
                      ..+            .-++|||..........   +...+..+..... ..+++++.... .    .  ......+.+..
T Consensus       180 ~~~------------~DvVIIDTaGrl~~d~~---lm~el~~i~~~~~pd~vlLVvDA~~-g----q--~a~~~a~~f~~  237 (443)
T 3dm5_A          180 SKG------------VDIIIVDTAGRHKEDKA---LIEEMKQISNVIHPHEVILVIDGTI-G----Q--QAYNQALAFKE  237 (443)
T ss_dssp             HTT------------CSEEEEECCCCSSCCHH---HHHHHHHHHHHHCCSEEEEEEEGGG-G----G--GHHHHHHHHHH
T ss_pred             hCC------------CCEEEEECCCcccchHH---HHHHHHHHHHhhcCceEEEEEeCCC-c----h--hHHHHHHHHHh
Confidence            311            23899999876643321   2222222222221 12444443321 1    1  01111222222


Q ss_pred             hcCeeEEEeCCCCHHHHHHHHHHHHHHhCCC---------------CCH-HHHHHHHHHcCCcHHHHHHHHHHHh
Q 005987          325 DAGARKVALNPITNGSIKRTLSKICRQEQYS---------------LST-EQIDLVAQASGGDIRQAITSLQFSS  383 (666)
Q Consensus       325 r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~---------------v~~-~~l~~Ia~~s~GDIR~AIn~LQf~~  383 (666)
                      ......|-++.++.+.-...+..++...++.               +++ ..+..|.  -.||+-..+...|-..
T Consensus       238 ~~~i~gVIlTKlD~~~~gG~~ls~~~~~g~PI~fig~Ge~vddL~~f~~~~~~~~ll--g~gd~~~l~e~~~~~~  310 (443)
T 3dm5_A          238 ATPIGSIIVTKLDGSAKGGGALSAVAATGAPIKFIGTGEKIDDIEPFDPPRFVSRLL--GLGDIQGLLEKFKELE  310 (443)
T ss_dssp             SCTTEEEEEECCSSCSSHHHHHHHHHTTCCCEEEEECSSSTTCEEECCHHHHHHHHT--TTTCHHHHHHHHHHHH
T ss_pred             hCCCeEEEEECCCCcccccHHHHHHHHHCCCEEEEEcCCChHHhhhCCHHHHHHHHc--CCCcHHHHHHHHHHhh
Confidence            2345667888887665444444444443332               223 3344443  4699999998877653

>2i3b_A HCR-ntpase, human cancer-related ntpase; AAA, rossmann, hydrolase; NMR {Homo sapiens} SCOP: c.37.1.11

Probab=97.35  E-value=0.0003  Score=67.97  Aligned_cols=23  Identities=35%  Similarity=0.598  Sum_probs=21.6

Q ss_pred             EEEEECCCCchHHHHHHHHHHHc
Q 005987          180 VLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      .+.|.||+|+||||+++.+|..+
T Consensus         3 ~i~i~G~nG~GKTTll~~l~g~~   25 (189)
T 2i3b_A            3 HVFLTGPPGVGKTTLIHKASEVL   25 (189)
T ss_dssp             CEEEESCCSSCHHHHHHHHHHHH
T ss_pred             EEEEECCCCChHHHHHHHHHhhc
Confidence            58899999999999999999987

>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=97.34  E-value=0.0015  Score=69.32  Aligned_cols=39  Identities=21%  Similarity=0.143  Sum_probs=31.2

Q ss_pred             CCCccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcCCC
Q 005987          175 KFSTNVLVITGQAGVGKTATVRQIASHL---GARLYEWDTPT  213 (666)
Q Consensus       175 ~~~~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~nasd  213 (666)
                      -++..+++|+||||+||||++..+|..+   +..++.++...
T Consensus        58 i~~G~i~~I~GppGsGKSTLal~la~~~~~~gg~VlyId~E~   99 (356)
T 3hr8_A           58 YPRGRIVEIFGQESSGKTTLALHAIAEAQKMGGVAAFIDAEH   99 (356)
T ss_dssp             EETTEEEEEEESTTSSHHHHHHHHHHHHHHTTCCEEEEESSC
T ss_pred             ccCCcEEEEECCCCCCHHHHHHHHHHHHHhcCCeEEEEeccc
Confidence            3445689999999999999999999875   66777776543

>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=97.34  E-value=0.00015  Score=68.48  Aligned_cols=31  Identities=23%  Similarity=0.457  Sum_probs=27.4

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEEEE
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLYEW  209 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~viE~  209 (666)
                      .+++|+||||+||||+++.||+.++..++.+
T Consensus         4 ~~i~l~G~~GsGKST~a~~La~~l~~~~~~~   34 (178)
T 1qhx_A            4 RMIILNGGSSAGKSGIVRCLQSVLPEPWLAF   34 (178)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHSSSCEEEE
T ss_pred             eEEEEECCCCCCHHHHHHHHHHhcCCCeEEe
Confidence            5899999999999999999999998765543

>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=97.29  E-value=0.00017  Score=67.51  Aligned_cols=31  Identities=10%  Similarity=0.213  Sum_probs=27.7

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEEEE
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLYEW  209 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~viE~  209 (666)
                      ..++|+||||+||||+++.||+.+++.++..
T Consensus         2 ~~i~l~G~~GsGKsT~~~~L~~~l~~~~i~~   32 (173)
T 3kb2_A            2 TLIILEGPDCCFKSTVAAKLSKELKYPIIKG   32 (173)
T ss_dssp             CEEEEECSSSSSHHHHHHHHHHHHCCCEEEC
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhCCeeecC
Confidence            3789999999999999999999999887643

>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=97.25  E-value=0.0002  Score=68.32  Aligned_cols=30  Identities=27%  Similarity=0.489  Sum_probs=27.5

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEEE
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLYE  208 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~viE  208 (666)
                      ..++|.||||+||||+++.|++.+++.++.
T Consensus         6 ~~I~l~G~~GsGKST~~~~L~~~l~~~~i~   35 (193)
T 2rhm_A            6 ALIIVTGHPATGKTTLSQALATGLRLPLLS   35 (193)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHHHTCCEEE
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHcCCeEec
Confidence            689999999999999999999999987765

>3vaa_A Shikimate kinase, SK; structural genomics, center for structural genomics of infec diseases, csgid, metal binding, transferase; 1.70A {Bacteroides thetaiotaomicron}

Probab=97.24  E-value=0.00021  Score=69.21  Aligned_cols=31  Identities=26%  Similarity=0.393  Sum_probs=28.2

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEEEE
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLYEW  209 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~viE~  209 (666)
                      +.++|.|||||||||+++.||+.+|+.++..
T Consensus        26 ~~i~l~G~~GsGKsTl~~~La~~l~~~~i~~   56 (199)
T 3vaa_A           26 VRIFLTGYMGAGKTTLGKAFARKLNVPFIDL   56 (199)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHHTCCEEEH
T ss_pred             CEEEEEcCCCCCHHHHHHHHHHHcCCCEEcc
Confidence            5899999999999999999999999887753

>1gvn_B Zeta; postsegregational killing system, plasmid; 1.95A {Streptococcus pyogenes} SCOP: c.37.1.21 PDB: 3q8x_B*

Probab=97.24  E-value=0.00046  Score=71.13  Aligned_cols=55  Identities=22%  Similarity=0.234  Sum_probs=34.9

Q ss_pred             HHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEc
Q 005987          156 KKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWD  210 (666)
Q Consensus       156 k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~n  210 (666)
                      .....+...+...+........+..++|+||||+||||+++.|+++++..++.++
T Consensus        11 ~~~~~~~~~~~~~l~~~~~~~~~~livl~G~sGsGKSTla~~L~~~~~~~~~~Is   65 (287)
T 1gvn_B           11 QFENRLNDNLEELIQGKKAVESPTAFLLGGQPGSGKTSLRSAIFEETQGNVIVID   65 (287)
T ss_dssp             HHHHHHHHHHHHHHTTCCCCSSCEEEEEECCTTSCTHHHHHHHHHHTTTCCEEEC
T ss_pred             HHHHHHHHHHHHHhccccCCCCCeEEEEECCCCCCHHHHHHHHHHHhCCCeEEEe
Confidence            3334444444444432212223368999999999999999999999843334444

>1zuh_A Shikimate kinase; alpha-beta protein, transferase; 1.80A {Helicobacter pylori} PDB: 1zui_A* 3hr7_A 3muf_A* 3mrs_A 3n2e_A*

Probab=97.18  E-value=0.00026  Score=66.30  Aligned_cols=31  Identities=23%  Similarity=0.379  Sum_probs=28.4

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEEEE
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLYEW  209 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~viE~  209 (666)
                      .+++|+|+|||||||+++.||+.+|+.++..
T Consensus         8 ~~i~l~G~~GsGKSTva~~La~~lg~~~id~   38 (168)
T 1zuh_A            8 QHLVLIGFMGSGKSSLAQELGLALKLEVLDT   38 (168)
T ss_dssp             CEEEEESCTTSSHHHHHHHHHHHHTCCEEEH
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHhCCCEEEC
Confidence            5899999999999999999999999988753

>1kag_A SKI, shikimate kinase I; transferase, structural genomics, PSI, protein structure initiative; 2.05A {Escherichia coli} SCOP: c.37.1.2

Probab=97.16  E-value=0.00026  Score=66.46  Aligned_cols=30  Identities=30%  Similarity=0.609  Sum_probs=26.8

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEEE
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLYE  208 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~viE  208 (666)
                      ..++|+||+||||||+++.||..+++.++.
T Consensus         5 ~~i~l~G~~GsGKSTl~~~La~~l~~~~id   34 (173)
T 1kag_A            5 RNIFLVGPMGAGKSTIGRQLAQQLNMEFYD   34 (173)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHHHTTCEEEE
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHhCCCEEe
Confidence            479999999999999999999999976553

>1via_A Shikimate kinase; structural genomics, transferase; HET: MSE; 1.57A {Campylobacter jejuni} SCOP: c.37.1.2

Probab=97.13  E-value=0.00027  Score=66.72  Aligned_cols=29  Identities=28%  Similarity=0.459  Sum_probs=26.7

Q ss_pred             EEEEECCCCchHHHHHHHHHHHcCCcEEE
Q 005987          180 VLVITGQAGVGKTATVRQIASHLGARLYE  208 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkelg~~viE  208 (666)
                      .++|.||||+||||+++.||+.+++.++.
T Consensus         6 ~i~i~G~~GsGKsTla~~La~~l~~~~~d   34 (175)
T 1via_A            6 NIVFIGFMGSGKSTLARALAKDLDLVFLD   34 (175)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHHTCEEEE
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHcCCCEEc
Confidence            58999999999999999999999987764

>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=97.13  E-value=0.00027  Score=67.22  Aligned_cols=31  Identities=32%  Similarity=0.484  Sum_probs=27.8

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEEEE
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLYEW  209 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~viE~  209 (666)
                      ..++|+|+||+||||+++.||+.+|+.++..
T Consensus         3 ~~I~l~G~~GsGKsT~a~~La~~lg~~~id~   33 (184)
T 2iyv_A            3 PKAVLVGLPGSGKSTIGRRLAKALGVGLLDT   33 (184)
T ss_dssp             CSEEEECSTTSSHHHHHHHHHHHHTCCEEEH
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHcCCCEEeC
Confidence            3699999999999999999999999887753

>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=97.12  E-value=0.00029  Score=66.78  Aligned_cols=30  Identities=33%  Similarity=0.563  Sum_probs=27.3

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEEE
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLYE  208 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~viE  208 (666)
                      +.++|+||||+||||+++.||+.+++.++.
T Consensus        12 ~~i~i~G~~GsGKst~~~~l~~~~~~~~~~   41 (180)
T 3iij_A           12 PNILLTGTPGVGKTTLGKELASKSGLKYIN   41 (180)
T ss_dssp             CCEEEECSTTSSHHHHHHHHHHHHCCEEEE
T ss_pred             CeEEEEeCCCCCHHHHHHHHHHHhCCeEEE
Confidence            579999999999999999999999987764

>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=97.11  E-value=0.003  Score=62.96  Aligned_cols=33  Identities=18%  Similarity=0.037  Sum_probs=28.0

Q ss_pred             EEEEECCCCchHHHHHHHHHHHcCCcEEEEcCC
Q 005987          180 VLVITGQAGVGKTATVRQIASHLGARLYEWDTP  212 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkelg~~viE~nas  212 (666)
                      .+||+||+|+|||.++..++..++..++-+...
T Consensus       110 ~~ll~~~tG~GKT~~a~~~~~~~~~~~liv~P~  142 (237)
T 2fz4_A          110 RGCIVLPTGSGKTHVAMAAINELSTPTLIVVPT  142 (237)
T ss_dssp             EEEEEESSSTTHHHHHHHHHHHSCSCEEEEESS
T ss_pred             CEEEEeCCCCCHHHHHHHHHHHcCCCEEEEeCC
Confidence            499999999999999999999987777766543

>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=97.10  E-value=0.00034  Score=65.17  Aligned_cols=30  Identities=30%  Similarity=0.535  Sum_probs=27.0

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEEEE
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLYEW  209 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~viE~  209 (666)
                      ..++|+||||+||||+++.| +.+|+.++..
T Consensus         2 ~~I~l~G~~GsGKsT~a~~L-~~~g~~~i~~   31 (179)
T 3lw7_A            2 KVILITGMPGSGKSEFAKLL-KERGAKVIVM   31 (179)
T ss_dssp             CEEEEECCTTSCHHHHHHHH-HHTTCEEEEH
T ss_pred             cEEEEECCCCCCHHHHHHHH-HHCCCcEEEH
Confidence            47899999999999999999 9999988764

>2dr3_A UPF0273 protein PH0284; RECA superfamily ATPase, hexamer, structural genomics; HET: ADP; 2.00A {Pyrococcus horikoshii}

Probab=97.07  E-value=0.0041  Score=61.44  Aligned_cols=37  Identities=24%  Similarity=0.240  Sum_probs=28.4

Q ss_pred             CccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcCCC
Q 005987          177 STNVLVITGQAGVGKTATVRQIASHL---GARLYEWDTPT  213 (666)
Q Consensus       177 ~~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~nasd  213 (666)
                      +...++|+||||+||||++..+|..+   +..++.++...
T Consensus        22 ~G~~~~i~G~~GsGKTtl~~~~~~~~~~~~~~v~~~~~e~   61 (247)
T 2dr3_A           22 ERNVVLLSGGPGTGKTIFSQQFLWNGLKMGEPGIYVALEE   61 (247)
T ss_dssp             TTCEEEEEECTTSSHHHHHHHHHHHHHHTTCCEEEEESSS
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHHhcCCeEEEEEccC
Confidence            34689999999999999988777654   66677666543

>2ze6_A Isopentenyl transferase; crown GALL tumor, cytokinin biosynthesis; HET: DST AMP; 2.10A {Agrobacterium tumefaciens} PDB: 2ze5_A* 2ze7_A* 2ze8_A

Probab=97.06  E-value=0.00034  Score=70.73  Aligned_cols=32  Identities=31%  Similarity=0.305  Sum_probs=28.6

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEEEEc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLYEWD  210 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~viE~n  210 (666)
                      ++++|.||||+||||+++.||+.+++.++..+
T Consensus         2 ~li~I~G~~GSGKSTla~~La~~~~~~~i~~D   33 (253)
T 2ze6_A            2 LLHLIYGPTCSGKTDMAIQIAQETGWPVVALD   33 (253)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHCCCEEECC
T ss_pred             eEEEEECCCCcCHHHHHHHHHhcCCCeEEecc
Confidence            47899999999999999999999998887554

>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=97.06  E-value=0.004  Score=66.36  Aligned_cols=38  Identities=21%  Similarity=0.153  Sum_probs=30.2

Q ss_pred             CCccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcCCC
Q 005987          176 FSTNVLVITGQAGVGKTATVRQIASHL---GARLYEWDTPT  213 (666)
Q Consensus       176 ~~~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~nasd  213 (666)
                      ++..+++|+||||+|||+++..+|..+   |..++.++...
T Consensus        72 ~~G~li~I~G~pGsGKTtlal~la~~~~~~g~~vlyi~~E~  112 (366)
T 1xp8_A           72 PRGRITEIYGPESGGKTTLALAIVAQAQKAGGTCAFIDAEH  112 (366)
T ss_dssp             ETTSEEEEEESTTSSHHHHHHHHHHHHHHTTCCEEEEESSC
T ss_pred             cCCcEEEEEcCCCCChHHHHHHHHHHHHHCCCeEEEEECCC
Confidence            344689999999999999999888765   66777776543

>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=97.05  E-value=0.00035  Score=65.50  Aligned_cols=30  Identities=27%  Similarity=0.500  Sum_probs=27.4

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEEE
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLYE  208 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~viE  208 (666)
                      +.++|+|+||+||||+++.||+.+|+.++.
T Consensus         3 ~~I~l~G~~GsGKsT~a~~La~~lg~~~id   32 (173)
T 1e6c_A            3 EPIFMVGARGCGMTTVGRELARALGYEFVD   32 (173)
T ss_dssp             CCEEEESCTTSSHHHHHHHHHHHHTCEEEE
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHhCCcEEc
Confidence            469999999999999999999999987764

>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=97.05  E-value=0.003  Score=66.94  Aligned_cols=37  Identities=22%  Similarity=0.184  Sum_probs=29.4

Q ss_pred             CCccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcCC
Q 005987          176 FSTNVLVITGQAGVGKTATVRQIASHL---GARLYEWDTP  212 (666)
Q Consensus       176 ~~~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~nas  212 (666)
                      ++..+++|+||||+||||++..+|..+   +..++.+...
T Consensus        59 ~~G~iv~I~G~pGsGKTtLal~la~~~~~~g~~vlyi~~E   98 (349)
T 2zr9_A           59 PRGRVIEIYGPESSGKTTVALHAVANAQAAGGIAAFIDAE   98 (349)
T ss_dssp             ETTSEEEEEESTTSSHHHHHHHHHHHHHHTTCCEEEEESS
T ss_pred             cCCeEEEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEECC
Confidence            345789999999999999999988765   5667766654

>3t61_A Gluconokinase; PSI-biology, structural genomics, protein structure initiati YORK structural genomics research consortium, nysgrc; 2.20A {Sinorhizobium meliloti}

Probab=97.04  E-value=0.00036  Score=67.49  Aligned_cols=30  Identities=30%  Similarity=0.467  Sum_probs=27.5

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEEE
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLYE  208 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~viE  208 (666)
                      ..++|+||+|+||||+++.|++.+|+.++.
T Consensus        19 ~~I~l~G~~GsGKSTla~~L~~~lg~~~i~   48 (202)
T 3t61_A           19 GSIVVMGVSGSGKSSVGEAIAEACGYPFIE   48 (202)
T ss_dssp             SCEEEECSTTSCHHHHHHHHHHHHTCCEEE
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhCCEEEe
Confidence            579999999999999999999999987765

>1ly1_A Polynucleotide kinase; PNK, phosphatase, transferase; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.1

Probab=97.04  E-value=0.00028  Score=66.40  Aligned_cols=29  Identities=21%  Similarity=0.361  Sum_probs=25.1

Q ss_pred             cEEEEECCCCchHHHHHHHHHH-HcCCcEE
Q 005987          179 NVLVITGQAGVGKTATVRQIAS-HLGARLY  207 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAk-elg~~vi  207 (666)
                      ..++|.||||+||||+++.|++ .+++.++
T Consensus         3 ~~I~i~G~~GsGKST~a~~L~~~~~~~~~i   32 (181)
T 1ly1_A            3 KIILTIGCPGSGKSTWAREFIAKNPGFYNI   32 (181)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHSTTEEEE
T ss_pred             eEEEEecCCCCCHHHHHHHHHhhcCCcEEe
Confidence            5799999999999999999999 5665554

>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=97.04  E-value=0.0033  Score=66.78  Aligned_cols=38  Identities=21%  Similarity=0.157  Sum_probs=30.5

Q ss_pred             CCCccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcCC
Q 005987          175 KFSTNVLVITGQAGVGKTATVRQIASHL---GARLYEWDTP  212 (666)
Q Consensus       175 ~~~~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~nas  212 (666)
                      -++..+++|+||||+||||++..+|.++   |..++.+...
T Consensus        60 l~~G~ii~I~G~pGsGKTtLal~la~~~~~~g~~vlyid~E  100 (356)
T 1u94_A           60 LPMGRIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDAE  100 (356)
T ss_dssp             EETTSEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEESS
T ss_pred             ccCCeEEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEeCC
Confidence            3345789999999999999999988765   6677777653

>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=97.03  E-value=0.00051  Score=66.38  Aligned_cols=31  Identities=23%  Similarity=0.351  Sum_probs=28.2

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEEEE
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLYEW  209 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~viE~  209 (666)
                      ..++|+||||+||||+++.||+.+++.++..
T Consensus        21 ~~I~l~G~~GsGKST~a~~La~~l~~~~i~~   51 (201)
T 2cdn_A           21 MRVLLLGPPGAGKGTQAVKLAEKLGIPQIST   51 (201)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHHTCCEEEH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhCCcEEeh
Confidence            5799999999999999999999999887754

>3cm0_A Adenylate kinase; ATP-binding, cytoplasm, nucleotide biosynthesis, nucleotide-binding, transferase, structural genomics; 1.80A {Thermus thermophilus}

Probab=97.03  E-value=0.00036  Score=66.27  Aligned_cols=30  Identities=23%  Similarity=0.494  Sum_probs=26.8

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEEE
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLYE  208 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~viE  208 (666)
                      ..++|+||||+||||+++.||+.+|+.++.
T Consensus         5 ~~I~l~G~~GsGKST~~~~La~~l~~~~i~   34 (186)
T 3cm0_A            5 QAVIFLGPPGAGKGTQASRLAQELGFKKLS   34 (186)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHHHTCEEEC
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhCCeEec
Confidence            479999999999999999999999976653

>1tev_A UMP-CMP kinase; ploop, NMP binding region, LID region, conformational changes, transferase; 2.10A {Homo sapiens} SCOP: c.37.1.1

Probab=97.02  E-value=0.00041  Score=66.12  Aligned_cols=30  Identities=23%  Similarity=0.382  Sum_probs=27.4

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEEE
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLYE  208 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~viE  208 (666)
                      ..++|+|+||+||||+++.||+.+|+.++.
T Consensus         4 ~~I~l~G~~GsGKsT~a~~L~~~~~~~~i~   33 (196)
T 1tev_A            4 LVVFVLGGPGAGKGTQCARIVEKYGYTHLS   33 (196)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHCCEEEE
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhCCeEEe
Confidence            579999999999999999999999987664

>2vli_A Antibiotic resistance protein; transferase, tunicamycin, phosphotransferase; 1.95A {Deinococcus radiodurans}

Probab=97.01  E-value=0.00032  Score=66.44  Aligned_cols=29  Identities=31%  Similarity=0.485  Sum_probs=23.1

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEE
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLY  207 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~vi  207 (666)
                      ..++|+|+||+||||+++.||+.+++.++
T Consensus         6 ~~I~l~G~~GsGKST~a~~La~~l~~~~i   34 (183)
T 2vli_A            6 PIIWINGPFGVGKTHTAHTLHERLPGSFV   34 (183)
T ss_dssp             CEEEEECCC----CHHHHHHHHHSTTCEE
T ss_pred             eEEEEECCCCCCHHHHHHHHHHhcCCCEE
Confidence            58999999999999999999999998776

>2c95_A Adenylate kinase 1; transferase, AP4A, nucleotide kinase, transferase ATP-bindi; HET: B4P; 1.71A {Homo sapiens} PDB: 1z83_A* 3adk_A

Probab=97.01  E-value=0.0004  Score=66.43  Aligned_cols=31  Identities=23%  Similarity=0.426  Sum_probs=27.9

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEEEE
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLYEW  209 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~viE~  209 (666)
                      ..++|.||||+||||+++.||+.+++.++..
T Consensus        10 ~~I~l~G~~GsGKsT~~~~La~~l~~~~i~~   40 (196)
T 2c95_A           10 NIIFVVGGPGSGKGTQCEKIVQKYGYTHLST   40 (196)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHHHCCEEEEH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHhCCeEEcH
Confidence            5899999999999999999999999877643

>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=97.01  E-value=0.00038  Score=66.53  Aligned_cols=30  Identities=37%  Similarity=0.482  Sum_probs=27.0

Q ss_pred             cEEEEECCCCchHHHHHHHHHHH-cCCcEEE
Q 005987          179 NVLVITGQAGVGKTATVRQIASH-LGARLYE  208 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAke-lg~~viE  208 (666)
                      ..++|+|+|||||||+++.||+. +|+.++.
T Consensus        11 ~~I~l~G~~GsGKSTv~~~La~~l~g~~~id   41 (184)
T 1y63_A           11 INILITGTPGTGKTSMAEMIAAELDGFQHLE   41 (184)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHSTTEEEEE
T ss_pred             CEEEEECCCCCCHHHHHHHHHHhcCCCEEee
Confidence            57999999999999999999999 7877664

>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=97.00  E-value=0.00039  Score=66.12  Aligned_cols=25  Identities=36%  Similarity=0.585  Sum_probs=23.7

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLG  203 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg  203 (666)
                      ..++|+||||+||||+++.||+.++
T Consensus         4 ~~I~i~G~~GsGKsT~~~~L~~~l~   28 (192)
T 1kht_A            4 KVVVVTGVPGVGSTTSSQLAMDNLR   28 (192)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHH
Confidence            5799999999999999999999987

>3be4_A Adenylate kinase; malaria, cryptosporidium parvum nonprotein inhibitors, nucleotide-binding, transferase; HET: AP5; 1.60A {Cryptosporidium parvum iowa II}

Probab=97.00  E-value=0.00044  Score=67.93  Aligned_cols=31  Identities=23%  Similarity=0.339  Sum_probs=28.0

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEEEE
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLYEW  209 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~viE~  209 (666)
                      ..++|.||||+||||+++.||+.+|+.++..
T Consensus         6 ~~I~l~G~~GsGKsT~a~~La~~l~~~~i~~   36 (217)
T 3be4_A            6 HNLILIGAPGSGKGTQCEFIKKEYGLAHLST   36 (217)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHHHCCEEEEH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhCceEEeh
Confidence            4789999999999999999999999887754

>4eun_A Thermoresistant glucokinase; putative sugar kinase, enzyme function initiative, EFI, STRU genomics, transferase; 1.60A {Janibacter SP}

Probab=97.00  E-value=0.00051  Score=66.53  Aligned_cols=30  Identities=30%  Similarity=0.491  Sum_probs=26.7

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEEE
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLYE  208 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~viE  208 (666)
                      .+++|.||+|+||||+++.|+..+|..++.
T Consensus        30 ~~i~l~G~~GsGKSTl~~~L~~~~g~~~i~   59 (200)
T 4eun_A           30 RHVVVMGVSGSGKTTIAHGVADETGLEFAE   59 (200)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHHCCEEEE
T ss_pred             cEEEEECCCCCCHHHHHHHHHHhhCCeEEc
Confidence            689999999999999999999999875553

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=96.98  E-value=0.002  Score=81.44  Aligned_cols=38  Identities=21%  Similarity=0.173  Sum_probs=31.2

Q ss_pred             CCccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcCCC
Q 005987          176 FSTNVLVITGQAGVGKTATVRQIASHL---GARLYEWDTPT  213 (666)
Q Consensus       176 ~~~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~nasd  213 (666)
                      .++++++|+||||||||++|.++|.+.   |..+..+....
T Consensus      1425 ~~g~~vll~GppGtGKT~LA~ala~ea~~~G~~v~Fi~~e~ 1465 (2050)
T 3cmu_A         1425 PMGRIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDAEH 1465 (2050)
T ss_dssp             ETTSEEEEECCTTSSHHHHHHHHHHHHHTTTCCEEEECTTS
T ss_pred             cCCeEEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEEEccc
Confidence            345799999999999999999998775   67777777654

>2bwj_A Adenylate kinase 5; phosphoryl transfer reaction, transferase; HET: AMP; 2.3A {Homo sapiens}

Probab=96.98  E-value=0.00044  Score=66.30  Aligned_cols=31  Identities=19%  Similarity=0.383  Sum_probs=27.9

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEEEE
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLYEW  209 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~viE~  209 (666)
                      ..++|+||||+||||+++.||+.+|+.++..
T Consensus        13 ~~I~l~G~~GsGKsT~a~~L~~~l~~~~i~~   43 (199)
T 2bwj_A           13 KIIFIIGGPGSGKGTQCEKLVEKYGFTHLST   43 (199)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHHHTCEEEEH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHhCCeEEcH
Confidence            5899999999999999999999999877643

>2p5t_B PEZT; postsegregational killing system, phosphoryltransferase, HEL helix motif, transcription regulator; 3.20A {Streptococcus pneumoniae}

Probab=96.97  E-value=0.001  Score=66.95  Aligned_cols=32  Identities=25%  Similarity=0.373  Sum_probs=27.1

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEEEEc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLYEWD  210 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~viE~n  210 (666)
                      ..++|.||||+||||+++.|++.++..++.++
T Consensus        33 ~~i~l~G~~GsGKSTla~~L~~~l~~~~~~~~   64 (253)
T 2p5t_B           33 IAILLGGQSGAGKTTIHRIKQKEFQGNIVIID   64 (253)
T ss_dssp             EEEEEESCGGGTTHHHHHHHHHHTTTCCEEEC
T ss_pred             eEEEEECCCCCCHHHHHHHHHHhcCCCcEEEe
Confidence            68999999999999999999999975444444

>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=96.97  E-value=0.00043  Score=65.82  Aligned_cols=31  Identities=26%  Similarity=0.365  Sum_probs=27.8

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEEEE
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLYEW  209 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~viE~  209 (666)
                      +.++|+|+||+||||+++.|++.+|+.++..
T Consensus         7 ~~I~l~G~~GsGKsT~~~~L~~~l~~~~i~~   37 (194)
T 1qf9_A            7 NVVFVLGGPGSGKGTQCANIVRDFGWVHLSA   37 (194)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHHHCCEEEEH
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHhCCeEeeH
Confidence            5899999999999999999999999877643

>3umf_A Adenylate kinase; rossmann fold, transferase; 2.05A {Schistosoma mansoni}

Probab=96.95  E-value=0.00049  Score=67.98  Aligned_cols=29  Identities=17%  Similarity=0.369  Sum_probs=26.9

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEE
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLY  207 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~vi  207 (666)
                      ++++|.||||+||+|.++.||+.+|+..+
T Consensus        30 kiI~llGpPGsGKgTqa~~L~~~~g~~hI   58 (217)
T 3umf_A           30 KVIFVLGGPGSGKGTQCEKLVQKFHFNHL   58 (217)
T ss_dssp             EEEEEECCTTCCHHHHHHHHHHHHCCEEE
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHHCCceE
Confidence            68999999999999999999999998765

>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=96.95  E-value=0.0052  Score=63.09  Aligned_cols=34  Identities=29%  Similarity=0.367  Sum_probs=27.5

Q ss_pred             ccEEEEECCCCchHHHHHHHHHHHc----CCcEEEEcC
Q 005987          178 TNVLVITGQAGVGKTATVRQIASHL----GARLYEWDT  211 (666)
Q Consensus       178 ~k~LLL~GPpG~GKTtla~~LAkel----g~~viE~na  211 (666)
                      ..+++|.||||+||||+++.+|..+    |..++.+..
T Consensus        35 G~~~~i~G~~G~GKTTl~~~ia~~~~~~~G~~v~~~~~   72 (296)
T 1cr0_A           35 GEVIMVTSGSGMGKSTFVRQQALQWGTAMGKKVGLAML   72 (296)
T ss_dssp             TCEEEEEESTTSSHHHHHHHHHHHHHHTSCCCEEEEES
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHHHHHHcCCeEEEEeC
Confidence            4689999999999999999998876    446665543

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A*

Probab=96.94  E-value=0.018  Score=68.63  Aligned_cols=43  Identities=19%  Similarity=0.189  Sum_probs=36.6

Q ss_pred             ccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHH
Q 005987          152 AVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       152 vg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAke  201 (666)
                      +|++..+++|..||...     ..  .+++.|+||+|+||||+|+.+++.
T Consensus       131 VGRe~eLeeL~elL~~~-----d~--~RVV~IvGmGGIGKTTLAk~Vy~d  173 (1221)
T 1vt4_I          131 VSRLQPYLKLRQALLEL-----RP--AKNVLIDGVLGSGKTWVALDVCLS  173 (1221)
T ss_dssp             CCCHHHHHHHHHHHHHC-----CS--SCEEEECCSTTSSHHHHHHHHHHH
T ss_pred             CCcHHHHHHHHHHHhcc-----CC--CeEEEEEcCCCccHHHHHHHHHHh
Confidence            89999999999999751     11  268999999999999999999864

>2r8r_A Sensor protein; KDPD, PFAM02702, MCSG, structural genomics, protein structure initiative, midwest center for structural genomics, kinase; 2.30A {Pseudomonas syringae PV}

Probab=96.93  E-value=0.0018  Score=64.03  Aligned_cols=32  Identities=28%  Similarity=0.318  Sum_probs=26.7

Q ss_pred             EEEEECCCCchHHHHHHHHHHHc---CCcEEEEcC
Q 005987          180 VLVITGQAGVGKTATVRQIASHL---GARLYEWDT  211 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkel---g~~viE~na  211 (666)
                      .+++.|+|||||||++-.+|..+   |+.++-+..
T Consensus         8 ~I~~~~kgGvGKTt~a~~la~~l~~~G~~V~v~d~   42 (228)
T 2r8r_A            8 KVFLGAAPGVGKTYAMLQAAHAQLRQGVRVMAGVV   42 (228)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHHHHHTTCCEEEEEC
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHHHCCCCEEEEEe
Confidence            59999999999999998888776   888765544

>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=96.92  E-value=0.00071  Score=63.68  Aligned_cols=30  Identities=30%  Similarity=0.585  Sum_probs=26.9

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEEE
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLYE  208 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~viE  208 (666)
                      ..++|.||+|+||||+++.|+..+|..++.
T Consensus         9 ~~i~l~G~~GsGKSTl~~~l~~~~g~~~i~   38 (175)
T 1knq_A            9 HIYVLMGVSGSGKSAVASEVAHQLHAAFLD   38 (175)
T ss_dssp             EEEEEECSTTSCHHHHHHHHHHHHTCEEEE
T ss_pred             cEEEEEcCCCCCHHHHHHHHHHhhCcEEEe
Confidence            689999999999999999999999876554

>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=96.91  E-value=0.0016  Score=81.51  Aligned_cols=35  Identities=23%  Similarity=0.231  Sum_probs=27.1

Q ss_pred             CccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcC
Q 005987          177 STNVLVITGQAGVGKTATVRQIASHL---GARLYEWDT  211 (666)
Q Consensus       177 ~~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~na  211 (666)
                      ..+++|||||||||||++|+++|.+.   |-..+.+..
T Consensus      1081 ~g~~~l~~G~~g~GKT~la~~~~~~~~~~g~~~~fi~~ 1118 (1706)
T 3cmw_A         1081 MGRIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDA 1118 (1706)
T ss_dssp             TTSEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEECT
T ss_pred             CCCEEEEEcCCCCChHHHHHHHHHHhhhcCCceeEEEc
Confidence            44679999999999999999999876   334444443

>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=96.90  E-value=0.01  Score=61.72  Aligned_cols=40  Identities=15%  Similarity=0.162  Sum_probs=29.1

Q ss_pred             CCCCccEEEEECCCCchHHHHHHHHHHHc-----CCcEEEEcCCC
Q 005987          174 DKFSTNVLVITGQAGVGKTATVRQIASHL-----GARLYEWDTPT  213 (666)
Q Consensus       174 g~~~~k~LLL~GPpG~GKTtla~~LAkel-----g~~viE~nasd  213 (666)
                      |..+..+++|+||||+||||++..++.+.     |..++.+.+..
T Consensus        24 GGl~~GiteI~G~pGsGKTtL~Lq~~~~~~~~g~g~~vlyId~E~   68 (333)
T 3io5_A           24 GGMQSGLLILAGPSKSFKSNFGLTMVSSYMRQYPDAVCLFYDSEF   68 (333)
T ss_dssp             CCBCSEEEEEEESSSSSHHHHHHHHHHHHHHHCTTCEEEEEESSC
T ss_pred             CCCcCCeEEEECCCCCCHHHHHHHHHHHHHhcCCCceEEEEeccc
Confidence            34443589999999999999987766554     56677776543

>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=96.89  E-value=0.019  Score=62.37  Aligned_cols=35  Identities=23%  Similarity=0.345  Sum_probs=29.4

Q ss_pred             ccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcCC
Q 005987          178 TNVLVITGQAGVGKTATVRQIASHL---GARLYEWDTP  212 (666)
Q Consensus       178 ~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~nas  212 (666)
                      +++++|.||+|+||||++..||..+   |.++.-+.+.
T Consensus        97 ~~vI~lvG~~GsGKTTt~~kLA~~l~~~G~kVllv~~D  134 (433)
T 3kl4_A           97 PFIIMLVGVQGSGKTTTAGKLAYFYKKRGYKVGLVAAD  134 (433)
T ss_dssp             SEEEEECCCTTSCHHHHHHHHHHHHHHTTCCEEEEEEC
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEecC
Confidence            4789999999999999999999876   7777766544

>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=96.89  E-value=0.00064  Score=66.43  Aligned_cols=30  Identities=27%  Similarity=0.348  Sum_probs=26.9

Q ss_pred             EEEEECCCCchHHHHHHHHHHHcCCcEEEE
Q 005987          180 VLVITGQAGVGKTATVRQIASHLGARLYEW  209 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkelg~~viE~  209 (666)
                      .++|+||||+||||+++.||+++|+.++..
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~~~~~~i~~   31 (216)
T 3dl0_A            2 NLVLMGLPGAGKGTQGERIVEKYGIPHIST   31 (216)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHSSCCEEEH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCcEEeH
Confidence            378999999999999999999999887754

>3fb4_A Adenylate kinase; psychrophIle, phosphotransferase, ATP-binding, nucleotide-binding, transferase; HET: AP5; 2.00A {Marinibacillus marinus}

Probab=96.88  E-value=0.0006  Score=66.55  Aligned_cols=30  Identities=23%  Similarity=0.294  Sum_probs=26.8

Q ss_pred             EEEEECCCCchHHHHHHHHHHHcCCcEEEE
Q 005987          180 VLVITGQAGVGKTATVRQIASHLGARLYEW  209 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkelg~~viE~  209 (666)
                      .++|+||||+||||+++.||+.+|+.++..
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~~~~~~i~~   31 (216)
T 3fb4_A            2 NIVLMGLPGAGKGTQAEQIIEKYEIPHIST   31 (216)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHCCCEEEH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCcEeeH
Confidence            478999999999999999999999887754

>1ukz_A Uridylate kinase; transferase; HET: ADP AMP; 1.90A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 1uky_A*

Probab=96.88  E-value=0.00067  Score=65.51  Aligned_cols=31  Identities=16%  Similarity=0.292  Sum_probs=27.8

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEEEE
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLYEW  209 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~viE~  209 (666)
                      ..++|+||||+||||+++.||+.+|+.++..
T Consensus        16 ~~I~l~G~~GsGKsT~~~~L~~~~g~~~i~~   46 (203)
T 1ukz_A           16 SVIFVLGGPGAGKGTQCEKLVKDYSFVHLSA   46 (203)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHSSCEEEEH
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHcCceEEeH
Confidence            5799999999999999999999999876653

>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=96.87  E-value=0.00079  Score=63.72  Aligned_cols=33  Identities=30%  Similarity=0.449  Sum_probs=28.9

Q ss_pred             ccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEc
Q 005987          178 TNVLVITGQAGVGKTATVRQIASHL---GARLYEWD  210 (666)
Q Consensus       178 ~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~n  210 (666)
                      +..++|+|++|+||||+++.|+..+   |+.++.++
T Consensus         5 g~~i~l~G~~GsGKST~~~~L~~~l~~~g~~~i~~d   40 (179)
T 2pez_A            5 GCTVWLTGLSGAGKTTVSMALEEYLVCHGIPCYTLD   40 (179)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHhhCCCcEEEEC
Confidence            3679999999999999999999998   88777654

>2pt5_A Shikimate kinase, SK; aromatic amino acid biosynthesis, P-loop kinase, SHI kinase, shikimate pathway; 2.10A {Aquifex aeolicus}

Probab=96.87  E-value=0.00073  Score=63.01  Aligned_cols=30  Identities=17%  Similarity=0.281  Sum_probs=27.2

Q ss_pred             EEEEECCCCchHHHHHHHHHHHcCCcEEEE
Q 005987          180 VLVITGQAGVGKTATVRQIASHLGARLYEW  209 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkelg~~viE~  209 (666)
                      .++|+|+||+||||+++.|++.+++.++..
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~l~~~~i~~   31 (168)
T 2pt5_A            2 RIYLIGFMCSGKSTVGSLLSRSLNIPFYDV   31 (168)
T ss_dssp             EEEEESCTTSCHHHHHHHHHHHHTCCEEEH
T ss_pred             eEEEECCCCCCHHHHHHHHHHHhCCCEEEC
Confidence            589999999999999999999999887753

>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=96.85  E-value=0.0051  Score=65.12  Aligned_cols=38  Identities=21%  Similarity=0.254  Sum_probs=30.2

Q ss_pred             CCccEEEEECCCCchHHHHHHHHHHHc---------CCcEEEEcCCC
Q 005987          176 FSTNVLVITGQAGVGKTATVRQIASHL---------GARLYEWDTPT  213 (666)
Q Consensus       176 ~~~k~LLL~GPpG~GKTtla~~LAkel---------g~~viE~nasd  213 (666)
                      ++..++.|+||||+||||+++.+|..+         +..++.++.-.
T Consensus       129 ~~G~i~~I~G~~GsGKTTL~~~l~~~~~~~~~~Gg~~G~vi~i~~e~  175 (349)
T 1pzn_A          129 ETQAITEVFGEFGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWIDTEN  175 (349)
T ss_dssp             ESSEEEEEEESTTSSHHHHHHHHHHHTTSCGGGTSCSCEEEEEESSS
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHhccchhcCCCCCeEEEEeCCC
Confidence            345789999999999999999999886         24667776543

>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=96.85  E-value=0.0055  Score=64.65  Aligned_cols=38  Identities=21%  Similarity=0.211  Sum_probs=30.3

Q ss_pred             CCccEEEEECCCCchHHHHHHHHHHHc---------CCcEEEEcCCC
Q 005987          176 FSTNVLVITGQAGVGKTATVRQIASHL---------GARLYEWDTPT  213 (666)
Q Consensus       176 ~~~k~LLL~GPpG~GKTtla~~LAkel---------g~~viE~nasd  213 (666)
                      ++..+++|+||||+|||+++..+|...         +..++.+....
T Consensus       120 ~~G~i~~I~G~~GsGKTtla~~la~~~~~~~~~gg~~~~vlyi~~E~  166 (343)
T 1v5w_A          120 ESMAITEAFGEFRTGKTQLSHTLCVTAQLPGAGGYPGGKIIFIDTEN  166 (343)
T ss_dssp             CSSEEEEEECCTTCTHHHHHHHHHHHTTSCBTTTBCCCEEEEEESSS
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHHhcccccCCCCCeEEEEECCC
Confidence            345689999999999999999999872         56777776544

>1zd8_A GTP:AMP phosphotransferase mitochondrial; ATP:AMP phosphotransferase, myokinase, structural genomics, structural genomics consortium, SGC; 1.48A {Homo sapiens} PDB: 2ak3_A*

Probab=96.85  E-value=0.00063  Score=67.19  Aligned_cols=31  Identities=26%  Similarity=0.349  Sum_probs=27.9

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEEEE
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLYEW  209 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~viE~  209 (666)
                      ..++|.||||+||||+++.||+.+|+.++..
T Consensus         8 ~~I~l~G~~GsGKsT~a~~La~~l~~~~i~~   38 (227)
T 1zd8_A            8 LRAVIMGAPGSGKGTVSSRITTHFELKHLSS   38 (227)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHHSSSEEEEH
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHcCCeEEec
Confidence            5799999999999999999999999877753

>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=96.84  E-value=0.00078  Score=66.12  Aligned_cols=31  Identities=19%  Similarity=0.288  Sum_probs=27.8

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEEEE
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLYEW  209 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~viE~  209 (666)
                      ..++|.||||+||||+++.||+.+++.++..
T Consensus         5 ~~I~l~G~~GsGKsT~a~~La~~l~~~~i~~   35 (220)
T 1aky_A            5 IRMVLIGPPGAGKGTQAPNLQERFHAAHLAT   35 (220)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHHCCEEEEH
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHcCceEEeh
Confidence            4799999999999999999999999877653

>2r6a_A DNAB helicase, replicative helicase; replication, DNAB; 2.90A {Geobacillus stearothermophilus} PDB: 2r6c_A 2r6d_A 2r6e_A 2vyf_A 2vye_A

Probab=96.82  E-value=0.0053  Score=67.31  Aligned_cols=37  Identities=19%  Similarity=0.328  Sum_probs=28.9

Q ss_pred             CCCccEEEEECCCCchHHHHHHHHHHHc----CCcEEEEcC
Q 005987          175 KFSTNVLVITGQAGVGKTATVRQIASHL----GARLYEWDT  211 (666)
Q Consensus       175 ~~~~k~LLL~GPpG~GKTtla~~LAkel----g~~viE~na  211 (666)
                      -.++..++|.||||+||||++..+|..+    |..++.+..
T Consensus       200 l~~G~liiI~G~pG~GKTtl~l~ia~~~~~~~g~~Vl~~s~  240 (454)
T 2r6a_A          200 FQRSDLIIVAARPSVGKTAFALNIAQNVATKTNENVAIFSL  240 (454)
T ss_dssp             BCTTCEEEEECCTTSCHHHHHHHHHHHHHHHSSCCEEEEES
T ss_pred             CCCCCEEEEECCCCCCHHHHHHHHHHHHHHhCCCcEEEEEC
Confidence            3345689999999999999999888764    556766654

>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=96.80  E-value=0.0034  Score=65.64  Aligned_cols=38  Identities=21%  Similarity=0.257  Sum_probs=30.8

Q ss_pred             CCccEEEEECCCCchHHHHHHHHHHHc---------CCcEEEEcCCC
Q 005987          176 FSTNVLVITGQAGVGKTATVRQIASHL---------GARLYEWDTPT  213 (666)
Q Consensus       176 ~~~k~LLL~GPpG~GKTtla~~LAkel---------g~~viE~nasd  213 (666)
                      ++..+++|+||||+|||+++..+|...         +..++.+....
T Consensus       105 ~~G~i~~i~G~~GsGKT~la~~la~~~~~~~~~gg~~~~vlyi~~e~  151 (324)
T 2z43_A          105 ETRTMTEFFGEFGSGKTQLCHQLSVNVQLPPEKGGLSGKAVYIDTEG  151 (324)
T ss_dssp             ETTSEEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSCEEEEEESSS
T ss_pred             CCCcEEEEECCCCCCHhHHHHHHHHHHhcccccCCCCCeEEEEECCC
Confidence            344689999999999999999999875         56777776654

>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=96.80  E-value=0.0072  Score=65.51  Aligned_cols=29  Identities=24%  Similarity=0.338  Sum_probs=26.6

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEE
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLY  207 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~vi  207 (666)
                      .+++|+||||+||||+++.|++.+++.++
T Consensus       259 ~lIil~G~pGSGKSTla~~L~~~~~~~~i  287 (416)
T 3zvl_A          259 EVVVAVGFPGAGKSTFIQEHLVSAGYVHV  287 (416)
T ss_dssp             CEEEEESCTTSSHHHHHHHHTGGGTCEEC
T ss_pred             EEEEEECCCCCCHHHHHHHHHHhcCcEEE
Confidence            68999999999999999999999987655

>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=96.77  E-value=0.007  Score=64.24  Aligned_cols=33  Identities=21%  Similarity=0.429  Sum_probs=26.6

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc----CCcEEEEcC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL----GARLYEWDT  211 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel----g~~viE~na  211 (666)
                      ..++|+||+|+||||++++++..+    +..++.+..
T Consensus       124 g~i~I~GptGSGKTTlL~~l~g~~~~~~~~~i~t~ed  160 (356)
T 3jvv_A          124 GLVLVTGPTGSGKSTTLAAMLDYLNNTKYHHILTIED  160 (356)
T ss_dssp             EEEEEECSTTSCHHHHHHHHHHHHHHHCCCEEEEEES
T ss_pred             CEEEEECCCCCCHHHHHHHHHhcccCCCCcEEEEccC
Confidence            489999999999999999999876    345555443

>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=96.75  E-value=0.0016  Score=65.20  Aligned_cols=31  Identities=13%  Similarity=0.100  Sum_probs=27.9

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEEEE
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLYEW  209 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~viE~  209 (666)
                      ..++|+||||+||||+++.|++.+|+.++..
T Consensus        30 ~~I~l~G~~GsGKsT~a~~L~~~~g~~~is~   60 (243)
T 3tlx_A           30 GRYIFLGAPGSGKGTQSLNLKKSHCYCHLST   60 (243)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHCCEEEEH
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHhCCeEEec
Confidence            5799999999999999999999999877643

>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=96.75  E-value=0.055  Score=56.05  Aligned_cols=34  Identities=24%  Similarity=0.401  Sum_probs=27.8

Q ss_pred             ccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcC
Q 005987          178 TNVLVITGQAGVGKTATVRQIASHL---GARLYEWDT  211 (666)
Q Consensus       178 ~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~na  211 (666)
                      +++++|.||+|+||||++..||..+   +.++.-..+
T Consensus       104 ~~vi~ivG~~GsGKTTl~~~LA~~l~~~g~kV~lv~~  140 (306)
T 1vma_A          104 PFVIMVVGVNGTGKTTSCGKLAKMFVDEGKSVVLAAA  140 (306)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEEEE
T ss_pred             CeEEEEEcCCCChHHHHHHHHHHHHHhcCCEEEEEcc
Confidence            4689999999999999999999876   566655443

>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=96.74  E-value=0.0032  Score=60.83  Aligned_cols=32  Identities=19%  Similarity=0.188  Sum_probs=27.5

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc---CCcEEEEc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL---GARLYEWD  210 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel---g~~viE~n  210 (666)
                      ++.+++||.|+||||++..+|+.+   |..++-+.
T Consensus         9 ~i~v~~G~mgsGKTT~ll~~a~r~~~~g~kV~v~k   43 (191)
T 1xx6_A            9 WVEVIVGPMYSGKSEELIRRIRRAKIAKQKIQVFK   43 (191)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             EEEEEECCCCCcHHHHHHHHHHHHHHCCCEEEEEE
Confidence            689999999999999998888876   77777665

>2q6t_A DNAB replication FORK helicase; hydrolase; 2.90A {Thermus aquaticus}

Probab=96.74  E-value=0.0098  Score=65.00  Aligned_cols=39  Identities=21%  Similarity=0.210  Sum_probs=29.7

Q ss_pred             CCCCccEEEEECCCCchHHHHHHHHHHHc----CCcEEEEcCC
Q 005987          174 DKFSTNVLVITGQAGVGKTATVRQIASHL----GARLYEWDTP  212 (666)
Q Consensus       174 g~~~~k~LLL~GPpG~GKTtla~~LAkel----g~~viE~nas  212 (666)
                      |-.+...++|+|+||+|||+++..+|...    |..++.+..-
T Consensus       196 Gl~~G~l~ii~G~pg~GKT~lal~ia~~~a~~~g~~vl~~slE  238 (444)
T 2q6t_A          196 TLGPGSLNIIAARPAMGKTAFALTIAQNAALKEGVGVGIYSLE  238 (444)
T ss_dssp             CCCTTCEEEEEECTTSCHHHHHHHHHHHHHHTTCCCEEEEESS
T ss_pred             CcCCCcEEEEEeCCCCCHHHHHHHHHHHHHHhCCCeEEEEECC
Confidence            44455789999999999999998888754    5567666543

>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=96.73  E-value=0.001  Score=65.20  Aligned_cols=29  Identities=28%  Similarity=0.469  Sum_probs=26.0

Q ss_pred             EEEEECCCCchHHHHHHHHHHHcCCcEEE
Q 005987          180 VLVITGQAGVGKTATVRQIASHLGARLYE  208 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkelg~~viE  208 (666)
                      +++|.||||+||+|.++.||+.+|+..+.
T Consensus         2 ~Iil~GpPGsGKgTqa~~La~~~g~~~is   30 (206)
T 3sr0_A            2 ILVFLGPPGAGKGTQAKRLAKEKGFVHIS   30 (206)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHCCEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHCCeEEc
Confidence            47889999999999999999999987664

>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=96.72  E-value=0.0011  Score=65.14  Aligned_cols=30  Identities=30%  Similarity=0.501  Sum_probs=26.8

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEEE
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLYE  208 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~viE  208 (666)
                      ..+.|+||+||||||+++.|++.+|+.++.
T Consensus         6 ~~i~i~G~~GsGKSTl~~~L~~~~g~~~~d   35 (227)
T 1cke_A            6 PVITIDGPSGAGKGTLCKAMAEALQWHLLD   35 (227)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHHTCEEEE
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhCCCccc
Confidence            479999999999999999999999976653

>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=96.72  E-value=0.0011  Score=65.91  Aligned_cols=31  Identities=19%  Similarity=0.237  Sum_probs=27.8

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEEEE
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLYEW  209 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~viE~  209 (666)
                      ..++|.|+||+||||+++.||+.+++.++..
T Consensus        17 ~~I~l~G~~GsGKsT~a~~La~~l~~~~i~~   47 (233)
T 1ak2_A           17 VRAVLLGPPGAGKGTQAPKLAKNFCVCHLAT   47 (233)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHHTCEEEEH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhCCceecH
Confidence            4799999999999999999999999877653

>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=96.70  E-value=0.00078  Score=64.21  Aligned_cols=33  Identities=24%  Similarity=0.533  Sum_probs=27.7

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEEEEcC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLYEWDT  211 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~viE~na  211 (666)
                      .+++|.||||+||||+++.||..++...+.++.
T Consensus        10 ~~i~l~G~~GsGKSTl~~~La~~~~~g~i~i~~   42 (191)
T 1zp6_A           10 NILLLSGHPGSGKSTIAEALANLPGVPKVHFHS   42 (191)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHTCSSSCEEEECT
T ss_pred             eEEEEECCCCCCHHHHHHHHHhccCCCeEEEcc
Confidence            689999999999999999999987655555553

>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=96.69  E-value=0.024  Score=58.50  Aligned_cols=34  Identities=26%  Similarity=0.398  Sum_probs=27.9

Q ss_pred             ccEEEEECCCCchHHHHHHHHHHHc----CCcEEEEcC
Q 005987          178 TNVLVITGQAGVGKTATVRQIASHL----GARLYEWDT  211 (666)
Q Consensus       178 ~k~LLL~GPpG~GKTtla~~LAkel----g~~viE~na  211 (666)
                      +++++|.||+|+||||++..||..+    |..+.-+..
T Consensus       105 g~vi~lvG~~GsGKTTl~~~LA~~l~~~~G~~V~lv~~  142 (296)
T 2px0_A          105 SKYIVLFGSTGAGKTTTLAKLAAISMLEKHKKIAFITT  142 (296)
T ss_dssp             SSEEEEEESTTSSHHHHHHHHHHHHHHTTCCCEEEEEC
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHhcCCEEEEEec
Confidence            4689999999999999999999765    556666554

>1nks_A Adenylate kinase; thermophilic, transferase; HET: AMP ADP; 2.57A {Sulfolobus acidocaldarius} SCOP: c.37.1.1

Probab=96.67  E-value=0.00066  Score=64.52  Aligned_cols=25  Identities=28%  Similarity=0.569  Sum_probs=23.1

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLG  203 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg  203 (666)
                      +.++|.||||+||||+++.|++.++
T Consensus         2 ~~I~i~G~~GsGKsT~~~~L~~~l~   26 (194)
T 1nks_A            2 KIGIVTGIPGVGKSTVLAKVKEILD   26 (194)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHH
Confidence            3689999999999999999999885

>1zak_A Adenylate kinase; ATP:AMP-phosphotransferase, transferase; HET: AP5; 3.50A {Zea mays} SCOP: c.37.1.1 g.41.2.1

Probab=96.66  E-value=0.00079  Score=66.15  Aligned_cols=29  Identities=17%  Similarity=0.218  Sum_probs=26.1

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEE
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLY  207 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~vi  207 (666)
                      ..++|.||||+||||+++.||+.+++..+
T Consensus         6 ~~I~l~G~~GsGKsT~~~~La~~l~~~~i   34 (222)
T 1zak_A            6 LKVMISGAPASGKGTQCELIKTKYQLAHI   34 (222)
T ss_dssp             CCEEEEESTTSSHHHHHHHHHHHHCCEEC
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhCCcee
Confidence            47999999999999999999999997544

>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=96.66  E-value=0.0012  Score=63.53  Aligned_cols=34  Identities=21%  Similarity=0.336  Sum_probs=29.3

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc-CCcEEEEcCC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL-GARLYEWDTP  212 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel-g~~viE~nas  212 (666)
                      ..++|.||+|+||||+++.|++.+ |+.++....+
T Consensus         5 ~~I~l~G~~GsGKsT~~~~L~~~l~g~~~~~~~~~   39 (204)
T 2v54_A            5 ALIVFEGLDKSGKTTQCMNIMESIPANTIKYLNFP   39 (204)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHTSCGGGEEEEESS
T ss_pred             cEEEEEcCCCCCHHHHHHHHHHHHCCCceEEEecC
Confidence            579999999999999999999998 6777766544

>2pbr_A DTMP kinase, thymidylate kinase; transferase, nucleotide biosynthesis, TMP-binding, A binding, structural genomics, NPPSFA; 1.96A {Aquifex aeolicus}

Probab=96.66  E-value=0.0014  Score=62.33  Aligned_cols=33  Identities=24%  Similarity=0.456  Sum_probs=29.1

Q ss_pred             EEEEECCCCchHHHHHHHHHHHc---CCcEEEEcCC
Q 005987          180 VLVITGQAGVGKTATVRQIASHL---GARLYEWDTP  212 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkel---g~~viE~nas  212 (666)
                      .++|+|++|+||||+++.|++.+   |+.++....+
T Consensus         2 ~I~l~G~~GsGKsT~~~~L~~~l~~~g~~~i~~d~~   37 (195)
T 2pbr_A            2 LIAFEGIDGSGKTTQAKKLYEYLKQKGYFVSLYREP   37 (195)
T ss_dssp             EEEEECSTTSCHHHHHHHHHHHHHHTTCCEEEEESS
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEeCC
Confidence            58999999999999999999998   8888876543

>1kgd_A CASK, peripheral plasma membrane CASK; maguk, guanylate kinase like domain, protein binding; 1.31A {Homo sapiens} SCOP: c.37.1.1

Probab=96.65  E-value=0.0011  Score=63.13  Aligned_cols=26  Identities=23%  Similarity=0.411  Sum_probs=23.5

Q ss_pred             ccEEEEECCCCchHHHHHHHHHHHcC
Q 005987          178 TNVLVITGQAGVGKTATVRQIASHLG  203 (666)
Q Consensus       178 ~k~LLL~GPpG~GKTtla~~LAkelg  203 (666)
                      ++.++|.||+|+||||+++.|+..+.
T Consensus         5 g~~i~i~GpsGsGKSTL~~~L~~~~~   30 (180)
T 1kgd_A            5 RKTLVLLGAHGVGRRHIKNTLITKHP   30 (180)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHCT
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhhCC
Confidence            46899999999999999999999763

>2jaq_A Deoxyguanosine kinase; transferase, deoxyribonucleoside kinase; HET: DCP; 2.3A {Mycoplasma mycoides subsp} PDB: 2jat_A* 2jas_A*

Probab=96.64  E-value=0.0012  Score=63.42  Aligned_cols=28  Identities=29%  Similarity=0.599  Sum_probs=25.5

Q ss_pred             EEEEECCCCchHHHHHHHHHHHcCCcEE
Q 005987          180 VLVITGQAGVGKTATVRQIASHLGARLY  207 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkelg~~vi  207 (666)
                      .++|.|++|+||||+++.||+.++..++
T Consensus         2 ~I~i~G~~GsGKsT~~~~L~~~l~~~~~   29 (205)
T 2jaq_A            2 KIAIFGTVGAGKSTISAEISKKLGYEIF   29 (205)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHCCEEE
T ss_pred             EEEEECCCccCHHHHHHHHHHhcCCcEE
Confidence            5889999999999999999999998654

>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=96.64  E-value=0.0011  Score=64.66  Aligned_cols=30  Identities=17%  Similarity=0.231  Sum_probs=26.9

Q ss_pred             EEEEECCCCchHHHHHHHHHHHcCCcEEEE
Q 005987          180 VLVITGQAGVGKTATVRQIASHLGARLYEW  209 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkelg~~viE~  209 (666)
                      .++|.||||+||||+++.||+.+|+.++..
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~~g~~~i~~   31 (214)
T 1e4v_A            2 RIILLGAPVAGKGTQAQFIMEKYGIPQIST   31 (214)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHCCCEEEH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCeEEeH
Confidence            378999999999999999999999887754

>2plr_A DTMP kinase, probable thymidylate kinase; TMP-binding, ATP-binding, structural GEN NPPSFA; HET: 1PE PGE EPE PG4; 1.60A {Sulfolobus tokodaii}

Probab=96.60  E-value=0.0016  Score=62.79  Aligned_cols=33  Identities=15%  Similarity=0.297  Sum_probs=27.5

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCC--cEEEEcC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGA--RLYEWDT  211 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~--~viE~na  211 (666)
                      ..++|.||||+||||+++.||+.++.  .++....
T Consensus         5 ~~I~i~G~~GsGKsT~~~~L~~~l~~~g~~~~~~~   39 (213)
T 2plr_A            5 VLIAFEGIDGSGKSSQATLLKDWIELKRDVYLTEW   39 (213)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHTTTSCEEEEET
T ss_pred             eEEEEEcCCCCCHHHHHHHHHHHHhhcCCEEEecC
Confidence            57999999999999999999999876  3554433

>2ga8_A Hypothetical 39.9 kDa protein; YFR007W, YFH7, unknown function; HET: CME; 1.77A {Saccharomyces cerevisiae} PDB: 2gaa_A*

Probab=96.60  E-value=0.00045  Score=73.01  Aligned_cols=54  Identities=15%  Similarity=0.366  Sum_probs=39.5

Q ss_pred             CHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcC
Q 005987          154 QRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDT  211 (666)
Q Consensus       154 ~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~na  211 (666)
                      -.+.++.+...+...+..  |..  ..++|.||||+||||++++||+.+++.++++++
T Consensus         4 ~~~L~~~il~~l~~~i~~--g~~--~~i~l~G~~G~GKTTl~~~la~~l~~~f~~l~a   57 (359)
T 2ga8_A            4 THKLADDVLQLLDNRIED--NYR--VCVILVGSPGSGKSTIAEELCQIINEKYHTFLS   57 (359)
T ss_dssp             HHHHHHHHHHHHHHTTTT--CSC--EEEEEECCTTSSHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhcc--CCe--eEEEEECCCCCcHHHHHHHHHHHhCCCeeeecc
Confidence            345566676776654431  333  369999999999999999999999877765544

>2xb4_A Adenylate kinase; ATP-binding, nucleotide-binding, transferase; HET: SRT; 1.80A {Desulfovibrio gigas} PDB: 3l0s_A* 3l0p_A*

Probab=96.59  E-value=0.0014  Score=64.67  Aligned_cols=30  Identities=20%  Similarity=0.232  Sum_probs=26.5

Q ss_pred             EEEEECCCCchHHHHHHHHHHHcCCcEEEE
Q 005987          180 VLVITGQAGVGKTATVRQIASHLGARLYEW  209 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkelg~~viE~  209 (666)
                      .++|.||||+||||+++.||+.+|+.++..
T Consensus         2 ~I~l~G~~GsGKsT~a~~La~~lg~~~i~~   31 (223)
T 2xb4_A            2 NILIFGPNGSGKGTQGNLVKDKYSLAHIES   31 (223)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHTCEEEEH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCeEEch
Confidence            589999999999999999999999866643

>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=96.59  E-value=0.0074  Score=65.06  Aligned_cols=38  Identities=16%  Similarity=0.157  Sum_probs=28.0

Q ss_pred             CCccEEEEECCCCchHHHHHHHHHHHc---------CCcEEEEcCCC
Q 005987          176 FSTNVLVITGQAGVGKTATVRQIASHL---------GARLYEWDTPT  213 (666)
Q Consensus       176 ~~~k~LLL~GPpG~GKTtla~~LAkel---------g~~viE~nasd  213 (666)
                      .+..+++|+|||||||||+++.+|-..         +..++.++.-+
T Consensus       176 ~~Gei~~I~G~sGsGKTTLl~~la~~~~~p~~~Gg~~~~viyid~E~  222 (400)
T 3lda_A          176 ETGSITELFGEFRTGKSQLCHTLAVTCQIPLDIGGGEGKCLYIDTEG  222 (400)
T ss_dssp             ETTSEEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSSEEEEEESSS
T ss_pred             CCCcEEEEEcCCCCChHHHHHHHHHHhccCcccCCCCCcEEEEeCCC
Confidence            345789999999999999999776432         34467766543

>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=96.58  E-value=0.0082  Score=57.82  Aligned_cols=24  Identities=29%  Similarity=0.317  Sum_probs=20.6

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      +.+++.+|+|+|||.++..++.++
T Consensus        49 ~~~li~~~tGsGKT~~~~~~~~~~   72 (216)
T 3b6e_A           49 KNIIICLPTGSGKTRVAVYIAKDH   72 (216)
T ss_dssp             CCEEEECSCHHHHHHHHHHHHHHH
T ss_pred             CCEEEEcCCCCCHHHHHHHHHHHH
Confidence            369999999999999998887764

>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=96.57  E-value=0.0014  Score=63.30  Aligned_cols=29  Identities=28%  Similarity=0.473  Sum_probs=26.2

Q ss_pred             EEEEECCCCchHHHHHHHHHHHcCCcEEEE
Q 005987          180 VLVITGQAGVGKTATVRQIASHLGARLYEW  209 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkelg~~viE~  209 (666)
                      .+.|+||+||||||+++.||+ +|+.++..
T Consensus         3 ~i~i~G~~GsGKSTl~~~L~~-~g~~~i~~   31 (204)
T 2if2_A            3 RIGLTGNIGCGKSTVAQMFRE-LGAYVLDA   31 (204)
T ss_dssp             EEEEEECTTSSHHHHHHHHHH-TTCEEEEH
T ss_pred             EEEEECCCCcCHHHHHHHHHH-CCCEEEEc
Confidence            689999999999999999999 99877754

>3bh0_A DNAB-like replicative helicase; ATPase, replication; 2.35A {Bacillus phage SPP1}

Probab=96.55  E-value=0.017  Score=60.10  Aligned_cols=38  Identities=18%  Similarity=0.186  Sum_probs=29.1

Q ss_pred             CCCCccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcC
Q 005987          174 DKFSTNVLVITGQAGVGKTATVRQIASHL---GARLYEWDT  211 (666)
Q Consensus       174 g~~~~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~na  211 (666)
                      |-.+...++|.|+||+|||+++..+|...   |..++.+..
T Consensus        64 Gl~~G~l~li~G~pG~GKTtl~l~ia~~~a~~g~~vl~~sl  104 (315)
T 3bh0_A           64 GYKRRNFVLIAARPSMGKTAFALKQAKNMSDNDDVVNLHSL  104 (315)
T ss_dssp             SBCTTCEEEEECCTTSSHHHHHHHHHHHHHTTTCEEEEEES
T ss_pred             CCCCCcEEEEEeCCCCCHHHHHHHHHHHHHHcCCeEEEEEC
Confidence            44445689999999999999999998765   455665553

>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=96.53  E-value=0.0017  Score=62.50  Aligned_cols=31  Identities=26%  Similarity=0.512  Sum_probs=27.8

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEEEE
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLYEW  209 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~viE~  209 (666)
                      +++.|+||+|+||||+++.||+.+|+.++..
T Consensus         3 ~~i~i~G~~GsGKst~~~~la~~lg~~~~d~   33 (208)
T 3ake_A            3 GIVTIDGPSASGKSSVARRVAAALGVPYLSS   33 (208)
T ss_dssp             SEEEEECSTTSSHHHHHHHHHHHHTCCEEEH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHhcCCceecc
Confidence            3799999999999999999999999877753

>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=96.53  E-value=0.0021  Score=62.16  Aligned_cols=24  Identities=29%  Similarity=0.457  Sum_probs=23.0

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      .++.|.||+||||||+++.||..+
T Consensus        26 ~~i~l~G~sGsGKSTl~~~La~~l   49 (200)
T 3uie_A           26 CVIWVTGLSGSGKSTLACALNQML   49 (200)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHH
Confidence            689999999999999999999998

>2efe_B Small GTP-binding protein-like; GEF, GTPase, VPS9, nucleotide, transport protein; HET: GNH; 2.08A {Arabidopsis thaliana} PDB: 2efd_B 2efc_B* 2efh_B*

Probab=96.52  E-value=0.037  Score=51.34  Aligned_cols=22  Identities=32%  Similarity=0.560  Sum_probs=20.0

Q ss_pred             EEEEECCCCchHHHHHHHHHHH
Q 005987          180 VLVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAke  201 (666)
                      .++|.|++|+||||++..+...
T Consensus        14 ki~v~G~~~~GKSsli~~l~~~   35 (181)
T 2efe_B           14 KLVLLGDVGAGKSSLVLRFVKD   35 (181)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHC
T ss_pred             EEEEECcCCCCHHHHHHHHHcC
Confidence            5899999999999999999875

>3lxx_A GTPase IMAP family member 4; structural genomics consortium, SGC, coiled coil, GTP- binding, nucleotide-binding, immune system; HET: GDP; 2.15A {Homo sapiens}

Probab=96.51  E-value=0.042  Score=54.27  Aligned_cols=24  Identities=33%  Similarity=0.480  Sum_probs=21.0

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      ..++|.|++|+||||++..|....
T Consensus        30 ~~i~lvG~~g~GKStlin~l~g~~   53 (239)
T 3lxx_A           30 LRIVLVGKTGAGKSATGNSILGRK   53 (239)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHTSC
T ss_pred             eEEEEECCCCCCHHHHHHHHcCCC
Confidence            368999999999999999998754

>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=96.50  E-value=0.0018  Score=64.55  Aligned_cols=30  Identities=40%  Similarity=0.673  Sum_probs=27.2

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEEE
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLYE  208 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~viE  208 (666)
                      ..+.|.||+||||||+++.||+.+|+.++.
T Consensus        10 ~~i~i~G~~GsGKsTla~~la~~lg~~~~d   39 (233)
T 3r20_A           10 LVVAVDGPAGTGKSSVSRGLARALGARYLD   39 (233)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHHTCEEEE
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhCCCccc
Confidence            479999999999999999999999987664

>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=96.50  E-value=0.0016  Score=65.11  Aligned_cols=29  Identities=31%  Similarity=0.453  Sum_probs=26.1

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEE
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLY  207 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~vi  207 (666)
                      ..++|.||+|+||||+++.||+.+|+..+
T Consensus        28 ~~i~l~G~~GsGKSTl~k~La~~lg~~~~   56 (246)
T 2bbw_A           28 LRAVILGPPGSGKGTVCQRIAQNFGLQHL   56 (246)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHHCCCCE
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHhCCeEe
Confidence            58999999999999999999999987543

>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=96.50  E-value=0.029  Score=51.04  Aligned_cols=23  Identities=30%  Similarity=0.463  Sum_probs=20.4

Q ss_pred             EEEEECCCCchHHHHHHHHHHHc
Q 005987          180 VLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      .+++.|++|+||||++..++..-
T Consensus         6 ~i~v~G~~~~GKssl~~~l~~~~   28 (168)
T 1u8z_A            6 KVIMVGSGGVGKSALTLQFMYDE   28 (168)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHHhCc
Confidence            58999999999999999998753

>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=96.48  E-value=0.0017  Score=65.64  Aligned_cols=32  Identities=22%  Similarity=0.378  Sum_probs=27.7

Q ss_pred             cEEEEECCCCchHHHHHHHHHHH---cCCcEEEEc
Q 005987          179 NVLVITGQAGVGKTATVRQIASH---LGARLYEWD  210 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAke---lg~~viE~n  210 (666)
                      ..++|+|+||+||||+++.|++.   .|+.++.++
T Consensus         5 ~lIvl~G~pGSGKSTla~~La~~L~~~g~~~i~~~   39 (260)
T 3a4m_A            5 MLIILTGLPGVGKSTFSKNLAKILSKNNIDVIVLG   39 (260)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEEC
T ss_pred             EEEEEEcCCCCCHHHHHHHHHHHHHhCCCEEEEEC
Confidence            58999999999999999999998   687776443

>3nwj_A ATSK2; P loop, shikimate, nucleoside monophosphate kinase, shikimat ATP binding, chloroplast, transferase; 2.35A {Arabidopsis thaliana}

Probab=96.48  E-value=0.0017  Score=65.60  Aligned_cols=31  Identities=26%  Similarity=0.498  Sum_probs=28.1

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEEEE
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLYEW  209 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~viE~  209 (666)
                      ..++|.||+|+||||+++.||+.+|+.++..
T Consensus        49 ~~i~l~G~~GsGKSTl~~~La~~lg~~~~d~   79 (250)
T 3nwj_A           49 RSMYLVGMMGSGKTTVGKIMARSLGYTFFDC   79 (250)
T ss_dssp             CCEEEECSTTSCHHHHHHHHHHHHTCEEEEH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHhcCCcEEeC
Confidence            5799999999999999999999999887753

>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=96.47  E-value=0.0014  Score=63.34  Aligned_cols=29  Identities=31%  Similarity=0.512  Sum_probs=25.6

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEEE
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLYE  208 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~viE  208 (666)
                      .++.|+||+|+||||+++.||+ +|+.++.
T Consensus         3 ~~i~l~G~~GsGKST~~~~La~-lg~~~id   31 (206)
T 1jjv_A            3 YIVGLTGGIGSGKTTIANLFTD-LGVPLVD   31 (206)
T ss_dssp             EEEEEECSTTSCHHHHHHHHHT-TTCCEEE
T ss_pred             cEEEEECCCCCCHHHHHHHHHH-CCCcccc
Confidence            3689999999999999999998 8887764

>2a9k_A RAS-related protein RAL-A; bacterial ADP-ribosyltransferase, RAL, RHO, GD binding; HET: GDP NAD; 1.73A {Homo sapiens} SCOP: c.37.1.8 PDB: 2a78_A*

Probab=96.47  E-value=0.025  Score=52.71  Aligned_cols=24  Identities=29%  Similarity=0.461  Sum_probs=20.9

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      -.++|.|++|+||||++..++..-
T Consensus        19 ~ki~v~G~~~~GKSsli~~l~~~~   42 (187)
T 2a9k_A           19 HKVIMVGSGGVGKSALTLQFMYDE   42 (187)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             eEEEEECCCCCCHHHHHHHHhhCC
Confidence            358999999999999999998753

>3clv_A RAB5 protein, putative; malaria, GTPase, structural genomics, GTP-binding, nucleotide-binding, signaling protein; HET: GDP; 1.89A {Plasmodium falciparum}

Probab=96.46  E-value=0.043  Score=51.63  Aligned_cols=22  Identities=27%  Similarity=0.508  Sum_probs=20.4

Q ss_pred             EEEEECCCCchHHHHHHHHHHH
Q 005987          180 VLVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAke  201 (666)
                      .++|.|++|+||||++..+...
T Consensus         9 ki~v~G~~~~GKSsli~~l~~~   30 (208)
T 3clv_A            9 KTVLLGESSVGKSSIVLRLTKD   30 (208)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            4899999999999999999886

>1w4r_A Thymidine kinase; type II, human, cytosolic, phosphorylation, transferase; HET: TTP; 1.83A {Homo sapiens} PDB: 1xbt_A* 2wvj_A* 2j87_A*

Probab=96.45  E-value=0.0029  Score=61.10  Aligned_cols=35  Identities=17%  Similarity=0.176  Sum_probs=27.5

Q ss_pred             ccEEEEECCCCchHH-HHHHHHHHHc--CCcEEEEcCC
Q 005987          178 TNVLVITGQAGVGKT-ATVRQIASHL--GARLYEWDTP  212 (666)
Q Consensus       178 ~k~LLL~GPpG~GKT-tla~~LAkel--g~~viE~nas  212 (666)
                      .+++++|||.|+||| .+++++.+..  +.+++.+.+.
T Consensus        20 g~l~fiyG~MgsGKTt~Ll~~i~n~~~~~~kvl~~kp~   57 (195)
T 1w4r_A           20 GQIQVILGPMFSGKSTELMRRVRRFQIAQYKCLVIKYA   57 (195)
T ss_dssp             CEEEEEEECTTSCHHHHHHHHHHHHHHTTCCEEEEEET
T ss_pred             eEEEEEECCCCCcHHHHHHHHHHHHHHcCCeEEEEccc
Confidence            379999999999999 7778876644  6777777643

>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=96.44  E-value=0.04  Score=50.01  Aligned_cols=23  Identities=35%  Similarity=0.517  Sum_probs=20.4

Q ss_pred             EEEEECCCCchHHHHHHHHHHHc
Q 005987          180 VLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      .++|.|++|+||||++..+....
T Consensus         5 ~i~v~G~~~~GKSsli~~l~~~~   27 (167)
T 1kao_A            5 KVVVLGSGGVGKSALTVQFVTGT   27 (167)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHHcCC
Confidence            48999999999999999988653

>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=96.43  E-value=0.0018  Score=61.67  Aligned_cols=27  Identities=41%  Similarity=0.749  Sum_probs=23.7

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGAR  205 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~  205 (666)
                      .+++|.||+|+||||+++.|+..++..
T Consensus         3 ~ii~l~G~~GaGKSTl~~~L~~~~~g~   29 (189)
T 2bdt_A            3 KLYIITGPAGVGKSTTCKRLAAQLDNS   29 (189)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHSSSE
T ss_pred             eEEEEECCCCCcHHHHHHHHhcccCCe
Confidence            478999999999999999999877653

>3a8t_A Adenylate isopentenyltransferase; rossmann fold protein; HET: ATP; 2.37A {Humulus lupulus}

Probab=96.41  E-value=0.0013  Score=68.98  Aligned_cols=32  Identities=28%  Similarity=0.501  Sum_probs=28.8

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEEEEc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLYEWD  210 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~viE~n  210 (666)
                      ++++|.||+|+|||+++..||+.++.+++...
T Consensus        41 ~lIvI~GPTgsGKTtLa~~LA~~l~~eiIs~D   72 (339)
T 3a8t_A           41 KLLVLMGATGTGKSRLSIDLAAHFPLEVINSD   72 (339)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHTTSCEEEEECC
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHCCCcEEccc
Confidence            58999999999999999999999998777544

>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=96.41  E-value=0.011  Score=58.49  Aligned_cols=35  Identities=20%  Similarity=0.332  Sum_probs=29.4

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcC--CcEEEEcCCC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLG--ARLYEWDTPT  213 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg--~~viE~nasd  213 (666)
                      ..++|.||||+||||+++.|++.++  +.++....+.
T Consensus        27 ~~i~i~G~~GsGKsT~~~~l~~~l~~~~~~~~~~~p~   63 (229)
T 4eaq_A           27 AFITFEGPEGSGKTTVINEVYHRLVKDYDVIMTREPG   63 (229)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHHHTTTSCEEEECTTT
T ss_pred             eEEEEEcCCCCCHHHHHHHHHHHHhcCCCceeecCCC
Confidence            5899999999999999999999986  5776555444

>3t5g_A GTP-binding protein RHEB; immunoglobulin-like beta sandwitch, PDE delta, RHEB; HET: GDP FAR; 1.70A {Homo sapiens} SCOP: c.37.1.8 PDB: 1xtq_A* 1xtr_A* 1xts_A* 2l0x_A* 3sea_A*

Probab=96.40  E-value=0.038  Score=51.38  Aligned_cols=23  Identities=26%  Similarity=0.343  Sum_probs=20.3

Q ss_pred             cEEEEECCCCchHHHHHHHHHHH
Q 005987          179 NVLVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAke  201 (666)
                      ..++|.|++|+||||++..+...
T Consensus         7 ~ki~~~G~~~~GKSsli~~l~~~   29 (181)
T 3t5g_A            7 RKIAILGYRSVGKSSLTIQFVEG   29 (181)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEEECcCCCCHHHHHHHHHcC
Confidence            35899999999999999999854

>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=96.38  E-value=0.0021  Score=62.08  Aligned_cols=31  Identities=26%  Similarity=0.464  Sum_probs=27.8

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEEEE
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLYEW  209 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~viE~  209 (666)
                      .++.|+|++||||||+++.|++.+|+.++..
T Consensus        13 ~iIgltG~~GSGKSTva~~L~~~lg~~vid~   43 (192)
T 2grj_A           13 MVIGVTGKIGTGKSTVCEILKNKYGAHVVNV   43 (192)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHHCCEEEEH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHhcCCEEEEC
Confidence            4788999999999999999999999888753

>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=96.37  E-value=0.0078  Score=62.67  Aligned_cols=26  Identities=31%  Similarity=0.318  Sum_probs=22.8

Q ss_pred             CCccEEEEECCCCchHHHHHHHHHHH
Q 005987          176 FSTNVLVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       176 ~~~k~LLL~GPpG~GKTtla~~LAke  201 (666)
                      ++..+++|+||||+|||+++..+|..
T Consensus        96 ~~g~i~~i~G~~gsGKT~la~~la~~  121 (322)
T 2i1q_A           96 ESQSVTEFAGVFGSGKTQIMHQSCVN  121 (322)
T ss_dssp             ETTEEEEEEESTTSSHHHHHHHHHHH
T ss_pred             cCCeEEEEECCCCCCHHHHHHHHHHH
Confidence            34468999999999999999999875

>4e22_A Cytidylate kinase; P-loop, CMP/ATP binding, transferase; 2.32A {Yersinia pseudotuberculosis}

Probab=96.36  E-value=0.0024  Score=64.36  Aligned_cols=29  Identities=31%  Similarity=0.550  Sum_probs=26.6

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEE
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLY  207 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~vi  207 (666)
                      ..+.|.||+||||||+++.||+.+|+..+
T Consensus        28 ~~I~I~G~~GsGKSTl~k~La~~Lg~~~~   56 (252)
T 4e22_A           28 PVITVDGPSGAGKGTLCKALAESLNWRLL   56 (252)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHTTCEEE
T ss_pred             cEEEEECCCCCCHHHHHHHHHHhcCCCcC
Confidence            57999999999999999999999998655

>2qor_A Guanylate kinase; phosphotransferase, purine metabolism, structural genomics, structural genomics of pathogenic protozoa consortium; HET: 5GP POP; 1.80A {Plasmodium vivax}

Probab=96.35  E-value=0.0017  Score=62.90  Aligned_cols=26  Identities=31%  Similarity=0.570  Sum_probs=23.8

Q ss_pred             ccEEEEECCCCchHHHHHHHHHHHcC
Q 005987          178 TNVLVITGQAGVGKTATVRQIASHLG  203 (666)
Q Consensus       178 ~k~LLL~GPpG~GKTtla~~LAkelg  203 (666)
                      +++++|.||||+||||+++.|++.++
T Consensus        12 ~~~i~l~G~sGsGKsTl~~~L~~~~~   37 (204)
T 2qor_A           12 IPPLVVCGPSGVGKGTLIKKVLSEFP   37 (204)
T ss_dssp             CCCEEEECCTTSCHHHHHHHHHHHCT
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHhCc
Confidence            36899999999999999999999984

>1rz3_A Hypothetical protein rbstp0775; MCSG, structural genomics, PSI, protein structure initiative; 1.90A {Geobacillus stearothermophilus} SCOP: c.37.1.6

Probab=96.31  E-value=0.0059  Score=59.03  Aligned_cols=50  Identities=22%  Similarity=0.252  Sum_probs=35.6

Q ss_pred             HHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc---CCcEEEE
Q 005987          155 RKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL---GARLYEW  209 (666)
Q Consensus       155 ~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~  209 (666)
                      .+.+++|.+++....     ..++.++.|+||+|+||||+++.|+..+   +..++-.
T Consensus         4 ~~~~~~l~~~~~~~~-----~~~~~~i~i~G~~GsGKstl~~~l~~~~~~~~~~v~~~   56 (201)
T 1rz3_A            4 RDRIDFLCKTILAIK-----TAGRLVLGIDGLSRSGKTTLANQLSQTLREQGISVCVF   56 (201)
T ss_dssp             HHHHHHHHHHHHTSC-----CSSSEEEEEEECTTSSHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             HHHHHHHHHHHHHhc-----cCCCeEEEEECCCCCCHHHHHHHHHHHHhhcCCeEEEe
Confidence            345666666666421     1123689999999999999999999976   6666544

>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=96.31  E-value=0.038  Score=52.52  Aligned_cols=23  Identities=30%  Similarity=0.463  Sum_probs=20.4

Q ss_pred             EEEEECCCCchHHHHHHHHHHHc
Q 005987          180 VLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      .++|.|++|+||||++..+...-
T Consensus        16 ki~v~G~~~~GKSsli~~l~~~~   38 (206)
T 2bov_A           16 KVIMVGSGGVGKSALTLQFMYDE   38 (206)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHHhCC
Confidence            58999999999999999998653

>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=96.31  E-value=0.051  Score=49.14  Aligned_cols=23  Identities=39%  Similarity=0.579  Sum_probs=20.5

Q ss_pred             EEEEECCCCchHHHHHHHHHHHc
Q 005987          180 VLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      .+++.|++|+||||++..++...
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            48999999999999999998753

>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=96.30  E-value=0.014  Score=62.35  Aligned_cols=24  Identities=46%  Similarity=0.653  Sum_probs=22.1

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      ..+.|.||+||||||++++||.-+
T Consensus        38 e~~~llGpnGsGKSTLLr~iaGl~   61 (372)
T 1v43_A           38 EFLVLLGPSGCGKTTTLRMIAGLE   61 (372)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHTSS
T ss_pred             CEEEEECCCCChHHHHHHHHHcCC
Confidence            589999999999999999999866

>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=96.29  E-value=0.0041  Score=66.56  Aligned_cols=33  Identities=15%  Similarity=0.250  Sum_probs=28.5

Q ss_pred             ccEEEEECCCCchHHHHHHHHHHHcCCcEEEEc
Q 005987          178 TNVLVITGQAGVGKTATVRQIASHLGARLYEWD  210 (666)
Q Consensus       178 ~k~LLL~GPpG~GKTtla~~LAkelg~~viE~n  210 (666)
                      ++.++|+||||+||||++++||..++..++..+
T Consensus       169 ~~~i~l~G~~GsGKSTl~~~l~~~~~g~~~~~~  201 (377)
T 1svm_A          169 KRYWLFKGPIDSGKTTLAAALLELCGGKALNVN  201 (377)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHHHHCCEEECCS
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhhcCCcEEEEe
Confidence            368999999999999999999999887766533

>2wwf_A Thymidilate kinase, putative; transferase, malaria; HET: TMP ADP; 1.89A {Plasmodium falciparum} PDB: 2wwg_A* 2wwh_A* 2wwi_A*

Probab=96.29  E-value=0.0016  Score=63.05  Aligned_cols=25  Identities=20%  Similarity=0.355  Sum_probs=23.3

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLG  203 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg  203 (666)
                      ..++|+|+||+||||+++.|++.++
T Consensus        11 ~~I~l~G~~GsGKST~~~~L~~~l~   35 (212)
T 2wwf_A           11 KFIVFEGLDRSGKSTQSKLLVEYLK   35 (212)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHHHHH
T ss_pred             CEEEEEcCCCCCHHHHHHHHHHHHH
Confidence            6899999999999999999999874

>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=96.25  E-value=0.0021  Score=62.58  Aligned_cols=26  Identities=23%  Similarity=0.425  Sum_probs=23.7

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGA  204 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~  204 (666)
                      .+++|.||+|+||||+++.|+..+..
T Consensus         9 ~~i~l~GpsGsGKsTl~~~L~~~~~~   34 (208)
T 3tau_A            9 LLIVLSGPSGVGKGTVREAVFKDPET   34 (208)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHSTTC
T ss_pred             cEEEEECcCCCCHHHHHHHHHhhCCC
Confidence            68999999999999999999998753

>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=96.24  E-value=0.0022  Score=61.66  Aligned_cols=25  Identities=24%  Similarity=0.551  Sum_probs=22.7

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLG  203 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg  203 (666)
                      +.++|+||+|+||||+++.|.++..
T Consensus         2 RpIVi~GPSG~GK~Tl~~~L~~~~~   26 (186)
T 1ex7_A            2 RPIVISGPSGTGKSTLLKKLFAEYP   26 (186)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHCT
T ss_pred             CEEEEECCCCCCHHHHHHHHHHhCC
Confidence            5799999999999999999998863

>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=96.23  E-value=0.02  Score=71.67  Aligned_cols=39  Identities=21%  Similarity=0.151  Sum_probs=31.0

Q ss_pred             CCCccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcCCC
Q 005987          175 KFSTNVLVITGQAGVGKTATVRQIASHL---GARLYEWDTPT  213 (666)
Q Consensus       175 ~~~~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~nasd  213 (666)
                      -.+...++|+||||+||||++..+|.++   +..++.++...
T Consensus       729 l~~G~lVlI~G~PG~GKTtLal~lA~~aa~~g~~VlyiS~Ee  770 (1706)
T 3cmw_A          729 LPMGRIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDAEH  770 (1706)
T ss_dssp             EETTSEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEECTTS
T ss_pred             cCCCceEEEECCCCCCcHHHHHHHHHHHHHcCCCeEEEeccc
Confidence            3455799999999999999999998875   55677766543

>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=96.23  E-value=0.0028  Score=61.86  Aligned_cols=30  Identities=27%  Similarity=0.508  Sum_probs=26.5

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEEEE
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLYEW  209 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~viE~  209 (666)
                      ..+.|+|++|+||||+++.|++ +|+.++..
T Consensus         5 ~~I~i~G~~GSGKST~~~~L~~-lg~~~id~   34 (218)
T 1vht_A            5 YIVALTGGIGSGKSTVANAFAD-LGINVIDA   34 (218)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHH-TTCEEEEH
T ss_pred             eEEEEECCCCCCHHHHHHHHHH-cCCEEEEc
Confidence            4799999999999999999998 88877653

>2fg5_A RAB-22B, RAS-related protein RAB-31; G-protein, GTP analogue, structural genomics, structural genomics consortium, SGC, signaling protein; HET: GNP; 2.80A {Homo sapiens} SCOP: c.37.1.8

Probab=96.22  E-value=0.039  Score=52.17  Aligned_cols=23  Identities=26%  Similarity=0.494  Sum_probs=20.4

Q ss_pred             EEEEECCCCchHHHHHHHHHHHc
Q 005987          180 VLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      .++|.|++|+||||++..+...-
T Consensus        25 ki~vvG~~~~GKSsli~~l~~~~   47 (192)
T 2fg5_A           25 KVCLLGDTGVGKSSIVCRFVQDH   47 (192)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHCC
T ss_pred             EEEEECcCCCCHHHHHHHHhcCC
Confidence            58999999999999999998653

>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=96.21  E-value=0.0028  Score=60.78  Aligned_cols=29  Identities=28%  Similarity=0.459  Sum_probs=26.2

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEEE
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLYE  208 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~viE  208 (666)
                      .++.|+|++|+||||+++.||+. |+.++.
T Consensus         9 ~~I~i~G~~GsGKST~~~~La~~-g~~~id   37 (203)
T 1uf9_A            9 IIIGITGNIGSGKSTVAALLRSW-GYPVLD   37 (203)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHHT-TCCEEE
T ss_pred             eEEEEECCCCCCHHHHHHHHHHC-CCEEEc
Confidence            57999999999999999999998 887764

>4dsu_A GTPase KRAS, isoform 2B; small G-protein, signaling, hydrolase; HET: GDP; 1.70A {Homo sapiens} PDB: 4dsn_A* 4dst_A* 4dso_A*

Probab=96.21  E-value=0.036  Score=51.70  Aligned_cols=23  Identities=39%  Similarity=0.567  Sum_probs=20.5

Q ss_pred             EEEEECCCCchHHHHHHHHHHHc
Q 005987          180 VLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      .++|.|++|+||||++..+....
T Consensus         6 ki~v~G~~~~GKSsli~~l~~~~   28 (189)
T 4dsu_A            6 KLVVVGADGVGKSALTIQLIQNH   28 (189)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHSS
T ss_pred             EEEEECCCCCCHHHHHHHHHhCC
Confidence            48999999999999999998654

>3con_A GTPase NRAS; structural genomics consortium, SGC, GDP, oncogene, disease mutation, golgi apparatus, GTP-binding, lipoprotein membrane, methylation; HET: GDP; 1.65A {Homo sapiens} PDB: 2pmx_A* 3gft_A* 4q21_A*

Probab=96.20  E-value=0.041  Score=51.71  Aligned_cols=23  Identities=39%  Similarity=0.579  Sum_probs=20.6

Q ss_pred             EEEEECCCCchHHHHHHHHHHHc
Q 005987          180 VLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      .+++.|++|+||||++..++...
T Consensus        23 ki~vvG~~~~GKSsli~~l~~~~   45 (190)
T 3con_A           23 KLVVVGAGGVGKSALTIQLIQNH   45 (190)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSS
T ss_pred             EEEEECcCCCCHHHHHHHHHcCC
Confidence            58899999999999999998753

>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=96.17  E-value=0.002  Score=62.41  Aligned_cols=32  Identities=25%  Similarity=0.423  Sum_probs=26.6

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc---CCcEEEEc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL---GARLYEWD  210 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel---g~~viE~n  210 (666)
                      ..++|+|++|+||||+++.|++.+   ++.+..+.
T Consensus        10 ~~I~l~G~~GsGKsT~~~~L~~~l~~~~~~v~~~~   44 (215)
T 1nn5_A           10 ALIVLEGVDRAGKSTQSRKLVEALCAAGHRAELLR   44 (215)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEee
Confidence            589999999999999999999986   45554443

>3vkw_A Replicase large subunit; alpha/beta domain, helicase, transferase; 1.90A {Tomato mosaic virus}

Probab=96.16  E-value=0.0043  Score=67.44  Aligned_cols=23  Identities=26%  Similarity=0.508  Sum_probs=20.4

Q ss_pred             ccEEEEECCCCchHHHHHHHHHH
Q 005987          178 TNVLVITGQAGVGKTATVRQIAS  200 (666)
Q Consensus       178 ~k~LLL~GPpG~GKTtla~~LAk  200 (666)
                      .++.++.|+||||||+++..+++
T Consensus       161 ~~v~~I~G~aGsGKTt~I~~~~~  183 (446)
T 3vkw_A          161 AKVVLVDGVPGCGKTKEILSRVN  183 (446)
T ss_dssp             SEEEEEEECTTSCHHHHHHHHCC
T ss_pred             ccEEEEEcCCCCCHHHHHHHHhc
Confidence            46899999999999999988775

>4a1f_A DNAB helicase, replicative DNA helicase; hydrolase, DNA replication, ATPase; HET: FLC; 2.50A {Helicobacter pylori}

Probab=96.14  E-value=0.037  Score=58.17  Aligned_cols=38  Identities=11%  Similarity=0.163  Sum_probs=29.6

Q ss_pred             CCCCccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcC
Q 005987          174 DKFSTNVLVITGQAGVGKTATVRQIASHL---GARLYEWDT  211 (666)
Q Consensus       174 g~~~~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~na  211 (666)
                      |-.+...++|.|+||+||||++..+|..+   |..++.++.
T Consensus        42 Gl~~G~LiiIaG~pG~GKTt~al~ia~~~a~~g~~Vl~fSl   82 (338)
T 4a1f_A           42 GFNKGSLVIIGARPSMGKTSLMMNMVLSALNDDRGVAVFSL   82 (338)
T ss_dssp             SBCTTCEEEEEECTTSCHHHHHHHHHHHHHHTTCEEEEEES
T ss_pred             CCCCCcEEEEEeCCCCCHHHHHHHHHHHHHHcCCeEEEEeC
Confidence            33445689999999999999999998874   666666554

>3bgw_A DNAB-like replicative helicase; ATPase, replication; 3.91A {Bacillus phage SPP1}

Probab=96.13  E-value=0.033  Score=60.82  Aligned_cols=38  Identities=18%  Similarity=0.186  Sum_probs=29.7

Q ss_pred             CCCCccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcC
Q 005987          174 DKFSTNVLVITGQAGVGKTATVRQIASHL---GARLYEWDT  211 (666)
Q Consensus       174 g~~~~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~na  211 (666)
                      |-.++..++|.|+||+|||+++..+|...   |..++.+..
T Consensus       193 Gl~~G~liiIaG~pG~GKTtlal~ia~~~a~~g~~vl~fSl  233 (444)
T 3bgw_A          193 GYKRRNFVLIAARPSMGKTAFALKQAKNMSDNDDVVNLHSL  233 (444)
T ss_dssp             SBCSSCEEEEEECSSSSHHHHHHHHHHHHHHTTCEEEEECS
T ss_pred             CCCCCcEEEEEeCCCCChHHHHHHHHHHHHHcCCEEEEEEC
Confidence            33445789999999999999998887765   667776653

>3oes_A GTPase rhebl1; small GTPase, structural genomics, structural genomics conso SGC, hydrolase; HET: GNP; 2.30A {Homo sapiens}

Probab=96.12  E-value=0.052  Score=51.76  Aligned_cols=23  Identities=35%  Similarity=0.356  Sum_probs=20.7

Q ss_pred             EEEEECCCCchHHHHHHHHHHHc
Q 005987          180 VLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      .++|.|++|+||||++..+...-
T Consensus        26 ki~vvG~~~~GKSsli~~l~~~~   48 (201)
T 3oes_A           26 KVVILGYRCVGKTSLAHQFVEGE   48 (201)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCcCHHHHHHHHHhCC
Confidence            58999999999999999998753

>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=96.11  E-value=0.003  Score=64.92  Aligned_cols=29  Identities=21%  Similarity=0.346  Sum_probs=25.1

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc-CCcEE
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL-GARLY  207 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel-g~~vi  207 (666)
                      ..++|.||||+||||+++.|++.+ ++.++
T Consensus         3 ~~I~l~G~~GsGKST~a~~L~~~~~~~~~i   32 (301)
T 1ltq_A            3 KIILTIGCPGSGKSTWAREFIAKNPGFYNI   32 (301)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHSTTEEEE
T ss_pred             eEEEEECCCCCCHHHHHHHHHHhCCCcEEe
Confidence            579999999999999999999974 65554

>3tr0_A Guanylate kinase, GMP kinase; purines, pyrimidines, nucleosides, nucleotides, transferase; HET: 5GP; 1.85A {Coxiella burnetii}

Probab=96.10  E-value=0.0032  Score=60.57  Aligned_cols=25  Identities=36%  Similarity=0.680  Sum_probs=22.9

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLG  203 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg  203 (666)
                      .++.|.||+|+||||+++.|+..+.
T Consensus         8 ~ii~l~Gp~GsGKSTl~~~L~~~~~   32 (205)
T 3tr0_A            8 NLFIISAPSGAGKTSLVRALVKALA   32 (205)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHSS
T ss_pred             cEEEEECcCCCCHHHHHHHHHhhCC
Confidence            5899999999999999999999863

>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=96.09  E-value=0.082  Score=49.80  Aligned_cols=23  Identities=35%  Similarity=0.469  Sum_probs=20.8

Q ss_pred             EEEEECCCCchHHHHHHHHHHHc
Q 005987          180 VLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      -++|.|++|+||||++..+...-
T Consensus        25 ki~v~G~~~~GKSsli~~l~~~~   47 (191)
T 3dz8_A           25 KLLIIGNSSVGKTSFLFRYADDT   47 (191)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHT
T ss_pred             EEEEECCCCcCHHHHHHHHhcCC
Confidence            48999999999999999998764

>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=96.08  E-value=0.05  Score=49.56  Aligned_cols=23  Identities=39%  Similarity=0.534  Sum_probs=20.3

Q ss_pred             EEEEECCCCchHHHHHHHHHHHc
Q 005987          180 VLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      .++|.|++|+||||++..+...-
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            48999999999999999998653

>3d3q_A TRNA delta(2)-isopentenylpyrophosphate transferase; alpha-beta protein, structural genomics, PSI-2; 2.70A {Staphylococcus epidermidis atcc 12228}

Probab=96.07  E-value=0.0034  Score=66.07  Aligned_cols=32  Identities=25%  Similarity=0.389  Sum_probs=27.7

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEEEEc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLYEWD  210 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~viE~n  210 (666)
                      ++++|.||+|+||||++..||+.++..++..+
T Consensus         8 ~lI~I~GptgSGKTtla~~La~~l~~~iis~D   39 (340)
T 3d3q_A            8 FLIVIVGPTASGKTELSIEVAKKFNGEIISGD   39 (340)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHTTEEEEECC
T ss_pred             ceEEEECCCcCcHHHHHHHHHHHcCCceeccc
Confidence            47999999999999999999999996665443

>2h92_A Cytidylate kinase; rossmann fold, transferase; HET: C5P PG4; 2.30A {Staphylococcus aureus}

Probab=96.05  E-value=0.0042  Score=60.53  Aligned_cols=30  Identities=23%  Similarity=0.409  Sum_probs=27.2

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEEE
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLYE  208 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~viE  208 (666)
                      ..+.|+|++||||||+++.||+.+|+.++.
T Consensus         4 ~~i~i~G~~gsGkst~~~~l~~~~g~~~~~   33 (219)
T 2h92_A            4 INIALDGPAAAGKSTIAKRVASELSMIYVD   33 (219)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHTTCEEEE
T ss_pred             eEEEEECCCCCCHHHHHHHHHHhcCCceec
Confidence            469999999999999999999999987764

>2j41_A Guanylate kinase; GMP, GMK, transferase, ATP-binding, nucleotide- binding; HET: 5GP; 1.9A {Staphylococcus aureus}

Probab=96.04  E-value=0.0031  Score=60.65  Aligned_cols=24  Identities=29%  Similarity=0.533  Sum_probs=22.6

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      ..+.|.||+|+||||+++.|+..+
T Consensus         7 ~~i~l~G~~GsGKSTl~~~L~~~~   30 (207)
T 2j41_A            7 LLIVLSGPSGVGKGTVRKRIFEDP   30 (207)
T ss_dssp             CEEEEECSTTSCHHHHHHHHHHCT
T ss_pred             CEEEEECCCCCCHHHHHHHHHHhh
Confidence            589999999999999999999987

>1q3t_A Cytidylate kinase; nucleotide monophosphate kinase, CMP kinase, transferase; NMR {Streptococcus pneumoniae} SCOP: c.37.1.1

Probab=96.04  E-value=0.0045  Score=61.44  Aligned_cols=30  Identities=27%  Similarity=0.438  Sum_probs=27.3

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEEE
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLYE  208 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~viE  208 (666)
                      ..+.|+|++|+||||+++.||+.+|+.++.
T Consensus        17 ~~i~i~G~~gsGKst~~~~l~~~lg~~~~d   46 (236)
T 1q3t_A           17 IQIAIDGPASSGKSTVAKIIAKDFGFTYLD   46 (236)
T ss_dssp             CEEEEECSSCSSHHHHHHHHHHHHCCEEEE
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHcCCceec
Confidence            579999999999999999999999987664

>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=96.03  E-value=0.0095  Score=58.41  Aligned_cols=34  Identities=15%  Similarity=0.090  Sum_probs=27.9

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcCC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL---GARLYEWDTP  212 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel---g~~viE~nas  212 (666)
                      ++.+++||.|+||||.+..+|..+   |.+++-+...
T Consensus        29 ~l~vitG~MgsGKTT~lL~~a~r~~~~g~kVli~k~~   65 (214)
T 2j9r_A           29 WIEVICGSMFSGKSEELIRRVRRTQFAKQHAIVFKPC   65 (214)
T ss_dssp             EEEEEECSTTSCHHHHHHHHHHHHHHTTCCEEEEECC
T ss_pred             EEEEEECCCCCcHHHHHHHHHHHHHHCCCEEEEEEec
Confidence            688999999999999998887765   7777777643

>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=96.00  E-value=0.0039  Score=62.61  Aligned_cols=27  Identities=22%  Similarity=0.432  Sum_probs=25.2

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGAR  205 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~  205 (666)
                      .++.|+||+|+||||+++.|++.+|+.
T Consensus        23 ~iI~I~G~~GSGKST~a~~L~~~lg~~   49 (252)
T 1uj2_A           23 FLIGVSGGTASGKSSVCAKIVQLLGQN   49 (252)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHTTGG
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHhhhh
Confidence            579999999999999999999999876

>3fdi_A Uncharacterized protein; cytidylate kinase like protein, PSI, MCSG, PRK04182 class ME structural genomics, protein structure initiative; 2.20A {Eubacterium ventriosum}

Probab=96.00  E-value=0.0045  Score=60.19  Aligned_cols=29  Identities=24%  Similarity=0.464  Sum_probs=27.5

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEE
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLY  207 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~vi  207 (666)
                      .++.|.||+||||||+++.||+.+|+.++
T Consensus         7 ~iI~i~g~~GsGk~ti~~~la~~lg~~~~   35 (201)
T 3fdi_A            7 IIIAIGREFGSGGHLVAKKLAEHYNIPLY   35 (201)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHHTTCCEE
T ss_pred             eEEEEeCCCCCCHHHHHHHHHHHhCcCEE
Confidence            48999999999999999999999999887

>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=95.99  E-value=0.0042  Score=60.30  Aligned_cols=26  Identities=27%  Similarity=0.461  Sum_probs=23.7

Q ss_pred             ccEEEEECCCCchHHHHHHHHHHHcC
Q 005987          178 TNVLVITGQAGVGKTATVRQIASHLG  203 (666)
Q Consensus       178 ~k~LLL~GPpG~GKTtla~~LAkelg  203 (666)
                      ++.++|.||+|+||||+++.|++.+.
T Consensus        19 g~~ivl~GPSGaGKsTL~~~L~~~~~   44 (197)
T 3ney_A           19 RKTLVLIGASGVGRSHIKNALLSQNP   44 (197)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHCT
T ss_pred             CCEEEEECcCCCCHHHHHHHHHhhCC
Confidence            47899999999999999999999874

>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=95.98  E-value=0.071  Score=48.47  Aligned_cols=22  Identities=41%  Similarity=0.573  Sum_probs=19.9

Q ss_pred             EEEEECCCCchHHHHHHHHHHH
Q 005987          180 VLVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAke  201 (666)
                      .+++.|++|+||||++..+...
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            4889999999999999999874

>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=95.98  E-value=0.082  Score=48.10  Aligned_cols=22  Identities=32%  Similarity=0.517  Sum_probs=20.0

Q ss_pred             EEEEECCCCchHHHHHHHHHHH
Q 005987          180 VLVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAke  201 (666)
                      .++|.|++|+||||++..+...
T Consensus         8 ~i~v~G~~~~GKssli~~l~~~   29 (170)
T 1r2q_A            8 KLVLLGESAVGKSSLVLRFVKG   29 (170)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            5899999999999999999864

>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=95.97  E-value=0.046  Score=60.57  Aligned_cols=38  Identities=21%  Similarity=0.175  Sum_probs=29.5

Q ss_pred             CCCCccEEEEECCCCchHHHHHHHHHHHc----CCcEEEEcC
Q 005987          174 DKFSTNVLVITGQAGVGKTATVRQIASHL----GARLYEWDT  211 (666)
Q Consensus       174 g~~~~k~LLL~GPpG~GKTtla~~LAkel----g~~viE~na  211 (666)
                      |-.+...++|.|+||+|||+++..+|..+    |..++.+..
T Consensus       238 Gl~~G~l~li~G~pG~GKT~lal~~a~~~a~~~g~~vl~~s~  279 (503)
T 1q57_A          238 GARGGEVIMVTSGSGMVMSTFVRQQALQWGTAMGKKVGLAML  279 (503)
T ss_dssp             CCCTTCEEEEEESSCHHHHHHHHHHHHHHTTTSCCCEEEEES
T ss_pred             ccCCCeEEEEeecCCCCchHHHHHHHHHHHHhcCCcEEEEec
Confidence            33455789999999999999999888775    456666654

>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=95.97  E-value=0.0033  Score=60.91  Aligned_cols=30  Identities=23%  Similarity=0.444  Sum_probs=26.1

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc-CCcEEE
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL-GARLYE  208 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel-g~~viE  208 (666)
                      ..+.|+||+|+||||+++.|++.+ ++.++.
T Consensus        22 ~~i~i~G~~GsGKSTl~~~L~~~~~~~~~i~   52 (207)
T 2qt1_A           22 FIIGISGVTNSGKTTLAKNLQKHLPNCSVIS   52 (207)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHTTSTTEEEEE
T ss_pred             eEEEEECCCCCCHHHHHHHHHHhcCCcEEEe
Confidence            578999999999999999999988 665554

>2yvu_A Probable adenylyl-sulfate kinase; transferase, structural genomics, NPPSFA, national P protein structural and functional analyses; 2.10A {Aeropyrum pernix}

Probab=95.95  E-value=0.0038  Score=59.29  Aligned_cols=31  Identities=35%  Similarity=0.464  Sum_probs=25.8

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc---CCcEEEE
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL---GARLYEW  209 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel---g~~viE~  209 (666)
                      ..++|.|++|+||||+++.||+.+   |+.+..+
T Consensus        14 ~~i~l~G~~GsGKsT~~~~L~~~l~~~~~~~~~~   47 (186)
T 2yvu_A           14 IVVWLTGLPGSGKTTIATRLADLLQKEGYRVEVL   47 (186)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             cEEEEEcCCCCCHHHHHHHHHHHHHhcCCeEEEe
Confidence            689999999999999999999987   4444443

>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=95.95  E-value=0.06  Score=50.27  Aligned_cols=22  Identities=32%  Similarity=0.511  Sum_probs=20.1

Q ss_pred             EEEEECCCCchHHHHHHHHHHH
Q 005987          180 VLVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAke  201 (666)
                      .++|.|++|+||||++..+...
T Consensus        13 ki~v~G~~~~GKSsli~~l~~~   34 (195)
T 3bc1_A           13 KFLALGDSGVGKTSVLYQYTDG   34 (195)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            5899999999999999999874

>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=95.93  E-value=0.0041  Score=63.74  Aligned_cols=30  Identities=33%  Similarity=0.569  Sum_probs=26.5

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEEEE
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLYEW  209 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~viE~  209 (666)
                      ..+.|+|++|+||||+++.|+ ++|+.++..
T Consensus        76 ~iI~I~G~~GSGKSTva~~La-~lg~~~id~  105 (281)
T 2f6r_A           76 YVLGLTGISGSGKSSVAQRLK-NLGAYIIDS  105 (281)
T ss_dssp             EEEEEEECTTSCHHHHHHHHH-HHTCEEEEH
T ss_pred             EEEEEECCCCCCHHHHHHHHH-HCCCcEEeh
Confidence            579999999999999999999 689877653

>3kkq_A RAS-related protein M-RAS; GTP-binding, GTPase, signaling protein; HET: GDP; 1.20A {Mus musculus} SCOP: c.37.1.8 PDB: 3kkp_A* 3kko_A* 3pit_A* 3pir_A* 1x1r_A* 1x1s_A*

Probab=95.92  E-value=0.057  Score=50.24  Aligned_cols=23  Identities=39%  Similarity=0.546  Sum_probs=20.5

Q ss_pred             cEEEEECCCCchHHHHHHHHHHH
Q 005987          179 NVLVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAke  201 (666)
                      -.++|.|++|+||||++..+...
T Consensus        19 ~ki~v~G~~~~GKSsl~~~l~~~   41 (183)
T 3kkq_A           19 YKLVVVGDGGVGKSALTIQFFQK   41 (183)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHS
T ss_pred             eEEEEECCCCCCHHHHHHHHHhC
Confidence            35899999999999999999865

>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=95.91  E-value=0.098  Score=49.12  Aligned_cols=23  Identities=17%  Similarity=0.293  Sum_probs=20.4

Q ss_pred             EEEEECCCCchHHHHHHHHHHHc
Q 005987          180 VLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      .++|.|++|+||||++..+....
T Consensus        23 ki~v~G~~~~GKSsli~~l~~~~   45 (190)
T 2h57_A           23 HVLCLGLDNSGKTTIINKLKPSN   45 (190)
T ss_dssp             EEEEEECTTSSHHHHHHHTSCGG
T ss_pred             EEEEECCCCCCHHHHHHHHhcCC
Confidence            58999999999999999987654

>2gf9_A RAS-related protein RAB-3D; G-protein, structural genomics, structural genomics consortium, SGC, protein transport; HET: GDP; 1.53A {Homo sapiens} PDB: 3rab_A*

Probab=95.90  E-value=0.077  Score=49.84  Aligned_cols=23  Identities=30%  Similarity=0.440  Sum_probs=20.5

Q ss_pred             EEEEECCCCchHHHHHHHHHHHc
Q 005987          180 VLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      .++|.|++|+||||++..++..-
T Consensus        24 ki~vvG~~~~GKSsli~~l~~~~   46 (189)
T 2gf9_A           24 KLLLIGNSSVGKTSFLFRYADDS   46 (189)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHHcCC
Confidence            58999999999999999998753

>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=95.90  E-value=0.0096  Score=61.32  Aligned_cols=25  Identities=36%  Similarity=0.458  Sum_probs=23.2

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLG  203 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg  203 (666)
                      .++.|.||+|+||||+++.|+..++
T Consensus        32 ~ii~I~G~sGsGKSTla~~L~~~l~   56 (290)
T 1odf_A           32 LFIFFSGPQGSGKSFTSIQIYNHLM   56 (290)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhh
Confidence            5899999999999999999999885

>2hup_A RAS-related protein RAB-43; G-protein, GDP, structural genomics, structural genomics consortium, SGC, signaling protein; HET: GDP; 2.05A {Homo sapiens}

Probab=95.89  E-value=0.098  Score=49.94  Aligned_cols=22  Identities=41%  Similarity=0.638  Sum_probs=19.8

Q ss_pred             EEEEECCCCchHHHHHHHHHHH
Q 005987          180 VLVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAke  201 (666)
                      .++|.|++|+||||++..+...
T Consensus        31 ki~vvG~~~vGKSsli~~l~~~   52 (201)
T 2hup_A           31 KLVLVGDASVGKTCVVQRFKTG   52 (201)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEEECcCCCCHHHHHHHHhhC
Confidence            4899999999999999999764

>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=95.89  E-value=0.0042  Score=66.71  Aligned_cols=31  Identities=32%  Similarity=0.531  Sum_probs=27.5

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEEEE
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLYEW  209 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~viE~  209 (666)
                      ++++|.||+|+||||++..||+.++..++..
T Consensus         3 ~~i~i~GptgsGKttla~~La~~~~~~iis~   33 (409)
T 3eph_A            3 KVIVIAGTTGVGKSQLSIQLAQKFNGEVINS   33 (409)
T ss_dssp             EEEEEEECSSSSHHHHHHHHHHHHTEEEEEC
T ss_pred             cEEEEECcchhhHHHHHHHHHHHCCCeEeec
Confidence            6899999999999999999999999776543

>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=95.86  E-value=0.099  Score=47.68  Aligned_cols=22  Identities=32%  Similarity=0.474  Sum_probs=20.1

Q ss_pred             EEEEECCCCchHHHHHHHHHHH
Q 005987          180 VLVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAke  201 (666)
                      .+++.|++|+||||++..+...
T Consensus         8 ~i~v~G~~~~GKssli~~l~~~   29 (170)
T 1z08_A            8 KVVLLGEGCVGKTSLVLRYCEN   29 (170)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHC
T ss_pred             EEEEECcCCCCHHHHHHHHHcC
Confidence            5899999999999999999865

>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=95.84  E-value=0.046  Score=50.05  Aligned_cols=21  Identities=24%  Similarity=0.564  Sum_probs=18.9

Q ss_pred             EEEEECCCCchHHHHHHHHHH
Q 005987          180 VLVITGQAGVGKTATVRQIAS  200 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAk  200 (666)
                      .++|.|++|+||||++..++.
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            388999999999999999864

>1lvg_A Guanylate kinase, GMP kinase; transferase; HET: ADP 5GP; 2.10A {Mus musculus} SCOP: c.37.1.1

Probab=95.83  E-value=0.0042  Score=60.06  Aligned_cols=25  Identities=20%  Similarity=0.513  Sum_probs=22.7

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLG  203 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg  203 (666)
                      +.+.|.||+|+||||+++.|+..+.
T Consensus         5 ~~i~lvGpsGaGKSTLl~~L~~~~~   29 (198)
T 1lvg_A            5 RPVVLSGPSGAGKSTLLKKLFQEHS   29 (198)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHHT
T ss_pred             CEEEEECCCCCCHHHHHHHHHhhCc
Confidence            5799999999999999999998763

>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=95.83  E-value=0.063  Score=51.71  Aligned_cols=24  Identities=21%  Similarity=0.411  Sum_probs=21.7

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      ..++|.|++|+||||++..++...
T Consensus        13 ~~i~~~G~~g~GKTsl~~~l~~~~   36 (218)
T 1nrj_B           13 PSIIIAGPQNSGKTSLLTLLTTDS   36 (218)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHSS
T ss_pred             CEEEEECCCCCCHHHHHHHHhcCC
Confidence            369999999999999999999865

>3c8u_A Fructokinase; YP_612366.1, putative fructose transport system kinase, STRU genomics, joint center for structural genomics, JCSG; 1.95A {Silicibacter SP}

Probab=95.82  E-value=0.0057  Score=59.42  Aligned_cols=25  Identities=24%  Similarity=0.542  Sum_probs=23.3

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLG  203 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg  203 (666)
                      ..+.|.||+|+||||++++|+..+.
T Consensus        23 ~~v~I~G~sGsGKSTl~~~l~~~~~   47 (208)
T 3c8u_A           23 QLVALSGAPGSGKSTLSNPLAAALS   47 (208)
T ss_dssp             EEEEEECCTTSCTHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHh
Confidence            5899999999999999999999885

>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=95.81  E-value=0.089  Score=49.46  Aligned_cols=22  Identities=41%  Similarity=0.377  Sum_probs=20.0

Q ss_pred             EEEEECCCCchHHHHHHHHHHH
Q 005987          180 VLVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAke  201 (666)
                      .++|.|++|+||||++..+...
T Consensus        24 ki~v~G~~~~GKSsli~~l~~~   45 (188)
T 1zd9_A           24 ELTLVGLQYSGKTTFVNVIASG   45 (188)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            4899999999999999999864

>3tkl_A RAS-related protein RAB-1A; vesicle trafficking, protein transport-protein binding compl; HET: GTP; 2.18A {Homo sapiens}

Probab=95.80  E-value=0.087  Score=49.50  Aligned_cols=23  Identities=30%  Similarity=0.573  Sum_probs=20.6

Q ss_pred             EEEEECCCCchHHHHHHHHHHHc
Q 005987          180 VLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      .++|.|++|+||||++..+...-
T Consensus        18 ki~v~G~~~~GKSsli~~l~~~~   40 (196)
T 3tkl_A           18 KLLLIGDSGVGKSCLLLRFADDT   40 (196)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEEECcCCCCHHHHHHHHHcCC
Confidence            58999999999999999998753

>2fn4_A P23, RAS-related protein R-RAS; GDP/GTP binding, GTP hydrolysis, structural genomics, structural genomics consortium, SGC, signaling protein; HET: GDP; 1.65A {Homo sapiens} SCOP: c.37.1.8 PDB: 2ery_A*

Probab=95.79  E-value=0.069  Score=49.26  Aligned_cols=23  Identities=39%  Similarity=0.566  Sum_probs=20.7

Q ss_pred             cEEEEECCCCchHHHHHHHHHHH
Q 005987          179 NVLVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAke  201 (666)
                      ..++|.|++|+||||++..+...
T Consensus        10 ~~i~v~G~~~~GKssli~~l~~~   32 (181)
T 2fn4_A           10 HKLVVVGGGGVGKSALTIQFIQS   32 (181)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHS
T ss_pred             eEEEEECCCCCCHHHHHHHHHhC
Confidence            35899999999999999999876

>3tui_C Methionine import ATP-binding protein METN; ABC-transporter, type I ABC type importer, methionine uptake transporter, membrane protein; HET: ADP; 2.90A {Escherichia coli} PDB: 3tuj_C 3tuz_C* 3dhw_C

Probab=95.77  E-value=0.025  Score=60.06  Aligned_cols=25  Identities=20%  Similarity=0.377  Sum_probs=22.6

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLG  203 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg  203 (666)
                      .++-|.||+|+||||++++++.-+.
T Consensus        55 ei~~IiGpnGaGKSTLlr~i~GL~~   79 (366)
T 3tui_C           55 QIYGVIGASGAGKSTLIRCVNLLER   79 (366)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHTSSC
T ss_pred             CEEEEEcCCCchHHHHHHHHhcCCC
Confidence            5899999999999999999998663

>2zts_A Putative uncharacterized protein PH0186; KAIC like protein, ATP-binding, nucleotide-binding, ATP- binding protein; HET: ADP; 2.07A {Pyrococcus horikoshii}

Probab=95.75  E-value=0.014  Score=57.68  Aligned_cols=36  Identities=22%  Similarity=0.203  Sum_probs=26.7

Q ss_pred             CCccEEEEECCCCchHHHHHHHHHHH----cCCcEEEEcC
Q 005987          176 FSTNVLVITGQAGVGKTATVRQIASH----LGARLYEWDT  211 (666)
Q Consensus       176 ~~~k~LLL~GPpG~GKTtla~~LAke----lg~~viE~na  211 (666)
                      ++...++|+|+||+|||+++.-+|..    .+..++.+..
T Consensus        28 ~~G~l~~i~G~pG~GKT~l~l~~~~~~~~~~~~~v~~~s~   67 (251)
T 2zts_A           28 PEGTTVLLTGGTGTGKTTFAAQFIYKGAEEYGEPGVFVTL   67 (251)
T ss_dssp             ETTCEEEEECCTTSSHHHHHHHHHHHHHHHHCCCEEEEES
T ss_pred             CCCeEEEEEeCCCCCHHHHHHHHHHHHHHhcCCCceeecc
Confidence            34568999999999999999876543    2556665543

>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=95.75  E-value=0.13  Score=52.86  Aligned_cols=35  Identities=29%  Similarity=0.362  Sum_probs=28.3

Q ss_pred             ccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcCC
Q 005987          178 TNVLVITGQAGVGKTATVRQIASHL---GARLYEWDTP  212 (666)
Q Consensus       178 ~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~nas  212 (666)
                      ++++.++||+|+||||++..||..+   +.++.-....
T Consensus        98 ~~~i~i~g~~G~GKTT~~~~la~~~~~~~~~v~l~~~d  135 (295)
T 1ls1_A           98 RNLWFLVGLQGSGKTTTAAKLALYYKGKGRRPLLVAAD  135 (295)
T ss_dssp             SEEEEEECCTTTTHHHHHHHHHHHHHHTTCCEEEEECC
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEecCC
Confidence            4688899999999999999999876   6666655543

>1z06_A RAS-related protein RAB-33B; RAB GTPase, RAB33B GTPase, vesicular trafficking, protein transport; HET: GNP; 1.81A {Mus musculus} SCOP: c.37.1.8 PDB: 2g77_B*

Probab=95.75  E-value=0.063  Score=50.47  Aligned_cols=22  Identities=23%  Similarity=0.478  Sum_probs=20.0

Q ss_pred             EEEEECCCCchHHHHHHHHHHH
Q 005987          180 VLVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAke  201 (666)
                      .++|.|++|+||||++..+...
T Consensus        22 ki~v~G~~~~GKSsli~~l~~~   43 (189)
T 1z06_A           22 KIIVIGDSNVGKTCLTYRFCAG   43 (189)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            5899999999999999999864

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=95.72  E-value=0.048  Score=69.24  Aligned_cols=39  Identities=21%  Similarity=0.151  Sum_probs=30.9

Q ss_pred             CCCccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcCCC
Q 005987          175 KFSTNVLVITGQAGVGKTATVRQIASHL---GARLYEWDTPT  213 (666)
Q Consensus       175 ~~~~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~nasd  213 (666)
                      -++..+++|+||||+||||++..+|.+.   |..++.++...
T Consensus       380 l~~G~lilI~G~pGsGKTtLaLqia~~~a~~G~~vlyis~E~  421 (2050)
T 3cmu_A          380 LPMGRIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDAEH  421 (2050)
T ss_dssp             EETTSEEEEECCTTSSHHHHHHHHHHHHHTTTCCEEEECTTS
T ss_pred             ccCCcEEEEEeCCCCCHHHHHHHHHHHHHhcCCeEEEEEcCC
Confidence            3455799999999999999999998876   45677776543

>3q72_A GTP-binding protein RAD; G-domain, CAV2 beta, signaling protein; HET: GNP; 1.66A {Homo sapiens} SCOP: c.37.1.8 PDB: 3q7p_A* 3q7q_A* 2gjs_A* 2dpx_A*

Probab=95.72  E-value=0.026  Score=51.63  Aligned_cols=21  Identities=33%  Similarity=0.593  Sum_probs=18.7

Q ss_pred             EEEEECCCCchHHHHHHHHHH
Q 005987          180 VLVITGQAGVGKTATVRQIAS  200 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAk  200 (666)
                      -++|.|++|+||||+++.+..
T Consensus         4 ki~~vG~~~~GKSsli~~l~~   24 (166)
T 3q72_A            4 KVLLLGAPGVGKSALARIFGG   24 (166)
T ss_dssp             EEEEEESTTSSHHHHHHHHCC
T ss_pred             EEEEECCCCCCHHHHHHHHcC
Confidence            489999999999999998863

>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=95.72  E-value=0.2  Score=51.58  Aligned_cols=35  Identities=26%  Similarity=0.377  Sum_probs=28.9

Q ss_pred             ccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcCC
Q 005987          178 TNVLVITGQAGVGKTATVRQIASHL---GARLYEWDTP  212 (666)
Q Consensus       178 ~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~nas  212 (666)
                      +.++++.||+|+||||++..||..+   |.++.-+...
T Consensus        98 ~~vi~i~G~~G~GKTT~~~~la~~~~~~g~~v~l~~~D  135 (297)
T 1j8m_F           98 PYVIMLVGVQGTGKTTTAGKLAYFYKKKGFKVGLVGAD  135 (297)
T ss_dssp             SEEEEEECSSCSSTTHHHHHHHHHHHHTTCCEEEEECC
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEecC
Confidence            3688899999999999999999876   7777766554

>2oil_A CATX-8, RAS-related protein RAB-25; G-protein, GDP, structural genomics, structural genomics consortium, SGC, protein transport; HET: GDP; 2.30A {Homo sapiens}

Probab=95.70  E-value=0.079  Score=49.88  Aligned_cols=23  Identities=30%  Similarity=0.562  Sum_probs=20.5

Q ss_pred             EEEEECCCCchHHHHHHHHHHHc
Q 005987          180 VLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      .++|.|++|+||||++..+...-
T Consensus        27 ki~v~G~~~~GKSsLi~~l~~~~   49 (193)
T 2oil_A           27 KVVLIGESGVGKTNLLSRFTRNE   49 (193)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHSC
T ss_pred             EEEEECcCCCCHHHHHHHHhcCC
Confidence            58999999999999999998753

>2y8e_A RAB-protein 6, GH09086P, RAB6; hydrolase, nucleotide binding, GTP binding; HET: GNP; 1.39A {Drosophila melanogaster} PDB: 3cwz_A* 1yzq_A* 2gil_A* 2e9s_A* 2fe4_A* 2ffq_A* 1d5c_A*

Probab=95.66  E-value=0.076  Score=48.85  Aligned_cols=22  Identities=32%  Similarity=0.495  Sum_probs=19.7

Q ss_pred             EEEEECCCCchHHHHHHHHHHH
Q 005987          180 VLVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAke  201 (666)
                      .++|.|++|+||||++..++..
T Consensus        16 ~i~v~G~~~~GKssli~~l~~~   37 (179)
T 2y8e_A           16 KLVFLGEQSVGKTSLITRFMYD   37 (179)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            4888999999999999999864

>1zu4_A FTSY; GTPase, signal recognition particle, SRP, receptor, protein transport; 1.95A {Mycoplasma mycoides} PDB: 1zu5_A

Probab=95.64  E-value=0.41  Score=49.69  Aligned_cols=35  Identities=23%  Similarity=0.442  Sum_probs=29.0

Q ss_pred             ccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcCC
Q 005987          178 TNVLVITGQAGVGKTATVRQIASHL---GARLYEWDTP  212 (666)
Q Consensus       178 ~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~nas  212 (666)
                      +++++|+||+|+||||++..||..+   |.+++-+.+.
T Consensus       105 ~~vI~ivG~~G~GKTT~~~~LA~~l~~~g~kVllid~D  142 (320)
T 1zu4_A          105 LNIFMLVGVNGTGKTTSLAKMANYYAELGYKVLIAAAD  142 (320)
T ss_dssp             CEEEEEESSTTSSHHHHHHHHHHHHHHTTCCEEEEECC
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEeCC
Confidence            4689999999999999999999876   6777666543

>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=95.62  E-value=0.18  Score=46.36  Aligned_cols=22  Identities=23%  Similarity=0.596  Sum_probs=20.1

Q ss_pred             EEEEECCCCchHHHHHHHHHHH
Q 005987          180 VLVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAke  201 (666)
                      .++|.|++|+||||++..+...
T Consensus         9 ~i~v~G~~~~GKSsli~~l~~~   30 (177)
T 1wms_A            9 KVILLGDGGVGKSSLMNRYVTN   30 (177)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            5899999999999999999865

>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=95.59  E-value=0.0063  Score=59.20  Aligned_cols=32  Identities=22%  Similarity=0.363  Sum_probs=26.6

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcC----CcEEEEc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLG----ARLYEWD  210 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg----~~viE~n  210 (666)
                      ..++|.|++|+||||+++.|++.++    +.++.++
T Consensus        26 ~~i~~~G~~GsGKsT~~~~l~~~l~~~~g~~~~~~~   61 (211)
T 1m7g_A           26 LTIWLTGLSASGKSTLAVELEHQLVRDRRVHAYRLD   61 (211)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHHHHHHCCCEEEEC
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHhccccCCcEEEEC
Confidence            5899999999999999999999874    4455554

>3asz_A Uridine kinase; cytidine phosphorylation, transferase; HET: C5P; 2.25A {Thermus thermophilus} PDB: 3asy_A*

Probab=95.59  E-value=0.0059  Score=59.14  Aligned_cols=25  Identities=36%  Similarity=0.513  Sum_probs=23.5

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLG  203 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg  203 (666)
                      .++.|.||+|+||||+++.|+..++
T Consensus         7 ~~i~i~G~~GsGKSTl~~~l~~~~~   31 (211)
T 3asz_A            7 FVIGIAGGTASGKTTLAQALARTLG   31 (211)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHHHG
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHhC
Confidence            5789999999999999999999987

>1zbd_A Rabphilin-3A; G protein, effector, RABCDR, synaptic exocytosis, RAB protein, RAB3A; HET: GTP; 2.60A {Rattus norvegicus} SCOP: c.37.1.8

Probab=95.59  E-value=0.073  Score=50.56  Aligned_cols=22  Identities=32%  Similarity=0.492  Sum_probs=19.8

Q ss_pred             EEEEECCCCchHHHHHHHHHHH
Q 005987          180 VLVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAke  201 (666)
                      .++|.|++|+||||++..+...
T Consensus        10 ki~v~G~~~~GKSsli~~l~~~   31 (203)
T 1zbd_A           10 KILIIGNSSVGKTSFLFRYADD   31 (203)
T ss_dssp             EEEEECSTTSSHHHHHHHHHTC
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            5899999999999999998764

>2atv_A RERG, RAS-like estrogen-regulated growth inhibitor; GDP/GTP binding, GTP hydrolysis, structural genomics, structural genomics consortium, SGC; HET: GDP; 1.90A {Homo sapiens} SCOP: c.37.1.8

Probab=95.58  E-value=0.11  Score=49.21  Aligned_cols=22  Identities=45%  Similarity=0.635  Sum_probs=20.2

Q ss_pred             EEEEECCCCchHHHHHHHHHHH
Q 005987          180 VLVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAke  201 (666)
                      .++|.|++|+||||++..+...
T Consensus        30 ki~v~G~~~vGKSsli~~l~~~   51 (196)
T 2atv_A           30 KLAIFGRAGVGKSALVVRFLTK   51 (196)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            5899999999999999999875

>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=95.58  E-value=0.065  Score=48.78  Aligned_cols=22  Identities=23%  Similarity=0.542  Sum_probs=20.0

Q ss_pred             EEEEECCCCchHHHHHHHHHHH
Q 005987          180 VLVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAke  201 (666)
                      .++|.|++|+||||++..+...
T Consensus         7 ~i~v~G~~~~GKssl~~~l~~~   28 (168)
T 1z2a_A            7 KMVVVGNGAVGKSSMIQRYCKG   28 (168)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHC
T ss_pred             EEEEECcCCCCHHHHHHHHHcC
Confidence            4889999999999999999875

>2fu5_C RAS-related protein RAB-8A; MSS4:RAB8 protein complex, GEF:GTPase nucleotide free complex; 2.00A {Mus musculus} SCOP: c.37.1.8 PDB: 3qbt_A* 3tnf_A*

Probab=95.57  E-value=0.098  Score=48.61  Aligned_cols=22  Identities=32%  Similarity=0.614  Sum_probs=9.2

Q ss_pred             EEEEECCCCchHHHHHHHHHHH
Q 005987          180 VLVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAke  201 (666)
                      .++|.|++|+||||++..+...
T Consensus        10 ki~v~G~~~~GKssl~~~l~~~   31 (183)
T 2fu5_C           10 KLLLIGDSGVGKTCVLFRFSED   31 (183)
T ss_dssp             EEEEECCCCC------------
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            5899999999999999988754

>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=95.54  E-value=0.19  Score=45.75  Aligned_cols=22  Identities=27%  Similarity=0.466  Sum_probs=20.0

Q ss_pred             EEEEECCCCchHHHHHHHHHHH
Q 005987          180 VLVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAke  201 (666)
                      .++|.|++|+||||++..+...
T Consensus         9 ~i~v~G~~~~GKssl~~~l~~~   30 (171)
T 1upt_A            9 RILILGLDGAGKTTILYRLQVG   30 (171)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            5899999999999999999764

>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=95.53  E-value=0.17  Score=47.14  Aligned_cols=23  Identities=22%  Similarity=0.393  Sum_probs=20.2

Q ss_pred             cEEEEECCCCchHHHHHHHHHHH
Q 005987          179 NVLVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAke  201 (666)
                      -.+++.|++|+||||++..+...
T Consensus        19 ~~i~v~G~~~~GKssl~~~l~~~   41 (186)
T 1ksh_A           19 LRLLMLGLDNAGKTTILKKFNGE   41 (186)
T ss_dssp             EEEEEECSTTSSHHHHHHHHTTC
T ss_pred             eEEEEECCCCCCHHHHHHHHhcC
Confidence            35899999999999999998754

>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=0.0077  Score=59.36  Aligned_cols=26  Identities=12%  Similarity=0.395  Sum_probs=23.7

Q ss_pred             ccEEEEECCCCchHHHHHHHHHHHcC
Q 005987          178 TNVLVITGQAGVGKTATVRQIASHLG  203 (666)
Q Consensus       178 ~k~LLL~GPpG~GKTtla~~LAkelg  203 (666)
                      +.++.|.||+|+||||++++|+..+.
T Consensus        16 G~ii~l~GpsGsGKSTLlk~L~g~~~   41 (219)
T 1s96_A           16 GTLYIVSAPSGAGKSSLIQALLKTQP   41 (219)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHHSC
T ss_pred             CcEEEEECCCCCCHHHHHHHHhccCC
Confidence            46899999999999999999999875

>4b3f_X DNA-binding protein smubp-2; hydrolase, helicase; 2.50A {Homo sapiens} PDB: 4b3g_A

Probab=95.51  E-value=0.022  Score=65.25  Aligned_cols=47  Identities=26%  Similarity=0.373  Sum_probs=33.1

Q ss_pred             cCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc---CCcEEEE
Q 005987          153 VQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL---GARLYEW  209 (666)
Q Consensus       153 g~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~  209 (666)
                      .++...+.|...|..          ....||.||||||||+++-.+..++   +..|+-.
T Consensus       190 LN~~Q~~AV~~al~~----------~~~~lI~GPPGTGKT~ti~~~I~~l~~~~~~ILv~  239 (646)
T 4b3f_X          190 LDTSQKEAVLFALSQ----------KELAIIHGPPGTGKTTTVVEIILQAVKQGLKVLCC  239 (646)
T ss_dssp             CCHHHHHHHHHHHHC----------SSEEEEECCTTSCHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             CCHHHHHHHHHHhcC----------CCceEEECCCCCCHHHHHHHHHHHHHhCCCeEEEE
Confidence            377777777776653          1379999999999999876665554   5555443

>1z0f_A RAB14, member RAS oncogene family; RAB GTPase, vesicular trafficking, protein transport; HET: GDP; 2.15A {Homo sapiens} SCOP: c.37.1.8 PDB: 2aed_A* 4drz_A*

Probab=95.50  E-value=0.11  Score=47.69  Aligned_cols=23  Identities=30%  Similarity=0.544  Sum_probs=20.7

Q ss_pred             EEEEECCCCchHHHHHHHHHHHc
Q 005987          180 VLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      .++|.|++|+||||++..+...-
T Consensus        17 ~i~v~G~~~~GKSsli~~l~~~~   39 (179)
T 1z0f_A           17 KYIIIGDMGVGKSCLLHQFTEKK   39 (179)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHHcCC
Confidence            58999999999999999998754

>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=95.47  E-value=0.0075  Score=58.45  Aligned_cols=28  Identities=36%  Similarity=0.497  Sum_probs=24.5

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEE
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLY  207 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~vi  207 (666)
                      +.++|+||+|+|||+++..|++..+ +++
T Consensus        35 ~~ilI~GpsGsGKStLA~~La~~g~-~iI   62 (205)
T 2qmh_A           35 LGVLITGDSGVGKSETALELVQRGH-RLI   62 (205)
T ss_dssp             EEEEEECCCTTTTHHHHHHHHTTTC-EEE
T ss_pred             EEEEEECCCCCCHHHHHHHHHHhCC-eEE
Confidence            6799999999999999999999865 544

>3hdt_A Putative kinase; structura genomics, PSI-2, protein structure initiative, midwest CENT structural genomics, MCSG; 2.79A {Clostridium symbiosum atcc 14940}

Probab=95.47  E-value=0.0086  Score=59.23  Aligned_cols=30  Identities=23%  Similarity=0.501  Sum_probs=27.7

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEEE
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLYE  208 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~viE  208 (666)
                      .++.|.|++||||||+++.||+.+|+.++.
T Consensus        15 ~iI~i~g~~gsGk~~i~~~la~~lg~~~~d   44 (223)
T 3hdt_A           15 LIITIEREYGSGGRIVGKKLAEELGIHFYD   44 (223)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHHHHTCEEEC
T ss_pred             eEEEEeCCCCCCHHHHHHHHHHHcCCcEEc
Confidence            489999999999999999999999998764

>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=95.45  E-value=0.16  Score=55.43  Aligned_cols=22  Identities=9%  Similarity=0.176  Sum_probs=19.7

Q ss_pred             EEEEECCCCchHHHHHHHH-HHHc
Q 005987          180 VLVITGQAGVGKTATVRQI-ASHL  202 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~L-Akel  202 (666)
                      ++||.|+||+ ||.+++.+ ++-+
T Consensus       241 hVLL~G~PGt-KS~Lar~i~~~i~  263 (506)
T 3f8t_A          241 HVLLAGYPVV-CSEILHHVLDHLA  263 (506)
T ss_dssp             CEEEESCHHH-HHHHHHHHHHHTC
T ss_pred             eEEEECCCCh-HHHHHHHHHHHhC
Confidence            6999999999 99999999 6654

>2a5j_A RAS-related protein RAB-2B; GTPase, signal transduction, structural genomics, structural genomics consortium, SGC, protein transport; HET: GDP; 1.50A {Homo sapiens} SCOP: c.37.1.8 PDB: 1z0a_A*

Probab=95.45  E-value=0.14  Score=48.12  Aligned_cols=23  Identities=30%  Similarity=0.525  Sum_probs=20.4

Q ss_pred             EEEEECCCCchHHHHHHHHHHHc
Q 005987          180 VLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      .++|.|++|+||||++..+...-
T Consensus        23 ki~v~G~~~~GKSsli~~l~~~~   45 (191)
T 2a5j_A           23 KYIIIGDTGVGKSCLLLQFTDKR   45 (191)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHSC
T ss_pred             EEEEECcCCCCHHHHHHHHhcCC
Confidence            48999999999999999998753

>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=95.44  E-value=0.15  Score=46.41  Aligned_cols=23  Identities=22%  Similarity=0.474  Sum_probs=20.6

Q ss_pred             EEEEECCCCchHHHHHHHHHHHc
Q 005987          180 VLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      .++|.|++|+||||++..+....
T Consensus         8 ~i~v~G~~~~GKSsli~~l~~~~   30 (170)
T 1z0j_A            8 KVCLLGDTGVGKSSIMWRFVEDS   30 (170)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHSC
T ss_pred             EEEEECcCCCCHHHHHHHHHcCC
Confidence            48999999999999999998764

>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=95.41  E-value=0.0088  Score=57.99  Aligned_cols=25  Identities=32%  Similarity=0.619  Sum_probs=23.0

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLG  203 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg  203 (666)
                      .++.|.||+|+||||++++|+..+.
T Consensus        21 ei~~l~GpnGsGKSTLl~~l~gl~~   45 (207)
T 1znw_A           21 RVVVLSGPSAVGKSTVVRCLRERIP   45 (207)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHST
T ss_pred             CEEEEECCCCCCHHHHHHHHHhhCC
Confidence            5899999999999999999999873

>1p9r_A General secretion pathway protein E; bacterial type II secretion system cytoplasmic protein - GSPE, putative ATPase/ ATP binding protein; 2.50A {Vibrio cholerae} SCOP: c.37.1.11 PDB: 1p9w_A*

Probab=95.40  E-value=0.015  Score=63.03  Aligned_cols=50  Identities=20%  Similarity=0.378  Sum_probs=36.7

Q ss_pred             CCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcC
Q 005987          145 PRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLG  203 (666)
Q Consensus       145 P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg  203 (666)
                      +-++++|-........++..+..         +..+++|+||+|+||||++++++..+.
T Consensus       143 ~~~l~~Lg~~~~~~~~L~~l~~~---------~ggii~I~GpnGSGKTTlL~allg~l~  192 (418)
T 1p9r_A          143 RLDLHSLGMTAHNHDNFRRLIKR---------PHGIILVTGPTGSGKSTTLYAGLQELN  192 (418)
T ss_dssp             CCCGGGSCCCHHHHHHHHHHHTS---------SSEEEEEECSTTSCHHHHHHHHHHHHC
T ss_pred             CCCHHHcCCCHHHHHHHHHHHHh---------cCCeEEEECCCCCCHHHHHHHHHhhcC
Confidence            45677877766655555554311         125899999999999999999999884

>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=95.40  E-value=0.021  Score=59.85  Aligned_cols=31  Identities=32%  Similarity=0.513  Sum_probs=25.9

Q ss_pred             ccEEEEECCCCchHHHHHHHHHHHc---CCcEEE
Q 005987          178 TNVLVITGQAGVGKTATVRQIASHL---GARLYE  208 (666)
Q Consensus       178 ~k~LLL~GPpG~GKTtla~~LAkel---g~~viE  208 (666)
                      +.++.|.||+|+||||+++.||..+   +.++.-
T Consensus       129 g~vi~lvG~nGaGKTTll~~Lag~l~~~~g~V~l  162 (328)
T 3e70_C          129 PYVIMFVGFNGSGKTTTIAKLANWLKNHGFSVVI  162 (328)
T ss_dssp             SEEEEEECCTTSSHHHHHHHHHHHHHHTTCCEEE
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHhcCCEEEE
Confidence            4789999999999999999999876   445543

>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=95.39  E-value=0.0046  Score=59.83  Aligned_cols=24  Identities=25%  Similarity=0.540  Sum_probs=22.4

Q ss_pred             EEEEECCCCchHHHHHHHHHHHcC
Q 005987          180 VLVITGQAGVGKTATVRQIASHLG  203 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkelg  203 (666)
                      .++|.||+|+||||+++.|++.++
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            689999999999999999999984

>1z6g_A Guanylate kinase; structural genomics, SGC, structural genom consortium, transferase; HET: EPE; 2.18A {Plasmodium falciparum}

Probab=95.38  E-value=0.0082  Score=58.95  Aligned_cols=24  Identities=33%  Similarity=0.631  Sum_probs=22.5

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      .++.|.||+|+||||++++|+..+
T Consensus        24 ~~~~lvGpsGsGKSTLl~~L~g~~   47 (218)
T 1z6g_A           24 YPLVICGPSGVGKGTLIKKLLNEF   47 (218)
T ss_dssp             CCEEEECSTTSSHHHHHHHHHHHS
T ss_pred             CEEEEECCCCCCHHHHHHHHHhhC
Confidence            579999999999999999999977

>3c5c_A RAS-like protein 12; GDP, GTPase, structural genomics consortium, SGC, limited proteolysis, GTP-binding, nucleotide-binding, signaling protein; HET: GDP; 1.85A {Homo sapiens}

Probab=95.37  E-value=0.092  Score=49.44  Aligned_cols=23  Identities=30%  Similarity=0.442  Sum_probs=20.3

Q ss_pred             EEEEECCCCchHHHHHHHHHHHc
Q 005987          180 VLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      -++|.|++|+||||++..+...-
T Consensus        23 ki~vvG~~~vGKTsLi~~l~~~~   45 (187)
T 3c5c_A           23 NLAILGRRGAGKSALTVKFLTKR   45 (187)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHSS
T ss_pred             EEEEECCCCCcHHHHHHHHHhCC
Confidence            58999999999999999988753

>3vkg_A Dynein heavy chain, cytoplasmic; AAA+ protein, molecular motor, microtubles, motor protein; HET: ADP SPM; 2.81A {Dictyostelium discoideum} PDB: 3vkh_A*

Probab=95.34  E-value=0.16  Score=67.18  Aligned_cols=141  Identities=11%  Similarity=0.144  Sum_probs=79.8

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCchhhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGES  258 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~  258 (666)
                      .++||.|..|+||++++|..|--.|++++.+.-+.             +.....-.+.++.++.++.           -.
T Consensus      1647 GhaLLVGvgGSGkqSLtrLAa~i~~~~vfqi~i~k-------------~Y~~~~f~eDLk~l~~~aG-----------~~ 1702 (3245)
T 3vkg_A         1647 GHALLIGVSGGGKSVLSRFVAWMNGLSIYTIKVNN-------------NYKSSDFDDDLRMLLKRAG-----------CK 1702 (3245)
T ss_dssp             CCEEEEESTTSSHHHHHHHHHHHTTCEEECCC-----------------CCHHHHHHHHHHHHHHHH-----------TS
T ss_pred             CCeEEecCCCCcHHHHHHHHHHHhCCeeEEEeeeC-------------CCCHHHHHHHHHHHHHHHh-----------cC
Confidence            57999999999999999999999999999876432             1111112223333443332           12


Q ss_pred             CCceEEEEeC--------------------CCCCcchhHHHHHHHHHHH------------------HHhcC--CCceEE
Q 005987          259 KSSAILLIDD--------------------LPVTNGRTAFERLRQCLLL------------------LVRST--HIPTAV  298 (666)
Q Consensus       259 ~~~~IIlIDE--------------------id~l~~~~~~~~l~~~L~~------------------l~~~~--~~PiVi  298 (666)
                      +++.++|++|                    +|+++..+.+..+.+.+..                  +++..  +..+|+
T Consensus      1703 ~~~~vFL~tD~qi~~e~FLE~IN~lL~sGEVP~LF~~dE~~~i~~~~r~~a~~~g~~~dt~~~l~~~Fi~rvr~NLHvVL 1782 (3245)
T 3vkg_A         1703 EEKICFIFDESNVLESSFLERMNTLLAGGEVPGLFEGEEFTALMHACKETAQRNGLILDSEEELYKYFTSQVRRNLHVVF 1782 (3245)
T ss_dssp             CCCEEEEEEGGGCSSTHHHHHHHHHHHHSCCTTSSCTTTHHHHHHHHHHHHHHTTCCCCCHHHHHHHHHHHHTTTCCEEE
T ss_pred             CCCEEEEEeccccccHHHHHHHHHHhccCCccccCCHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHcCEEEE
Confidence            3567888875                    4555544444444332222                  22221  346777


Q ss_pred             EEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHH
Q 005987          299 VLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICR  350 (666)
Q Consensus       299 Iit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~  350 (666)
                      +++..+...  ....|.+   +++++  +|.+-=|.+=+.+.+..+-.+.+.
T Consensus      1783 ~mSPvg~~f--R~R~r~f---PaLvn--cctIDWf~~Wp~eAL~~Va~~fl~ 1827 (3245)
T 3vkg_A         1783 TMNPASPDF--HNRSATS---PALFN--RCVLDWFGEWSPEALFQVGSEFTR 1827 (3245)
T ss_dssp             EECTTSTTT--TC----C---THHHH--HSEEEEEESCCHHHHHHHHHHHTT
T ss_pred             EECCCCHHH--HHHHHHC---hHHhh--CceeeecCCCCHHHHHHHHHHHHh
Confidence            776543221  1122333   34444  378888999998888777666554

>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=95.34  E-value=0.11  Score=47.42  Aligned_cols=22  Identities=23%  Similarity=0.564  Sum_probs=19.8

Q ss_pred             EEEEECCCCchHHHHHHHHHHH
Q 005987          180 VLVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAke  201 (666)
                      .++|.|++|+||||++..+...
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            4899999999999999999864

>3t1o_A Gliding protein MGLA; G domain containing protein, bacterial GTPase, bacterial POL motility, POLE localisation, alpha/beta protein; HET: GDP; 1.90A {Thermus thermophilus} PDB: 3t12_A* 3t1q_A* 3t1t_A* 3t1v_A*

Probab=95.29  E-value=0.19  Score=46.89  Aligned_cols=23  Identities=30%  Similarity=0.364  Sum_probs=20.5

Q ss_pred             EEEEECCCCchHHHHHHHHHHHc
Q 005987          180 VLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      .++|.|++|+||||+++.+....
T Consensus        16 ki~vvG~~~~GKssL~~~l~~~~   38 (198)
T 3t1o_A           16 KIVYYGPGLSGKTTNLKWIYSKV   38 (198)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHTS
T ss_pred             EEEEECCCCCCHHHHHHHHHhhc
Confidence            48999999999999999888765

>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=95.28  E-value=0.011  Score=55.15  Aligned_cols=24  Identities=25%  Similarity=0.473  Sum_probs=22.7

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      .++.|.||.|+||||++++++..+
T Consensus        34 e~v~L~G~nGaGKTTLlr~l~g~l   57 (158)
T 1htw_A           34 IMVYLNGDLGAGKTTLTRGMLQGI   57 (158)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHT
T ss_pred             CEEEEECCCCCCHHHHHHHHHHhC
Confidence            589999999999999999999987

>4gp7_A Metallophosphoesterase; polynucleotide kinase phosphatase, RNA repair, transferase; HET: ATP CIT; 2.00A {Clostridium thermocellum} PDB: 4gp6_A*

Probab=95.27  E-value=0.0089  Score=56.22  Aligned_cols=21  Identities=24%  Similarity=0.526  Sum_probs=18.8

Q ss_pred             cEEEEECCCCchHHHHHHHHH
Q 005987          179 NVLVITGQAGVGKTATVRQIA  199 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LA  199 (666)
                      .++.|.||+|+||||+++++.
T Consensus        10 ei~~l~G~nGsGKSTl~~~~~   30 (171)
T 4gp7_A           10 SLVVLIGSSGSGKSTFAKKHF   30 (171)
T ss_dssp             EEEEEECCTTSCHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHc
Confidence            589999999999999999744

>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=95.26  E-value=0.07  Score=50.76  Aligned_cols=23  Identities=26%  Similarity=0.536  Sum_probs=20.7

Q ss_pred             EEEEECCCCchHHHHHHHHHHHc
Q 005987          180 VLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      .++|.||+|+||||+++.++...
T Consensus         7 kv~lvG~~g~GKSTLl~~l~~~~   29 (199)
T 2f9l_A            7 KVVLIGDSGVGKSNLLSRFTRNE   29 (199)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHSC
T ss_pred             EEEEECcCCCCHHHHHHHHhcCC
Confidence            48899999999999999999863

>3thx_B DNA mismatch repair protein MSH3; ABC family ATPase, mismatch recognition, mismatched unpaired DNA binding protein-DNA complex; HET: DNA ADP; 2.70A {Homo sapiens} PDB: 3thw_B* 3thy_B* 3thz_B*

Probab=95.23  E-value=0.086  Score=62.52  Aligned_cols=23  Identities=35%  Similarity=0.547  Sum_probs=20.7

Q ss_pred             ccEEEEECCCCchHHHHHHHHHH
Q 005987          178 TNVLVITGQAGVGKTATVRQIAS  200 (666)
Q Consensus       178 ~k~LLL~GPpG~GKTtla~~LAk  200 (666)
                      ..+++|+||.|+||||+++.++.
T Consensus       673 g~i~~ItGPNGaGKSTlLr~i~~  695 (918)
T 3thx_B          673 ERVMIITGPNMGGKSSYIKQVAL  695 (918)
T ss_dssp             CCEEEEESCCCHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCchHHHHHHHHH
Confidence            36899999999999999999874

>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=95.21  E-value=0.06  Score=63.99  Aligned_cols=23  Identities=30%  Similarity=0.354  Sum_probs=20.4

Q ss_pred             ccEEEEECCCCchHHHHHHHHHH
Q 005987          178 TNVLVITGQAGVGKTATVRQIAS  200 (666)
Q Consensus       178 ~k~LLL~GPpG~GKTtla~~LAk  200 (666)
                      +.+++|+||.|+||||+++.+|-
T Consensus       662 g~i~~ItGpNGsGKSTlLr~ial  684 (934)
T 3thx_A          662 QMFHIITGPNMGGKSTYIRQTGV  684 (934)
T ss_dssp             BCEEEEECCTTSSHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH
Confidence            36899999999999999999853

>3gmt_A Adenylate kinase; ssgcid, ATP-BIN cytoplasm, nucleotide biosynthesis, nucleotide-BIND transferase, structural genomics; 2.10A {Burkholderia pseudomallei 1710B}

Probab=95.20  E-value=0.012  Score=58.40  Aligned_cols=30  Identities=23%  Similarity=0.366  Sum_probs=26.8

Q ss_pred             EEEEECCCCchHHHHHHHHHHHcCCcEEEE
Q 005987          180 VLVITGQAGVGKTATVRQIASHLGARLYEW  209 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkelg~~viE~  209 (666)
                      .|-|.||||+||||.++.||+.+|+..+..
T Consensus        10 ~~~~~G~pGsGKsT~a~~L~~~~g~~~is~   39 (230)
T 3gmt_A           10 RLILLGAPGAGKGTQANFIKEKFGIPQIST   39 (230)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHTCCEECH
T ss_pred             ceeeECCCCCCHHHHHHHHHHHhCCCeeec
Confidence            488999999999999999999999887743

>3reg_A RHO-like small GTPase; cytoskeleton, nucleotide-binding, GTP-binding, signaling Pro lipoprotein, prenylation; HET: GSP; 1.80A {Entamoeba histolytica} PDB: 3ref_B* 4dvg_A*

Probab=95.18  E-value=0.17  Score=47.68  Aligned_cols=23  Identities=26%  Similarity=0.413  Sum_probs=20.7

Q ss_pred             EEEEECCCCchHHHHHHHHHHHc
Q 005987          180 VLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      .++|.|++|+||||++..+...-
T Consensus        25 ki~~vG~~~~GKSsl~~~l~~~~   47 (194)
T 3reg_A           25 KIVVVGDGAVGKTCLLLAFSKGE   47 (194)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEEECcCCCCHHHHHHHHhcCC
Confidence            58999999999999999998754

>3lnc_A Guanylate kinase, GMP kinase; ALS collaborative crystallography, emerald biostructures, ATP-binding, cytoplasm, nucleotide-binding; HET: 5GP; 1.95A {Anaplasma phagocytophilum}

Probab=95.14  E-value=0.0074  Score=59.50  Aligned_cols=25  Identities=24%  Similarity=0.488  Sum_probs=16.2

Q ss_pred             cEEEEECCCCchHHHHHHHHH-HHcC
Q 005987          179 NVLVITGQAGVGKTATVRQIA-SHLG  203 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LA-kelg  203 (666)
                      .++.|.||+|+||||+++.|+ ..+.
T Consensus        28 ~ii~l~Gp~GsGKSTl~~~L~~~~~~   53 (231)
T 3lnc_A           28 VILVLSSPSGCGKTTVANKLLEKQKN   53 (231)
T ss_dssp             CEEEEECSCC----CHHHHHHC----
T ss_pred             CEEEEECCCCCCHHHHHHHHHhcCCC
Confidence            589999999999999999999 7653

>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=95.13  E-value=0.011  Score=57.71  Aligned_cols=26  Identities=23%  Similarity=0.383  Sum_probs=22.9

Q ss_pred             CccEEEEECCCCchHHHHHHHHHHHc
Q 005987          177 STNVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       177 ~~k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      +..++.|.||+|+||||+++.++..+
T Consensus        24 ~G~~~~l~G~nGsGKSTll~~l~g~~   49 (231)
T 4a74_A           24 TQAITEVFGEFGSGKTQLAHTLAVMV   49 (231)
T ss_dssp             SSEEEEEEESTTSSHHHHHHHHHHHT
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHH
Confidence            34689999999999999999999854

>2ew1_A RAS-related protein RAB-30; G-protein, GTP analogue, structural genomics, structural genomics consortium, SGC, signaling protein; HET: GNP; 2.00A {Homo sapiens} SCOP: c.37.1.8

Probab=95.11  E-value=0.2  Score=47.98  Aligned_cols=23  Identities=48%  Similarity=0.752  Sum_probs=20.4

Q ss_pred             EEEEECCCCchHHHHHHHHHHHc
Q 005987          180 VLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      .++|.|++|+||||++..+....
T Consensus        28 ki~lvG~~~vGKSsLi~~l~~~~   50 (201)
T 2ew1_A           28 KIVLIGNAGVGKTCLVRRFTQGL   50 (201)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHSS
T ss_pred             EEEEECcCCCCHHHHHHHHHhCC
Confidence            58999999999999999998753

>2eyu_A Twitching motility protein PILT; pilus retraction motor, C-terminal domain PILT, protein transport; 1.87A {Aquifex aeolicus}

Probab=95.10  E-value=0.012  Score=59.65  Aligned_cols=24  Identities=25%  Similarity=0.624  Sum_probs=22.4

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      ..++|.||+|+||||++++++..+
T Consensus        26 ~~v~i~Gp~GsGKSTll~~l~g~~   49 (261)
T 2eyu_A           26 GLILVTGPTGSGKSTTIASMIDYI   49 (261)
T ss_dssp             EEEEEECSTTCSHHHHHHHHHHHH
T ss_pred             CEEEEECCCCccHHHHHHHHHHhC
Confidence            589999999999999999999876

>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=95.10  E-value=0.019  Score=56.20  Aligned_cols=36  Identities=22%  Similarity=0.354  Sum_probs=29.4

Q ss_pred             ccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcCCC
Q 005987          178 TNVLVITGQAGVGKTATVRQIASHL---GARLYEWDTPT  213 (666)
Q Consensus       178 ~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~nasd  213 (666)
                      +..++|.||+|+||||.++.|++.+   |+.++....|.
T Consensus         6 g~~i~~eG~~gsGKsT~~~~l~~~l~~~~~~v~~~~~p~   44 (213)
T 4edh_A            6 GLFVTLEGPEGAGKSTNRDYLAERLRERGIEVQLTREPG   44 (213)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHHHTTTCCEEEEESSC
T ss_pred             ceEEEEEcCCCCCHHHHHHHHHHHHHHcCCCcccccCCC
Confidence            3689999999999999999999988   56776555443

>3b9q_A Chloroplast SRP receptor homolog, alpha subunit CPFTSY; protein translocation, GTP-binding, nucleotide-binding, protein transport; 1.75A {Arabidopsis thaliana}

Probab=95.09  E-value=0.027  Score=58.23  Aligned_cols=31  Identities=32%  Similarity=0.599  Sum_probs=25.8

Q ss_pred             ccEEEEECCCCchHHHHHHHHHHHc---CCcEEE
Q 005987          178 TNVLVITGQAGVGKTATVRQIASHL---GARLYE  208 (666)
Q Consensus       178 ~k~LLL~GPpG~GKTtla~~LAkel---g~~viE  208 (666)
                      +.++.|.||+|+||||+++.||..+   +.++.-
T Consensus       100 g~vi~lvG~nGsGKTTll~~Lag~l~~~~g~V~l  133 (302)
T 3b9q_A          100 PAVIMIVGVNGGGKTTSLGKLAHRLKNEGTKVLM  133 (302)
T ss_dssp             CEEEEEECCTTSCHHHHHHHHHHHHHHTTCCEEE
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHHHHHcCCeEEE
Confidence            4689999999999999999999876   445443

>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=95.08  E-value=0.077  Score=49.72  Aligned_cols=23  Identities=30%  Similarity=0.489  Sum_probs=20.4

Q ss_pred             cEEEEECCCCchHHHHHHHHHHH
Q 005987          179 NVLVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAke  201 (666)
                      -.++|.|++|+||||+++.++..
T Consensus        17 ~ki~ivG~~~vGKSsL~~~l~~~   39 (181)
T 1fzq_A           17 VRILLLGLDNAGKTTLLKQLASE   39 (181)
T ss_dssp             EEEEEEESTTSSHHHHHHHHCCS
T ss_pred             eEEEEECCCCCCHHHHHHHHhcC
Confidence            35999999999999999998765

>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=95.05  E-value=0.094  Score=48.12  Aligned_cols=22  Identities=36%  Similarity=0.566  Sum_probs=19.6

Q ss_pred             EEEEECCCCchHHHHHHHHHHH
Q 005987          180 VLVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAke  201 (666)
                      .++|.|++|+||||++..+...
T Consensus         6 ki~i~G~~~vGKSsl~~~l~~~   27 (175)
T 2nzj_A            6 RVVLLGDPGVGKTSLASLFAGK   27 (175)
T ss_dssp             EEEEECCTTSSHHHHHHHHHCC
T ss_pred             EEEEECCCCccHHHHHHHHhcC
Confidence            4899999999999999998754

>2bme_A RAB4A, RAS-related protein RAB4A; GTP-binding protein, vesicular transport, endocytosis, prenylation, protein transport, transport; HET: GNP; 1.57A {Homo sapiens} SCOP: c.37.1.8 PDB: 2bmd_A* 1yu9_A* 1z0k_A*

Probab=95.04  E-value=0.16  Score=47.10  Aligned_cols=23  Identities=26%  Similarity=0.514  Sum_probs=20.4

Q ss_pred             EEEEECCCCchHHHHHHHHHHHc
Q 005987          180 VLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      .++|.|++|+||||++..+...-
T Consensus        12 ki~v~G~~~~GKSsli~~l~~~~   34 (186)
T 2bme_A           12 KFLVIGNAGTGKSCLLHQFIEKK   34 (186)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHSS
T ss_pred             EEEEECCCCCCHHHHHHHHHcCC
Confidence            58999999999999999998653

>3ihw_A Centg3; RAS, centaurin, GTPase, structural genomics, structural genomics consortium, SGC, alternative splicing, ANK repeat, cytoplasm, GTP-binding; 1.92A {Homo sapiens} SCOP: c.37.1.0

Probab=95.03  E-value=0.34  Score=45.36  Aligned_cols=23  Identities=26%  Similarity=0.307  Sum_probs=20.1

Q ss_pred             EEEEECCCCchHHHHHHHHHHHc
Q 005987          180 VLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      -++|.|++|+||||++..++...
T Consensus        22 ki~ivG~~~vGKSsL~~~~~~~~   44 (184)
T 3ihw_A           22 KVGIVGNLSSGKSALVHRYLTGT   44 (184)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHSS
T ss_pred             EEEEECCCCCCHHHHHHHHhcCC
Confidence            58999999999999998887653

>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=95.00  E-value=0.019  Score=65.26  Aligned_cols=33  Identities=30%  Similarity=0.449  Sum_probs=29.5

Q ss_pred             ccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEc
Q 005987          178 TNVLVITGQAGVGKTATVRQIASHL---GARLYEWD  210 (666)
Q Consensus       178 ~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~n  210 (666)
                      +..++|+|+||+||||+++.|++.+   |+.++.+.
T Consensus        52 g~lIvLtGlsGSGKSTlAr~La~~L~~~G~~~v~lD   87 (630)
T 1x6v_B           52 GCTVWLTGLSGAGKTTVSMALEEYLVCHGIPCYTLD   87 (630)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEES
T ss_pred             CCEEEEEeCCCCCHHHHHHHHHHHHHhcCCeEEEec
Confidence            3689999999999999999999999   88877664

>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=95.00  E-value=0.3  Score=44.16  Aligned_cols=22  Identities=18%  Similarity=0.339  Sum_probs=19.8

Q ss_pred             EEEECCCCchHHHHHHHHHHHc
Q 005987          181 LVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       181 LLL~GPpG~GKTtla~~LAkel  202 (666)
                      ++|.|++|+||||++..+...-
T Consensus         3 i~~~G~~~~GKssl~~~l~~~~   24 (164)
T 1r8s_A            3 ILMVGLDAAGKTTILYKLKLGE   24 (164)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHC
T ss_pred             EEEECCCCCCHHHHHHHHHcCC
Confidence            7899999999999999998654

>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=95.00  E-value=0.021  Score=53.97  Aligned_cols=32  Identities=25%  Similarity=0.273  Sum_probs=27.0

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc---CCcEEEEc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL---GARLYEWD  210 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel---g~~viE~n  210 (666)
                      +.+.|.|++|+||||++..|+..+   |+.+..+.
T Consensus         5 ~~i~i~G~sGsGKTTl~~~L~~~l~~~g~~v~~ik   39 (169)
T 1xjc_A            5 NVWQVVGYKHSGKTTLMEKWVAAAVREGWRVGTVK   39 (169)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             EEEEEECCCCCCHHHHHHHHHHhhHhcCCeeeEEE
Confidence            589999999999999999999876   66665554

>3tqc_A Pantothenate kinase; biosynthesis of cofactors, prosthetic groups, carriers, TRAN; HET: ADP; 2.30A {Coxiella burnetii}

Probab=94.98  E-value=0.032  Score=58.18  Aligned_cols=25  Identities=32%  Similarity=0.523  Sum_probs=23.1

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLG  203 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg  203 (666)
                      .++-|.||+||||||+++.|+..++
T Consensus        93 ~iigI~GpsGSGKSTl~~~L~~ll~  117 (321)
T 3tqc_A           93 YIIGIAGSVAVGKSTTSRVLKALLS  117 (321)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHT
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHhc
Confidence            5899999999999999999999875

>3pqc_A Probable GTP-binding protein ENGB; rossmann fold, GTPase, cell cycle, hydrolase; HET: GDP; 1.90A {Thermotoga maritima} PDB: 3pr1_A

Probab=94.97  E-value=0.49  Score=43.98  Aligned_cols=24  Identities=17%  Similarity=0.380  Sum_probs=20.8

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      ..++|.|++|+||||++..+...-
T Consensus        24 ~~i~v~G~~~~GKSsli~~l~~~~   47 (195)
T 3pqc_A           24 GEVAFVGRSNVGKSSLLNALFNRK   47 (195)
T ss_dssp             CEEEEEEBTTSSHHHHHHHHHTSC
T ss_pred             eEEEEECCCCCCHHHHHHHHHcCc
Confidence            358999999999999999987653

>3tw8_B RAS-related protein RAB-35; longin domain, RAB GTPase, guanine exchange factor; 2.10A {Homo sapiens}

Probab=94.94  E-value=0.19  Score=46.24  Aligned_cols=22  Identities=36%  Similarity=0.658  Sum_probs=19.4

Q ss_pred             EEEEECCCCchHHHHHHHHHHH
Q 005987          180 VLVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAke  201 (666)
                      .++|.|++|+||||++..+...
T Consensus        11 ~i~v~G~~~~GKssl~~~l~~~   32 (181)
T 3tw8_B           11 KLLIIGDSGVGKSSLLLRFADN   32 (181)
T ss_dssp             EEEEECCTTSCHHHHHHHHCSC
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            5899999999999999998653

>2p5s_A RAS and EF-hand domain containing; G-protein, RAB, GDP, structural genomics, SGC, structural genomics consortium, signaling protein; HET: GDP; 2.15A {Homo sapiens}

Probab=94.92  E-value=0.37  Score=45.52  Aligned_cols=23  Identities=26%  Similarity=0.512  Sum_probs=20.4

Q ss_pred             EEEEECCCCchHHHHHHHHHHHc
Q 005987          180 VLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      .++|.|++|+||||++..+...-
T Consensus        30 ki~v~G~~~~GKSsli~~l~~~~   52 (199)
T 2p5s_A           30 KIVLAGDAAVGKSSFLMRLCKNE   52 (199)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHCC
T ss_pred             EEEEECcCCCCHHHHHHHHHhCC
Confidence            58999999999999999998653

>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=94.92  E-value=0.76  Score=49.63  Aligned_cols=35  Identities=29%  Similarity=0.374  Sum_probs=28.8

Q ss_pred             CccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcC
Q 005987          177 STNVLVITGQAGVGKTATVRQIASHL---GARLYEWDT  211 (666)
Q Consensus       177 ~~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~na  211 (666)
                      ++++++|.||+|+||||++..||..+   |..+.-+.+
T Consensus        97 ~~~vi~i~G~~GsGKTT~~~~LA~~l~~~g~~Vllvd~  134 (425)
T 2ffh_A           97 DRNLWFLVGLQGSGKTTTAAKLALYYKGKGRRPLLVAA  134 (425)
T ss_dssp             SSEEEEEECCTTSSHHHHHHHHHHHHHTTTCCEEEEEC
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEeec
Confidence            34688899999999999999999877   667766655

>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=94.91  E-value=0.031  Score=55.33  Aligned_cols=33  Identities=15%  Similarity=0.154  Sum_probs=25.4

Q ss_pred             ccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEc
Q 005987          178 TNVLVITGQAGVGKTATVRQIASHL---GARLYEWD  210 (666)
Q Consensus       178 ~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~n  210 (666)
                      ..+.+++||.|+||||.+-.++..+   |.+++-+.
T Consensus        19 g~l~v~~G~MgsGKTT~lL~~~~r~~~~g~kvli~k   54 (234)
T 2orv_A           19 GQIQVILGPMFSGKSTELMRRVRRFQIAQYKCLVIK   54 (234)
T ss_dssp             CEEEEEECCTTSCHHHHHHHHHHHHHTTTCCEEEEE
T ss_pred             eEEEEEECCCCCcHHHHHHHHHHHHHHCCCeEEEEe
Confidence            3689999999999998876665544   66776665

>1x3s_A RAS-related protein RAB-18; GTPase, GNP, structural genomics, NPPSFA, national project on protein structural and functional analyses; HET: GNP; 1.32A {Homo sapiens} SCOP: c.37.1.8

Probab=94.91  E-value=0.085  Score=49.43  Aligned_cols=23  Identities=26%  Similarity=0.567  Sum_probs=20.6

Q ss_pred             EEEEECCCCchHHHHHHHHHHHc
Q 005987          180 VLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      .++|.|++|+||||++..+...-
T Consensus        17 ~i~v~G~~~~GKssli~~l~~~~   39 (195)
T 1x3s_A           17 KILIIGESGVGKSSLLLRFTDDT   39 (195)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHHcCC
Confidence            58999999999999999998753

>2e87_A Hypothetical protein PH1320; GTP-binding, GTPase, OBG, bundle, GDP, complex, structural G NPPSFA; HET: GDP; 2.35A {Pyrococcus horikoshii}

Probab=94.87  E-value=0.82  Score=48.00  Aligned_cols=24  Identities=25%  Similarity=0.524  Sum_probs=21.2

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      ..++|.|+||+||||++..++...
T Consensus       168 ~~v~lvG~~gvGKSTLin~L~~~~  191 (357)
T 2e87_A          168 PTVVIAGHPNVGKSTLLKALTTAK  191 (357)
T ss_dssp             CEEEEECSTTSSHHHHHHHHCSSC
T ss_pred             CEEEEECCCCCCHHHHHHHHhCCC
Confidence            479999999999999999998653

>2jeo_A Uridine-cytidine kinase 1; UCK, transferase, ATP-binding, nucleoside kinase, nucleotide-binding; 2.50A {Homo sapiens} PDB: 2uvq_A*

Probab=94.86  E-value=0.015  Score=58.04  Aligned_cols=27  Identities=22%  Similarity=0.428  Sum_probs=24.3

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGAR  205 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~  205 (666)
                      .++-|.||+|+||||+++.|+..+|..
T Consensus        26 ~iigI~G~~GsGKSTl~k~L~~~lG~~   52 (245)
T 2jeo_A           26 FLIGVSGGTASGKSTVCEKIMELLGQN   52 (245)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHHTGG
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHhchh
Confidence            478999999999999999999988753

>2xxa_A Signal recognition particle protein; protein transport, RNA/RNA binding protein, hydrolase, gtpas; HET: GCP; 3.94A {Escherichia coli} PDB: 2j28_9

Probab=94.86  E-value=0.72  Score=49.97  Aligned_cols=36  Identities=22%  Similarity=0.426  Sum_probs=29.5

Q ss_pred             ccEEEEECCCCchHHHHHHHHHHHc----CCcEEEEcCCC
Q 005987          178 TNVLVITGQAGVGKTATVRQIASHL----GARLYEWDTPT  213 (666)
Q Consensus       178 ~k~LLL~GPpG~GKTtla~~LAkel----g~~viE~nasd  213 (666)
                      ++.+++.|++|+||||++-.||..+    |.++.-+.+-.
T Consensus       100 ~~vI~ivG~~GvGKTT~a~~LA~~l~~~~G~kVllvd~D~  139 (433)
T 2xxa_A          100 PAVVLMAGLQGAGKTTSVGKLGKFLREKHKKKVLVVSADV  139 (433)
T ss_dssp             SEEEEEECSTTSSHHHHHHHHHHHHHHTSCCCEEEEECCC
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHhcCCeEEEEecCC
Confidence            3688899999999999999998765    77887776543

>2yc2_C IFT27, small RAB-related GTPase; transport protein, cilium, IFT complex; 2.59A {Chlamydomonas reinhardtii} PDB: 2yc4_C

Probab=94.83  E-value=0.26  Score=46.48  Aligned_cols=22  Identities=32%  Similarity=0.531  Sum_probs=4.3

Q ss_pred             EEEEECCCCchHHHHHHHHHHH
Q 005987          180 VLVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAke  201 (666)
                      .++|.|++|+||||++..+...
T Consensus        22 ~i~v~G~~~~GKssli~~l~~~   43 (208)
T 2yc2_C           22 KVAVVGEATVGKSALISMFTSK   43 (208)
T ss_dssp             EEEEC-----------------
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            5899999999999999988765

>2og2_A Putative signal recognition particle receptor; nucleotide-binding, protein transport; 2.00A {Arabidopsis thaliana}

Probab=94.83  E-value=0.037  Score=58.63  Aligned_cols=31  Identities=32%  Similarity=0.599  Sum_probs=25.9

Q ss_pred             ccEEEEECCCCchHHHHHHHHHHHc---CCcEEE
Q 005987          178 TNVLVITGQAGVGKTATVRQIASHL---GARLYE  208 (666)
Q Consensus       178 ~k~LLL~GPpG~GKTtla~~LAkel---g~~viE  208 (666)
                      +.++.|.||+|+||||+++.||..+   +..|.-
T Consensus       157 g~vi~lvG~nGsGKTTll~~Lag~l~~~~G~V~l  190 (359)
T 2og2_A          157 PAVIMIVGVNGGGKTTSLGKLAHRLKNEGTKVLM  190 (359)
T ss_dssp             SEEEEEECCTTSCHHHHHHHHHHHHHHTTCCEEE
T ss_pred             CeEEEEEcCCCChHHHHHHHHHhhccccCCEEEE
Confidence            4689999999999999999999976   445443

>2wsm_A Hydrogenase expression/formation protein (HYPB); metal binding protein; 2.30A {Archaeoglobus fulgidus}

Probab=94.81  E-value=0.019  Score=55.75  Aligned_cols=45  Identities=27%  Similarity=0.381  Sum_probs=33.6

Q ss_pred             cccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcC
Q 005987          151 LAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLG  203 (666)
Q Consensus       151 Lvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg  203 (666)
                      |..+.+..+.++..+..      .+.  +.++|.|++|+||||++..|+..+.
T Consensus        11 l~~~~~~~~~~~~~~~~------~~~--~~i~i~G~~g~GKTTl~~~l~~~~~   55 (221)
T 2wsm_A           11 LAENKRLAEKNREALRE------SGT--VAVNIMGAIGSGKTLLIERTIERIG   55 (221)
T ss_dssp             CHHHHHHHHHHHHHHHH------HTC--EEEEEEECTTSCHHHHHHHHHHHHT
T ss_pred             HhhcHHHHHHHHHhhcc------cCc--eEEEEEcCCCCCHHHHHHHHHHHhc
Confidence            44566667777766653      222  4799999999999999999998863

>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=94.78  E-value=0.021  Score=59.21  Aligned_cols=31  Identities=23%  Similarity=0.430  Sum_probs=26.8

Q ss_pred             ccEEEEECCCCchHHHHHHHHHHHcCCcEEE
Q 005987          178 TNVLVITGQAGVGKTATVRQIASHLGARLYE  208 (666)
Q Consensus       178 ~k~LLL~GPpG~GKTtla~~LAkelg~~viE  208 (666)
                      +..+.|.||+|+||||++++|+..+...|+-
T Consensus       126 Ge~vaIvGpsGsGKSTLl~lL~gl~~G~I~~  156 (305)
T 2v9p_A          126 KNCLAFIGPPNTGKSMLCNSLIHFLGGSVLS  156 (305)
T ss_dssp             CSEEEEECSSSSSHHHHHHHHHHHHTCEEEC
T ss_pred             CCEEEEECCCCCcHHHHHHHHhhhcCceEEE
Confidence            3689999999999999999999998666653

>2g6b_A RAS-related protein RAB-26; G-protein, GTP analogue, structural genomics, structural genomics consortium, SGC, unknown function; HET: GNP; 2.00A {Homo sapiens} SCOP: c.37.1.8

Probab=94.77  E-value=0.27  Score=45.22  Aligned_cols=23  Identities=26%  Similarity=0.499  Sum_probs=20.4

Q ss_pred             EEEEECCCCchHHHHHHHHHHHc
Q 005987          180 VLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      .++|.|++|+||||++..+...-
T Consensus        12 ~i~v~G~~~~GKssli~~l~~~~   34 (180)
T 2g6b_A           12 KVMLVGDSGVGKTCLLVRFKDGA   34 (180)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEEECcCCCCHHHHHHHHHhCC
Confidence            58999999999999999998753

>3v9p_A DTMP kinase, thymidylate kinase; ssgcid, STRU genomics, seattle structural genomics center for infectious transferase; 1.90A {Burkholderia thailandensis}

Probab=94.77  E-value=0.021  Score=56.55  Aligned_cols=34  Identities=24%  Similarity=0.438  Sum_probs=25.6

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc-------CCcEEEEcCC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL-------GARLYEWDTP  212 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel-------g~~viE~nas  212 (666)
                      ..++|.||+|+||||.++.|++.+       |+.++....|
T Consensus        26 ~~I~~eG~~GsGKsT~~~~l~~~l~~~~~~~g~~v~~~rep   66 (227)
T 3v9p_A           26 KFITFEGIDGAGKTTHLQWFCDRLQERLGPAGRHVVVTREP   66 (227)
T ss_dssp             CEEEEECCC---CHHHHHHHHHHHHHHHGGGTCCEEEEESS
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHhhccccceeeeeecCC
Confidence            589999999999999999999988       6666655544

>4dhe_A Probable GTP-binding protein ENGB; melioidosis, RAS-like GTPase, cell division, cell cycle, SEP GTP-binding; 2.20A {Burkholderia thailandensis}

Probab=94.77  E-value=0.42  Score=45.85  Aligned_cols=23  Identities=13%  Similarity=0.453  Sum_probs=20.4

Q ss_pred             cEEEEECCCCchHHHHHHHHHHH
Q 005987          179 NVLVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAke  201 (666)
                      ..++|.|++|+||||++..+...
T Consensus        30 ~~i~v~G~~~~GKSslin~l~~~   52 (223)
T 4dhe_A           30 PEIAFAGRSNAGKSTAINVLCNQ   52 (223)
T ss_dssp             CEEEEEESCHHHHHHHHHHHTTC
T ss_pred             CEEEEEcCCCCCHHHHHHHHhCC
Confidence            36889999999999999998765

>4bas_A ADP-ribosylation factor, putative (small GTPase, putative); hydrolase; HET: GNP; 2.00A {Trypanosoma brucei TREU927}

Probab=94.77  E-value=0.41  Score=44.81  Aligned_cols=23  Identities=26%  Similarity=0.400  Sum_probs=20.2

Q ss_pred             cEEEEECCCCchHHHHHHHHHHH
Q 005987          179 NVLVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAke  201 (666)
                      ..++|.|++|+||||++..+...
T Consensus        18 ~ki~v~G~~~~GKSsl~~~l~~~   40 (199)
T 4bas_A           18 LQVVMCGLDNSGKTTIINQVKPA   40 (199)
T ss_dssp             EEEEEECCTTSCHHHHHHHHSCC
T ss_pred             cEEEEECCCCCCHHHHHHHHhcC
Confidence            46999999999999999988653

>1a7j_A Phosphoribulokinase; transferase, calvin cycle; 2.50A {Rhodobacter sphaeroides} SCOP: c.37.1.6

Probab=94.75  E-value=0.0084  Score=61.74  Aligned_cols=25  Identities=16%  Similarity=0.422  Sum_probs=20.3

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLG  203 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg  203 (666)
                      .++.|+||+|+||||+++.|++.++
T Consensus         6 ~iIgItG~sGSGKSTva~~L~~~lg   30 (290)
T 1a7j_A            6 PIISVTGSSGAGTSTVKHTFDQIFR   30 (290)
T ss_dssp             CEEEEESCC---CCTHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHh
Confidence            4799999999999999999999886

>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=94.73  E-value=0.028  Score=63.47  Aligned_cols=31  Identities=29%  Similarity=0.482  Sum_probs=25.9

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc---CCcEEEE
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL---GARLYEW  209 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel---g~~viE~  209 (666)
                      +.++|+|||||||||++..++..+   +..++-.
T Consensus       205 ~~~~I~G~pGTGKTt~i~~l~~~l~~~g~~Vl~~  238 (574)
T 3e1s_A          205 RLVVLTGGPGTGKSTTTKAVADLAESLGLEVGLC  238 (574)
T ss_dssp             SEEEEECCTTSCHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             CEEEEEcCCCCCHHHHHHHHHHHHHhcCCeEEEe
Confidence            589999999999999999998865   6666643

>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=94.70  E-value=0.019  Score=54.44  Aligned_cols=31  Identities=26%  Similarity=0.377  Sum_probs=25.4

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc---CCcEEEE
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL---GARLYEW  209 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel---g~~viE~  209 (666)
                      +.++|+||+|+||||++..|+..+   ++.+..+
T Consensus         7 ~~i~i~G~sGsGKTTl~~~l~~~l~~~g~~v~~i   40 (174)
T 1np6_A            7 PLLAFAAWSGTGKTTLLKKLIPALCARGIRPGLI   40 (174)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             eEEEEEeCCCCCHHHHHHHHHHhccccCCceeEE
Confidence            589999999999999999999875   5555443

>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=94.69  E-value=0.35  Score=45.52  Aligned_cols=22  Identities=23%  Similarity=0.391  Sum_probs=20.2

Q ss_pred             EEEEECCCCchHHHHHHHHHHH
Q 005987          180 VLVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAke  201 (666)
                      .++|.|++|+||||+++.++..
T Consensus        25 ki~~vG~~~vGKSsli~~l~~~   46 (190)
T 1m2o_B           25 KLLFLGLDNAGKTTLLHMLKND   46 (190)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            5899999999999999999874

>2lkc_A Translation initiation factor IF-2; NMR {Geobacillus stearothermophilus} PDB: 2lkd_A*

Probab=94.69  E-value=0.8  Score=41.82  Aligned_cols=23  Identities=30%  Similarity=0.430  Sum_probs=20.4

Q ss_pred             cEEEEECCCCchHHHHHHHHHHH
Q 005987          179 NVLVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAke  201 (666)
                      ..++|.|++|+||||++..+...
T Consensus         9 ~~i~v~G~~~~GKssl~~~l~~~   31 (178)
T 2lkc_A            9 PVVTIMGHVDHGKTTLLDAIRHS   31 (178)
T ss_dssp             CEEEEESCTTTTHHHHHHHHHTT
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            46999999999999999999764

>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=94.67  E-value=0.088  Score=50.64  Aligned_cols=22  Identities=32%  Similarity=0.522  Sum_probs=19.7

Q ss_pred             EEEEECCCCchHHHHHHHHHHH
Q 005987          180 VLVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAke  201 (666)
                      .++|.|++|+||||++..+...
T Consensus        27 ki~vvG~~~~GKSsLi~~l~~~   48 (217)
T 2f7s_A           27 KLLALGDSGVGKTTFLYRYTDN   48 (217)
T ss_dssp             EEEEESCTTSSHHHHHHHHHCS
T ss_pred             EEEEECcCCCCHHHHHHHHhcC
Confidence            4899999999999999998864

>1rj9_A FTSY, signal recognition protein; SRP-GTPase domain, heterodimer, nucleotide twinning, protein complex, protein transport; HET: GCP; 1.90A {Thermus aquaticus} SCOP: a.24.13.1 c.37.1.10 PDB: 2q9c_A* 2q9b_A* 2q9a_A* 1okk_D* 2xkv_D 2iyl_D* 2cnw_D* 2j7p_D*

Probab=94.65  E-value=0.021  Score=59.18  Aligned_cols=25  Identities=32%  Similarity=0.593  Sum_probs=22.9

Q ss_pred             ccEEEEECCCCchHHHHHHHHHHHc
Q 005987          178 TNVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       178 ~k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      +..+.|.||+||||||+++.||..+
T Consensus       102 g~vi~lvG~nGsGKTTll~~Lagll  126 (304)
T 1rj9_A          102 GRVVLVVGVNGVGKTTTIAKLGRYY  126 (304)
T ss_dssp             SSEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCcHHHHHHHHHHHH
Confidence            3689999999999999999999876

>4a2p_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2 RNA helicase, ATP and dsRNA binding antiviral signalling pathway; 3.00A {Anas platyrhynchos} PDB: 4a36_A*

Probab=94.62  E-value=0.48  Score=52.22  Aligned_cols=32  Identities=25%  Similarity=0.239  Sum_probs=23.8

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc--------CCcEEEEc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL--------GARLYEWD  210 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel--------g~~viE~n  210 (666)
                      +.+|+.+|+|+|||.++-..+.+.        +..++-+.
T Consensus        23 ~~~l~~~~tGsGKT~~~~~~~~~~~~~~~~~~~~~~lil~   62 (556)
T 4a2p_A           23 KNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLA   62 (556)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHHHHHHTCCSSCCCCEEEEC
T ss_pred             CCEEEEcCCCChHHHHHHHHHHHHHHhCcccCCCeEEEEe
Confidence            359999999999999877666554        55555553

>3e2i_A Thymidine kinase; Zn-binding, ATP-binding, DNA synthesis, nucleotide-B transferase; HET: MSE; 2.01A {Staphylococcus aureus}

Probab=94.62  E-value=0.036  Score=54.31  Aligned_cols=33  Identities=15%  Similarity=0.123  Sum_probs=23.4

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL---GARLYEWDT  211 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel---g~~viE~na  211 (666)
                      .+.+++||-|+||||.+-..+..+   +.+++-++.
T Consensus        29 ~I~vitG~M~sGKTT~Llr~~~r~~~~g~kvli~kp   64 (219)
T 3e2i_A           29 WIECITGSMFSGKSEELIRRLRRGIYAKQKVVVFKP   64 (219)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHHHHHHTTCCEEEEEE
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHcCCceEEEEe
Confidence            689999999999999543334433   666665553

>2erx_A GTP-binding protein DI-RAS2; GTP hydrolysis, transport protein; HET: GDP; 1.65A {Homo sapiens} SCOP: c.37.1.8

Probab=94.60  E-value=0.23  Score=45.09  Aligned_cols=22  Identities=27%  Similarity=0.475  Sum_probs=19.7

Q ss_pred             EEEEECCCCchHHHHHHHHHHH
Q 005987          180 VLVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAke  201 (666)
                      .+++.|++|+||||++..++..
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            4889999999999999999863

>2bcg_Y Protein YP2, GTP-binding protein YPT1; RABGTPase, geranylgeranylation, vesicular transport, protein transport; HET: GDP GER; 1.48A {Saccharomyces cerevisiae} SCOP: c.37.1.8 PDB: 1ukv_Y* 3cue_F* 1yzn_A* 3sfv_A* 2wwx_A 2fol_A* 3nkv_A* 3jza_A* 2rhd_A*

Probab=94.56  E-value=0.26  Score=46.74  Aligned_cols=23  Identities=26%  Similarity=0.551  Sum_probs=20.4

Q ss_pred             EEEEECCCCchHHHHHHHHHHHc
Q 005987          180 VLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      .++|.|++|+||||++..+...-
T Consensus        10 ki~v~G~~~~GKSsli~~l~~~~   32 (206)
T 2bcg_Y           10 KLLLIGNSGVGKSCLLLRFSDDT   32 (206)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHCC
T ss_pred             EEEEECCCCCCHHHHHHHHhcCC
Confidence            58999999999999999998753

>2ocp_A DGK, deoxyguanosine kinase; protein-nucleotide complex, transferase; HET: DTP; 2.80A {Homo sapiens} SCOP: c.37.1.1

Probab=94.54  E-value=0.023  Score=56.41  Aligned_cols=25  Identities=28%  Similarity=0.420  Sum_probs=23.4

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLG  203 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg  203 (666)
                      ..++|.|++|+||||+++.|++.+.
T Consensus         3 ~~i~~~G~~g~GKtt~~~~l~~~l~   27 (241)
T 2ocp_A            3 RRLSIEGNIAVGKSTFVKLLTKTYP   27 (241)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHHCT
T ss_pred             eEEEEEcCCCCCHHHHHHHHHHHcC
Confidence            5799999999999999999999993

>3cbq_A GTP-binding protein REM 2; FLJ38964A, structural genomics consortium, SGC, GDP, membrane, nucleotide-binding, nucleotide binding protein; HET: GDP; 1.82A {Homo sapiens}

Probab=94.50  E-value=0.15  Score=48.51  Aligned_cols=21  Identities=24%  Similarity=0.564  Sum_probs=18.9

Q ss_pred             EEEEECCCCchHHHHHHHHHH
Q 005987          180 VLVITGQAGVGKTATVRQIAS  200 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAk  200 (666)
                      -++|.|++|+||||++..++.
T Consensus        25 ki~vvG~~~vGKSsLi~~l~~   45 (195)
T 3cbq_A           25 KVMLVGESGVGKSTLAGTFGG   45 (195)
T ss_dssp             EEEEECSTTSSHHHHHHHTCC
T ss_pred             EEEEECCCCCCHHHHHHHHHh
Confidence            589999999999999999853

>3llu_A RAS-related GTP-binding protein C; structural genomics consortium, SGC, cytoplasm, nucleotide-binding, nucleus, phosphoprotein; HET: GNP; 1.40A {Homo sapiens} PDB: 2q3f_A*

Probab=94.42  E-value=0.46  Score=44.81  Aligned_cols=23  Identities=13%  Similarity=0.330  Sum_probs=20.1

Q ss_pred             EEEEECCCCchHHHHHHHHHHHc
Q 005987          180 VLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      -++|.|++|+||||+++.+....
T Consensus        22 ki~~vG~~~vGKTsLi~~l~~~~   44 (196)
T 3llu_A           22 RILLMGLRRSGKSSIQKVVFHKM   44 (196)
T ss_dssp             EEEEEESTTSSHHHHHHHHHSCC
T ss_pred             EEEEECCCCCCHHHHHHHHHhcC
Confidence            59999999999999999877643

>2hxs_A RAB-26, RAS-related protein RAB-28; GTPase, signaling protein; HET: G3D; 1.10A {Homo sapiens} PDB: 2hy4_A* 3e5h_A*

Probab=94.36  E-value=0.37  Score=44.17  Aligned_cols=22  Identities=27%  Similarity=0.415  Sum_probs=19.8

Q ss_pred             EEEEECCCCchHHHHHHHHHHH
Q 005987          180 VLVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAke  201 (666)
                      .++|.|++|+||||++..+...
T Consensus         8 ki~v~G~~~~GKssl~~~l~~~   29 (178)
T 2hxs_A            8 KIVVLGDGASGKTSLTTCFAQE   29 (178)
T ss_dssp             EEEEECCTTSSHHHHHHHHHGG
T ss_pred             EEEEECcCCCCHHHHHHHHHhC
Confidence            5899999999999999999754

>4dkx_A RAS-related protein RAB-6A; GTP binding fold, membrane trafficking, GTP, cytosol, protei transport; HET: GDP; 1.90A {Homo sapiens} PDB: 3bbp_A*

Probab=94.36  E-value=0.26  Score=48.13  Aligned_cols=21  Identities=33%  Similarity=0.545  Sum_probs=19.0

Q ss_pred             EEEECCCCchHHHHHHHHHHH
Q 005987          181 LVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       181 LLL~GPpG~GKTtla~~LAke  201 (666)
                      ++|.|.+|||||+++..+...
T Consensus        16 ivlvGd~~VGKTsLi~r~~~~   36 (216)
T 4dkx_A           16 LVFLGEQSVGKTSLITRFMYD   36 (216)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECcCCcCHHHHHHHHHhC
Confidence            788899999999999998764

>2gco_A H9, RHO-related GTP-binding protein RHOC; GTPase,signaling protein, signaling Pro; HET: GNP; 1.40A {Homo sapiens} PDB: 2gcn_A* 2gcp_A* 1z2c_A* 1x86_B 2rgn_C* 1lb1_B 1s1c_A* 3kz1_E* 3lxr_A* 3lwn_A* 3lw8_A* 1cxz_A* 1a2b_A* 1ow3_B* 1ftn_A* 1cc0_A* 3msx_A* 1xcg_B 3t06_B 1tx4_B* ...

Probab=94.32  E-value=0.57  Score=44.35  Aligned_cols=23  Identities=30%  Similarity=0.416  Sum_probs=20.6

Q ss_pred             EEEEECCCCchHHHHHHHHHHHc
Q 005987          180 VLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      .++|.|++|+||||++..++..-
T Consensus        27 ki~vvG~~~~GKSsli~~l~~~~   49 (201)
T 2gco_A           27 KLVIVGDGACGKTCLLIVFSKDQ   49 (201)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHSS
T ss_pred             EEEEECCCCCCHHHHHHHHHhCc
Confidence            58999999999999999998753

>1g5t_A COB(I)alamin adenosyltransferase; P-loop protein, cobalamin biosynthesis, RECA fold; HET: ATP; 1.80A {Salmonella typhimurium} SCOP: c.37.1.11 PDB: 1g5r_A* 1g64_A*

Probab=94.31  E-value=0.4  Score=46.14  Aligned_cols=31  Identities=19%  Similarity=0.263  Sum_probs=26.6

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc---CCcEEEE
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL---GARLYEW  209 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel---g~~viE~  209 (666)
                      ..+++++++|.||||+|-.+|-..   |++|.-+
T Consensus        29 g~i~v~tG~GkGKTTaA~GlalRA~g~G~rV~~v   62 (196)
T 1g5t_A           29 GIIIVFTGNGKGKTTAAFGTAARAVGHGKNVGVV   62 (196)
T ss_dssp             CCEEEEESSSSCHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEE
Confidence            468999999999999999888765   8888777

>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=94.30  E-value=0.023  Score=60.55  Aligned_cols=24  Identities=25%  Similarity=0.624  Sum_probs=22.5

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      ..++|.||+|+||||++++++..+
T Consensus       137 ~~i~ivG~~GsGKTTll~~l~~~~  160 (372)
T 2ewv_A          137 GLILVTGPTGSGKSTTIASMIDYI  160 (372)
T ss_dssp             EEEEEECSSSSSHHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHhhc
Confidence            589999999999999999999876

>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=94.30  E-value=0.051  Score=59.07  Aligned_cols=34  Identities=29%  Similarity=0.445  Sum_probs=28.7

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcCC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL---GARLYEWDTP  212 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel---g~~viE~nas  212 (666)
                      +.++|.||+|+||||++..||..+   |.++.-+.+.
T Consensus       100 ~vI~ivG~~GvGKTTla~~La~~l~~~G~kVllv~~D  136 (432)
T 2v3c_C          100 NVILLVGIQGSGKTTTAAKLARYIQKRGLKPALIAAD  136 (432)
T ss_dssp             CCEEEECCSSSSTTHHHHHHHHHHHHHHCCEEEECCS
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEecc
Confidence            589999999999999999999876   5777766653

>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=94.27  E-value=0.031  Score=63.80  Aligned_cols=24  Identities=42%  Similarity=0.603  Sum_probs=20.6

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      +..+|.||||||||+++..++..+
T Consensus       196 ~~~li~GppGTGKT~~~~~~i~~l  219 (624)
T 2gk6_A          196 PLSLIQGPPGTGKTVTSATIVYHL  219 (624)
T ss_dssp             SEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CCeEEECCCCCCHHHHHHHHHHHH
Confidence            478999999999999988777664

>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=94.25  E-value=0.012  Score=59.32  Aligned_cols=28  Identities=18%  Similarity=0.255  Sum_probs=24.6

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc-CCcE
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL-GARL  206 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel-g~~v  206 (666)
                      ..++|.|++|+||||+++.|++.+ ++.+
T Consensus        25 ~~I~ieG~~GsGKST~~~~L~~~l~~~~~   53 (263)
T 1p5z_B           25 KKISIEGNIAAGKSTFVNILKQLCEDWEV   53 (263)
T ss_dssp             EEEEEECSTTSSHHHHHTTTGGGCTTEEE
T ss_pred             eEEEEECCCCCCHHHHHHHHHHhcCCCEE
Confidence            589999999999999999999998 4433

>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=94.22  E-value=0.23  Score=54.06  Aligned_cols=33  Identities=18%  Similarity=0.037  Sum_probs=28.0

Q ss_pred             EEEEECCCCchHHHHHHHHHHHcCCcEEEEcCC
Q 005987          180 VLVITGQAGVGKTATVRQIASHLGARLYEWDTP  212 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkelg~~viE~nas  212 (666)
                      .+||.||+|+|||.++-.++..++..++-+-+.
T Consensus       110 ~~ll~~~TGsGKT~~~l~~i~~~~~~~Lvl~P~  142 (472)
T 2fwr_A          110 RGCIVLPTGSGKTHVAMAAINELSTPTLIVVPT  142 (472)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHCSCEEEEESS
T ss_pred             CEEEEeCCCCCHHHHHHHHHHHcCCCEEEEECC
Confidence            599999999999999998888888777766543

>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=94.22  E-value=0.021  Score=56.76  Aligned_cols=25  Identities=24%  Similarity=0.367  Sum_probs=22.6

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLG  203 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg  203 (666)
                      ..+.|.||+|+||||++++++.-+.
T Consensus        32 e~~~iiG~nGsGKSTLl~~l~Gl~~   56 (235)
T 3tif_A           32 EFVSIMGPSGSGKSTMLNIIGCLDK   56 (235)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTTSSC
T ss_pred             CEEEEECCCCCcHHHHHHHHhcCCC
Confidence            5899999999999999999998763

>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=94.17  E-value=0.022  Score=57.82  Aligned_cols=25  Identities=24%  Similarity=0.387  Sum_probs=22.2

Q ss_pred             ccEEEEECCCCchHHHHHHHHHHHc
Q 005987          178 TNVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       178 ~k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      ..+++|+||||+||||++..+|..+
T Consensus        30 G~i~~i~G~~GsGKTtl~~~l~~~~   54 (279)
T 1nlf_A           30 GTVGALVSPGGAGKSMLALQLAAQI   54 (279)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHHH
Confidence            4689999999999999999998754

>1wb9_A DNA mismatch repair protein MUTS; DNA-binding, ATP-binding, DNA binding, DNA repair, mismatch recognition; HET: DNA ADP; 2.10A {Escherichia coli} SCOP: a.113.1.1 c.37.1.12 c.55.6.1 d.75.2.1 PDB: 1wbb_A* 1e3m_A* 1oh5_A* 1oh6_A* 1oh7_A* 1oh8_A* 1w7a_A* 2wtu_A* 1wbd_A* 1ng9_A* 3k0s_A*

Probab=94.14  E-value=0.26  Score=57.70  Aligned_cols=24  Identities=38%  Similarity=0.433  Sum_probs=21.6

Q ss_pred             ccEEEEECCCCchHHHHHHHHHHH
Q 005987          178 TNVLVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       178 ~k~LLL~GPpG~GKTtla~~LAke  201 (666)
                      +.+++|+||.|+||||+++.++--
T Consensus       607 g~i~~ItGpNGsGKSTlLr~iagl  630 (800)
T 1wb9_A          607 RRMLIITGPNMGGKSTYMRQTALI  630 (800)
T ss_dssp             SCEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CcEEEEECCCCCChHHHHHHHHHH
Confidence            368999999999999999999864

>2oap_1 GSPE-2, type II secretion system protein; hexameric ATPase, hydrolase; HET: ANP; 2.95A {Archaeoglobus fulgidus} PDB: 2oaq_1

Probab=94.14  E-value=0.028  Score=62.54  Aligned_cols=32  Identities=19%  Similarity=0.360  Sum_probs=25.5

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCC--cEEEEc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGA--RLYEWD  210 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~--~viE~n  210 (666)
                      .+++|.||+|+||||++++++..+..  .++.+.
T Consensus       261 ~~i~I~GptGSGKTTlL~aL~~~i~~~~giitie  294 (511)
T 2oap_1          261 FSAIVVGETASGKTTTLNAIMMFIPPDAKVVSIE  294 (511)
T ss_dssp             CCEEEEESTTSSHHHHHHHHGGGSCTTCCEEEEE
T ss_pred             CEEEEECCCCCCHHHHHHHHHhhCCCCCCEEEEc
Confidence            46999999999999999999988732  344444

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus}

Probab=94.13  E-value=0.67  Score=50.90  Aligned_cols=32  Identities=22%  Similarity=0.289  Sum_probs=24.0

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc--------CCcEEEEc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL--------GARLYEWD  210 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel--------g~~viE~n  210 (666)
                      +.+|+.+|+|+|||.++-..+.+.        +..++-+-
T Consensus        20 ~~~l~~~~tGsGKT~~~~~~~~~~~~~~~~~~~~~~lil~   59 (555)
T 3tbk_A           20 KNTIICAPTGCGKTFVSLLICEHHLKKFPCGQKGKVVFFA   59 (555)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHHHHHHTCCSSCCCCEEEEC
T ss_pred             CCEEEEeCCCChHHHHHHHHHHHHHHhcccCCCCEEEEEe
Confidence            469999999999999877666554        55555554

>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=94.13  E-value=0.053  Score=54.01  Aligned_cols=35  Identities=26%  Similarity=0.539  Sum_probs=27.9

Q ss_pred             ccEEEEECCCCchHHHHHHHHHHHc---CCc-EEEEcCC
Q 005987          178 TNVLVITGQAGVGKTATVRQIASHL---GAR-LYEWDTP  212 (666)
Q Consensus       178 ~k~LLL~GPpG~GKTtla~~LAkel---g~~-viE~nas  212 (666)
                      +..++|.||+|+||||.++.|++.+   |+. ++....|
T Consensus        27 ~~~i~~eG~~GsGKsT~~~~l~~~l~~~~~~~~~~~rep   65 (236)
T 3lv8_A           27 AKFIVIEGLEGAGKSTAIQVVVETLQQNGIDHITRTREP   65 (236)
T ss_dssp             CCEEEEEESTTSCHHHHHHHHHHHHHHTTCCCEEEEESS
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHhcCCCeeeeecCC
Confidence            3689999999999999999999987   556 4444433

>2qu8_A Putative nucleolar GTP-binding protein 1; GTPase, malaria, structural genomics, structural genomics consortium, SGC, unknown function; HET: GDP; 2.01A {Plasmodium falciparum}

Probab=94.13  E-value=0.87  Score=44.10  Aligned_cols=23  Identities=17%  Similarity=0.507  Sum_probs=20.3

Q ss_pred             cEEEEECCCCchHHHHHHHHHHH
Q 005987          179 NVLVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAke  201 (666)
                      ..++|.|++|+||||++..++..
T Consensus        30 ~kI~vvG~~~vGKSsLin~l~~~   52 (228)
T 2qu8_A           30 KTIILSGAPNVGKSSFMNIVSRA   52 (228)
T ss_dssp             EEEEEECSTTSSHHHHHHHHTTT
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            46999999999999999998764

>2pcj_A ABC transporter, lipoprotein-releasing system ATP-binding protein; structural genomics; 1.70A {Aquifex aeolicus} PDB: 2pcl_A

Probab=94.13  E-value=0.021  Score=56.42  Aligned_cols=25  Identities=20%  Similarity=0.306  Sum_probs=22.4

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLG  203 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg  203 (666)
                      .++.|.||+|+||||++++++.-+.
T Consensus        31 e~~~iiG~nGsGKSTLl~~l~Gl~~   55 (224)
T 2pcj_A           31 EFVSIIGASGSGKSTLLYILGLLDA   55 (224)
T ss_dssp             CEEEEEECTTSCHHHHHHHHTTSSC
T ss_pred             CEEEEECCCCCCHHHHHHHHhcCCC
Confidence            5799999999999999999997663

>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=94.09  E-value=0.029  Score=52.70  Aligned_cols=26  Identities=31%  Similarity=0.395  Sum_probs=23.5

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGA  204 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~  204 (666)
                      ...+|+||.|+||||++.+|+-.++.
T Consensus        27 g~~~i~G~NGsGKStll~ai~~~l~~   52 (182)
T 3kta_A           27 GFTAIVGANGSGKSNIGDAILFVLGG   52 (182)
T ss_dssp             SEEEEEECTTSSHHHHHHHHHHHTTC
T ss_pred             CcEEEECCCCCCHHHHHHHHHHHHcC
Confidence            48899999999999999999998863

>2o52_A RAS-related protein RAB-4B; G-protein, GDP, structural genomics, structural genomics consortium, SGC, protein transport; HET: GDP; 2.20A {Homo sapiens}

Probab=94.09  E-value=0.23  Score=47.21  Aligned_cols=22  Identities=27%  Similarity=0.570  Sum_probs=19.1

Q ss_pred             EEEEECCCCchHHHHHHHHHHH
Q 005987          180 VLVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAke  201 (666)
                      .++|.|++|+||||++..+...
T Consensus        27 ki~v~G~~~~GKSsLi~~l~~~   48 (200)
T 2o52_A           27 KFLVIGSAGTGKSCLLHQFIEN   48 (200)
T ss_dssp             EEEEEESTTSSHHHHHHHHHC-
T ss_pred             EEEEECcCCCCHHHHHHHHHhC
Confidence            5889999999999999998743

>2gf0_A GTP-binding protein DI-RAS1; GDP/GTP binding, GTP hydrolysis, structural genomics, structural genomics consortium, SGC, transport protein; HET: GDP; 1.90A {Homo sapiens} SCOP: c.37.1.8

Probab=94.06  E-value=0.32  Score=45.64  Aligned_cols=22  Identities=32%  Similarity=0.525  Sum_probs=20.0

Q ss_pred             EEEEECCCCchHHHHHHHHHHH
Q 005987          180 VLVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAke  201 (666)
                      .++|.|++|+||||++..+...
T Consensus        10 ki~vvG~~~~GKSsli~~l~~~   31 (199)
T 2gf0_A           10 RVVVFGAGGVGKSSLVLRFVKG   31 (199)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCcHHHHHHHHHcC
Confidence            5899999999999999999874

>3tmk_A Thymidylate kinase; phosphotransferase; HET: T5A; 2.00A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 2tmk_A* 1tmk_A*

Probab=94.05  E-value=0.043  Score=53.88  Aligned_cols=31  Identities=19%  Similarity=0.259  Sum_probs=26.7

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEEEE
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLYEW  209 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~viE~  209 (666)
                      ..++|.||+|+||||.++.|++.++..+..+
T Consensus         6 ~~i~~eG~~g~GKst~~~~l~~~l~~~~~~~   36 (216)
T 3tmk_A            6 KLILIEGLDRTGKTTQCNILYKKLQPNCKLL   36 (216)
T ss_dssp             CEEEEEECSSSSHHHHHHHHHHHHCSSEEEE
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhcccceEE
Confidence            5899999999999999999999998644333

>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=94.03  E-value=0.035  Score=61.52  Aligned_cols=26  Identities=12%  Similarity=0.058  Sum_probs=24.3

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGA  204 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~  204 (666)
                      ..++|+|++||||||++++||+.|+.
T Consensus       396 ~~I~l~GlsGsGKSTIa~~La~~L~~  421 (511)
T 1g8f_A          396 FSIVLGNSLTVSREQLSIALLSTFLQ  421 (511)
T ss_dssp             EEEEECTTCCSCHHHHHHHHHHHHTT
T ss_pred             eEEEecccCCCCHHHHHHHHHHHHHH
Confidence            47999999999999999999999985

>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=94.01  E-value=0.025  Score=56.35  Aligned_cols=24  Identities=21%  Similarity=0.569  Sum_probs=22.2

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      ..+.|.||+|+||||++++|+..+
T Consensus        32 e~~~i~G~nGsGKSTLl~~l~Gl~   55 (237)
T 2cbz_A           32 ALVAVVGQVGCGKSSLLSALLAEM   55 (237)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTTCS
T ss_pred             CEEEEECCCCCCHHHHHHHHhcCC
Confidence            589999999999999999998875

>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=94.00  E-value=0.028  Score=58.45  Aligned_cols=25  Identities=28%  Similarity=0.508  Sum_probs=22.9

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLG  203 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg  203 (666)
                      .++.|.||+|+||||++++|+..+.
T Consensus        91 ~ivgI~G~sGsGKSTL~~~L~gll~  115 (312)
T 3aez_A           91 FIIGVAGSVAVGKSTTARVLQALLA  115 (312)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHHHH
T ss_pred             EEEEEECCCCchHHHHHHHHHhhcc
Confidence            5899999999999999999999873

>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=93.98  E-value=0.027  Score=58.27  Aligned_cols=25  Identities=32%  Similarity=0.571  Sum_probs=23.2

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLG  203 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg  203 (666)
                      .++.|.||+|+||||+++.|+..++
T Consensus        81 ~iigI~G~~GsGKSTl~~~L~~~l~  105 (308)
T 1sq5_A           81 YIISIAGSVAVGKSTTARVLQALLS  105 (308)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHHHT
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHh
Confidence            5899999999999999999999876

>2ged_A SR-beta, signal recognition particle receptor beta subunit; protein transport, G protein, proline isomerization, circular permutation; 2.20A {Saccharomyces cerevisiae}

Probab=93.94  E-value=0.051  Score=51.13  Aligned_cols=24  Identities=21%  Similarity=0.411  Sum_probs=21.4

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      ..++|.|++|+||||++..++...
T Consensus        49 ~~i~vvG~~g~GKSsll~~l~~~~   72 (193)
T 2ged_A           49 PSIIIAGPQNSGKTSLLTLLTTDS   72 (193)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHSS
T ss_pred             CEEEEECCCCCCHHHHHHHHhcCC
Confidence            469999999999999999998764

>2f1r_A Molybdopterin-guanine dinucleotide biosynthesis protein B (MOBB); structural genomics, PSI, protein structure initiative; 2.10A {Archaeoglobus fulgidus}

Probab=93.92  E-value=0.023  Score=53.72  Aligned_cols=24  Identities=29%  Similarity=0.472  Sum_probs=22.2

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      +.+.|.||+|+||||+++.|+..+
T Consensus         3 ~~v~IvG~SGsGKSTL~~~L~~~~   26 (171)
T 2f1r_A            3 LILSIVGTSDSGKTTLITRMMPIL   26 (171)
T ss_dssp             CEEEEEESCHHHHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHh
Confidence            478999999999999999999987

>3cpj_B GTP-binding protein YPT31/YPT8; RAB GTPase, prenylation, vesicular transport, acetylation, golgi apparatus, lipoprotein, membrane; HET: GDP; 2.35A {Saccharomyces cerevisiae}

Probab=93.92  E-value=0.34  Score=46.85  Aligned_cols=23  Identities=26%  Similarity=0.554  Sum_probs=20.4

Q ss_pred             EEEEECCCCchHHHHHHHHHHHc
Q 005987          180 VLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      .++|.|++|+||||++..++..-
T Consensus        15 ki~v~G~~~vGKSsli~~l~~~~   37 (223)
T 3cpj_B           15 KIVLIGDSGVGKSNLLSRFTKNE   37 (223)
T ss_dssp             EEEEESCTTSSHHHHHHHHHHCC
T ss_pred             EEEEECcCCCCHHHHHHHHhcCC
Confidence            58999999999999999998753

>3b85_A Phosphate starvation-inducible protein; PHOH2, ATPase, PFAM: PF02562, ST genomics, PSI-2, protein structure initiative; 2.35A {Corynebacterium glutamicum atcc 13032}

Probab=93.92  E-value=0.023  Score=55.43  Aligned_cols=23  Identities=30%  Similarity=0.315  Sum_probs=21.0

Q ss_pred             cEEEEECCCCchHHHHHHHHHHH
Q 005987          179 NVLVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAke  201 (666)
                      .++.|.||+|+||||++++++..
T Consensus        23 e~~~liG~nGsGKSTLl~~l~Gl   45 (208)
T 3b85_A           23 TIVFGLGPAGSGKTYLAMAKAVQ   45 (208)
T ss_dssp             SEEEEECCTTSSTTHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHhcC
Confidence            47899999999999999999875

>3q3j_B RHO-related GTP-binding protein RHO6; RAS-binding domain, plexin, small GTPase, structural genomic consortium, SGC; HET: GNP; 1.97A {Homo sapiens} PDB: 2rex_B* 2cls_A*

Probab=93.91  E-value=0.83  Score=43.86  Aligned_cols=22  Identities=36%  Similarity=0.557  Sum_probs=20.1

Q ss_pred             EEEEECCCCchHHHHHHHHHHH
Q 005987          180 VLVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAke  201 (666)
                      -++|.|++|+||||++..+...
T Consensus        29 ki~vvG~~~vGKSsL~~~l~~~   50 (214)
T 3q3j_B           29 KLVLVGDVQCGKTAMLQVLAKD   50 (214)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECcCCCCHHHHHHHHhcC
Confidence            5899999999999999999875

>2hf9_A Probable hydrogenase nickel incorporation protein HYPB; alpha and beta protein; HET: GSP; 1.90A {Methanocaldococcus jannaschii} PDB: 2hf8_A*

Probab=93.90  E-value=0.046  Score=53.09  Aligned_cols=42  Identities=17%  Similarity=0.351  Sum_probs=30.2

Q ss_pred             cCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc
Q 005987          153 VQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       153 g~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      -++...+.++..+..      .+.  ..++|.|++|+||||++..++..+
T Consensus        21 ~~~~~a~~~r~~~~~------~~~--~~i~ivG~~gvGKTtl~~~l~~~~   62 (226)
T 2hf9_A           21 ANKRLADKNRKLLNK------HGV--VAFDFMGAIGSGKTLLIEKLIDNL   62 (226)
T ss_dssp             HHHHHHHHHHHHHHH------TTC--EEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHh------CCC--eEEEEEcCCCCCHHHHHHHHHHHh
Confidence            345555666665543      222  468888999999999999999886

>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=93.87  E-value=0.041  Score=61.31  Aligned_cols=25  Identities=28%  Similarity=0.461  Sum_probs=23.3

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLG  203 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg  203 (666)
                      .+++|.|+||+||||+++.||+.++
T Consensus        36 ~lIvlvGlpGSGKSTia~~La~~L~   60 (520)
T 2axn_A           36 TVIVMVGLPARGKTYISKKLTRYLN   60 (520)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHh
Confidence            5899999999999999999999984

>1b0u_A Histidine permease; ABC transporter, transport protein; HET: ATP; 1.50A {Salmonella typhimurium} SCOP: c.37.1.12

Probab=93.82  E-value=0.027  Score=56.95  Aligned_cols=25  Identities=32%  Similarity=0.444  Sum_probs=22.4

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLG  203 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg  203 (666)
                      .++.|.||+|+||||++++++.-+.
T Consensus        33 e~~~liG~nGsGKSTLlk~l~Gl~~   57 (262)
T 1b0u_A           33 DVISIIGSSGSGKSTFLRCINFLEK   57 (262)
T ss_dssp             CEEEEECCTTSSHHHHHHHHTTSSC
T ss_pred             CEEEEECCCCCCHHHHHHHHhcCCC
Confidence            5899999999999999999998663

>2onk_A Molybdate/tungstate ABC transporter, ATP-binding protein; membrane protein; 3.10A {Archaeoglobus fulgidus} SCOP: c.37.1.12

Probab=93.79  E-value=0.031  Score=55.84  Aligned_cols=25  Identities=28%  Similarity=0.445  Sum_probs=22.5

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLG  203 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg  203 (666)
                      .++.|.||+|+||||++++++.-+.
T Consensus        25 e~~~liG~nGsGKSTLl~~l~Gl~~   49 (240)
T 2onk_A           25 DYCVLLGPTGAGKSVFLELIAGIVK   49 (240)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHTSSC
T ss_pred             EEEEEECCCCCCHHHHHHHHhCCCC
Confidence            4789999999999999999998763

>1svi_A GTP-binding protein YSXC; ENGB, GTPase, GDP, hydrolase; HET: GDP; 1.95A {Bacillus subtilis} SCOP: c.37.1.8 PDB: 1sul_A* 1svw_A*

Probab=93.78  E-value=0.32  Score=45.55  Aligned_cols=23  Identities=17%  Similarity=0.491  Sum_probs=20.4

Q ss_pred             cEEEEECCCCchHHHHHHHHHHH
Q 005987          179 NVLVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAke  201 (666)
                      ..++|.|++|+||||++..+...
T Consensus        24 ~~i~v~G~~~~GKSsli~~l~~~   46 (195)
T 1svi_A           24 PEIALAGRSNVGKSSFINSLINR   46 (195)
T ss_dssp             CEEEEEEBTTSSHHHHHHHHHTC
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            36999999999999999999764

>1sgw_A Putative ABC transporter; structural genomics, P protein structure initiative, southeast collaboratory for S genomics, secsg; 1.70A {Pyrococcus furiosus} SCOP: c.37.1.12

Probab=93.73  E-value=0.027  Score=55.27  Aligned_cols=25  Identities=36%  Similarity=0.623  Sum_probs=22.3

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLG  203 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg  203 (666)
                      .++.|.||+|+||||++++++.-+.
T Consensus        36 e~~~iiG~NGsGKSTLlk~l~Gl~~   60 (214)
T 1sgw_A           36 NVVNFHGPNGIGKTTLLKTISTYLK   60 (214)
T ss_dssp             CCEEEECCTTSSHHHHHHHHTTSSC
T ss_pred             CEEEEECCCCCCHHHHHHHHhcCCC
Confidence            4789999999999999999988763

>4tmk_A Protein (thymidylate kinase); ATP:DTMP phosphotransferase, transferase; HET: T5A; 1.98A {Escherichia coli} SCOP: c.37.1.1 PDB: 5tmp_A*

Probab=93.73  E-value=0.07  Score=52.22  Aligned_cols=34  Identities=29%  Similarity=0.451  Sum_probs=27.3

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc---CC-cEEEEcCC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL---GA-RLYEWDTP  212 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel---g~-~viE~nas  212 (666)
                      ..++|.|++|+||||.++.|++.+   |+ .++....|
T Consensus         4 ~~i~~eG~~gsGKsT~~~~l~~~l~~~~~~~v~~~rep   41 (213)
T 4tmk_A            4 KYIVIEGLEGAGKTTARNVVVETLEQLGIRDMVFTREP   41 (213)
T ss_dssp             CEEEEEECTTSCHHHHHHHHHHHHHHTTCCCEEEEESS
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHcCCCcceeeeCC
Confidence            589999999999999999999987   55 55444433

>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=93.73  E-value=0.029  Score=59.43  Aligned_cols=24  Identities=38%  Similarity=0.612  Sum_probs=22.3

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      ..+.|.||+||||||++++||.-+
T Consensus        31 e~~~llGpsGsGKSTLLr~iaGl~   54 (359)
T 3fvq_A           31 EILFIIGASGCGKTTLLRCLAGFE   54 (359)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHTSS
T ss_pred             CEEEEECCCCchHHHHHHHHhcCC
Confidence            589999999999999999999876

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19

Probab=93.72  E-value=0.24  Score=47.80  Aligned_cols=21  Identities=29%  Similarity=0.251  Sum_probs=16.7

Q ss_pred             cEEEEECCCCchHHHHHHHHH
Q 005987          179 NVLVITGQAGVGKTATVRQIA  199 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LA  199 (666)
                      +.+++.+|+|+|||.++-..+
T Consensus        42 ~~~lv~a~TGsGKT~~~~~~~   62 (219)
T 1q0u_A           42 ESMVGQSQTGTGKTHAYLLPI   62 (219)
T ss_dssp             CCEEEECCSSHHHHHHHHHHH
T ss_pred             CCEEEECCCCChHHHHHHHHH
Confidence            468999999999999754433

>2r2a_A Uncharacterized protein; zonular occludens toxin, structural genomics, APC84050.2, PS protein structure initiative; HET: MSE; 1.82A {Neisseria meningitidis MC58}

Probab=93.71  E-value=0.037  Score=53.61  Aligned_cols=23  Identities=30%  Similarity=0.557  Sum_probs=19.4

Q ss_pred             cEEEEECCCCchHHHHHHHHHHH
Q 005987          179 NVLVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAke  201 (666)
                      -+.|++|+||+|||+.+..++.+
T Consensus         6 mi~l~tG~pGsGKT~~a~~~~~~   28 (199)
T 2r2a_A            6 EICLITGTPGSGKTLKMVSMMAN   28 (199)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHH
T ss_pred             eEEEEEeCCCCCHHHHHHHHHHH
Confidence            37899999999999998776544

>2zu0_C Probable ATP-dependent transporter SUFC; iron-sulfur cluster, ABC-ATPase, ATP-binding, cytoplasm, nucleotide-binding; HET: MES; 2.20A {Escherichia coli} PDB: 2d3w_A

Probab=93.71  E-value=0.036  Score=56.24  Aligned_cols=23  Identities=30%  Similarity=0.476  Sum_probs=21.5

Q ss_pred             cEEEEECCCCchHHHHHHHHHHH
Q 005987          179 NVLVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAke  201 (666)
                      .++.|.||+|+||||++++|+.-
T Consensus        47 e~~~l~G~NGsGKSTLlk~l~Gl   69 (267)
T 2zu0_C           47 EVHAIMGPNGSGKSTLSATLAGR   69 (267)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHTC
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            58999999999999999999985

>1c9k_A COBU, adenosylcobinamide kinase; alpha/beta structure rossmann fold P-loop, transferase; HET: 5GP; 2.20A {Salmonella typhimurium} SCOP: c.37.1.11 PDB: 1cbu_A

Probab=93.71  E-value=0.034  Score=52.99  Aligned_cols=31  Identities=19%  Similarity=0.344  Sum_probs=27.4

Q ss_pred             EEEECCCCchHHHHHHHHHHHcCCcEEEEcCC
Q 005987          181 LVITGQAGVGKTATVRQIASHLGARLYEWDTP  212 (666)
Q Consensus       181 LLL~GPpG~GKTtla~~LAkelg~~viE~nas  212 (666)
                      +|++|++|+|||++|..+|.. +..++.+...
T Consensus         2 ilV~Gg~~SGKS~~A~~la~~-~~~~~yiaT~   32 (180)
T 1c9k_A            2 ILVTGGARSGKSRHAEALIGD-APQVLYIATS   32 (180)
T ss_dssp             EEEEECTTSSHHHHHHHHHCS-CSSEEEEECC
T ss_pred             EEEECCCCCcHHHHHHHHHhc-CCCeEEEecC
Confidence            789999999999999999988 8888887654

>2d2e_A SUFC protein; ABC-ATPase, SUF protein, 310-helix, riken structural genomics/proteomics initiative, RSGI, structural genomics, binding; 1.70A {Thermus thermophilus} PDB: 2d2f_A*

Probab=93.70  E-value=0.034  Score=55.76  Aligned_cols=23  Identities=26%  Similarity=0.459  Sum_probs=21.4

Q ss_pred             cEEEEECCCCchHHHHHHHHHHH
Q 005987          179 NVLVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAke  201 (666)
                      .++.|.||+|+||||++++|+.-
T Consensus        30 e~~~l~G~nGsGKSTLlk~l~Gl   52 (250)
T 2d2e_A           30 EVHALMGPNGAGKSTLGKILAGD   52 (250)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHTC
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            58999999999999999999985

>3tqf_A HPR(Ser) kinase; transferase, hydrolase; 2.80A {Coxiella burnetii}

Probab=93.70  E-value=0.044  Score=51.83  Aligned_cols=28  Identities=29%  Similarity=0.462  Sum_probs=23.8

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEE
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLY  207 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~vi  207 (666)
                      +.+||+||+|+||||++..|.+. |+.++
T Consensus        17 ~gvli~G~SGaGKStlal~L~~r-G~~lv   44 (181)
T 3tqf_A           17 MGVLITGEANIGKSELSLALIDR-GHQLV   44 (181)
T ss_dssp             EEEEEEESSSSSHHHHHHHHHHT-TCEEE
T ss_pred             EEEEEEcCCCCCHHHHHHHHHHc-CCeEe
Confidence            57999999999999999999884 65543

>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=93.68  E-value=0.32  Score=45.14  Aligned_cols=22  Identities=27%  Similarity=0.445  Sum_probs=20.1

Q ss_pred             EEEEECCCCchHHHHHHHHHHH
Q 005987          180 VLVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAke  201 (666)
                      .++|.|++|+||||++..+...
T Consensus        23 ~i~v~G~~~~GKSsli~~l~~~   44 (181)
T 2h17_A           23 KVIIVGLDNAGKTTILYQFSMN   44 (181)
T ss_dssp             EEEEEEETTSSHHHHHHHHHTT
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            5899999999999999999864

>2pze_A Cystic fibrosis transmembrane conductance regulat; NBD, ABC transporter, CFTR, hydrolase; HET: ATP; 1.70A {Homo sapiens} PDB: 2pzg_A* 2pzf_A* 1ckx_A 1cky_A 1ckw_A 1ckz_A

Probab=93.65  E-value=0.031  Score=55.29  Aligned_cols=25  Identities=32%  Similarity=0.573  Sum_probs=22.7

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLG  203 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg  203 (666)
                      ..+.|.||.|+||||++++++..+.
T Consensus        35 e~~~i~G~nGsGKSTLl~~l~Gl~~   59 (229)
T 2pze_A           35 QLLAVAGSTGAGKTSLLMMIMGELE   59 (229)
T ss_dssp             CEEEEECCTTSSHHHHHHHHTTSSC
T ss_pred             CEEEEECCCCCCHHHHHHHHhCCCc
Confidence            5899999999999999999998763

>1g6h_A High-affinity branched-chain amino acid transport ATP-binding protein; beta-core domain; HET: ADP; 1.60A {Methanocaldococcus jannaschii} SCOP: c.37.1.12 PDB: 1gaj_A 1g9x_A*

Probab=93.63  E-value=0.031  Score=56.38  Aligned_cols=25  Identities=32%  Similarity=0.554  Sum_probs=22.5

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLG  203 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg  203 (666)
                      .++.|.||+|+||||++++++.-+.
T Consensus        34 e~~~liG~nGsGKSTLlk~l~Gl~~   58 (257)
T 1g6h_A           34 DVTLIIGPNGSGKSTLINVITGFLK   58 (257)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTTSSC
T ss_pred             CEEEEECCCCCCHHHHHHHHhCCCC
Confidence            5899999999999999999998763

>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=93.61  E-value=0.081  Score=55.82  Aligned_cols=32  Identities=34%  Similarity=0.568  Sum_probs=26.4

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc---CCcEEEEc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL---GARLYEWD  210 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel---g~~viE~n  210 (666)
                      ..+.|+|+||+||||++..|+..+   |.++.-+.
T Consensus        80 ~~I~i~G~~G~GKSTl~~~L~~~l~~~g~kV~vi~  114 (355)
T 3p32_A           80 HRVGITGVPGVGKSTAIEALGMHLIERGHRVAVLA  114 (355)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHHTTTCCEEEEE
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHhCCCceEEEe
Confidence            479999999999999999999886   66655443

>1ji0_A ABC transporter; ATP binding protein, structural genomics, PSI, protein structure initiative, midwest center for structural genomics, MCSG; HET: ATP; 2.00A {Thermotoga maritima} SCOP: c.37.1.12

Probab=93.60  E-value=0.031  Score=55.69  Aligned_cols=24  Identities=33%  Similarity=0.613  Sum_probs=22.1

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      .++.|.||+|+||||++++|+.-+
T Consensus        33 e~~~l~G~nGsGKSTLl~~l~Gl~   56 (240)
T 1ji0_A           33 QIVTLIGANGAGKTTTLSAIAGLV   56 (240)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             CEEEEECCCCCCHHHHHHHHhCCC
Confidence            589999999999999999999876

>3gfo_A Cobalt import ATP-binding protein CBIO 1; structural genomics, cell membrane, cobalt transport, hydrolase, ION transport; 2.30A {Clostridium perfringens atcc 13124}

Probab=93.59  E-value=0.032  Score=56.96  Aligned_cols=25  Identities=32%  Similarity=0.478  Sum_probs=22.5

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLG  203 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg  203 (666)
                      .++.|.||+|+||||++++|+.-+.
T Consensus        35 e~~~iiGpnGsGKSTLl~~l~Gl~~   59 (275)
T 3gfo_A           35 EVTAILGGNGVGKSTLFQNFNGILK   59 (275)
T ss_dssp             SEEEEECCTTSSHHHHHHHHTTSSC
T ss_pred             CEEEEECCCCCCHHHHHHHHHcCCC
Confidence            5899999999999999999998663

>1ewq_A DNA mismatch repair protein MUTS; multiple domains of protein, mostly mixed alpha-beta structures, one domain is entirely helical; HET: DNA; 2.20A {Thermus aquaticus} SCOP: a.113.1.1 c.37.1.12 c.55.6.1 d.75.2.1 PDB: 1nne_A* 1fw6_A* 1ewr_A*

Probab=93.59  E-value=0.33  Score=56.48  Aligned_cols=23  Identities=35%  Similarity=0.463  Sum_probs=21.0

Q ss_pred             cEEEEECCCCchHHHHHHHHHHH
Q 005987          179 NVLVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAke  201 (666)
                      .+++|+||+|+||||+++.+|--
T Consensus       577 ~i~~I~GpNGsGKSTlLr~iagl  599 (765)
T 1ewq_A          577 ELVLITGPNMAGKSTFLRQTALI  599 (765)
T ss_dssp             CEEEEESCSSSSHHHHHHHHHHH
T ss_pred             cEEEEECCCCCChHHHHHHHHhh
Confidence            68999999999999999999864

>2olj_A Amino acid ABC transporter; ABC domain, ATPase, hydrolase; HET: ADP; 2.05A {Geobacillus stearothermophilus} PDB: 2olk_A* 2ouk_A 2q0h_A* 3c4j_A* 3c41_J*

Probab=93.56  E-value=0.034  Score=56.35  Aligned_cols=25  Identities=28%  Similarity=0.464  Sum_probs=22.6

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLG  203 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg  203 (666)
                      .++.|.||+|+||||++++|+.-+.
T Consensus        51 ei~~liG~NGsGKSTLlk~l~Gl~~   75 (263)
T 2olj_A           51 EVVVVIGPSGSGKSTFLRCLNLLED   75 (263)
T ss_dssp             CEEEEECCTTSSHHHHHHHHTTSSC
T ss_pred             CEEEEEcCCCCcHHHHHHHHHcCCC
Confidence            5899999999999999999998763

>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=93.55  E-value=0.034  Score=58.71  Aligned_cols=25  Identities=36%  Similarity=0.436  Sum_probs=22.5

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLG  203 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg  203 (666)
                      ..+.|.||+||||||++++||.-+.
T Consensus        27 e~~~llGpnGsGKSTLLr~iaGl~~   51 (348)
T 3d31_A           27 EYFVILGPTGAGKTLFLELIAGFHV   51 (348)
T ss_dssp             CEEEEECCCTHHHHHHHHHHHTSSC
T ss_pred             CEEEEECCCCccHHHHHHHHHcCCC
Confidence            5899999999999999999998663

>2ff7_A Alpha-hemolysin translocation ATP-binding protein HLYB; ABC-transporter, transport protein; HET: ADP; 1.60A {Escherichia coli} SCOP: c.37.1.12 PDB: 2ffb_A* 2fgk_A* 2ffa_A* 2fgj_A* 2pmk_A* 3b5j_A* 1mt0_A 1xef_A*

Probab=93.55  E-value=0.032  Score=55.88  Aligned_cols=25  Identities=28%  Similarity=0.445  Sum_probs=22.6

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLG  203 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg  203 (666)
                      .++.|.||+|+||||++++|+.-+.
T Consensus        36 e~~~i~G~nGsGKSTLl~~l~Gl~~   60 (247)
T 2ff7_A           36 EVIGIVGRSGSGKSTLTKLIQRFYI   60 (247)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTTSSC
T ss_pred             CEEEEECCCCCCHHHHHHHHhcCCC
Confidence            5899999999999999999988763

>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=93.54  E-value=0.05  Score=63.79  Aligned_cols=24  Identities=42%  Similarity=0.603  Sum_probs=20.7

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      +..+|.||||||||+++..++..+
T Consensus       372 ~~~lI~GppGTGKT~ti~~~i~~l  395 (800)
T 2wjy_A          372 PLSLIQGPPGTGKTVTSATIVYHL  395 (800)
T ss_dssp             SEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CeEEEEcCCCCCHHHHHHHHHHHH
Confidence            478999999999999988777664

>1mv5_A LMRA, multidrug resistance ABC transporter ATP-binding and permease protein; asymmetric dimer, tetramer, P-glycoprotein; HET: ATP ADP; 3.10A {Lactococcus lactis} SCOP: c.37.1.12

Probab=93.54  E-value=0.033  Score=55.62  Aligned_cols=24  Identities=17%  Similarity=0.437  Sum_probs=22.1

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      ..+.|.||+|+||||++++|+.-+
T Consensus        29 e~~~i~G~nGsGKSTLl~~l~Gl~   52 (243)
T 1mv5_A           29 SIIAFAGPSGGGKSTIFSLLERFY   52 (243)
T ss_dssp             EEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CEEEEECCCCCCHHHHHHHHhcCC
Confidence            589999999999999999999865

>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=93.51  E-value=0.36  Score=54.00  Aligned_cols=24  Identities=25%  Similarity=0.487  Sum_probs=21.7

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      .++|+.|.+|+|||++++.+...+
T Consensus       215 pHlLIaG~TGSGKS~~L~tlI~sL  238 (574)
T 2iut_A          215 PHLLVAGTTGSGKSVGVNAMLLSI  238 (574)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CeeEEECCCCCCHHHHHHHHHHHH
Confidence            479999999999999999987766

>1z47_A CYSA, putative ABC-transporter ATP-binding protein; alpha/beta motif, beta sandwich, ligand binding protein; 1.90A {Alicyclobacillus acidocaldarius}

Probab=93.50  E-value=0.036  Score=58.60  Aligned_cols=25  Identities=32%  Similarity=0.453  Sum_probs=22.4

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLG  203 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg  203 (666)
                      ..+.|.||+||||||++++||.-+.
T Consensus        42 e~~~llGpnGsGKSTLLr~iaGl~~   66 (355)
T 1z47_A           42 EMVGLLGPSGSGKTTILRLIAGLER   66 (355)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHTSSC
T ss_pred             CEEEEECCCCCcHHHHHHHHhCCCC
Confidence            5899999999999999999998663

>2it1_A 362AA long hypothetical maltose/maltodextrin transport ATP-binding protein; structural genomics, NPPSFA; 1.94A {Pyrococcus horikoshii}

Probab=93.50  E-value=0.037  Score=58.74  Aligned_cols=25  Identities=24%  Similarity=0.436  Sum_probs=22.6

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLG  203 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg  203 (666)
                      ..+.|.||+||||||++++||.-+.
T Consensus        30 e~~~llGpnGsGKSTLLr~iaGl~~   54 (362)
T 2it1_A           30 EFMALLGPSGSGKSTLLYTIAGIYK   54 (362)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHTSSC
T ss_pred             CEEEEECCCCchHHHHHHHHhcCCC
Confidence            5899999999999999999998763

>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=93.49  E-value=0.037  Score=59.07  Aligned_cols=25  Identities=32%  Similarity=0.513  Sum_probs=22.6

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLG  203 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg  203 (666)
                      ..+.|.||+||||||++++||.-+.
T Consensus        30 e~~~llGpsGsGKSTLLr~iaGl~~   54 (381)
T 3rlf_A           30 EFVVFVGPSGCGKSTLLRMIAGLET   54 (381)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHTSSC
T ss_pred             CEEEEEcCCCchHHHHHHHHHcCCC
Confidence            5899999999999999999998763

>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=93.47  E-value=0.25  Score=46.68  Aligned_cols=21  Identities=19%  Similarity=0.390  Sum_probs=19.1

Q ss_pred             EEEEECCCCchHHHHHHHHHH
Q 005987          180 VLVITGQAGVGKTATVRQIAS  200 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAk  200 (666)
                      .++|.|++|+||||++..+..
T Consensus        31 ki~v~G~~~vGKSsLi~~l~~   51 (192)
T 2b6h_A           31 RILMVGLDAAGKTTILYKLKL   51 (192)
T ss_dssp             EEEEEESTTSSHHHHHHHHCS
T ss_pred             EEEEECCCCCCHHHHHHHHHh
Confidence            599999999999999999864

>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=93.46  E-value=0.49  Score=44.04  Aligned_cols=23  Identities=26%  Similarity=0.443  Sum_probs=20.3

Q ss_pred             cEEEEECCCCchHHHHHHHHHHH
Q 005987          179 NVLVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAke  201 (666)
                      -.++|.|++|+||||++..+...
T Consensus        17 ~~i~v~G~~~~GKssl~~~l~~~   39 (187)
T 1zj6_A           17 HKVIIVGLDNAGKTTILYQFSMN   39 (187)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHTT
T ss_pred             cEEEEECCCCCCHHHHHHHHhcC
Confidence            36999999999999999999853

>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=93.44  E-value=0.035  Score=55.74  Aligned_cols=25  Identities=24%  Similarity=0.507  Sum_probs=22.5

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLG  203 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg  203 (666)
                      .++.|.||+|+||||++++++.-+.
T Consensus        27 e~~~liG~NGsGKSTLlk~l~Gl~~   51 (249)
T 2qi9_C           27 EILHLVGPNGAGKSTLLARMAGMTS   51 (249)
T ss_dssp             CEEEEECCTTSSHHHHHHHHTTSSC
T ss_pred             CEEEEECCCCCcHHHHHHHHhCCCC
Confidence            5899999999999999999988764

>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=93.44  E-value=0.038  Score=58.61  Aligned_cols=24  Identities=29%  Similarity=0.499  Sum_probs=22.1

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      ..+.|.||+||||||++++||.-+
T Consensus        30 e~~~llGpnGsGKSTLLr~iaGl~   53 (359)
T 2yyz_A           30 EFVALLGPSGCGKTTTLLMLAGIY   53 (359)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHTSS
T ss_pred             CEEEEEcCCCchHHHHHHHHHCCC
Confidence            579999999999999999999866

>2ixe_A Antigen peptide transporter 1; ABC ATPase, hydrolase; HET: ATP; 2.0A {Rattus norvegicus} PDB: 2ixg_A* 2ixf_A* 1jj7_A*

Probab=93.40  E-value=0.036  Score=56.34  Aligned_cols=25  Identities=20%  Similarity=0.373  Sum_probs=22.7

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLG  203 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg  203 (666)
                      .++.|.||+|+||||++++|+..+.
T Consensus        46 e~~~i~G~nGsGKSTLlk~l~Gl~~   70 (271)
T 2ixe_A           46 KVTALVGPNGSGKSTVAALLQNLYQ   70 (271)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTTSSC
T ss_pred             CEEEEECCCCCCHHHHHHHHhcCCC
Confidence            5899999999999999999998763

>2ghi_A Transport protein; multidrug resistance protein, MDR, structural genomics, structural genomics consortium, SGC; 2.20A {Plasmodium yoelii yoelii str}

Probab=93.39  E-value=0.037  Score=55.92  Aligned_cols=24  Identities=17%  Similarity=0.400  Sum_probs=22.0

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      ..+.|.||+|+||||++++|+.-+
T Consensus        47 e~~~i~G~nGsGKSTLl~~l~Gl~   70 (260)
T 2ghi_A           47 TTCALVGHTGSGKSTIAKLLYRFY   70 (260)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             CEEEEECCCCCCHHHHHHHHhccC
Confidence            589999999999999999998765

>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=93.39  E-value=0.038  Score=55.76  Aligned_cols=25  Identities=32%  Similarity=0.589  Sum_probs=22.5

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLG  203 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg  203 (666)
                      .++.|.||+|+||||++++|+.-+.
T Consensus        42 ei~~l~G~NGsGKSTLlk~l~Gl~~   66 (256)
T 1vpl_A           42 EIFGLIGPNGAGKTTTLRIISTLIK   66 (256)
T ss_dssp             CEEEEECCTTSSHHHHHHHHTTSSC
T ss_pred             cEEEEECCCCCCHHHHHHHHhcCCC
Confidence            5899999999999999999998763

>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=93.35  E-value=0.07  Score=60.16  Aligned_cols=25  Identities=28%  Similarity=0.409  Sum_probs=23.5

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLG  203 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg  203 (666)
                      ..++|+|++|+||||+++.|++.++
T Consensus       397 ~~I~l~GlsGSGKSTiA~~La~~L~  421 (573)
T 1m8p_A          397 FTIFLTGYMNSGKDAIARALQVTLN  421 (573)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             eEEEeecCCCCCHHHHHHHHHHHhc
Confidence            5799999999999999999999986

>2ihy_A ABC transporter, ATP-binding protein; ATPase, ABC cassette, hydrolase; HET: MSE; 1.90A {Staphylococcus aureus}

Probab=93.35  E-value=0.037  Score=56.59  Aligned_cols=25  Identities=20%  Similarity=0.322  Sum_probs=22.5

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLG  203 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg  203 (666)
                      .++.|.||+|+||||++++|+..+.
T Consensus        48 e~~~liG~NGsGKSTLlk~l~Gl~~   72 (279)
T 2ihy_A           48 DKWILYGLNGAGKTTLLNILNAYEP   72 (279)
T ss_dssp             CEEEEECCTTSSHHHHHHHHTTSSC
T ss_pred             CEEEEECCCCCcHHHHHHHHhCCCC
Confidence            5799999999999999999998763

>4a2q_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2 RNA helicase, ATP and dsRNA binding antiviral signalling pathway; 3.40A {Anas platyrhynchos}

Probab=93.34  E-value=0.76  Score=53.74  Aligned_cols=32  Identities=25%  Similarity=0.239  Sum_probs=24.3

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc--------CCcEEEEc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL--------GARLYEWD  210 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel--------g~~viE~n  210 (666)
                      +.+|+.+|+|+|||.++-..+.+.        +..++-+.
T Consensus       264 ~~~ll~~~TGsGKTl~~~~~i~~~l~~~~~~~~~~~Lvl~  303 (797)
T 4a2q_A          264 KNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLA  303 (797)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHHHHHHTCCSSCCCCEEEEC
T ss_pred             CCEEEEeCCCChHHHHHHHHHHHHHHhccccCCCeEEEEe
Confidence            369999999999999877766655        55565554

>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=93.34  E-value=0.045  Score=56.52  Aligned_cols=24  Identities=21%  Similarity=0.498  Sum_probs=21.6

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLG  203 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg  203 (666)
                      ..+.|.||+|+||||++++|+ .+.
T Consensus       166 ~i~~l~G~sG~GKSTLln~l~-~~~  189 (302)
T 2yv5_A          166 FICILAGPSGVGKSSILSRLT-GEE  189 (302)
T ss_dssp             CEEEEECSTTSSHHHHHHHHH-SCC
T ss_pred             cEEEEECCCCCCHHHHHHHHH-Hhh
Confidence            589999999999999999999 653

>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=93.33  E-value=0.037  Score=56.14  Aligned_cols=24  Identities=29%  Similarity=0.580  Sum_probs=22.1

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      .++.|.||+|+||||++++++.-+
T Consensus        38 e~~~liG~nGsGKSTLl~~l~Gl~   61 (266)
T 4g1u_C           38 EMVAIIGPNGAGKSTLLRLLTGYL   61 (266)
T ss_dssp             CEEEEECCTTSCHHHHHHHHTSSS
T ss_pred             CEEEEECCCCCcHHHHHHHHhcCC
Confidence            589999999999999999999866

>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=93.33  E-value=0.48  Score=45.57  Aligned_cols=24  Identities=21%  Similarity=0.241  Sum_probs=19.4

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      +.+++.+|+|+|||.++-..+-+.
T Consensus        52 ~~~li~~~TGsGKT~~~~~~~~~~   75 (220)
T 1t6n_A           52 MDVLCQAKSGMGKTAVFVLATLQQ   75 (220)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CCEEEECCCCCchhhhhhHHHHHh
Confidence            359999999999999876666554

>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=93.26  E-value=0.042  Score=58.59  Aligned_cols=24  Identities=38%  Similarity=0.632  Sum_probs=22.1

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      .++.|.||+||||||++++||.-+
T Consensus        30 e~~~llGpnGsGKSTLLr~iaGl~   53 (372)
T 1g29_1           30 EFMILLGPSGCGKTTTLRMIAGLE   53 (372)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHTSS
T ss_pred             CEEEEECCCCcHHHHHHHHHHcCC
Confidence            589999999999999999999866

>1lw7_A Transcriptional regulator NADR; NMN, NMN adenylyl transferase, ribosylnicotinamide KINA transferase; HET: NAD; 2.90A {Haemophilus influenzae} SCOP: c.26.1.3 c.37.1.1

Probab=93.26  E-value=0.05  Score=57.62  Aligned_cols=27  Identities=22%  Similarity=0.406  Sum_probs=24.2

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGAR  205 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~  205 (666)
                      ..+.|.||+|+||||++++|+..+...
T Consensus       171 ~k~~IvG~nGsGKSTLlk~L~gl~~~~  197 (365)
T 1lw7_A          171 KTVAILGGESSGKSVLVNKLAAVFNTT  197 (365)
T ss_dssp             EEEEEECCTTSHHHHHHHHHHHHTTCE
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHhCCC
Confidence            579999999999999999999988653

>2yz2_A Putative ABC transporter ATP-binding protein TM_0; cobalt transport, TM02 hydrolase, inner membrane, membrane, nucleotide-binding; 2.30A {Thermotoga maritima}

Probab=93.19  E-value=0.041  Score=55.75  Aligned_cols=24  Identities=25%  Similarity=0.594  Sum_probs=22.0

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      .++.|.||+|+||||++++++.-+
T Consensus        34 e~~~liG~nGsGKSTLl~~i~Gl~   57 (266)
T 2yz2_A           34 ECLLVAGNTGSGKSTLLQIVAGLI   57 (266)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             CEEEEECCCCCcHHHHHHHHhCCC
Confidence            589999999999999999998865

>2nq2_C Hypothetical ABC transporter ATP-binding protein HI1470; putative iron chelatin ABC transporter, nucleotide binding domain; 2.40A {Haemophilus influenzae}

Probab=93.19  E-value=0.041  Score=55.39  Aligned_cols=25  Identities=24%  Similarity=0.457  Sum_probs=22.5

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLG  203 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg  203 (666)
                      .++.|.||+|+||||++++++.-+.
T Consensus        32 e~~~l~G~nGsGKSTLl~~l~Gl~~   56 (253)
T 2nq2_C           32 DILAVLGQNGCGKSTLLDLLLGIHR   56 (253)
T ss_dssp             CEEEEECCSSSSHHHHHHHHTTSSC
T ss_pred             CEEEEECCCCCCHHHHHHHHhCCCC
Confidence            5799999999999999999998763

>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=93.18  E-value=0.035  Score=58.77  Aligned_cols=24  Identities=38%  Similarity=0.425  Sum_probs=22.0

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      ..+.|.||+||||||++++||.-+
T Consensus        32 e~~~llGpnGsGKSTLLr~iaGl~   55 (353)
T 1oxx_K           32 ERFGILGPSGAGKTTFMRIIAGLD   55 (353)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHTSS
T ss_pred             CEEEEECCCCCcHHHHHHHHhCCC
Confidence            589999999999999999999865

>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=93.18  E-value=0.042  Score=56.66  Aligned_cols=25  Identities=28%  Similarity=0.529  Sum_probs=22.3

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLG  203 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg  203 (666)
                      ..+.|.||+|+||||++++|+....
T Consensus       170 eiv~l~G~sG~GKSTll~~l~g~~~  194 (301)
T 1u0l_A          170 KISTMAGLSGVGKSSLLNAINPGLK  194 (301)
T ss_dssp             SEEEEECSTTSSHHHHHHHHSTTCC
T ss_pred             CeEEEECCCCCcHHHHHHHhccccc
Confidence            5899999999999999999987654

>4i1u_A Dephospho-COA kinase; structural genomics, niaid, national institute of allergy AN infectious diseases; 2.05A {Burkholderia vietnamiensis} PDB: 4i1v_A*

Probab=93.16  E-value=0.063  Score=52.45  Aligned_cols=30  Identities=37%  Similarity=0.493  Sum_probs=26.8

Q ss_pred             EEEEECCCCchHHHHHHHHHHHcCCcEEEEc
Q 005987          180 VLVITGQAGVGKTATVRQIASHLGARLYEWD  210 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkelg~~viE~n  210 (666)
                      .+-|+|..||||||+++.|++ +|+.++..+
T Consensus        11 ~iglTGgigsGKStv~~~l~~-~g~~vidaD   40 (210)
T 4i1u_A           11 AIGLTGGIGSGKTTVADLFAA-RGASLVDTD   40 (210)
T ss_dssp             EEEEECCTTSCHHHHHHHHHH-TTCEEEEHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH-CCCcEEECc
Confidence            689999999999999999998 999888543

>2yhs_A FTSY, cell division protein FTSY; cell cycle, protein targeting, simibi class GTPase, GTP-BIND membrane, nucleotide-binding; 1.60A {Escherichia coli} PDB: 2qy9_A 2xxa_B* 1fts_A

Probab=93.10  E-value=0.047  Score=60.11  Aligned_cols=30  Identities=33%  Similarity=0.635  Sum_probs=25.2

Q ss_pred             ccEEEEECCCCchHHHHHHHHHHHc---CCcEE
Q 005987          178 TNVLVITGQAGVGKTATVRQIASHL---GARLY  207 (666)
Q Consensus       178 ~k~LLL~GPpG~GKTtla~~LAkel---g~~vi  207 (666)
                      +.+++|.||+|+||||+++.||..+   +..|.
T Consensus       293 GeVI~LVGpNGSGKTTLl~~LAgll~~~~G~V~  325 (503)
T 2yhs_A          293 PFVILMVGVNGVGKTTTIGKLARQFEQQGKSVM  325 (503)
T ss_dssp             TEEEEEECCTTSSHHHHHHHHHHHHHHTTCCEE
T ss_pred             CeEEEEECCCcccHHHHHHHHHHHhhhcCCeEE
Confidence            3689999999999999999999876   44544

>3ld9_A DTMP kinase, thymidylate kinase; ssgcid, NIH, niaid, SBRI, UW, emerald biostructures, ehrlich chaffeensis; 2.15A {Ehrlichia chaffeensis}

Probab=93.08  E-value=0.052  Score=53.59  Aligned_cols=30  Identities=23%  Similarity=0.273  Sum_probs=25.7

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCC----cEEE
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGA----RLYE  208 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~----~viE  208 (666)
                      ..++|.|++|+||||.++.|++.++.    .++.
T Consensus        22 ~~i~~~G~~g~GKst~~~~l~~~l~~~~g~~v~~   55 (223)
T 3ld9_A           22 MFITFEGIDGSGKTTQSHLLAEYLSEIYGVNNVV   55 (223)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHHHHHHCGGGEE
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHhhccCceeeE
Confidence            68999999999999999999998643    5555

>2il1_A RAB12; G-protein, GDP, GTPase, predicted, structural genomics, structural genomics consortium, SGC, protein transport; HET: GDP; 2.10A {Homo sapiens}

Probab=93.07  E-value=0.47  Score=44.55  Aligned_cols=22  Identities=32%  Similarity=0.623  Sum_probs=19.0

Q ss_pred             EEEEECCCCchHHHHHHHHHHH
Q 005987          180 VLVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAke  201 (666)
                      .++|.|++|+||||++..+...
T Consensus        28 ki~vvG~~~~GKSsLi~~l~~~   49 (192)
T 2il1_A           28 QVIIIGSRGVGKTSLMERFTDD   49 (192)
T ss_dssp             EEEEECSTTSSHHHHHHHHCC-
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            4899999999999999998653

>4a2w_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2 RNA helicase, ATP and dsRNA binding antiviral signalling pathway; 3.70A {Anas platyrhynchos}

Probab=93.07  E-value=0.89  Score=54.26  Aligned_cols=24  Identities=29%  Similarity=0.321  Sum_probs=20.4

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      +.+|+.+|+|+|||.++-..+.+.
T Consensus       264 ~~~ll~a~TGsGKTl~~~~~i~~~  287 (936)
T 4a2w_A          264 KNALICAPTGSGKTFVSILICEHH  287 (936)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHHTT
T ss_pred             CCEEEEeCCCchHHHHHHHHHHHH
Confidence            359999999999999987777665

>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=93.03  E-value=0.049  Score=61.91  Aligned_cols=24  Identities=42%  Similarity=0.671  Sum_probs=20.9

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      +.++++|||||||||++..+...+
T Consensus       165 ~~~vi~G~pGTGKTt~l~~ll~~l  188 (608)
T 1w36_D          165 RISVISGGPGTGKTTTVAKLLAAL  188 (608)
T ss_dssp             SEEEEECCTTSTHHHHHHHHHHHH
T ss_pred             CCEEEEeCCCCCHHHHHHHHHHHH
Confidence            589999999999999988776654

>2rcn_A Probable GTPase ENGC; YJEQ, circularly permuted, GTP-binding, hydrolase, nucleotide-binding; HET: GDP; 2.25A {Salmonella typhimurium} PDB: 2ykr_W 4a2i_V

Probab=93.03  E-value=0.038  Score=58.50  Aligned_cols=25  Identities=24%  Similarity=0.512  Sum_probs=22.1

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLG  203 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg  203 (666)
                      ..+.|.||+|+||||++++|+..+.
T Consensus       216 ~~~~lvG~sG~GKSTLln~L~g~~~  240 (358)
T 2rcn_A          216 RISIFAGQSGVGKSSLLNALLGLQN  240 (358)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHCCSS
T ss_pred             CEEEEECCCCccHHHHHHHHhcccc
Confidence            5799999999999999999986553

>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=93.01  E-value=1.3  Score=45.38  Aligned_cols=24  Identities=21%  Similarity=0.452  Sum_probs=21.0

Q ss_pred             ccEEEEECCCCchHHHHHHHHHHH
Q 005987          178 TNVLVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       178 ~k~LLL~GPpG~GKTtla~~LAke  201 (666)
                      ...+.|.|+||+||||++..|...
T Consensus        10 ~g~v~ivG~~nvGKSTLin~l~g~   33 (308)
T 3iev_A           10 VGYVAIVGKPNVGKSTLLNNLLGT   33 (308)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHTS
T ss_pred             CCEEEEECCCCCcHHHHHHHHhCC
Confidence            357999999999999999998764

>2gza_A Type IV secretion system protein VIRB11; ATPase, hydrolase; 2.60A {Brucella suis}

Probab=93.00  E-value=0.035  Score=58.89  Aligned_cols=25  Identities=28%  Similarity=0.636  Sum_probs=22.9

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLG  203 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg  203 (666)
                      ..++|.||+|+||||++++|+..+.
T Consensus       176 ~~i~ivG~sGsGKSTll~~l~~~~~  200 (361)
T 2gza_A          176 RVIVVAGETGSGKTTLMKALMQEIP  200 (361)
T ss_dssp             CCEEEEESSSSCHHHHHHHHHTTSC
T ss_pred             CEEEEECCCCCCHHHHHHHHHhcCC
Confidence            4799999999999999999999874

>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=92.98  E-value=0.11  Score=50.40  Aligned_cols=35  Identities=20%  Similarity=0.364  Sum_probs=29.1

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc--CCcEEEEcCCC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL--GARLYEWDTPT  213 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel--g~~viE~nasd  213 (666)
                      +.+.|-|+.|+||||.++.|++.+  |+.++....|.
T Consensus         3 kFI~~EG~dGsGKsTq~~~L~~~L~~~~~v~~~~eP~   39 (205)
T 4hlc_A            3 AFITFEGPEGSGKTTVINEVYHRLVKDYDVIMTREPG   39 (205)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHHHTTTSCEEEEESST
T ss_pred             CEEEEECCCCCcHHHHHHHHHHHHHCCCCEEEeeCCC
Confidence            468899999999999999999988  67777665543

>3cr8_A Sulfate adenylyltranferase, adenylylsulfate kinase; APS kinase, transferase, sulfate metabolism, nucleotide 2 kinase; 2.95A {Thiobacillus denitrificans}

Probab=92.94  E-value=0.043  Score=61.58  Aligned_cols=25  Identities=32%  Similarity=0.504  Sum_probs=23.4

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLG  203 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg  203 (666)
                      .++.|.||+||||||++++||..++
T Consensus       370 ~iI~LiG~sGSGKSTLar~La~~L~  394 (552)
T 3cr8_A          370 FTVFFTGLSGAGKSTLARALAARLM  394 (552)
T ss_dssp             EEEEEEESSCHHHHHHHHHHHHHHH
T ss_pred             eEEEEECCCCChHHHHHHHHHHhhc
Confidence            5799999999999999999999984

>2v6i_A RNA helicase; membrane, hydrolase, transmembrane, RNA replication, viral replication, nucleotide-binding; 2.10A {Kokobera virus} PDB: 2v6j_A

Probab=92.92  E-value=0.16  Score=54.99  Aligned_cols=32  Identities=25%  Similarity=0.269  Sum_probs=22.8

Q ss_pred             cEEEEECCCCchHHHHH-HHHHH---HcCCcEEEEc
Q 005987          179 NVLVITGQAGVGKTATV-RQIAS---HLGARLYEWD  210 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla-~~LAk---elg~~viE~n  210 (666)
                      +.+|+.||+|+|||.++ ..+.+   .-|..++-+.
T Consensus         3 ~~~lv~a~TGsGKT~~~l~~~l~~~~~~g~~~lvl~   38 (431)
T 2v6i_A            3 ELTVLDLHPGAGKTRRVLPQLVREAVKKRLRTVILA   38 (431)
T ss_dssp             CEEEEECCTTSCTTTTHHHHHHHHHHHTTCCEEEEE
T ss_pred             CEEEEEcCCCCCHHHHHHHHHHHHHHhCCCCEEEEC
Confidence            58999999999999986 43442   2355666554

>3sop_A Neuronal-specific septin-3; hydrolase; HET: GDP; 2.88A {Homo sapiens}

Probab=92.86  E-value=0.05  Score=55.25  Aligned_cols=23  Identities=26%  Similarity=0.540  Sum_probs=21.2

Q ss_pred             EEEEECCCCchHHHHHHHHHHHc
Q 005987          180 VLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      .+.|.||+|+||||++++|+...
T Consensus         4 ~v~lvG~nGaGKSTLln~L~g~~   26 (270)
T 3sop_A            4 NIMVVGQSGLGKSTLVNTLFKSQ   26 (270)
T ss_dssp             EEEEEESSSSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhCCC
Confidence            47899999999999999999876

>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=92.85  E-value=0.049  Score=58.38  Aligned_cols=24  Identities=21%  Similarity=0.372  Sum_probs=21.8

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      ..+.|.||+||||||++++||.-+
T Consensus        48 e~~~llGpsGsGKSTLLr~iaGl~   71 (390)
T 3gd7_A           48 QRVGLLGRTGSGKSTLLSAFLRLL   71 (390)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHTCS
T ss_pred             CEEEEECCCCChHHHHHHHHhCCC
Confidence            589999999999999999999754

>2pjz_A Hypothetical protein ST1066; ATP binding protein, structural genomics, NPPSFA; 1.90A {Sulfolobus tokodaii}

Probab=92.84  E-value=0.047  Score=55.25  Aligned_cols=24  Identities=38%  Similarity=0.612  Sum_probs=22.2

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      ..+.|.||+|+||||++++++..+
T Consensus        31 e~~~i~G~NGsGKSTLlk~l~Gl~   54 (263)
T 2pjz_A           31 EKVIILGPNGSGKTTLLRAISGLL   54 (263)
T ss_dssp             SEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             EEEEEECCCCCCHHHHHHHHhCCC
Confidence            589999999999999999999876

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A*

Probab=92.83  E-value=1.6  Score=49.81  Aligned_cols=24  Identities=29%  Similarity=0.354  Sum_probs=19.8

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      +.+|+.+|+|+|||.++-.++.+.
T Consensus        29 ~~~iv~~~TGsGKTl~~~~~i~~~   52 (696)
T 2ykg_A           29 KNTIICAPTGCGKTFVSLLICEHH   52 (696)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CCEEEEcCCCchHHHHHHHHHHHH
Confidence            469999999999999887766543

>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=92.83  E-value=0.05  Score=51.64  Aligned_cols=23  Identities=26%  Similarity=0.536  Sum_probs=21.0

Q ss_pred             EEEEECCCCchHHHHHHHHHHHc
Q 005987          180 VLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      .++|.||+|+||||+++.++...
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            58899999999999999999864

>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=92.80  E-value=0.91  Score=52.97  Aligned_cols=24  Identities=29%  Similarity=0.531  Sum_probs=20.0

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      +.+++.||+|+||||++..++.+.
T Consensus       110 ~~vii~gpTGSGKTtllp~ll~~~  133 (773)
T 2xau_A          110 QIMVFVGETGSGKTTQIPQFVLFD  133 (773)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHh
Confidence            479999999999999877775543

>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=92.79  E-value=0.15  Score=58.71  Aligned_cols=32  Identities=16%  Similarity=0.123  Sum_probs=22.8

Q ss_pred             cEEEEECCCCchHHHHHHHHH-HHc--CCcEEEEc
Q 005987          179 NVLVITGQAGVGKTATVRQIA-SHL--GARLYEWD  210 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LA-kel--g~~viE~n  210 (666)
                      +.++++||+|+|||+++-..+ +.+  +..++.+.
T Consensus        41 ~~~lv~apTGsGKT~~~~l~il~~~~~~~~~l~i~   75 (702)
T 2p6r_A           41 KNLLLAMPTAAGKTLLAEMAMVREAIKGGKSLYVV   75 (702)
T ss_dssp             SCEEEECSSHHHHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             CcEEEEcCCccHHHHHHHHHHHHHHHhCCcEEEEe
Confidence            579999999999999984433 333  55555554

>3def_A T7I23.11 protein; chloroplast, TOC33, GTPase, hydrolase; HET: GDP; 1.96A {Arabidopsis thaliana} PDB: 3bb3_A* 3bb4_A* 2j3e_A*

Probab=92.68  E-value=0.87  Score=45.44  Aligned_cols=24  Identities=29%  Similarity=0.581  Sum_probs=21.0

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      -.++|.|++|+||||++.++...-
T Consensus        37 ~~I~lvG~~g~GKSSLin~l~~~~   60 (262)
T 3def_A           37 MTVLVLGKGGVGKSSTVNSLIGEQ   60 (262)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHTSC
T ss_pred             cEEEEECCCCCCHHHHHHHHhCCC
Confidence            368999999999999999998654

>2xzl_A ATP-dependent helicase NAM7; hydrolase-RNA complex, NMD, RNA degradation, allosteric REGU; HET: ADP 1PE; 2.40A {Saccharomyces cerevisiae}

Probab=92.64  E-value=0.07  Score=62.59  Aligned_cols=24  Identities=42%  Similarity=0.603  Sum_probs=19.6

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      +.+++.||||||||+++..++..+
T Consensus       376 ~~~lI~GppGTGKT~~i~~~i~~l  399 (802)
T 2xzl_A          376 PLSLIQGPPGTGKTVTSATIVYHL  399 (802)
T ss_dssp             SEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CCEEEECCCCCCHHHHHHHHHHHH
Confidence            478999999999999987665543

>1tq4_A IIGP1, interferon-inducible GTPase; interferon gamma, dimer, immunology, signaling protein; HET: GDP; 1.95A {Mus musculus} SCOP: c.37.1.8 PDB: 1tqd_A* 1tq6_A* 1tpz_A* 1tq2_A*

Probab=92.64  E-value=0.095  Score=56.56  Aligned_cols=39  Identities=15%  Similarity=0.213  Sum_probs=27.8

Q ss_pred             HHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc
Q 005987          158 VEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       158 i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      ...+++.|+.....      ...+.|.||+|+||||++++|+..+
T Consensus        55 ~~~i~~~L~~~~~~------~~~valvG~nGaGKSTLln~L~Gl~   93 (413)
T 1tq4_A           55 NSAISDALKEIDSS------VLNVAVTGETGSGKSSFINTLRGIG   93 (413)
T ss_dssp             HHHHHHHHHHHHHC------CEEEEEEECTTSSHHHHHHHHHTCC
T ss_pred             chhhhhhhhhcccC------CeEEEEECCCCCcHHHHHHHHhCCC
Confidence            34455555544321      1378999999999999999999843

>3szr_A Interferon-induced GTP-binding protein MX1; interferon-induced antiviral GTPase, membrane associated, PR binding; 3.50A {Homo sapiens} PDB: 3zys_B

Probab=92.61  E-value=0.27  Score=55.79  Aligned_cols=24  Identities=13%  Similarity=0.374  Sum_probs=21.3

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      +.+.|.||+|+||||++++|+..+
T Consensus        46 p~iaIvG~nGsGKSTLL~~I~Gl~   69 (608)
T 3szr_A           46 PAIAVIGDQSSGKSSVLEALSGVA   69 (608)
T ss_dssp             CCEECCCCTTSCHHHHHHHHHSCC
T ss_pred             CeEEEECCCCChHHHHHHHHhCCC
Confidence            359999999999999999998754

>2j37_W Signal recognition particle 54 kDa protein (SRP54); ribosome, SRP, translation/RNA; 8.00A {Canis SP} PDB: 1wgw_A

Probab=92.59  E-value=0.19  Score=55.61  Aligned_cols=33  Identities=30%  Similarity=0.380  Sum_probs=27.8

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL---GARLYEWDT  211 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel---g~~viE~na  211 (666)
                      +.++|.|+||+||||++..||..+   |.++.-+.+
T Consensus       102 ~vI~ivG~~GvGKTTl~~kLA~~l~~~G~kVllVd~  137 (504)
T 2j37_W          102 NVIMFVGLQGSGKTTTCSKLAYYYQRKGWKTCLICA  137 (504)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEEE
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEec
Confidence            589999999999999999999776   777766654

>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=92.55  E-value=0.65  Score=48.46  Aligned_cols=22  Identities=27%  Similarity=0.368  Sum_probs=17.8

Q ss_pred             cEEEEECCCCchHHHHHHHHHH
Q 005987          179 NVLVITGQAGVGKTATVRQIAS  200 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAk  200 (666)
                      +.+++.+|+|+|||.++-..+-
T Consensus        45 ~~~lv~a~TGsGKT~~~~~~~~   66 (395)
T 3pey_A           45 RNMIAQSQSGTGKTAAFSLTML   66 (395)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHH
T ss_pred             CeEEEECCCCCcHHHHHHHHHH
Confidence            5799999999999997654443

>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=92.48  E-value=0.6  Score=56.12  Aligned_cols=21  Identities=29%  Similarity=0.420  Sum_probs=19.6

Q ss_pred             cEEEEECCCCchHHHHHHHHH
Q 005987          179 NVLVITGQAGVGKTATVRQIA  199 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LA  199 (666)
                      .+++|+||.|+||||+++.++
T Consensus       790 ~i~~ItGpNgsGKSTlLr~iG  810 (1022)
T 2o8b_B          790 YCVLVTGPNMGGKSTLMRQAG  810 (1022)
T ss_dssp             CEEEEECCTTSSHHHHHHHHH
T ss_pred             cEEEEECCCCCChHHHHHHHH
Confidence            689999999999999999984

>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=92.46  E-value=0.071  Score=48.95  Aligned_cols=24  Identities=33%  Similarity=0.516  Sum_probs=21.9

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      ...+|+||.|+|||+++.++.-.+
T Consensus        24 g~~~I~G~NGsGKStil~Ai~~~l   47 (149)
T 1f2t_A           24 GINLIIGQNGSGKSSLLDAILVGL   47 (149)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHH
Confidence            588999999999999999998766

>2dyk_A GTP-binding protein; GTPase, ribosome-binding protein, structural genomics; HET: GDP; 1.96A {Thermus thermophilus}

Probab=92.45  E-value=0.072  Score=48.15  Aligned_cols=23  Identities=26%  Similarity=0.476  Sum_probs=20.6

Q ss_pred             EEEEECCCCchHHHHHHHHHHHc
Q 005987          180 VLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      .+++.|++|+||||++..++...
T Consensus         3 ki~v~G~~~~GKSsli~~l~~~~   25 (161)
T 2dyk_A            3 KVVIVGRPNVGKSSLFNRLLKKR   25 (161)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHCC
T ss_pred             EEEEECCCCCCHHHHHHHHhCCC
Confidence            58999999999999999998754

>2bbs_A Cystic fibrosis transmembrane conductance regulator; ATP binding cassette, transport protein; HET: ATP; 2.05A {Homo sapiens} PDB: 2bbt_A* 1xmi_A* 1xmj_A* 2bbo_A* 3si7_A* 1r0w_A 1q3h_A 1r0x_A* 1r0y_A* 1r0z_A* 1r10_A* 1xf9_A* 1xfa_A*

Probab=92.45  E-value=0.054  Score=55.63  Aligned_cols=24  Identities=33%  Similarity=0.607  Sum_probs=22.1

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      ..+.|.||.|+||||++++|+..+
T Consensus        65 e~~~i~G~NGsGKSTLlk~l~Gl~   88 (290)
T 2bbs_A           65 QLLAVAGSTGAGKTSLLMMIMGEL   88 (290)
T ss_dssp             CEEEEEESTTSSHHHHHHHHTTSS
T ss_pred             CEEEEECCCCCcHHHHHHHHhcCC
Confidence            589999999999999999998876

>1dek_A Deoxynucleoside monophosphate kinase; transferase, phosphotransferase; HET: DGP; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.1 PDB: 1del_A*

Probab=92.39  E-value=0.067  Score=53.41  Aligned_cols=29  Identities=28%  Similarity=0.413  Sum_probs=25.7

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEE
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLY  207 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~vi  207 (666)
                      .++.|+|++|+||||+++.|+..+|+.++
T Consensus         2 ~~i~ltG~~~sGK~tv~~~l~~~~g~~~~   30 (241)
T 1dek_A            2 KLIFLSGVKRSGKDTTADFIMSNYSAVKY   30 (241)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHSCEEEC
T ss_pred             eEEEEECCCCCCHHHHHHHHHHhcCCeEE
Confidence            36889999999999999999999997763

>2vp4_A Deoxynucleoside kinase; ATP-binding, DNA synthesis, phosphoprotein, feedback inhibition, deoxyribonucleoside kinase, salvage pathway; HET: DCP; 2.20A {Drosophila melanogaster} SCOP: c.37.1.1 PDB: 1j90_A* 2jj8_A* 2vp2_A* 1oe0_A* 2vp5_A* 2vp6_A* 2vp9_A* 2vpp_A* 2vqs_A* 2vp0_A* 1ot3_A* 2jcs_A* 1zm7_A* 1zmx_A*

Probab=92.39  E-value=0.073  Score=52.38  Aligned_cols=32  Identities=19%  Similarity=0.282  Sum_probs=26.2

Q ss_pred             ccEEEEECCCCchHHHHHHHHHHHcCCcEEEEc
Q 005987          178 TNVLVITGQAGVGKTATVRQIASHLGARLYEWD  210 (666)
Q Consensus       178 ~k~LLL~GPpG~GKTtla~~LAkelg~~viE~n  210 (666)
                      +..+.|.||.|+||||+++.|+.. +..+.-..
T Consensus        20 g~~i~i~G~~GsGKSTl~~~L~~~-~g~v~~~~   51 (230)
T 2vp4_A           20 PFTVLIEGNIGSGKTTYLNHFEKY-KNDICLLT   51 (230)
T ss_dssp             CEEEEEECSTTSCHHHHHHTTGGG-TTTEEEEC
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhc-cCCeEEEe
Confidence            368999999999999999999987 65555444

>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=92.36  E-value=0.04  Score=57.71  Aligned_cols=33  Identities=21%  Similarity=0.476  Sum_probs=26.2

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCC--cEEEEcC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGA--RLYEWDT  211 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~--~viE~na  211 (666)
                      ..++|.||+|+||||++++|+..+..  ..+.++.
T Consensus       172 ~~v~i~G~~GsGKTTll~~l~g~~~~~~g~i~i~~  206 (330)
T 2pt7_A          172 KNVIVCGGTGSGKTTYIKSIMEFIPKEERIISIED  206 (330)
T ss_dssp             CCEEEEESTTSCHHHHHHHGGGGSCTTSCEEEEES
T ss_pred             CEEEEECCCCCCHHHHHHHHhCCCcCCCcEEEECC
Confidence            47999999999999999999998742  3444543

>3hjn_A DTMP kinase, thymidylate kinase; ATP-binding, nucleotide biosynth nucleotide-binding, transferase, structural genomics; HET: ADP TYD; 2.10A {Thermotoga maritima}

Probab=92.34  E-value=0.14  Score=49.21  Aligned_cols=33  Identities=24%  Similarity=0.462  Sum_probs=28.5

Q ss_pred             EEEECCCCchHHHHHHHHHHHc---CCcEEEEcCCC
Q 005987          181 LVITGQAGVGKTATVRQIASHL---GARLYEWDTPT  213 (666)
Q Consensus       181 LLL~GPpG~GKTtla~~LAkel---g~~viE~nasd  213 (666)
                      +.|-|+-|+||||.++.|++.|   |..++....|.
T Consensus         3 I~~EG~DGsGKsTq~~~L~~~L~~~g~~v~~treP~   38 (197)
T 3hjn_A            3 ITFEGIDGSGKSTQIQLLAQYLEKRGKKVILKREPG   38 (197)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEESSC
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCCcEEEEECCC
Confidence            6789999999999999999887   78888776665

>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=92.26  E-value=0.058  Score=50.65  Aligned_cols=22  Identities=36%  Similarity=0.620  Sum_probs=19.7

Q ss_pred             EEEEECCCCchHHHHHHHHHHH
Q 005987          180 VLVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAke  201 (666)
                      -++|.|++||||||+++.++..
T Consensus         4 kv~ivG~~gvGKStLl~~l~~~   25 (184)
T 2zej_A            4 KLMIVGNTGSGKTTLLQQLMKT   25 (184)
T ss_dssp             EEEEESCTTSSHHHHHHHHTCC
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            4889999999999999999863

>4f4c_A Multidrug resistance protein PGP-1; ABC transporter, ATPase, multi-drug transporter, exporter, A binding, hydrolase,protein transport; HET: NDG NAG BMA MAN 0SA; 3.40A {Caenorhabditis elegans}

Probab=92.12  E-value=0.19  Score=62.35  Aligned_cols=26  Identities=15%  Similarity=0.410  Sum_probs=23.7

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGA  204 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~  204 (666)
                      ..+.|.||+|+||||++++|.+.+..
T Consensus       445 ~~vaivG~sGsGKSTll~ll~~~~~~  470 (1321)
T 4f4c_A          445 QTVALVGSSGCGKSTIISLLLRYYDV  470 (1321)
T ss_dssp             CEEEEEECSSSCHHHHHHHHTTSSCC
T ss_pred             cEEEEEecCCCcHHHHHHHhcccccc
Confidence            68999999999999999999998844

>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=92.08  E-value=0.074  Score=48.94  Aligned_cols=22  Identities=18%  Similarity=0.460  Sum_probs=20.0

Q ss_pred             EEEEECCCCchHHHHHHHHHHH
Q 005987          180 VLVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAke  201 (666)
                      .++|.|++|+||||+++.++..
T Consensus         5 ~v~lvG~~gvGKStL~~~l~~~   26 (165)
T 2wji_A            5 EIALIGNPNVGKSTIFNALTGE   26 (165)
T ss_dssp             EEEEECSTTSSHHHHHHHHHCC
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            5899999999999999999864

>1bif_A 6-phosphofructo-2-kinase/ fructose-2,6-bisphospha; transferase (phospho), phosphatase, hydrolase (phosp glycolysis, bifunctional enzyme; HET: AGS; 2.00A {Rattus norvegicus} SCOP: c.37.1.7 c.60.1.4 PDB: 3bif_A* 2bif_A* 1k6m_A* 1c80_A* 1c7z_A* 1c81_A* 1tip_A* 1fbt_A

Probab=92.07  E-value=0.076  Score=58.28  Aligned_cols=25  Identities=24%  Similarity=0.440  Sum_probs=23.1

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLG  203 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg  203 (666)
                      ..++|.|.||+||||+++.||+.++
T Consensus        40 ~~IvlvGlpGsGKSTia~~La~~l~   64 (469)
T 1bif_A           40 TLIVMVGLPARGKTYISKKLTRYLN   64 (469)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHh
Confidence            4799999999999999999999875

>3nh6_A ATP-binding cassette SUB-family B member 6, mitoc; ABC-transporter, ABCB6, nucleotide binding domain, heme BIOS transport protein; 2.00A {Homo sapiens} PDB: 3nh9_A* 3nha_A* 3nhb_A*

Probab=92.05  E-value=0.066  Score=55.44  Aligned_cols=25  Identities=24%  Similarity=0.511  Sum_probs=22.8

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLG  203 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg  203 (666)
                      ..+.|.||+|+||||++++|+..+.
T Consensus        81 e~vaivG~sGsGKSTLl~ll~gl~~  105 (306)
T 3nh6_A           81 QTLALVGPSGAGKSTILRLLFRFYD  105 (306)
T ss_dssp             CEEEEESSSCHHHHHHHHHHTTSSC
T ss_pred             CEEEEECCCCchHHHHHHHHHcCCC
Confidence            5899999999999999999998764

>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=91.92  E-value=0.15  Score=50.69  Aligned_cols=32  Identities=25%  Similarity=0.361  Sum_probs=27.2

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc--CCcEEEEc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL--GARLYEWD  210 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel--g~~viE~n  210 (666)
                      .++++.|.+|+||||++..||..+  |.++.-++
T Consensus        15 ~i~~~~GkgGvGKTTl~~~La~~l~~g~~v~vvd   48 (262)
T 1yrb_A           15 MIVVFVGTAGSGKTTLTGEFGRYLEDNYKVAYVN   48 (262)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHHTTTSCEEEEE
T ss_pred             EEEEEeCCCCCCHHHHHHHHHHHHHCCCeEEEEe
Confidence            689999999999999999999776  66666555

>2obl_A ESCN; ATPase, hydrolase; 1.80A {Escherichia coli O127} PDB: 2obm_A*

Probab=91.86  E-value=0.12  Score=54.34  Aligned_cols=29  Identities=24%  Similarity=0.328  Sum_probs=25.5

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEE
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLY  207 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~vi  207 (666)
                      ..+.|.||+|+||||+++.|+..+.....
T Consensus        72 q~~gIiG~nGaGKTTLl~~I~g~~~~~~g  100 (347)
T 2obl_A           72 QRIGIFAGSGVGKSTLLGMICNGASADII  100 (347)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHHSCCSEE
T ss_pred             CEEEEECCCCCCHHHHHHHHhcCCCCCEE
Confidence            47999999999999999999999866543

>3r7w_A Gtpase1, GTP-binding protein GTR1; RAG gtpases, GTR1P, GTR2P, MTOR, protein transport; HET: GNP; 2.77A {Saccharomyces cerevisiae} PDB: 4arz_A*

Probab=91.76  E-value=1.9  Score=44.08  Aligned_cols=22  Identities=32%  Similarity=0.514  Sum_probs=19.7

Q ss_pred             EEEEECCCCchHHHHHHHHHHH
Q 005987          180 VLVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAke  201 (666)
                      -++|.|+||+||||++..+...
T Consensus         5 KI~lvG~~~vGKSSLi~~l~~~   26 (307)
T 3r7w_A            5 KLLLMGRSGSGKSSMRSIIFSN   26 (307)
T ss_dssp             EEEEECCTTSSHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            5899999999999999998764

>3ch4_B Pmkase, phosphomevalonate kinase; parallel beta-sheet with the strand order 23145, walker A motif, cholesterol biosynthesis, lipid synthesis; 1.76A {Homo sapiens}

Probab=91.76  E-value=0.11  Score=50.42  Aligned_cols=28  Identities=32%  Similarity=0.482  Sum_probs=25.1

Q ss_pred             CccEEEEECCCCchHHHHHHHHHHHcCC
Q 005987          177 STNVLVITGQAGVGKTATVRQIASHLGA  204 (666)
Q Consensus       177 ~~k~LLL~GPpG~GKTtla~~LAkelg~  204 (666)
                      |..+++|+|.||+||++++..+.+.+|.
T Consensus        10 ~~~II~itGk~~SGKd~va~~l~~~~g~   37 (202)
T 3ch4_B           10 PRLVLLFSGKRKSGKDFVTEALQSRLGA   37 (202)
T ss_dssp             CSEEEEEEECTTSSHHHHHHHHHHHHCT
T ss_pred             CCEEEEEECCCCCChHHHHHHHHHHcCC
Confidence            4579999999999999999999988864

>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=91.71  E-value=0.5  Score=51.53  Aligned_cols=32  Identities=25%  Similarity=0.247  Sum_probs=22.2

Q ss_pred             cEEEEECCCCchHHHH-HHHHHHH---cCCcEEEEc
Q 005987          179 NVLVITGQAGVGKTAT-VRQIASH---LGARLYEWD  210 (666)
Q Consensus       179 k~LLL~GPpG~GKTtl-a~~LAke---lg~~viE~n  210 (666)
                      +.+|+.||+|+|||++ +-.+...   -+..++.+.
T Consensus        22 ~~vlv~a~TGsGKT~~~~l~il~~~~~~~~~~lvl~   57 (459)
T 2z83_A           22 QMTVLDLHPGSGKTRKILPQIIKDAIQQRLRTAVLA   57 (459)
T ss_dssp             CEEEECCCTTSCTTTTHHHHHHHHHHHTTCCEEEEE
T ss_pred             CcEEEECCCCCCHHHHHHHHHHHHHHhCCCcEEEEC
Confidence            5899999999999997 3343332   255565554

>2qm8_A GTPase/ATPase; G protein, G3E, metallochaperone, chaperone; HET: MSE; 1.70A {Methylobacterium extorquens} SCOP: c.37.1.10 PDB: 2qm7_A*

Probab=91.71  E-value=0.093  Score=55.06  Aligned_cols=24  Identities=42%  Similarity=0.559  Sum_probs=22.1

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      ..+.|.||||+||||++++|+..+
T Consensus        56 ~~v~i~G~~GaGKSTLl~~l~g~~   79 (337)
T 2qm8_A           56 IRVGITGVPGVGKSTTIDALGSLL   79 (337)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHhh
Confidence            589999999999999999999765

>2wjg_A FEOB, ferrous iron transport protein B homolog; membrane G-proteins, cell membrane, ION transport, transmembrane; HET: GDP; 2.20A {Methanocaldococcus jannaschii}

Probab=91.35  E-value=0.097  Score=48.86  Aligned_cols=23  Identities=17%  Similarity=0.420  Sum_probs=20.6

Q ss_pred             cEEEEECCCCchHHHHHHHHHHH
Q 005987          179 NVLVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAke  201 (666)
                      ..++|.|++|+||||+++.++..
T Consensus         8 ~~i~lvG~~gvGKStL~~~l~~~   30 (188)
T 2wjg_A            8 YEIALIGNPNVGKSTIFNALTGE   30 (188)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHTT
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            36999999999999999999864

>1ky3_A GTP-binding protein YPT7P; vesicular traffic, GTP hydrolysis, YPT/RAB protein, endocytosis, hydrolase, endocytosis/exocytosis complex; HET: GDP; 1.35A {Saccharomyces cerevisiae} SCOP: c.37.1.8 PDB: 1ky2_A*

Probab=91.29  E-value=0.11  Score=47.94  Aligned_cols=23  Identities=30%  Similarity=0.564  Sum_probs=20.4

Q ss_pred             EEEEECCCCchHHHHHHHHHHHc
Q 005987          180 VLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      .++|.|++|+||||++..+....
T Consensus        10 ~i~v~G~~~~GKSsli~~l~~~~   32 (182)
T 1ky3_A           10 KVIILGDSGVGKTSLMHRYVNDK   32 (182)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHHhCc
Confidence            58999999999999999988753

>2gks_A Bifunctional SAT/APS kinase; transferase, sulfurylase; HET: ADP; 2.31A {Aquifex aeolicus}

Probab=91.26  E-value=0.14  Score=57.24  Aligned_cols=25  Identities=24%  Similarity=0.310  Sum_probs=23.1

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLG  203 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg  203 (666)
                      ..++|+|++|+||||+++.|++.++
T Consensus       373 ~~I~l~G~~GsGKSTia~~La~~L~  397 (546)
T 2gks_A          373 FCVWLTGLPCAGKSTIAEILATMLQ  397 (546)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             eEEEccCCCCCCHHHHHHHHHHHhh
Confidence            5799999999999999999999874

>2dpy_A FLII, flagellum-specific ATP synthase; beta barrel, alpha-beta structure, hydrolase; HET: ADP; 2.40A {Salmonella typhimurium}

Probab=91.24  E-value=0.15  Score=55.44  Aligned_cols=29  Identities=21%  Similarity=0.263  Sum_probs=25.2

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEE
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLY  207 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~vi  207 (666)
                      ..+.|.||+||||||+++.||........
T Consensus       158 q~~~IvG~sGsGKSTLl~~Iag~~~~~~G  186 (438)
T 2dpy_A          158 QRMGLFAGSGVGKSVLLGMMARYTRADVI  186 (438)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHHSCCSEE
T ss_pred             CEEEEECCCCCCHHHHHHHHhcccCCCeE
Confidence            47999999999999999999999865543

>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin nucleotide-binding; 2.30A {Sulfolobus solfataricus}

Probab=91.18  E-value=0.56  Score=54.06  Aligned_cols=32  Identities=28%  Similarity=0.269  Sum_probs=22.8

Q ss_pred             cEEEEECCCCchHHHHHHHHH-HH---cCCcEEEEc
Q 005987          179 NVLVITGQAGVGKTATVRQIA-SH---LGARLYEWD  210 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LA-ke---lg~~viE~n  210 (666)
                      +.+|++||+|+|||+.+-..+ +.   -+..++.+.
T Consensus        47 ~~~lv~apTGsGKT~~~~l~il~~~~~~~~~il~i~   82 (715)
T 2va8_A           47 NRLLLTSPTGSGKTLIAEMGIISFLLKNGGKAIYVT   82 (715)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHHHHHHHSCSEEEEEC
T ss_pred             CcEEEEcCCCCcHHHHHHHHHHHHHHHCCCeEEEEe
Confidence            579999999999999984443 22   255555544

>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=91.14  E-value=0.84  Score=48.69  Aligned_cols=32  Identities=25%  Similarity=0.265  Sum_probs=25.2

Q ss_pred             EEEEECCCCchHHHHHHHHHHHc----CCcEEEEcC
Q 005987          180 VLVITGQAGVGKTATVRQIASHL----GARLYEWDT  211 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkel----g~~viE~na  211 (666)
                      .+|+.+|+|+|||.++-.++.++    +..++-+-.
T Consensus        25 ~~ll~~~tG~GKT~~~~~~~~~~~~~~~~~~liv~P   60 (494)
T 1wp9_A           25 NCLIVLPTGLGKTLIAMMIAEYRLTKYGGKVLMLAP   60 (494)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHHHHHSCSCEEEECS
T ss_pred             CEEEEcCCCCCHHHHHHHHHHHHHhcCCCeEEEEEC
Confidence            58999999999999998887765    556665543

>2www_A Methylmalonic aciduria type A protein, mitochondrial; transport protein, nucleotide-binding; HET: GDP 2PE; 2.64A {Homo sapiens}

Probab=91.08  E-value=0.28  Score=51.58  Aligned_cols=24  Identities=21%  Similarity=0.375  Sum_probs=22.0

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      ..+.|.|+||+||||++..|+..+
T Consensus        75 ~~v~lvG~pgaGKSTLln~L~~~~   98 (349)
T 2www_A           75 FRVGLSGPPGAGKSTFIEYFGKML   98 (349)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             eEEEEEcCCCCCHHHHHHHHHHHh
Confidence            579999999999999999999865

>2zpa_A Uncharacterized protein YPFI; RNA modification enzyme, RNA helicase, acetyltransferase, GCN5 acetyltransferase; HET: ACO ADP; 2.35A {Escherichia coli K12}

Probab=91.03  E-value=0.37  Score=54.93  Aligned_cols=35  Identities=29%  Similarity=0.399  Sum_probs=28.5

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTP  214 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~  214 (666)
                      .+.+|+|++|.|||+++-.++..+...+ -+.+|..
T Consensus       193 ~~~vlta~RGRGKSa~lG~~~a~~~~~~-~vtAP~~  227 (671)
T 2zpa_A          193 GVAAVTAARGRGKSALAGQLISRIAGRA-IVTAPAK  227 (671)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHHSSSCE-EEECSSC
T ss_pred             CeEEEecCCCCCHHHHHHHHHHHHHhCc-EEECCCH
Confidence            4689999999999999999999886553 5566653

>1nij_A Hypothetical protein YJIA; structural genomics, P-loop protein, GTP binding, structure function project, S2F, unknown function; 2.00A {Escherichia coli} SCOP: c.37.1.10 d.237.1.1

Probab=90.87  E-value=0.093  Score=54.52  Aligned_cols=24  Identities=38%  Similarity=0.559  Sum_probs=22.0

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      ++++|+||.|+||||+++.|+...
T Consensus         5 ~v~~i~G~~GaGKTTll~~l~~~~   28 (318)
T 1nij_A            5 AVTLLTGFLGAGKTTLLRHILNEQ   28 (318)
T ss_dssp             EEEEEEESSSSSCHHHHHHHHHSC
T ss_pred             cEEEEEecCCCCHHHHHHHHHhhc
Confidence            489999999999999999999865

>2npi_A Protein CLP1; CLP1-PCF11 complex, ATP binding, ternary complex, transcript; HET: ATP; 2.95A {Saccharomyces cerevisiae}

Probab=90.87  E-value=0.1  Score=57.20  Aligned_cols=24  Identities=33%  Similarity=0.416  Sum_probs=22.0

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      ..+.|.||+||||||++++|+.-+
T Consensus       139 e~v~IvGpnGsGKSTLlr~L~Gl~  162 (460)
T 2npi_A          139 PRVVIVGGSQTGKTSLSRTLCSYA  162 (460)
T ss_dssp             CCEEEEESTTSSHHHHHHHHHHTT
T ss_pred             CEEEEECCCCCCHHHHHHHHhCcc
Confidence            479999999999999999999865

>3ug7_A Arsenical pump-driving ATPase; tail-anchored, membrane protein, targeting factor, ATP-bindi TRC40, ARSA, nucleotide-binding; HET: ADP; 2.90A {Methanocaldococcus jannaschii} PDB: 3ug6_A*

Probab=90.70  E-value=0.21  Score=52.58  Aligned_cols=35  Identities=29%  Similarity=0.402  Sum_probs=29.5

Q ss_pred             ccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcCC
Q 005987          178 TNVLVITGQAGVGKTATVRQIASHL---GARLYEWDTP  212 (666)
Q Consensus       178 ~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~nas  212 (666)
                      ..+++++|..|+||||++..+|..+   |.+++-+++-
T Consensus        26 ~~i~v~sgKGGvGKTTvA~~LA~~lA~~G~rVLlvD~D   63 (349)
T 3ug7_A           26 TKYIMFGGKGGVGKTTMSAATGVYLAEKGLKVVIVSTD   63 (349)
T ss_dssp             CEEEEEECSSSTTHHHHHHHHHHHHHHSSCCEEEEECC
T ss_pred             CEEEEEeCCCCccHHHHHHHHHHHHHHCCCeEEEEeCC
Confidence            3688999999999999999988776   8888877653

>3cio_A ETK, tyrosine-protein kinase ETK; WZC, escherichia coli tyrosine kinase domain, signaling protein, transferase, inner membrane, membrane; 2.50A {Escherichia coli}

Probab=90.64  E-value=0.44  Score=48.89  Aligned_cols=53  Identities=23%  Similarity=0.310  Sum_probs=36.9

Q ss_pred             HHHHHHHHHHHHhhcCCCCCCCccEEEEECC-CCchHHHHHHHHHHHc---CCcEEEEcCC
Q 005987          156 KKVEEVRAWFEERLGDSKDKFSTNVLVITGQ-AGVGKTATVRQIASHL---GARLYEWDTP  212 (666)
Q Consensus       156 k~i~el~~wL~~~~~~~~g~~~~k~LLL~GP-pG~GKTtla~~LAkel---g~~viE~nas  212 (666)
                      +.++.|+.-|.-...   +.. .++++++|+ +|+||||++..||..+   |.+|+-+++-
T Consensus        86 Ea~r~lrt~l~~~~~---~~~-~kvI~vts~kgG~GKTtva~nLA~~lA~~G~rVLLID~D  142 (299)
T 3cio_A           86 EAVRALRTSLHFAMM---ETE-NNILMITGATPDSGKTFVSSTLAAVIAQSDQKVLFIDAD  142 (299)
T ss_dssp             HHHHHHHHHHHHHTS---SCS-CCEEEEEESSSSSCHHHHHHHHHHHHHHTTCCEEEEECC
T ss_pred             HHHHHHHHHHHHhcc---CCC-CeEEEEECCCCCCChHHHHHHHHHHHHhCCCcEEEEECC
Confidence            456666666654322   222 268888887 8999999998888876   7888877653

>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=90.62  E-value=0.12  Score=48.14  Aligned_cols=23  Identities=26%  Similarity=0.494  Sum_probs=20.5

Q ss_pred             cEEEEECCCCchHHHHHHHHHHH
Q 005987          179 NVLVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAke  201 (666)
                      -.++|.|+||+||||++..++..
T Consensus         5 ~ki~ivG~~g~GKStLl~~l~~~   27 (172)
T 2gj8_A            5 MKVVIAGRPNAGKSSLLNALAGR   27 (172)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHTS
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            35889999999999999999875

>1pui_A ENGB, probable GTP-binding protein ENGB; structural genomics, nysgxrc T16, GTPase, PSI, protein structure initiative; 2.00A {Escherichia coli} SCOP: c.37.1.8

Probab=90.58  E-value=0.059  Score=51.53  Aligned_cols=23  Identities=13%  Similarity=0.423  Sum_probs=20.1

Q ss_pred             cEEEEECCCCchHHHHHHHHHHH
Q 005987          179 NVLVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAke  201 (666)
                      ..+.|.|++|+||||+++.++..
T Consensus        27 ~~v~lvG~~g~GKSTLl~~l~g~   49 (210)
T 1pui_A           27 IEVAFAGRSNAGKSSALNTLTNQ   49 (210)
T ss_dssp             EEEEEEECTTSSHHHHHTTTCCC
T ss_pred             cEEEEECCCCCCHHHHHHHHhCC
Confidence            46999999999999999988643

>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=90.54  E-value=0.47  Score=47.93  Aligned_cols=53  Identities=23%  Similarity=0.263  Sum_probs=37.2

Q ss_pred             HHHHHHHHHHHHhhcCCCCCCCccEEEEECC-CCchHHHHHHHHHHHc---CCcEEEEcCC
Q 005987          156 KKVEEVRAWFEERLGDSKDKFSTNVLVITGQ-AGVGKTATVRQIASHL---GARLYEWDTP  212 (666)
Q Consensus       156 k~i~el~~wL~~~~~~~~g~~~~k~LLL~GP-pG~GKTtla~~LAkel---g~~viE~nas  212 (666)
                      +.++.|+.-|.-...   ++. .+.++++|+ +|+||||++..||..+   |.+|+-+++-
T Consensus        64 Ea~r~lrt~l~~~~~---~~~-~kvI~vts~kgG~GKTt~a~nLA~~lA~~G~rVLLID~D  120 (271)
T 3bfv_A           64 EKFRGIRSNIMFANP---DSA-VQSIVITSEAPGAGKSTIAANLAVAYAQAGYKTLIVDGD  120 (271)
T ss_dssp             HHHHHHHHHHHHSST---TCC-CCEEEEECSSTTSSHHHHHHHHHHHHHHTTCCEEEEECC
T ss_pred             HHHHHHHHHHHhhcc---CCC-CeEEEEECCCCCCcHHHHHHHHHHHHHhCCCeEEEEeCC
Confidence            556666666654221   222 367888876 8999999999888876   7888877653

>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=90.53  E-value=0.51  Score=54.46  Aligned_cols=33  Identities=15%  Similarity=0.173  Sum_probs=23.1

Q ss_pred             cEEEEECCCCchHHHHHH-HHHHHc---CCcEEEEcC
Q 005987          179 NVLVITGQAGVGKTATVR-QIASHL---GARLYEWDT  211 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~-~LAkel---g~~viE~na  211 (666)
                      +.+|++||+|+|||+++. .+.+.+   +..++.+.+
T Consensus        40 ~~~lv~apTGsGKT~~~~l~il~~~~~~~~~~l~i~P   76 (720)
T 2zj8_A           40 KNALISIPTASGKTLIAEIAMVHRILTQGGKAVYIVP   76 (720)
T ss_dssp             CEEEEECCGGGCHHHHHHHHHHHHHHHHCSEEEEECS
T ss_pred             CcEEEEcCCccHHHHHHHHHHHHHHHhCCCEEEEEcC
Confidence            589999999999999873 333222   556665543

>1m7b_A RND3/RHOE small GTP-binding protein; small GTPase, signaling protein; HET: GTP; 2.00A {Homo sapiens} SCOP: c.37.1.8 PDB: 2v55_B*

Probab=90.52  E-value=0.13  Score=48.17  Aligned_cols=22  Identities=32%  Similarity=0.507  Sum_probs=20.1

Q ss_pred             EEEEECCCCchHHHHHHHHHHH
Q 005987          180 VLVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAke  201 (666)
                      .++|.|++|+||||+++.++..
T Consensus         9 ki~v~G~~~vGKSsli~~l~~~   30 (184)
T 1m7b_A            9 KIVVVGDSQCGKTALLHVFAKD   30 (184)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            4889999999999999999875

>3qks_A DNA double-strand break repair RAD50 ATPase; RECA-like fold, coiled-coils, ATPase, exonuclease, endonucle binding, DNA binding; HET: DNA; 2.10A {Pyrococcus furiosus} PDB: 3qkr_A*

Probab=90.47  E-value=0.14  Score=49.37  Aligned_cols=26  Identities=31%  Similarity=0.379  Sum_probs=23.3

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGA  204 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~  204 (666)
                      ...+|+||.|+||||++.+|.-.++.
T Consensus        24 ~~~~I~G~NgsGKStil~ai~~~l~g   49 (203)
T 3qks_A           24 GINLIIGQNGSGKSSLLDAILVGLYW   49 (203)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHHT
T ss_pred             CeEEEEcCCCCCHHHHHHHHHHHhcC
Confidence            58999999999999999999887754

>1udx_A The GTP-binding protein OBG; TGS domain, riken structural genomics/proteomics initiative, RSGI, structural genomics; 2.07A {Thermus thermophilus} SCOP: b.117.1.1 c.37.1.8 d.242.1.1

Probab=90.46  E-value=0.88  Score=49.02  Aligned_cols=22  Identities=14%  Similarity=0.279  Sum_probs=20.2

Q ss_pred             EEEEECCCCchHHHHHHHHHHH
Q 005987          180 VLVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAke  201 (666)
                      .+.|.||||+||||++++|+..
T Consensus       159 ~VgLVG~~gAGKSTLL~~Lsg~  180 (416)
T 1udx_A          159 DVGLVGYPNAGKSSLLAAMTRA  180 (416)
T ss_dssp             SEEEECCGGGCHHHHHHHHCSS
T ss_pred             EEEEECCCCCcHHHHHHHHHcC
Confidence            5889999999999999999875

---

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	666
d1sxja2	253	c.37.1.20 (A:295-547) Replication factor C1 {Baker	2e-17
d1sxje2	252	c.37.1.20 (E:4-255) Replication factor C5 {Baker's	4e-15
d1sxjd2	237	c.37.1.20 (D:26-262) Replication factor C2 {Baker'	6e-12
d1njfa_	239	c.37.1.20 (A:) delta prime subunit of DNA polymera	4e-11
d1iqpa2	231	c.37.1.20 (A:2-232) Replication factor C {Archaeon	1e-09
d1sxjb2	224	c.37.1.20 (B:7-230) Replication factor C4 {Baker's	1e-09
d1sxjc2	227	c.37.1.20 (C:12-238) Replication factor C3 {Baker'	5e-08
d1w5sa2	287	c.37.1.20 (A:7-293) CDC6-like protein APE0152, N-t	1e-06
d1a5ta2	207	c.37.1.20 (A:1-207) delta prime subunit of DNA pol	2e-04
d1fnna2	276	c.37.1.20 (A:1-276) CDC6, N-domain {Archaeon Pyrob	6e-04
d1ixsb2	239	c.37.1.20 (B:4-242) Holliday junction helicase Ruv	0.001
d1in4a2	238	c.37.1.20 (A:17-254) Holliday junction helicase Ru	0.001

>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 = 80.6 bits (197), Expect = 2e-17
 Identities = 49/262 (18%), Positives = 85/262 (32%), Gaps = 35/262 (13%)

Query: 137 QLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFS---------TNVLVITGQA 187
           +LW  KY P +L+++   +  V +++ W        K+ F              ++ G  
Sbjct: 2   KLWTVKYAPTNLQQVCGNKGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPP 61

Query: 188 GVGKTATVRQIASHLGARLYEWDTPTPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRY 247
           G+GKT     +A  LG  + E +              K  L+  S +  F++  E     
Sbjct: 62  GIGKTTAAHLVAQELGYDILEQNASDVRSKTLLNAGVKNALDNMSVVGYFKHNEEAQNLN 121

Query: 248 GSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHIPTAVVLTECGKAD 307
           G              ++++D++   +G       +        ST +          K  
Sbjct: 122 GKHF-----------VIIMDEVDGMSGGDRGGVGQLAQFCRKTSTPLILICNERNLPKMR 170

Query: 308 SVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQA 367
             D      +                      SIK  L  I  +E++ L    ID + Q 
Sbjct: 171 PFDRVCLDIQF---------------RRPDANSIKSRLMTIAIREKFKLDPNVIDRLIQT 215

Query: 368 SGGDIRQAITSLQFSSLKQDPM 389
           + GDIRQ I  L   S     +
Sbjct: 216 TRGDIRQVINLLSTISTTTKTI 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 = 73.3 bits (178), Expect = 4e-15
 Identities = 36/264 (13%), Positives = 88/264 (33%), Gaps = 19/264 (7%)

Query: 139 WAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQI 198
           W +KY+P+SL  L+   +    +++  +      + +   ++L + G  G GK      +
Sbjct: 1   WVDKYRPKSLNALSHNEELTNFLKSLSD------QPRDLPHLL-LYGPNGTGKKTRCMAL 53

Query: 199 ASHLGARLYEWDTPTPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGES 258
              +               ++++      LE       +   +       +    I    
Sbjct: 54  LESIFGPGVYRL---KIDVRQFVTASNRKLELNVVSSPYHLEITPSDMGNNDRIVIQELL 110

Query: 259 KSSAILLIDDLPVTNGRTAFERLRQCLLLLV-----RSTHIPTAVVLTECGKADSVDSTA 313
           K  A   ++ +   + +       +C+++       +         + +  K   +    
Sbjct: 111 KEVAQ--MEQVDFQDSKDGLAHRYKCVIINEANSLTKDAQAALRRTMEKYSKNIRLIMVC 168

Query: 314 QSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQ-IDLVAQASGGDI 372
            S   + + +           P  +       S +   E+  L T+  +  +AQAS G++
Sbjct: 169 DSMSPIIAPIKSQCLLIRCPAPSDSEISTIL-SDVVTNERIQLETKDILKRIAQASNGNL 227

Query: 373 RQAITSLQFSSLKQDPMLNLSLSI 396
           R ++  L+  +L  +  L  S  I
Sbjct: 228 RVSLLMLESMALNNELALKSSSPI 251

>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 = 64.0 bits (154), Expect = 6e-12
 Identities = 39/253 (15%), Positives = 74/253 (29%), Gaps = 32/253 (12%)

Query: 139 WAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQI 198
           W EKY+P++L+E+  Q   V  ++   +              ++  G  G GKT+T+  +
Sbjct: 2   WVEKYRPKNLDEVTAQDHAVTVLKKTLK------SANLPH--MLFYGPPGTGKTSTILAL 53

Query: 199 ASHLGARLYEWDTPTPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGES 258
              L         P     +    N       +   ++ +NF        S         
Sbjct: 54  TKELYG-------PDLMKSRILELNASDERGISIVREKVKNFARLTVSKPSKHDLENYPC 106

Query: 259 KSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHIPTAVVLTECGKADSVDSTAQSFEE 318
               I+++D+             R        +        +T                 
Sbjct: 107 PPYKIIILDEADSMTADAQSALRRTMETYSGVTRFCLICNYVTRIIDPL----------- 155

Query: 319 LQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASGGDIRQAITS 378
                  +   K     +   +    L  I  QE        ++ +   S GD+R+ IT 
Sbjct: 156 ------ASQCSKFRFKALDASNAIDRLRFISEQENVKCDDGVLERILDISAGDLRRGITL 209

Query: 379 LQFSSLKQDPMLN 391
           LQ +S     + +
Sbjct: 210 LQSASKGAQYLGD 222

>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 = 61.3 bits (148), Expect = 4e-11
 Identities = 40/249 (16%), Positives = 78/249 (31%), Gaps = 25/249 (10%)

Query: 139 WAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQI 198
            A K++P++  ++  Q   +  +             +   +  + +G  GVGKT+  R +
Sbjct: 2   LARKWRPQTFADVVGQEHVLTALANGLS------LGRIH-HAYLFSGTRGVGKTSIARLL 54

Query: 199 ASHLGARLYEWDTPTPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGES 258
           A  L        TP               ++           VE  R         P   
Sbjct: 55  AKGLNCETGITATPCGVCDNCREIEQGRFVDLIEIDAASRTKVEDTRDLLDNVQYAPARG 114

Query: 259 KSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHIPTAVVLTECGKADSVDSTAQSFEE 318
           +   + LID++ + + R +F  L + L              L        +  T  S   
Sbjct: 115 RFK-VYLIDEVHMLS-RHSFNALLKTL-----EEPPEHVKFLLATTDPQKLPVTILSRCL 167

Query: 319 LQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASGGDIRQAITS 378
              +             +    I+  L  I  +E  +     + L+A+A+ G +R A++ 
Sbjct: 168 QFHL-----------KALDVEQIRHQLEHILNEEHIAHEPRALQLLARAAEGSLRDALSL 216

Query: 379 LQFSSLKQD 387
              +    D
Sbjct: 217 TDQAIASGD 225

>d1iqpa2 c.37.1.20 (A:2-232) Replication factor C {Archaeon Pyrococcus furiosus [TaxId: 2261]} Length = 231

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]

 Score = 57.3 bits (137), Expect = 1e-09
 Identities = 45/248 (18%), Positives = 81/248 (32%), Gaps = 43/248 (17%)

Query: 136 QQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATV 195
           ++ W EKY+P+ L+++  Q   V+ ++ + +              L+  G  GVGKT   
Sbjct: 11  EKPWVEKYRPQRLDDIVGQEHIVKRLKHYVK------TGSMP--HLLFAGPPGVGKTTAA 62

Query: 196 RQIASHLGARLYEWDTPTPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIP 255
             +A  L                 +  N +      +  DE    V R +          
Sbjct: 63  LALAREL-----------------FGENWRHNFLELNASDERGINVIREKVKEFARTKPI 105

Query: 256 GESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHIPTAVVLTECGKADSVDSTAQS 315
           G +    I L +   +T          Q  L             +  C  +  +    QS
Sbjct: 106 GGASFKIIFLDEADALTQD-------AQQALRRTMEMFSSNVRFILSCNYSSKIIEPIQS 158

Query: 316 FEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASGGDIRQA 375
              +               P+ +  I + L  I   E   L+ E +  +   + GD+R+A
Sbjct: 159 RCAIFRF-----------RPLRDEDIAKRLRYIAENEGLELTEEGLQAILYIAEGDMRRA 207

Query: 376 ITSLQFSS 383
           I  LQ ++
Sbjct: 208 INILQAAA 215

>d1sxjb2 c.37.1.20 (B:7-230) Replication factor C4 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 224

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]

 Score = 56.6 bits (135), Expect = 1e-09
 Identities = 34/245 (13%), Positives = 89/245 (36%), Gaps = 42/245 (17%)

Query: 139 WAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQI 198
           W EKY+P+ L ++   ++ ++ ++   ++         +   ++I+G  G+GKT +V  +
Sbjct: 5   WVEKYRPQVLSDIVGNKETIDRLQQIAKDG--------NMPHMIISGMPGIGKTTSVHCL 56

Query: 199 ASHLGARLYEWDTPTPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGES 258
           A  L                      +        +D   N ++   +     P    + 
Sbjct: 57  AHELLG------------RSYADGVLELNASDDRGIDVVRNQIKHFAQKKLHLPPGKHK- 103

Query: 259 KSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHIPTAVVLTECGKADSVDSTAQSFEE 318
               I+++D+              Q  L      +  +      C +++ +         
Sbjct: 104 ----IVILDEADSMTAG------AQQALRRTMELYSNSTRFAFACNQSNKIIEP------ 147

Query: 319 LQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASGGDIRQAITS 378
                + +    +  + +++  + + L +I + E    + + ++ +   + GD+RQAI +
Sbjct: 148 -----LQSQCAILRYSKLSDEDVLKRLLQIIKLEDVKYTNDGLEAIIFTAEGDMRQAINN 202

Query: 379 LQFSS 383
           LQ + 
Sbjct: 203 LQSTV 207

>d1sxjc2 c.37.1.20 (C:12-238) Replication factor C3 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 227

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]

 Score = 52.0 bits (123), Expect = 5e-08
 Identities = 43/249 (17%), Positives = 82/249 (32%), Gaps = 43/249 (17%)

Query: 139 WAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQI 198
           W EKY+P +L+E+  Q + +  VR + +      + K     L+  G  G GKT+T+  +
Sbjct: 4   WVEKYRPETLDEVYGQNEVITTVRKFVD------EGKLPH--LLFYGPPGTGKTSTIVAL 55

Query: 199 ASHLGARLYEWDTPTPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGES 258
           A  +  + Y           E   +   G++      +      +I   G          
Sbjct: 56  AREIYGKNYSNM------VLELNASDDRGIDVVRNQIKDFASTRQIFSKGFK-------- 101

Query: 259 KSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHIPTAVVLTECGKADSVDSTAQSFEE 318
               ++++D+              Q  L  V   +            A  +     S   
Sbjct: 102 ----LIILDEADAMTNA------AQNALRRVIERYTKNTRFCVLANYAHKLTPALLSQCT 151

Query: 319 LQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASGGDIRQAITS 378
                           P+   +I+R ++ +   E+  LS      + + S GD+R+ +  
Sbjct: 152 RFRF-----------QPLPQEAIERRIANVLVHEKLKLSPNAEKALIELSNGDMRRVLNV 200

Query: 379 LQFSSLKQD 387
           LQ      D
Sbjct: 201 LQSCKATLD 209

>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 = 48.2 bits (113), Expect = 1e-06
 Identities = 29/257 (11%), Positives = 72/257 (28%), Gaps = 15/257 (5%)

Query: 137 QLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVR 196
           +++ E Y P  L     + + +   R +    L  +       +    G+ G+GKT   +
Sbjct: 7   RVFDENYIPPELRVRRGEAEAL--ARIYLNRLLSGAGLSDVNMIYGSIGRVGIGKTTLAK 64

Query: 197 QIASHLGARLYEWDTPTPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPG 256
                +     +        +    +        +  + +    ++              
Sbjct: 65  FTVKRVSEAAAKEGLTVKQAYVNAFNAPNLYTILSLIVRQTGYPIQVRGAPALDILKALV 124

Query: 257 ESKSSA------ILLIDDLPVTNGRTAFERLRQCLLLLVRSTHIPTAVVLTECGKADSVD 310
           ++          IL      +++ R A E L   L +            +     A  V 
Sbjct: 125 DNLYVENHYLLVILDEFQSMLSSPRIAAEDLYTLLRVHEEIPSRDGVNRIGFLLVASDVR 184

Query: 311 STAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICR-QEQYSLSTEQIDLVAQASG 369
           + +   E++  +    G +       +         +              ++L++   G
Sbjct: 185 ALSYMREKIPQVESQIGFKLHLPAYKSRELYTILEQRAELGLRDTVWEPRHLELISDVYG 244

Query: 370 ------GDIRQAITSLQ 380
                 G  R+AI +L+
Sbjct: 245 EDKGGDGSARRAIVALK 261

>d1a5ta2 c.37.1.20 (A:1-207) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]} Length = 207

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 = 41.3 bits (95), Expect = 2e-04
 Identities = 22/205 (10%), Positives = 49/205 (23%), Gaps = 26/205 (12%)

Query: 179 NVLVITGQAGVGKTATVRQIA---SHLGARLYEWDTPTPTIWQEYMHNCKTGLEYTSKLD 235
           + L+I    G+G  A +  ++        + ++                        +  
Sbjct: 25  HALLIQALPGMGDDALIYALSRYLLCQQPQGHKSCGHCRGCQLMQAGTHPDYYTLAPEKG 84

Query: 236 EFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHIP 295
           +    V+ +R              +  +       VT+     +     LL  +      
Sbjct: 85  KNTLGVDAVREVTEKLNEHARLGGAKVVW------VTDAALLTDAAANALLKTLEEPPAE 138

Query: 296 TAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYS 355
           T   L        + +                 R   L P         L       + +
Sbjct: 139 TWFFLATREPERLLATLRSRC------------RLHYLAPPPEQYAVTWL-----SREVT 181

Query: 356 LSTEQIDLVAQASGGDIRQAITSLQ 380
           +S + +    + S G    A+   Q
Sbjct: 182 MSQDALLAALRLSAGSPGAALALFQ 206

>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 = 39.8 bits (91), Expect = 6e-04
 Identities = 11/68 (16%), Positives = 30/68 (44%), Gaps = 5/68 (7%)

Query: 138 LWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQ 197
           +++  Y P+ L     + ++++++       L +    +      + G+ G GKT T+R+
Sbjct: 8   VFSPSYVPKRLPH---REQQLQQLDILLGNWLRNPGHHY--PRATLLGRPGTGKTVTLRK 62

Query: 198 IASHLGAR 205
           +      +
Sbjct: 63  LWELYKDK 70

>d1ixsb2 c.37.1.20 (B:4-242) Holliday junction helicase RuvB {Thermus thermophilus [TaxId: 274]} 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: Holliday junction helicase RuvB
species: Thermus thermophilus [TaxId: 274]

 Score = 38.8 bits (89), Expect = 0.001
 Identities = 33/238 (13%), Positives = 67/238 (28%), Gaps = 35/238 (14%)

Query: 145 PRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGA 204
           P++L+E   Q +  +++R + E      +       L++ G  G+GKT     IA  LG 
Sbjct: 5   PKTLDEYIGQERLKQKLRVYLEAAKARKEPLEH---LLLFGPPGLGKTTLAHVIAHELGV 61

Query: 205 RLYEWDTPTPT-IWQEYMHNCKTGLEYTS-KLDEFENFVERIRRYGSTSPSIPGESKSSA 262
            L     P              +  E     +DE      +   +               
Sbjct: 62  NLRVTSGPAIEKPGDLAAILANSLEEGDILFIDEIHRLSRQAEEHL-------------- 107

Query: 263 ILLIDDLPVTNGRTAFERLRQCLLLLVRSTHIPTAVVLTECGKADSVDSTAQSFEELQSI 322
                  P          + Q          +P   ++    +   + +   S   +   
Sbjct: 108 ------YPAMEDFVMDIVIGQGPAARTIRLELPRFTLIGATTRPGLITAPLLSRFGIVEH 161

Query: 323 LVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASGGDIRQAITSLQ 380
                     L   T   + + + +  R     ++ E    + + S G +R A    +
Sbjct: 162 ----------LEYYTPEELAQGVMRDARLLGVRITEEAALEIGRRSRGTMRVAKRLFR 209

>d1in4a2 c.37.1.20 (A:17-254) Holliday junction helicase RuvB {Thermotoga maritima [TaxId: 2336]} Length = 238

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]

 Score = 38.4 bits (88), Expect = 0.001
 Identities = 35/240 (14%), Positives = 73/240 (30%), Gaps = 32/240 (13%)

Query: 141 EKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIAS 200
           +  +P+SL+E   Q    +++    E      + +   +VL + G  G+GKT     IAS
Sbjct: 1   QFLRPKSLDEFIGQENVKKKLSLALE--AAKMRGEVLDHVL-LAGPPGLGKTTLAHIIAS 57

Query: 201 HLGARLYEWDTPTPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKS 260
            L   ++    P      +                 F + + R+ +          E   
Sbjct: 58  ELQTNIHVTSGPVLVKQGD---MAAILTSLERGDVLFIDEIHRLNK--------AVEELL 106

Query: 261 SAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHIPTAVVLTECGKADSVDSTAQSFEELQ 320
            + +    + +  G+    +        +R    P  +V                F    
Sbjct: 107 YSAIEDFQIDIMIGKGPSAKS-------IRIDIQPFTLVGATTRSGLLSSPLRSRF---- 155

Query: 321 SILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASGGDIRQAITSLQ 380
                     + L+  T   +K  + +        +     +++A+ S G  R AI   +
Sbjct: 156 -------GIILELDFYTVKELKEIIKRAASLMDVEIEDAAAEMIAKRSRGTPRIAIRLTK 208

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	666
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	99.97
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	99.97
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	99.97
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	99.96
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	99.96
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	99.94
d1sxje2	252	Replication factor C5 {Baker's yeast (Saccharomyce	99.94
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	99.9
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	99.9
d1a5ta2	207	delta prime subunit of DNA polymerase III, N-domai	99.75
d1ixza_	247	AAA domain of cell division protein FtsH {Thermus	99.72
d1lv7a_	256	AAA domain of cell division protein FtsH {Escheric	99.69
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	99.69
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	99.68
d1e32a2	258	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	99.67
d1r7ra3	265	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	99.6
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	99.58
d1d2na_	246	Hexamerization domain of N-ethylmalemide-sensitive	99.48
d1r6bx2	268	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	99.39
d1qvra2	387	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	99.31
d1jbka_	195	ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}	99.24
d1r6bx3	315	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	99.23
d1svma_	362	Papillomavirus large T antigen helicase domain {Si	99.23
d2gnoa2	198	gamma subunit of DNA polymerase III, N-domain {The	99.21
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	99.18
d1qvra3	315	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	99.09
d1um8a_	364	ClpX {Helicobacter pylori [TaxId: 210]}	98.89
d2fnaa2	283	Archaeal ATPase SSO1545 {Sulfolobus solfataricus [	98.85
d1w44a_	321	NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}	98.85
d1sxja1	146	Replication factor C1 {Baker's yeast (Saccharomyce	98.83
d1ny5a2	247	Transcriptional activator sigm54 (NtrC1), C-termin	98.6
d1g41a_	443	HslU {Haemophilus influenzae [TaxId: 727]}	98.56
d1gvnb_	273	Plasmid maintenance system epsilon/zeta, toxin zet	98.41
d1ye8a1	178	Hypothetical kinase-like protein Aq_1292 {Aquifex	98.36
d1g8pa_	333	ATPase subunit of magnesium chelatase, BchI {Rhodo	98.26
d2a5yb3	277	CED-4, NB-ARC domain {Caenorhabditis elegans [TaxI	98.11
d1kaga_	169	Shikimate kinase (AroK) {Escherichia coli [TaxId:	98.02
d1tuea_	205	Replication protein E1 helicase domain {Human papi	98.01
d1lw7a2	192	Transcriptional regulator NadR, ribosylnicotinamid	97.84
d1rkba_	173	Adenylate kinase {Human (Homo sapiens), isoenzyme	97.82
d2bdta1	176	Hypothetical protein BH3686 {Bacillus halodurans [	97.79
d1zp6a1	176	Hypothetical protein Atu3015 {Agrobacterium tumefa	97.78
d1knqa_	171	Gluconate kinase {Escherichia coli [TaxId: 562]}	97.75
d1qhxa_	178	Chloramphenicol phosphotransferase {Streptomyces v	97.72
d1e6ca_	170	Shikimate kinase (AroK) {Erwinia chrysanthemi [Tax	97.69
d1viaa_	161	Shikimate kinase (AroK) {Campylobacter jejuni [Tax	97.64
d1yj5a2	172	5' polynucleotide kinase-3' phosphatase, C-termina	97.61
d2iyva1	165	Shikimate kinase (AroK) {Mycobacterium tuberculosi	97.6
d1y63a_	174	Probable kinase LmjF30.1890 {Leishmania major [Tax	97.55
d2i3ba1	189	Cancer-related NTPase, C1orf57 {Human (Homo sapien	97.52
d1qf9a_	194	UMP/CMP kinase {Dictyostelium discoideum [TaxId: 4	97.5
d1ls1a2	207	GTPase domain of the signal sequence recognition p	97.47
d1j8yf2	211	GTPase domain of the signal sequence recognition p	97.43
d1ukza_	196	Uridylate kinase {Baker's yeast (Saccharomyces cer	97.41
d3adka_	194	Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}	97.4
d1m8pa3	183	ATP sulfurylase C-terminal domain {Fungus (Penicil	97.38
d1zina1	182	Adenylate kinase {Bacillus stearothermophilus [Tax	97.37
d1ly1a_	152	Polynucleotide kinase, kinase domain {Bacteriophag	97.35
d1x6va3	195	Adenosine-5'phosphosulfate kinase (APS kinase) {Hu	97.34
d1ak2a1	190	Adenylate kinase {Cow (Bos taurus), mitochondrial	97.32
d1teva_	194	UMP/CMP kinase {Human (Homo sapiens) [TaxId: 9606]	97.31
d1ckea_	225	CMP kinase {Escherichia coli [TaxId: 562]}	97.27
d1p9ra_	401	Extracellular secretion NTPase EpsE {Vibrio choler	97.27
d1zaka1	189	Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}	97.26
d2qy9a2	211	GTPase domain of the signal recognition particle r	97.26
d2cdna1	181	Adenylate kinase {Mycobacterium tuberculosis [TaxI	97.25
d1vmaa2	213	GTPase domain of the signal recognition particle r	97.22
d1s3ga1	182	Adenylate kinase {Bacillus globisporus [TaxId: 145	97.2
d1bifa1	213	6-phosphofructo-2-kinase/fructose-2,6-bisphosphata	97.19
d1akya1	180	Adenylate kinase {Baker's yeast (Saccharomyces cer	97.19
d2ak3a1	189	Adenylate kinase {Cow (Bos taurus), mitochondrial	97.17
d1q3ta_	223	CMP kinase {Streptococcus pneumoniae [TaxId: 1313]	97.13
d1khta_	190	Adenylate kinase {Archaeon Methanococcus voltae [T	97.12
d1e4va1	179	Adenylate kinase {Escherichia coli [TaxId: 562]}	97.1
d1okkd2	207	GTPase domain of the signal recognition particle r	97.09
d1u94a1	263	RecA protein, ATPase-domain {Escherichia coli [Tax	97.07
d1np6a_	170	Molybdopterin-guanine dinucleotide biosynthesis pr	97.03
d1a1va1	136	HCV helicase domain {Human hepatitis C virus (HCV)	97.0
d1v43a3	239	Hypothetical protein PH0022, N-terminal domain {Py	96.92
d1wp9a1	200	putative ATP-dependent RNA helicase PF2015 {Pyroco	96.92
d1nksa_	194	Adenylate kinase {Archaeon Sulfolobus acidocaldari	96.87
d2awna2	232	Maltose transport protein MalK, N-terminal domain	96.85
d1r8sa_	160	ADP-ribosylation factor {Human (Homo sapiens), ARF	96.83
d1wb9a2	234	DNA repair protein MutS, the C-terminal domain {Es	96.81
d1u0ja_	267	Rep 40 protein helicase domain {Adeno-associated v	96.81
d2onka1	240	Molybdate/tungstate import ATP-binding protein Wtp	96.81
d1rz3a_	198	Hypothetical protein rbstp0775 {Bacillus stearothe	96.8
d1tf7a2	242	Circadian clock protein KaiC {Synechococcus sp. st	96.72
d1ksha_	165	ADP-ribosylation factor {Mouse (Mus musculus), ARL	96.67
d2fz4a1	206	DNA repair protein RAD25 {Archaeoglobus fulgidus [	96.66
d1xp8a1	268	RecA protein, ATPase-domain {Deinococcus radiodura	96.64
d1mo6a1	269	RecA protein, ATPase-domain {Mycobacterium tubercu	96.6
d1kaoa_	167	Rap2a {Human (Homo sapiens) [TaxId: 9606]}	96.53
d1u8za_	168	Ras-related protein RalA {Cotton-top tamarin (Sagu	96.52
d1ctqa_	166	cH-p21 Ras protein {Human (Homo sapiens) [TaxId: 9	96.51
d1zj6a1	177	ADP-ribosylation factor {Human (Homo sapiens), ARL	96.49
d1gkya_	186	Guanylate kinase {Baker's yeast (Saccharomyces cer	96.48
d1lvga_	190	Guanylate kinase {Mouse (Mus musculus) [TaxId: 100	96.38
d1g2912	240	Maltose transport protein MalK, N-terminal domain	96.38
d1znwa1	182	Guanylate kinase {Mycobacterium tuberculosis [TaxI	96.36
d1ewqa2	224	DNA repair protein MutS, the C-terminal domain {Th	96.35
d1xtqa1	167	GTP-binding protein RheB {Human (Homo sapiens) [Ta	96.33
d1upta_	169	ADP-ribosylation factor {Human (Homo sapiens), ARL	96.3
d1xjca_	165	Molybdopterin-guanine dinucleotide biosynthesis pr	96.29
d1e0sa_	173	ADP-ribosylation factor {Human (Homo sapiens), ARF	96.21
d2erya1	171	r-Ras2 {Human (Homo sapiens) [TaxId: 9606]}	96.19
d1htwa_	158	Hypothetical protein HI0065 {Haemophilus influenza	96.14
d1m7ga_	208	Adenosine-5'phosphosulfate kinase (APS kinase) {Fu	96.13
d2gjsa1	168	Rad {Human (Homo sapiens) [TaxId: 9606]}	96.07
d1nlfa_	274	Hexameric replicative helicase repA {Escherichia c	96.05
d1yksa1	140	YFV helicase domain {Yellow fever virus [TaxId: 11	96.0
d2pmka1	241	Haemolysin B ATP-binding protein {Escherichia coli	95.99
d1nrjb_	209	Signal recognition particle receptor beta-subunit	95.93
d1cr2a_	277	Gene 4 protein (g4p, DNA primase), helicase domain	95.91
d2a5ja1	173	Rab2b {Human (Homo sapiens) [TaxId: 9606]}	95.87
d2p6ra3	202	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	95.76
d1w36d1	359	Exodeoxyribonuclease V alpha chain (RecD) {Escheri	95.74
d2ew1a1	171	Rab30 {Human (Homo sapiens) [TaxId: 9606]}	95.7
d1odfa_	286	Hypothetical protein Ygr205W {Baker's yeast (Sacch	95.69
d2atva1	168	Ras-like estrogen-regulated growth inhibitor, RERG	95.67
d1n0wa_	242	DNA repair protein Rad51, catalytic domain {Human	95.58
d1z08a1	167	Rab21 {Human (Homo sapiens) [TaxId: 9606]}	95.57
d1z0fa1	166	Rab14 {Human (Homo sapiens) [TaxId: 9606]}	95.57
d1uj2a_	213	Uridine-cytidine kinase 2 {Human (Homo sapiens) [T	95.55
d1kgda_	178	Guanylate kinase-like domain of Cask {Human (Homo	95.55
d1s96a_	205	Guanylate kinase {Escherichia coli [TaxId: 562]}	95.55
d1uf9a_	191	Dephospho-CoA kinase {Thermus thermophilus [TaxId:	95.49
d1r2qa_	170	Rab5a {Human (Homo sapiens) [TaxId: 9606]}	95.48
d1tf7a1	242	Circadian clock protein KaiC {Synechococcus sp. st	95.47
d1yzqa1	164	Rab6 {Human (Homo sapiens) [TaxId: 9606]}	95.43
d2fn4a1	173	r-Ras {Human (Homo sapiens) [TaxId: 9606]}	95.42
d1zd9a1	164	ADP-ribosylation factor {Human (Homo sapiens), ARL	95.41
d1z2aa1	164	Rab23 {Mouse (Mus musculus) [TaxId: 10090]}	95.4
d1ji0a_	240	Branched chain aminoacid ABC transporter {Thermoto	95.37
d1c1ya_	167	Rap1A {Human (Homo sapiens) [TaxId: 9606]}	95.36
d2f7sa1	186	Rab27b {Human (Homo sapiens) [TaxId: 9606]}	95.34
d3raba_	169	Rab3a {Rat (Rattus norvegicus) [TaxId: 10116]}	95.3
d1szpa2	251	DNA repair protein Rad51, catalytic domain {Baker'	95.26
d1sq5a_	308	Pantothenate kinase PanK {Escherichia coli [TaxId:	95.26
d1fzqa_	176	ADP-ribosylation factor {Mouse (Mus musculus), ARL	95.2
d1pzna2	254	DNA repair protein Rad51, catalytic domain {Archae	95.18
d1mkya1	171	Probable GTPase Der, N-terminal and middle domains	95.16
d2g3ya1	172	GTP-binding protein GEM {Human (Homo sapiens) [Tax	95.15
d1v5wa_	258	Meiotic recombination protein DMC1/LIM15 homolog {	95.11
d1u0la2	225	Probable GTPase EngC (YjeQ), C-terminal domain {Th	95.08
d2bmea1	174	Rab4a {Human (Homo sapiens) [TaxId: 9606]}	95.06
d1z0ja1	167	Rab-22a {Mouse (Mus musculus) [TaxId: 10090]}	94.91
d1nn5a_	209	Thymidylate kinase {Human (Homo sapiens) [TaxId: 9	94.89
d1yrba1	244	ATP(GTP)-binding protein PAB0955 {Pyrococcus abyss	94.89
d1deka_	241	Deoxynucleoside monophosphate kinase {Bacteriophag	94.82
d1gsia_	208	Thymidylate kinase {Mycobacterium tuberculosis [Ta	94.72
d1g6oa_	323	Hexameric traffic ATPase, HP0525 {Helicobacter pyl	94.68
d1vhta_	208	Dephospho-CoA kinase {Escherichia coli [TaxId: 562	94.56
d2vp4a1	197	Deoxyribonucleoside kinase {Fruit fly (Drosophila	94.52
d1moza_	182	ADP-ribosylation factor {Baker's yeast (Saccharomy	94.49
d1wf3a1	178	GTPase Era, N-terminal domain {Thermus thermophilu	94.46
d2f9la1	175	Rab11b {Human (Homo sapiens) [TaxId: 9606]}	94.42
d1sgwa_	200	Putative ABC transporter PF0895 {Pyrococcus furios	94.4
d1kkma_	176	HPr kinase HprK C-terminal domain {Lactobacillus c	94.39
d1x1ra1	169	Ras-related protein M-Ras (XRas) {Mouse (Mus muscu	94.29
d1ek0a_	170	Ypt51 {Baker's yeast (Saccharomyces cerevisiae) [T	94.25
d2i1qa2	258	DNA repair protein Rad51, catalytic domain {Archae	94.18
d2erxa1	171	di-Ras2 {Human (Homo sapiens) [TaxId: 9606]}	94.14
d2fu5c1	173	Rab8a {Mouse (Mus musculus) [TaxId: 10090]}	94.13
d1svia_	195	Probable GTPase EngB {Bacillus subtilis [TaxId: 14	94.12
d1jjva_	205	Dephospho-CoA kinase {Haemophilus influenzae [TaxI	94.03
d2bcgy1	194	GTPase Ytp1 {Baker's yeast (Saccharomyces cerevisi	94.03
d2gj8a1	161	Probable tRNA modification GTPase TrmE (MnmE), G d	93.94
d4tmka_	210	Thymidylate kinase {Escherichia coli [TaxId: 562]}	93.92
d1l2ta_	230	MJ0796 {Archaeon Methanococcus jannaschii [TaxId:	93.89
d2ocpa1	241	Deoxyguanosine kinase {Human (Homo sapiens) [TaxId	93.88
d3d31a2	229	Sulfate/molybdate ABC transporter, ATP-binding pro	93.84
d1knxa2	177	HPr kinase HprK C-terminal domain {Mycoplasma pneu	93.79
d2g6ba1	170	Rab26 {Human (Homo sapiens) [TaxId: 9606]}	93.61
d1ko7a2	169	HPr kinase HprK C-terminal domain {Staphylococcus	93.57
d1x3sa1	177	Rab18 {Human (Homo sapiens) [TaxId: 9606]}	93.53
d3dhwc1	240	Methionine import ATP-binding protein MetN {Escher	93.5
d1i2ma_	170	Ran {Human (Homo sapiens) [TaxId: 9606]}	93.42
d2p67a1	327	LAO/AO transport system kinase ArgK {Escherichia c	93.42
d1uaaa1	306	DEXX box DNA helicase {Escherichia coli, RepD [Tax	93.36
d1oxxk2	242	Glucose transport protein GlcV, N-terminal domain	93.36
d2qtvb1	166	SAR1 {Baker's yeast (Saccharomyces cerevisiae) [Ta	93.35
d1tmka_	214	Thymidylate kinase {Baker's yeast (Saccharomyces c	93.25
d2qm8a1	323	Metallochaperone MeaB {Methylobacterium extorquens	93.19
d1udxa2	180	Obg GTP-binding protein middle domain {Thermus the	93.16
d2fh5b1	207	Signal recognition particle receptor beta-subunit	93.11
d1r0wa_	281	Cystic fibrosis transmembrane conductance regulato	92.96
d2bmfa2	305	Dengue virus helicase {Dengue virus type 2 [TaxId:	92.96
d1p5zb_	241	Deoxycytidine kinase {Human (Homo sapiens) [TaxId:	92.92
d1mv5a_	242	Multidrug resistance ABC transporter LmrA, C-termi	92.88
d1t9ha2	231	Probable GTPase EngC (YjeQ), C-terminal domain {Ba	92.84
d3b60a1	253	Multidrug resistance ABC transporter MsbA, C-termi	92.83
d1jj7a_	251	Peptide transporter Tap1, C-terminal ABC domain {H	92.57
d1byia_	224	Dethiobiotin synthetase {Escherichia coli [TaxId:	92.5
d1f6ba_	186	SAR1 {Chinese hamster (Cricetulus griseus) [TaxId:	92.42
d1pjra1	318	DEXX box DNA helicase {Bacillus stearothermophilus	92.33
d2b8ta1	139	Thymidine kinase, TK1, N-terminal domain {Ureaplas	92.24
d1h65a_	257	Chloroplast protein translocon GTPase Toc34 {Garde	92.22
d1b0ua_	258	ATP-binding subunit of the histidine permease {Sal	91.98
d1ky3a_	175	Rab-related protein ypt7p {Baker's yeast (Saccharo	91.31
d1g16a_	166	Rab-related protein Sec4 {Baker's yeast (Saccharom	91.28
d1ihua1	296	Arsenite-translocating ATPase ArsA {Escherichia co	91.26
d2hyda1	255	Putative multidrug export ATP-binding/permease pro	91.1
d1vpla_	238	Putative ABC transporter TM0544 {Thermotoga mariti	90.94
d1ihua2	279	Arsenite-translocating ATPase ArsA {Escherichia co	90.84
d1vg8a_	184	Rab7 {Rat (Rattus norvegicus) [TaxId: 10116]}	90.81
d1z06a1	165	Rab-33b {Mouse (Mus musculus) [TaxId: 10090]}	90.77
d1g6ha_	254	MJ1267 {Archaeon Methanococcus jannaschii [TaxId:	90.74
g1f2t.1	292	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	90.69
d1wmsa_	174	Rab9a {Human (Homo sapiens) [TaxId: 9606]}	90.68
d1kmqa_	177	RhoA {Human (Homo sapiens) [TaxId: 9606]}	90.47
d2cxxa1	184	GTP-binding protein engB {Pyrococcus horikoshii [T	90.39
d2bv3a2	276	Elongation factor G (EF-G), N-terminal (G) domain	90.25
d1l7vc_	231	ABC transporter involved in vitamin B12 uptake, Bt	90.15
d1a7ja_	288	Phosphoribulokinase {Rhodobacter sphaeroides [TaxI	90.11
d1mh1a_	183	Rac {Human (Homo sapiens) [TaxId: 9606]}	89.69
d1xbta1	133	Thymidine kinase, TK1, N-terminal domain {Human (H	89.62
g1ii8.1	369	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	89.41
d1qhla_	222	Cell division protein MukB {Escherichia coli [TaxI	89.36
d1m7ba_	179	RhoE (RND3) {Mouse (Mus musculus) [TaxId: 10090]}	89.29
d1nija1	222	Hypothetical protein YjiA, N-terminal domain {Esch	89.25
d2atxa1	185	RhoQ {Human (Homo sapiens) [TaxId: 9606]}	89.01
d2ngra_	191	CDC42 {Human (Homo sapiens) [TaxId: 9606]}	88.68
g1xew.1	329	Smc head domain {Pyrococcus furiosus [TaxId: 2261]	88.35
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	87.99
d1xzpa2	160	TrmE GTPase domain {Thermotoga maritima [TaxId: 23	87.96
d1e69a_	308	Smc head domain {Thermotoga maritima [TaxId: 2336]	87.62
d1egaa1	179	GTPase Era, N-terminal domain {Escherichia coli [T	87.54
d1e9ra_	433	Bacterial conjugative coupling protein TrwB {Esche	87.22
d1mkya2	186	Probable GTPase Der, N-terminal and middle domains	86.24
d2dy1a2	267	Elongation factor G (EF-G), N-terminal (G) domain	85.95
d1gm5a3	264	RecG helicase domain {Thermotoga maritima [TaxId:	85.92
d1zcba2	200	Transducin (alpha subunit) {Mouse (Mus musculus) [	85.75
d1lnza2	185	Obg GTP-binding protein middle domain {Bacillus su	85.56
d1puia_	188	Probable GTPase EngB {Escherichia coli [TaxId: 562	85.19
d1wb1a4	179	Elongation factor SelB, N-terminal domain {Methano	85.05
d2bmja1	175	Centaurin gamma 1, G domain {Human (Homo sapiens)	84.94
d2bcjq2	200	Transducin (alpha subunit) {Mouse (Mus musculus) [	84.61
d1lkxa_	684	Myosin S1, motor domain {Dictyostelium discoideum,	84.59
d1p6xa_	333	Thymidine kinase {Equine herpesvirus type 4 [TaxId	84.24
d1azta2	221	Transducin (alpha subunit) {Cow (Bos taurus) [TaxI	83.95
d1cp2a_	269	Nitrogenase iron protein {Clostridium pasteurianum	83.2
d1g7sa4	227	Initiation factor IF2/eIF5b, N-terminal (G) domain	82.8
d1osna_	331	Thymidine kinase {Varicella-zoster virus [TaxId: 1	82.4
d1w1wa_	427	Smc head domain {Baker's yeast (Saccharomyces cere	82.0
d1ys7a2	121	Transcriptional regulatory protein PrrA, N-termina	81.74
d2afhe1	289	Nitrogenase iron protein {Azotobacter vinelandii [	80.76
d1gkub1	237	Helicase-like "domain" of reverse gyrase {Archaeon	80.66
d1mvoa_	121	PhoP receiver domain {Bacillus subtilis [TaxId: 14	80.52

>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=99.97  E-value=1.8e-31  Score=269.83  Aligned_cols=225  Identities=20%  Similarity=0.304  Sum_probs=157.7

Q ss_pred             CCccccccCCCCccccccCHHHHHHHHHHHHHhhcC---------CCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcE
Q 005987          136 QQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGD---------SKDKFSTNVLVITGQAGVGKTATVRQIASHLGARL  206 (666)
Q Consensus       136 ~~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~---------~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~v  206 (666)
                      +++|+|||+|++++||+|+++++++|+.||+.|...         ..+....+++||+|||||||||+|+++|+++++.+
T Consensus         1 ~~lW~eky~P~~~~dlig~~~~~~~L~~~l~~~~~~~~~~~~~~~~~~~~~~~~lll~GPpG~GKTt~a~~la~~~~~~~   80 (253)
T d1sxja2           1 DKLWTVKYAPTNLQQVCGNKGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAAHLVAQELGYDI   80 (253)
T ss_dssp             CCCHHHHTCCSSGGGCCSCHHHHHHHHHHHHTHHHHHHTTTCCCCTTSTTSCSEEEEECSTTSSHHHHHHHHHHHTTCEE
T ss_pred             CCccccCcCCCCHHHhcCCHHHHHHHHHHHHhhhhcchhhhhhhcccCCCCCceEEEECCCCCCHHHHHHHHHHHHHhhh
Confidence            368999999999999999999999999999876421         11233346899999999999999999999999999


Q ss_pred             EEEcCCCchhhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHH
Q 005987          207 YEWDTPTPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLL  286 (666)
Q Consensus       207 iE~nasd~~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~  286 (666)
                      ++++.++.+.....................+   ....        ..........++++||++.+....  ......+.
T Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~--------~~~~~~~~~~vi~ide~~~~~~~~--~~~~~~~~  147 (253)
T d1sxja2          81 LEQNASDVRSKTLLNAGVKNALDNMSVVGYF---KHNE--------EAQNLNGKHFVIIMDEVDGMSGGD--RGGVGQLA  147 (253)
T ss_dssp             EEECTTSCCCHHHHHHTGGGGTTBCCSTTTT---TC------------CCSSTTSEEEEECSGGGCCTTS--TTHHHHHH
T ss_pred             hccccccchhhHHHHHHHHHHhhcchhhhhh---hhhh--------hcccccccceEEEeeeccccccch--hhhhHHHh
Confidence            9999886432111100000000000000000   0000        001112346799999999875432  11222344


Q ss_pred             HHHhcCCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHH
Q 005987          287 LLVRSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQ  366 (666)
Q Consensus       287 ~l~~~~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~  366 (666)
                      ........|+++++++...        ..+..++    + +|..|+|++|+.+++.++|++||.+|++.+++++++.|+.
T Consensus       148 ~~~~~~~~~ii~i~~~~~~--------~~~~~l~----~-~~~~i~f~~~~~~~i~~~l~~i~~~e~i~i~~~~l~~i~~  214 (253)
T d1sxja2         148 QFCRKTSTPLILICNERNL--------PKMRPFD----R-VCLDIQFRRPDANSIKSRLMTIAIREKFKLDPNVIDRLIQ  214 (253)
T ss_dssp             HHHHHCSSCEEEEESCTTS--------STTGGGT----T-TSEEEECCCCCHHHHHHHHHHHHHHHTCCCCTTHHHHHHH
T ss_pred             hhhcccccccccccccccc--------ccccccc----c-eeeeeeccccchhHHHHHHHHHHHHhCCCCCHHHHHHHHH
Confidence            5556666788877765322        1222222    2 6999999999999999999999999999999999999999


Q ss_pred             HcCCcHHHHHHHHHHHhcCC
Q 005987          367 ASGGDIRQAITSLQFSSLKQ  386 (666)
Q Consensus       367 ~s~GDIR~AIn~LQf~~~~~  386 (666)
                      .++||+|+|||.||+++...
T Consensus       215 ~s~GDiR~ai~~L~~~~~~~  234 (253)
T d1sxja2         215 TTRGDIRQVINLLSTISTTT  234 (253)
T ss_dssp             HTTTCHHHHHHHHTHHHHHS
T ss_pred             hCCCcHHHHHHHHHHHHHcC
Confidence            99999999999999998643

>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=99.97  E-value=2.1e-30  Score=258.03  Aligned_cols=203  Identities=19%  Similarity=0.319  Sum_probs=150.5

Q ss_pred             CCccccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCC-----cEEEEc
Q 005987          136 QQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGA-----RLYEWD  210 (666)
Q Consensus       136 ~~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~-----~viE~n  210 (666)
                      +.||+|||||++++|++||++.++.|+.|++.      ++.+  ++||+|||||||||+|+++|++++.     .+++.|
T Consensus         2 ~~pw~eKyrP~~~~d~ig~~~~~~~L~~~~~~------~~~~--~~ll~Gp~G~GKTt~a~~la~~l~~~~~~~~~~~~n   73 (224)
T d1sxjb2           2 QLPWVEKYRPQVLSDIVGNKETIDRLQQIAKD------GNMP--HMIISGMPGIGKTTSVHCLAHELLGRSYADGVLELN   73 (224)
T ss_dssp             CCCHHHHTCCSSGGGCCSCTHHHHHHHHHHHS------CCCC--CEEEECSTTSSHHHHHHHHHHHHHGGGHHHHEEEEC
T ss_pred             CCchHhHhCCCCHHHhcCCHHHHHHHHHHHHc------CCCC--eEEEECCCCCCchhhHHHHHHHHhcccccccccccc
Confidence            57899999999999999999999999999986      4444  6999999999999999999999864     588999


Q ss_pred             CCCchhhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHh
Q 005987          211 TPTPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVR  290 (666)
Q Consensus       211 asd~~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~  290 (666)
                      +++.+..                 ..+...+.........    . ...+.++++|||+|.+...     .+.+|+..++
T Consensus        74 ~~~~~~~-----------------~~i~~~~~~~~~~~~~----~-~~~~~kviiiDe~d~~~~~-----~~~~ll~~~e  126 (224)
T d1sxjb2          74 ASDDRGI-----------------DVVRNQIKHFAQKKLH----L-PPGKHKIVILDEADSMTAG-----AQQALRRTME  126 (224)
T ss_dssp             TTSCCSH-----------------HHHHTHHHHHHHBCCC----C-CTTCCEEEEEESGGGSCHH-----HHHTTHHHHH
T ss_pred             ccccCCc-----------------eehhhHHHHHHHhhcc----C-CCcceEEEEEecccccchh-----HHHHHhhhcc
Confidence            8873321                 1111111111111111    1 1234679999999988653     2334555555


Q ss_pred             cCCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCC
Q 005987          291 STHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASGG  370 (666)
Q Consensus       291 ~~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~s~G  370 (666)
                      ....+.+++++...       ..+.++.|++     ||..|+|++|+.+++.++|.++|.+|++.+++++++.|+..|+|
T Consensus       127 ~~~~~~~~i~~~~~-------~~~i~~~l~s-----r~~~i~~~~~~~~~i~~~l~~i~~~e~~~i~~~~l~~I~~~s~G  194 (224)
T d1sxjb2         127 LYSNSTRFAFACNQ-------SNKIIEPLQS-----QCAILRYSKLSDEDVLKRLLQIIKLEDVKYTNDGLEAIIFTAEG  194 (224)
T ss_dssp             HTTTTEEEEEEESC-------GGGSCHHHHT-----TSEEEECCCCCHHHHHHHHHHHHHHHTCCBCHHHHHHHHHHHTT
T ss_pred             ccccceeeeeccCc-------hhhhhhHHHH-----HHHHhhhcccchhhhHHHHHHHHHhcccCCCHHHHHHHHHHcCC
Confidence            55444333333311       2233344443     69999999999999999999999999999999999999999999


Q ss_pred             cHHHHHHHHHHHhcC
Q 005987          371 DIRQAITSLQFSSLK  385 (666)
Q Consensus       371 DIR~AIn~LQf~~~~  385 (666)
                      |+|.||+.||+++.+
T Consensus       195 d~R~ai~~Lq~~~~~  209 (224)
T d1sxjb2         195 DMRQAINNLQSTVAG  209 (224)
T ss_dssp             CHHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHc
Confidence            999999999998754

>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=99.97  E-value=1.4e-29  Score=252.87  Aligned_cols=202  Identities=21%  Similarity=0.328  Sum_probs=153.5

Q ss_pred             CCccccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcC-----CcEEEEc
Q 005987          136 QQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLG-----ARLYEWD  210 (666)
Q Consensus       136 ~~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg-----~~viE~n  210 (666)
                      .++|+|||+|++++||+||+++++.|+.|++.      ++.+  ++||+||||+||||+|+++|++++     ..++|+|
T Consensus        11 ~~~w~~ky~P~~~~diig~~~~~~~l~~~i~~------~~~~--~lll~Gp~G~GKTtla~~iak~l~~~~~~~~~~e~n   82 (231)
T d1iqpa2          11 EKPWVEKYRPQRLDDIVGQEHIVKRLKHYVKT------GSMP--HLLFAGPPGVGKTTAALALARELFGENWRHNFLELN   82 (231)
T ss_dssp             TSCHHHHTCCCSTTTCCSCHHHHHHHHHHHHH------TCCC--EEEEESCTTSSHHHHHHHHHHHHHGGGHHHHEEEEE
T ss_pred             hchHHHHhCCCCHHHccCcHHHHHHHHHHHHc------CCCC--eEEEECCCCCcHHHHHHHHHHHHHhcccCCCeeEEe
Confidence            57899999999999999999999999999987      4443  799999999999999999999974     4788999


Q ss_pred             CCCchhhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHh
Q 005987          211 TPTPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVR  290 (666)
Q Consensus       211 asd~~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~  290 (666)
                      +++.+..                 ..+.........+..      .....+.||+|||+|.+...     .+..|+.++.
T Consensus        83 ~s~~~~~-----------------~~~~~~~~~~~~~~~------~~~~~~~iilide~d~~~~~-----~~~~ll~~l~  134 (231)
T d1iqpa2          83 ASDERGI-----------------NVIREKVKEFARTKP------IGGASFKIIFLDEADALTQD-----AQQALRRTME  134 (231)
T ss_dssp             TTCHHHH-----------------HTTHHHHHHHHHSCC------GGGCSCEEEEEETGGGSCHH-----HHHHHHHHHH
T ss_pred             cCcccch-----------------hHHHHHHHHHHhhhh------ccCCCceEEeehhhhhcchh-----HHHHHhhhcc
Confidence            8763321                 111122222211111      01124579999999987653     2334666667


Q ss_pred             cCCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCC
Q 005987          291 STHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASGG  370 (666)
Q Consensus       291 ~~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~s~G  370 (666)
                      ....++++|++...       ..+.+..|++     ||..|.|++++..++.++|++++.++++.+++++++.|++.++|
T Consensus       135 ~~~~~~~~i~~~n~-------~~~i~~~l~s-----R~~~i~~~~~~~~~~~~~l~~~~~~e~i~i~~~~l~~I~~~~~g  202 (231)
T d1iqpa2         135 MFSSNVRFILSCNY-------SSKIIEPIQS-----RCAIFRFRPLRDEDIAKRLRYIAENEGLELTEEGLQAILYIAEG  202 (231)
T ss_dssp             HTTTTEEEEEEESC-------GGGSCHHHHH-----TEEEEECCCCCHHHHHHHHHHHHHTTTCEECHHHHHHHHHHHTT
T ss_pred             cCCcceEEEeccCC-------hhhchHhHhC-----ccccccccccchhhHHHHHHHHHHHhCCCCCHHHHHHHHHHcCC
Confidence            66666665555422       1233333433     69999999999999999999999999999999999999999999


Q ss_pred             cHHHHHHHHHHHhcC
Q 005987          371 DIRQAITSLQFSSLK  385 (666)
Q Consensus       371 DIR~AIn~LQf~~~~  385 (666)
                      |+|.|||.||+++..
T Consensus       203 diR~ai~~Lq~~~~~  217 (231)
T d1iqpa2         203 DMRRAINILQAAAAL  217 (231)
T ss_dssp             CHHHHHHHHHHHHTT
T ss_pred             CHHHHHHHHHHHHHc
Confidence            999999999998764

>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=99.96  E-value=2.1e-29  Score=250.81  Aligned_cols=199  Identities=22%  Similarity=0.369  Sum_probs=146.4

Q ss_pred             CccccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCC-----cEEEEcC
Q 005987          137 QLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGA-----RLYEWDT  211 (666)
Q Consensus       137 ~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~-----~viE~na  211 (666)
                      .||+|||+|++++|++||++.++.|+.|++.      +..+  ++||+||||+||||+|+++|++++.     .+++.+.
T Consensus         2 ~pw~ekyrP~~~~divg~~~~~~~L~~~i~~------~~~~--~lLl~Gp~G~GKttl~~~la~~l~~~~~~~~~~e~~~   73 (227)
T d1sxjc2           2 LPWVEKYRPETLDEVYGQNEVITTVRKFVDE------GKLP--HLLFYGPPGTGKTSTIVALAREIYGKNYSNMVLELNA   73 (227)
T ss_dssp             CCHHHHTCCSSGGGCCSCHHHHHHHHHHHHT------TCCC--CEEEECSSSSSHHHHHHHHHHHHHTTSHHHHEEEECT
T ss_pred             CchhhhhCCCCHHHccCcHHHHHHHHHHHHc------CCCC--eEEEECCCCCChhHHHHHHHHHhhcCCCcceeEEecc
Confidence            5799999999999999999999999999986      4444  5899999999999999999999853     3677776


Q ss_pred             CCchhhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhc
Q 005987          212 PTPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRS  291 (666)
Q Consensus       212 sd~~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~  291 (666)
                      ++..           +..      ...............      .....++|+|||++.+.... ..    .|+..++.
T Consensus        74 ~~~~-----------~~~------~~~~~~~~~~~~~~~------~~~~~kiiiiDe~d~~~~~~-~~----~Ll~~le~  125 (227)
T d1sxjc2          74 SDDR-----------GID------VVRNQIKDFASTRQI------FSKGFKLIILDEADAMTNAA-QN----ALRRVIER  125 (227)
T ss_dssp             TSCC-----------SHH------HHHTHHHHHHHBCCS------SSCSCEEEEETTGGGSCHHH-HH----HHHHHHHH
T ss_pred             cccC-----------Cee------eeecchhhccccccc------cCCCeEEEEEeccccchhhH-HH----HHHHHhhh
Confidence            6521           111      111112222122111      11235799999999886542 23    34444444


Q ss_pred             C-CCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCC
Q 005987          292 T-HIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASGG  370 (666)
Q Consensus       292 ~-~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~s~G  370 (666)
                      . ..++++++++.        ....++.+++     ||..+.|++++.+++.++|.+|+..|++.+++++++.|++.++|
T Consensus       126 ~~~~~~~~~~~~~--------~~~i~~~i~s-----r~~~i~~~~~~~~~i~~~l~~I~~~e~i~i~~~~l~~i~~~s~G  192 (227)
T d1sxjc2         126 YTKNTRFCVLANY--------AHKLTPALLS-----QCTRFRFQPLPQEAIERRIANVLVHEKLKLSPNAEKALIELSNG  192 (227)
T ss_dssp             TTTTEEEEEEESC--------GGGSCHHHHT-----TSEEEECCCCCHHHHHHHHHHHHHTTTCCBCHHHHHHHHHHHTT
T ss_pred             cccceeeccccCc--------HHHhHHHHHH-----HHhhhccccccccccccccccccccccccCCHHHHHHHHHHcCC
Confidence            3 34455555542        1233333332     69999999999999999999999999999999999999999999


Q ss_pred             cHHHHHHHHHHHhc
Q 005987          371 DIRQAITSLQFSSL  384 (666)
Q Consensus       371 DIR~AIn~LQf~~~  384 (666)
                      |+|.|||.||++..
T Consensus       193 d~R~ain~Lq~~~~  206 (227)
T d1sxjc2         193 DMRRVLNVLQSCKA  206 (227)
T ss_dssp             CHHHHHHHTTTTTT
T ss_pred             cHHHHHHHHHHHHH
Confidence            99999999998764

>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=99.96  E-value=2.8e-28  Score=243.52  Aligned_cols=205  Identities=21%  Similarity=0.338  Sum_probs=145.8

Q ss_pred             ccccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc------CCcEEEEcC
Q 005987          138 LWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL------GARLYEWDT  211 (666)
Q Consensus       138 ~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel------g~~viE~na  211 (666)
                      ||+|||+|++++||+||+++++.|+.|++.      ++.+  .+||+|||||||||+++++|+++      ....++++.
T Consensus         1 ~w~~ky~P~~~~diig~~~~~~~l~~~i~~------~~~~--~lll~Gp~G~GKTtl~~~i~~~l~~~~~~~~~~~~~~~   72 (237)
T d1sxjd2           1 PWVEKYRPKNLDEVTAQDHAVTVLKKTLKS------ANLP--HMLFYGPPGTGKTSTILALTKELYGPDLMKSRILELNA   72 (237)
T ss_dssp             CHHHHTCCSSTTTCCSCCTTHHHHHHHTTC------TTCC--CEEEECSTTSSHHHHHHHHHHHHHHHHHHTTSEEEECS
T ss_pred             CcchhhCCCCHHHccCcHHHHHHHHHHHHc------CCCC--eEEEECCCCCChHHHHHHHHHHHcCCcccccchhheec
Confidence            799999999999999999999999999875      3333  59999999999999999999997      567788887


Q ss_pred             CCchhhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCC----CCCCCCceEEEEeCCCCCcchhHHHHHHHHHHH
Q 005987          212 PTPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSI----PGESKSSAILLIDDLPVTNGRTAFERLRQCLLL  287 (666)
Q Consensus       212 sd~~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~----~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~  287 (666)
                      +..+.....             ...+..+.    .........    .-.....++|||||++.+... ...    .+..
T Consensus        73 ~~~~~~~~~-------------~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~viiiDe~d~l~~~-~~~----~l~~  130 (237)
T d1sxjd2          73 SDERGISIV-------------REKVKNFA----RLTVSKPSKHDLENYPCPPYKIIILDEADSMTAD-AQS----ALRR  130 (237)
T ss_dssp             SSCCCHHHH-------------TTHHHHHH----HSCCCCCCTTHHHHSCCCSCEEEEETTGGGSCHH-HHH----HHHH
T ss_pred             cccccchHH-------------HHHHHHHh----hhhhhhhhHHHHhhccccCceEEEEecccccCHH-HHH----HHhh
Confidence            653221100             00111111    010000000    001224569999999988653 222    3334


Q ss_pred             HHhcCC-CceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHH
Q 005987          288 LVRSTH-IPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQ  366 (666)
Q Consensus       288 l~~~~~-~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~  366 (666)
                      ++.... .+.++++++.        ..+.+..+++     ||..|+|++++.+++.++|.+++.++++.+++++++.|++
T Consensus       131 ~~~~~~~~~~~i~~~~~--------~~~~~~~l~s-----r~~~i~f~~~~~~~~~~~L~~i~~~e~i~i~~~~l~~ia~  197 (237)
T d1sxjd2         131 TMETYSGVTRFCLICNY--------VTRIIDPLAS-----QCSKFRFKALDASNAIDRLRFISEQENVKCDDGVLERILD  197 (237)
T ss_dssp             HHHHTTTTEEEEEEESC--------GGGSCHHHHH-----HSEEEECCCCCHHHHHHHHHHHHHTTTCCCCHHHHHHHHH
T ss_pred             ccccccccccccccccc--------cccccccccc-----hhhhhccccccccccchhhhhhhhhhcCcCCHHHHHHHHH
Confidence            444333 3344444431        2334444544     4899999999999999999999999999999999999999


Q ss_pred             HcCCcHHHHHHHHHHHhcC
Q 005987          367 ASGGDIRQAITSLQFSSLK  385 (666)
Q Consensus       367 ~s~GDIR~AIn~LQf~~~~  385 (666)
                      .++||+|+|||.||+++..
T Consensus       198 ~s~gd~R~ai~~L~~~~~~  216 (237)
T d1sxjd2         198 ISAGDLRRGITLLQSASKG  216 (237)
T ss_dssp             HTSSCHHHHHHHHHHTHHH
T ss_pred             HcCCCHHHHHHHHHHHHHh
Confidence            9999999999999998754

>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=99.94  E-value=1.1e-26  Score=233.67  Aligned_cols=213  Identities=17%  Similarity=0.259  Sum_probs=146.4

Q ss_pred             cccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCc-h-h
Q 005987          139 WAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTP-T-I  216 (666)
Q Consensus       139 W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~-~-~  216 (666)
                      +.+||||++|+||+||++.++.++.|++.      ++.+ +.+||+||||+|||++|+++|++++........+.. . .
T Consensus         2 ~~~KyrP~~~~dlig~~~~~~~L~~~i~~------~~~~-~~~Ll~Gp~G~GKtt~a~~~~~~l~~~~~~~~~~~~~~~~   74 (239)
T d1njfa_           2 LARKWRPQTFADVVGQEHVLTALANGLSL------GRIH-HAYLFSGTRGVGKTSIARLLAKGLNCETGITATPCGVCDN   74 (239)
T ss_dssp             HHHHTCCSSGGGSCSCHHHHHHHHHHHHT------TCCC-SEEEEECSTTSSHHHHHHHHHHHHHCTTCSCSSCCSCSHH
T ss_pred             chhhhCCCCHHHccChHHHHHHHHHHHHc------CCCC-eeEEEECCCCCcHHHHHHHHHHHhcCccccccCccccchH
Confidence            56899999999999999999999999986      5555 679999999999999999999998543211111100 0 0


Q ss_pred             hhhhhhcccCCc-----cccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhc
Q 005987          217 WQEYMHNCKTGL-----EYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRS  291 (666)
Q Consensus       217 ~~e~l~~~~~g~-----~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~  291 (666)
                      ...........+     ......+.++++++.+. +.    ..   .+..+|+||||+|.+...     .++.|+..++.
T Consensus        75 ~~~i~~~~~~~~~~~~~~~~~~i~~ir~~~~~~~-~~----~~---~~~~kviiIde~d~l~~~-----~q~~Llk~lE~  141 (239)
T d1njfa_          75 CREIEQGRFVDLIEIDAASRTKVEDTRDLLDNVQ-YA----PA---RGRFKVYLIDEVHMLSRH-----SFNALLKTLEE  141 (239)
T ss_dssp             HHHHHHTCCTTEEEEETTCSSSHHHHHHHHHSCC-CS----CS---SSSSEEEEEETGGGSCHH-----HHHHHHHHHHS
T ss_pred             HHHHHcCCCCeEEEecchhcCCHHHHHHHHHHHH-hc----cc---cCCCEEEEEECcccCCHH-----HHHHHHHHHhc
Confidence            000000000000     00122345555554432 11    11   124579999999998643     23456677776


Q ss_pred             CCC-ceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCC
Q 005987          292 THI-PTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASGG  370 (666)
Q Consensus       292 ~~~-PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~s~G  370 (666)
                      ... ..+|++++.        ..+.++.|++     ||..+.|++++.+++++++.+++..|++.+++++++.|+..|+|
T Consensus       142 ~~~~~~~il~tn~--------~~~i~~~i~S-----Rc~~i~~~~~~~~~i~~~l~~i~~~e~~~~~~~~l~~i~~~s~G  208 (239)
T d1njfa_         142 PPEHVKFLLATTD--------PQKLPVTILS-----RCLQFHLKALDVEQIRHQLEHILNEEHIAHEPRALQLLARAAEG  208 (239)
T ss_dssp             CCTTEEEEEEESC--------GGGSCHHHHT-----TSEEEECCCCCHHHHHHHHHHHHHHHTCCBCHHHHHHHHHHTTT
T ss_pred             CCCCeEEEEEcCC--------ccccChhHhh-----hhcccccccCcHHHhhhHHHHHHhhhccCCCHHHHHHHHHHcCC
Confidence            533 344444441        2334444443     69999999999999999999999999999999999999999999


Q ss_pred             cHHHHHHHHHHHhc
Q 005987          371 DIRQAITSLQFSSL  384 (666)
Q Consensus       371 DIR~AIn~LQf~~~  384 (666)
                      |+|.|||.||.+..
T Consensus       209 d~R~ain~l~~~~~  222 (239)
T d1njfa_         209 SLRDALSLTDQAIA  222 (239)
T ss_dssp             CHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHH
Confidence            99999999987553

>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=99.94  E-value=1.5e-26  Score=233.13  Aligned_cols=224  Identities=14%  Similarity=0.220  Sum_probs=136.3

Q ss_pred             cccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCC---cEEEEcCCCch
Q 005987          139 WAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGA---RLYEWDTPTPT  215 (666)
Q Consensus       139 W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~---~viE~nasd~~  215 (666)
                      |+|||+|++++|++||++.++.|+.|+..      +... +.+||+|||||||||+|+++|+++..   ...+.+.....
T Consensus         1 W~eky~P~~~~diig~~~~~~~L~~~~~~------~~~~-~~lll~Gp~G~GKTt~~~~la~~l~~~~~~~~~~~~~~~~   73 (252)
T d1sxje2           1 WVDKYRPKSLNALSHNEELTNFLKSLSDQ------PRDL-PHLLLYGPNGTGKKTRCMALLESIFGPGVYRLKIDVRQFV   73 (252)
T ss_dssp             CTTTTCCCSGGGCCSCHHHHHHHHTTTTC------TTCC-CCEEEECSTTSSHHHHHHTHHHHHSCTTCCC---------
T ss_pred             CCcccCCCCHHHccCcHHHHHHHHHHHHc------CCCC-CeEEEECCCCCCHHHHHHHHHHhhcCcccccccccccccc
Confidence            99999999999999999988888877653      2223 46999999999999999999999722   11111111100


Q ss_pred             hhhh---hhhcccCC-------ccc-cchhHHHHHHHHHHHhhcCCCC--CCCCCCCCceEEEEeCCCCCcchhHHHHHH
Q 005987          216 IWQE---YMHNCKTG-------LEY-TSKLDEFENFVERIRRYGSTSP--SIPGESKSSAILLIDDLPVTNGRTAFERLR  282 (666)
Q Consensus       216 ~~~e---~l~~~~~g-------~~~-~s~~~~f~~fl~~a~~~~~l~~--s~~~~~~~~~IIlIDEid~l~~~~~~~~l~  282 (666)
                      ....   .+......       ... ......+...+........+..  ...+.....++++|||+|.+... ...   
T Consensus        74 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iiiide~d~l~~~-~~~---  149 (252)
T d1sxje2          74 TASNRKLELNVVSSPYHLEITPSDMGNNDRIVIQELLKEVAQMEQVDFQDSKDGLAHRYKCVIINEANSLTKD-AQA---  149 (252)
T ss_dssp             ---------CCEECSSEEEECCC----CCHHHHHHHHHHHTTTTC------------CCEEEEEECTTSSCHH-HHH---
T ss_pred             ccccchhhhhhccCCccceeeecccccCCcceeeehhhhhhhhhhhhhhhcccccCCCceEEEeccccccccc-cch---
Confidence            0000   00000000       000 0111112222222222111110  11112234579999999998643 223   


Q ss_pred             HHHHHHHhcCCCc-eEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCC-HHH
Q 005987          283 QCLLLLVRSTHIP-TAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLS-TEQ  360 (666)
Q Consensus       283 ~~L~~l~~~~~~P-iViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~-~~~  360 (666)
                       .|..+++..... .+|++++..        .+.+..|++     ||..|+|++++.+++.++|..++..|++.+. +++
T Consensus       150 -~l~~~~e~~~~~~~~Il~tn~~--------~~i~~~l~s-----R~~~i~~~~~~~~~~~~~l~~i~~~e~~~~~~~~~  215 (252)
T d1sxje2         150 -ALRRTMEKYSKNIRLIMVCDSM--------SPIIAPIKS-----QCLLIRCPAPSDSEISTILSDVVTNERIQLETKDI  215 (252)
T ss_dssp             -HHHHHHHHSTTTEEEEEEESCS--------CSSCHHHHT-----TSEEEECCCCCHHHHHHHHHHHHHHHTCEECCSHH
T ss_pred             -hhhcccccccccccceeeeccc--------cchhhhhhc-----chheeeecccchhhHHHHHHHHHHHcCCCCCcHHH
Confidence             344444444333 344444311        223333432     5899999999999999999999999998875 788


Q ss_pred             HHHHHHHcCCcHHHHHHHHHHHhcCCC
Q 005987          361 IDLVAQASGGDIRQAITSLQFSSLKQD  387 (666)
Q Consensus       361 l~~Ia~~s~GDIR~AIn~LQf~~~~~~  387 (666)
                      ++.|+..++||+|+||+.||+++..+.
T Consensus       216 l~~i~~~s~Gd~R~ai~~Lq~~~~~~~  242 (252)
T d1sxje2         216 LKRIAQASNGNLRVSLLMLESMALNNE  242 (252)
T ss_dssp             HHHHHHHHTTCHHHHHHHHTHHHHTTT
T ss_pred             HHHHHHHcCCcHHHHHHHHHHHHHcCC
Confidence            999999999999999999999998654

>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=99.90  E-value=4.1e-23  Score=206.33  Aligned_cols=191  Identities=17%  Similarity=0.214  Sum_probs=139.4

Q ss_pred             cCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCchhhhhhhh
Q 005987          143 YKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTIWQEYMH  222 (666)
Q Consensus       143 Y~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~~~~e~l~  222 (666)
                      -||++++|++||++.++.++.|++.+...  +... +++|||||||||||++|+++|+++++.+.++++++..       
T Consensus         3 ~RP~~~~divGqe~~~~~l~~~i~~~~~~--~~~~-~~~L~~GPpGtGKT~lA~~la~~~~~~~~~~~~~~~~-------   72 (238)
T d1in4a2           3 LRPKSLDEFIGQENVKKKLSLALEAAKMR--GEVL-DHVLLAGPPGLGKTTLAHIIASELQTNIHVTSGPVLV-------   72 (238)
T ss_dssp             TSCSSGGGCCSCHHHHHHHHHHHHHHHHH--TCCC-CCEEEESSTTSSHHHHHHHHHHHHTCCEEEEETTTCC-------
T ss_pred             CCCCcHHHcCChHHHHHHHHHHHHHHHhc--CCCC-CeEEEECCCCCcHHHHHHHHHhccCCCcccccCcccc-------
Confidence            58999999999999999999999876532  2222 5799999999999999999999999999999987621       


Q ss_pred             cccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhc-----------
Q 005987          223 NCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRS-----------  291 (666)
Q Consensus       223 ~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~-----------  291 (666)
                                ....+..++..   .           +.+.+++|||++.+....     .+.+...++.           
T Consensus        73 ----------~~~~~~~~~~~---~-----------~~~~~~~ide~~~~~~~~-----~~~l~~~~~~~~~~~~~~~~~  123 (238)
T d1in4a2          73 ----------KQGDMAAILTS---L-----------ERGDVLFIDEIHRLNKAV-----EELLYSAIEDFQIDIMIGKGP  123 (238)
T ss_dssp             ----------SHHHHHHHHHH---C-----------CTTCEEEEETGGGCCHHH-----HHHHHHHHHTSCCCC------
T ss_pred             ----------cHHHHHHHHHh---h-----------ccCCchHHHHHHHhhhHH-----HhhcccceeeeeeeeeecCcc
Confidence                      11223333322   1           134689999999875421     1222222222           


Q ss_pred             -------CCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHH
Q 005987          292 -------THIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLV  364 (666)
Q Consensus       292 -------~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~I  364 (666)
                             ...|+++|++....       ...   ...++.+ .+..+.|++++..++..++..++..+++.+++++++.|
T Consensus       124 ~~~~~~~~~~~~~~I~at~~~-------~~~---~~~~~~r-~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~i  192 (238)
T d1in4a2         124 SAKSIRIDIQPFTLVGATTRS-------GLL---SSPLRSR-FGIILELDFYTVKELKEIIKRAASLMDVEIEDAAAEMI  192 (238)
T ss_dssp             ---------CCCEEEEEESCG-------GGS---CHHHHTT-CSEEEECCCCCHHHHHHHHHHHHHHTTCCBCHHHHHHH
T ss_pred             cccccccCCCCeEEEEecCCC-------ccc---cccceee-eeEEEEecCCCHHHHHHHHHHhhhhccchhhHHHHHHH
Confidence                   12355666554321       111   1233333 46678999999999999999999999999999999999


Q ss_pred             HHHcCCcHHHHHHHHHHHh
Q 005987          365 AQASGGDIRQAITSLQFSS  383 (666)
Q Consensus       365 a~~s~GDIR~AIn~LQf~~  383 (666)
                      +..++||+|.|+|.||.++
T Consensus       193 ~~~s~gd~R~ai~~l~~~~  211 (238)
T d1in4a2         193 AKRSRGTPRIAIRLTKRVR  211 (238)
T ss_dssp             HHTSTTCHHHHHHHHHHHH
T ss_pred             HHhCCCCHHHHHHHHHHHH
Confidence            9999999999999998764

>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=99.90  E-value=5e-23  Score=205.99  Aligned_cols=193  Identities=20%  Similarity=0.214  Sum_probs=137.2

Q ss_pred             CCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCchhhhhhhhc
Q 005987          144 KPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTIWQEYMHN  223 (666)
Q Consensus       144 ~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~~~~e~l~~  223 (666)
                      ||++|+|++||++.+++|+.|+..+..   ++.+.+++||+|||||||||+|+++|+++++.+.++++++...       
T Consensus         4 RP~~~ddivGq~~~~~~L~~~i~~~~~---~~~~~~~~Ll~GPpG~GKTtla~~la~~~~~~~~~~~~~~~~~-------   73 (239)
T d1ixsb2           4 RPKTLDEYIGQERLKQKLRVYLEAAKA---RKEPLEHLLLFGPPGLGKTTLAHVIAHELGVNLRVTSGPAIEK-------   73 (239)
T ss_dssp             CCCSGGGSCSCHHHHHHHHHHHHHHTT---SSSCCCCEEEECCTTSCHHHHHHHHHHHHTCCEEEEETTTCCS-------
T ss_pred             CCCCHHHhCCHHHHHHHHHHHHHHHHh---cCCCCCeEEEECCCCCCHHHHHHHHHHHhCCCeEeccCCcccc-------
Confidence            899999999999999999999987543   2222357999999999999999999999999999998765211       


Q ss_pred             ccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHH--------------
Q 005987          224 CKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLV--------------  289 (666)
Q Consensus       224 ~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~--------------  289 (666)
                                .......+.   ...          ....+++|||++.+... ....+...+....              
T Consensus        74 ----------~~~~~~~~~---~~~----------~~~~i~~iDe~~~~~~~-~~~~l~~~~e~~~~~~~~~~~~~~~~~  129 (239)
T d1ixsb2          74 ----------PGDLAAILA---NSL----------EEGDILFIDEIHRLSRQ-AEEHLYPAMEDFVMDIVIGQGPAARTI  129 (239)
T ss_dssp             ----------HHHHHHHHH---TTC----------CTTCEEEEETGGGCCHH-HHHHHHHHHHHSEEEEECSCTTCCCEE
T ss_pred             ----------chhhHHHHH---hhc----------cCCCeeeeecccccchh-HHHhhhhhhhhhhhhhhhccchhhhhc
Confidence                      111111221   111          12458999999987543 2223333333211              


Q ss_pred             --hcCCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHH
Q 005987          290 --RSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQA  367 (666)
Q Consensus       290 --~~~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~  367 (666)
                        +.++.++++.+++....        ..    ..+. .+|..+.|.+++.+++.+++.++|..+++.++++.++.|+..
T Consensus       130 ~~~~~~~~~i~~~~~~~~~--------~~----~~l~-~~~~~~~~~~~~~~~~~~i~~~~~~~~~i~~~~~~l~~ia~~  196 (239)
T d1ixsb2         130 RLELPRFTLIGATTRPGLI--------TA----PLLS-RFGIVEHLEYYTPEELAQGVMRDARLLGVRITEEAALEIGRR  196 (239)
T ss_dssp             EEECCCCEEEEEESCCSSC--------SC----GGGG-GCSEEEECCCCCHHHHHHHHHHHHGGGCCCBCHHHHHHHHHH
T ss_pred             ccCCCCEEEEeeccCcccc--------cc----hhhc-ccceeeEeeccChhhhhHHHHHHHHHhCCccchHHHHHHHHH
Confidence              11122333333321111        11    1122 269999999999999999999999999999999999999999


Q ss_pred             cCCcHHHHHHHHHHHh
Q 005987          368 SGGDIRQAITSLQFSS  383 (666)
Q Consensus       368 s~GDIR~AIn~LQf~~  383 (666)
                      ++||+|.|+|.||.+.
T Consensus       197 s~gd~R~a~~~l~~~~  212 (239)
T d1ixsb2         197 SRGTMRVAKRLFRRVR  212 (239)
T ss_dssp             TTSSHHHHHHHHHHHH
T ss_pred             cCCCHHHHHHHHHHHH
Confidence            9999999999999864

>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=99.75  E-value=2.5e-17  Score=160.95  Aligned_cols=190  Identities=16%  Similarity=0.161  Sum_probs=122.3

Q ss_pred             cCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCC--ch---hhhhhhhc----
Q 005987          153 VQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPT--PT---IWQEYMHN----  223 (666)
Q Consensus       153 g~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd--~~---~~~e~l~~----  223 (666)
                      .|++..+.+...++.      ++.+ +.+||+||||+||||+|+.+|+.+...-.+-..+.  ..   ......+.    
T Consensus         6 w~~~~~~~l~~~~~~------~~l~-h~lLl~Gp~G~GKtt~a~~~a~~l~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~   78 (207)
T d1a5ta2           6 WLRPDFEKLVASYQA------GRGH-HALLIQALPGMGDDALIYALSRYLLCQQPQGHKSCGHCRGCQLMQAGTHPDYYT   78 (207)
T ss_dssp             GGHHHHHHHHHHHHT------TCCC-SEEEEECCTTSCHHHHHHHHHHHHTCSSCBTTBCCSCSHHHHHHHHTCCTTEEE
T ss_pred             ccHHHHHHHHHHHHc------CCcC-eEEEEECCCCCcHHHHHHHHHHhcccccccccccccccchhhhhhhccccccch
Confidence            577788888888876      6666 67999999999999999999999843211100000  00   00000000    


Q ss_pred             c-cCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcCCCceEEE-Ee
Q 005987          224 C-KTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHIPTAVV-LT  301 (666)
Q Consensus       224 ~-~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~~~PiViI-it  301 (666)
                      . ..+..-....+.++++++.+....        .....+|+||||+|.+...     .++.|+.+++.....++|| ++
T Consensus        79 ~~~~~~~~~i~~~~ir~l~~~~~~~~--------~~~~~kviIide~d~l~~~-----a~n~Llk~lEep~~~~~fIl~t  145 (207)
T d1a5ta2          79 LAPEKGKNTLGVDAVREVTEKLNEHA--------RLGGAKVVWVTDAALLTDA-----AANALLKTLEEPPAETWFFLAT  145 (207)
T ss_dssp             ECCCTTCSSBCHHHHHHHHHHTTSCC--------TTSSCEEEEESCGGGBCHH-----HHHHHHHHHTSCCTTEEEEEEE
T ss_pred             hhhhhcccccccchhhHHhhhhhhcc--------ccCccceEEechhhhhhhh-----hhHHHHHHHHhhcccceeeeee
Confidence            0 000011123445555554432111        1224679999999998643     3445777777764434444 44


Q ss_pred             cCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCcHHHHHHHHH
Q 005987          302 ECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASGGDIRQAITSLQ  380 (666)
Q Consensus       302 ~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~s~GDIR~AIn~LQ  380 (666)
                      + +       ..+.++.|++     ||..|.|++++.+++.++|+     +.+.+++++++.|+..++||+|.||+.||
T Consensus       146 ~-~-------~~~ll~tI~S-----Rc~~i~~~~~~~~~~~~~L~-----~~~~~~~~~~~~i~~~s~Gs~r~al~~le  206 (207)
T d1a5ta2         146 R-E-------PERLLATLRS-----RCRLHYLAPPPEQYAVTWLS-----REVTMSQDALLAALRLSAGSPGAALALFQ  206 (207)
T ss_dssp             S-C-------GGGSCHHHHT-----TSEEEECCCCCHHHHHHHHH-----HHCCCCHHHHHHHHHHTTTCHHHHHHTTS
T ss_pred             c-C-------hhhhhhhhcc-----eeEEEecCCCCHHHHHHHHH-----HcCCCCHHHHHHHHHHcCCCHHHHHHHhC
Confidence            3 1       2334444443     69999999999999999886     45678999999999999999999999876

>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=99.72  E-value=1.3e-17  Score=167.26  Aligned_cols=202  Identities=16%  Similarity=0.235  Sum_probs=129.5

Q ss_pred             CCccccccCHHHHHHHHHHHHHhhcC-----CCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCchhhhhh
Q 005987          146 RSLEELAVQRKKVEEVRAWFEERLGD-----SKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTIWQEY  220 (666)
Q Consensus       146 ~sl~eLvg~~k~i~el~~wL~~~~~~-----~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~~~~e~  220 (666)
                      .+|+||+|.++.+++|.+.+.- +..     .-|...++.+||+||||||||++|+++|+++++.+++++.++.      
T Consensus         6 ~~~~di~G~~~~k~~l~~~i~~-l~~~~~~~~~g~~~~~giLl~GppGtGKT~la~aia~~~~~~~~~i~~~~l------   78 (247)
T d1ixza_           6 VTFKDVAGAEEAKEELKEIVEF-LKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEARVPFITASGSDF------   78 (247)
T ss_dssp             CCGGGCCSCHHHHHHHHHHHHH-HHCHHHHHHTTCCCCSEEEEECCTTSSHHHHHHHHHHHTTCCEEEEEHHHH------
T ss_pred             CcHHHHccHHHHHHHHHHHHHH-HHCHHHHHHcCCCCCceEEEecCCCCChhHHHHHHHHHcCCCEEEEEhHHh------
Confidence            4899999999998888776542 111     0133334789999999999999999999999999999986531      


Q ss_pred             hhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcch---------hHHHHHHHHHHHHHhc
Q 005987          221 MHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGR---------TAFERLRQCLLLLVRS  291 (666)
Q Consensus       221 l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~---------~~~~~l~~~L~~l~~~  291 (666)
                       ..    ..+......++.+++.+..+            .|.||+|||+|.+...         ....++...|+..++.
T Consensus        79 -~~----~~~g~~~~~l~~~f~~a~~~------------~p~Ii~iDeid~l~~~r~~~~~~~~~~~~~~~~~ll~~~d~  141 (247)
T d1ixza_          79 -VE----MFVGVGAARVRDLFETAKRH------------APCIVFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMDG  141 (247)
T ss_dssp             -HH----SCTTHHHHHHHHHHHHHTTS------------SSEEEEEETHHHHHC---------CHHHHHHHHHHHHHHHT
T ss_pred             -hh----ccccHHHHHHHHHHHHHHHc------------CCEEEEEEChhhhCccCCCCCCCCcHHHHHHHHHHHHHhhC
Confidence             11    11122334566666666432            4789999999854221         1122344445555543


Q ss_pred             C--CCceEEEEecCCCCCCccchhhhhhHHHHHHhhc-Ce-eEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHH
Q 005987          292 T--HIPTAVVLTECGKADSVDSTAQSFEELQSILVDA-GA-RKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQA  367 (666)
Q Consensus       292 ~--~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~-r~-~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~  367 (666)
                      .  +.++++|++ ++....          +.+.+.|+ |+ ..|.|++|+.++..++|+..+...... .+..++.|++.
T Consensus       142 ~~~~~~vivi~t-Tn~~~~----------ld~al~R~~Rf~~~i~~~~P~~~eR~~il~~~l~~~~~~-~~~~~~~la~~  209 (247)
T d1ixza_         142 FEKDTAIVVMAA-TNRPDI----------LDPALLRPGRFDRQIAIDAPDVKGREQILRIHARGKPLA-EDVDLALLAKR  209 (247)
T ss_dssp             CCTTCCEEEEEE-ESCGGG----------SCGGGGSTTSSCEEEECCSCCHHHHHHHHHHHHTTSCBC-TTCCHHHHHHT
T ss_pred             CCCCCCEEEEEe-CCCccc----------cCHhHcCCCCCcEEEEECCcCHHHHHHHHHHHhcccCCc-cccCHHHHHHH
Confidence            2  234444433 332221          22222221 33 589999999999999999888665433 33457888988


Q ss_pred             cCC----cHHHHHHHHHHHh
Q 005987          368 SGG----DIRQAITSLQFSS  383 (666)
Q Consensus       368 s~G----DIR~AIn~LQf~~  383 (666)
                      +.|    ||+.+++.-.+.+
T Consensus       210 t~g~s~~di~~lv~~A~l~a  229 (247)
T d1ixza_         210 TPGFVGADLENLLNEAALLA  229 (247)
T ss_dssp             CTTCCHHHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHHH
Confidence            776    8998887554444

>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=99.69  E-value=1.8e-16  Score=159.62  Aligned_cols=199  Identities=15%  Similarity=0.205  Sum_probs=129.2

Q ss_pred             CCCccccccCHHHHHHHHHHHHHhhcC-----CCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCchhhhh
Q 005987          145 PRSLEELAVQRKKVEEVRAWFEERLGD-----SKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTIWQE  219 (666)
Q Consensus       145 P~sl~eLvg~~k~i~el~~wL~~~~~~-----~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~~~~e  219 (666)
                      +.|++|++|.+...++|.+.+.- +..     ..|...++.+||+||||||||++|+++|++++..++.++.++..    
T Consensus         8 ~~t~~Di~Gl~~~k~~l~e~v~~-~~~~~~~~~~g~~~~~~iLL~GppGtGKT~la~~iA~~~~~~~~~i~~~~l~----   82 (256)
T d1lv7a_           8 KTTFADVAGCDEAKEEVAELVEY-LREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGEAKVPFFTISGSDFV----   82 (256)
T ss_dssp             CCCGGGSCSCHHHHHHTHHHHHH-HHCGGGC-----CCCCEEEEECCTTSCHHHHHHHHHHHHTCCEEEECSCSST----
T ss_pred             CCCHHHHhchHHHHHHHHHHHHH-HHCHHHHHHcCCCCCCeEEeeCCCCCCccHHHHHHHHHcCCCEEEEEhHHhh----
Confidence            45789999999999888876542 211     11333347899999999999999999999999999999987621    


Q ss_pred             hhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcc---------hhHHHHHHHHHHHHHh
Q 005987          220 YMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNG---------RTAFERLRQCLLLLVR  290 (666)
Q Consensus       220 ~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~---------~~~~~~l~~~L~~l~~  290 (666)
                             +..+......++.+++.+...            .|.||+|||+|.+..         .....++...|+..++
T Consensus        83 -------~~~~g~~~~~l~~~f~~A~~~------------~P~il~iDeiD~l~~~r~~~~~~~~~~~~~~~~~ll~~~d  143 (256)
T d1lv7a_          83 -------EMFVGVGASRVRDMFEQAKKA------------APCIIFIDEIDAVGRQRGAGLGGGHDEREQTLNQMLVEMD  143 (256)
T ss_dssp             -------TSCCCCCHHHHHHHHHHHHTT------------CSEEEEETTHHHHTCCCSTTSCCTTCHHHHHHHHHHHHHH
T ss_pred             -------hcchhHHHHHHHHHHHHHHHc------------CCEEEEEEChhhhCccCCCCCCCCcHHHHHHHHHHHHHhh
Confidence                   111223345667777777543            478999999985321         1122334444555554


Q ss_pred             c--CCCceEEEEecCCCCCCccchhhhhhHHHHHHhhc-C-eeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHH
Q 005987          291 S--THIPTAVVLTECGKADSVDSTAQSFEELQSILVDA-G-ARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQ  366 (666)
Q Consensus       291 ~--~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~-r-~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~  366 (666)
                      .  ...++++|+++ +.+..          |.+.+.|+ | -..|.|++|+.++..++|+..+.+..+. .+..+..|++
T Consensus       144 ~~~~~~~v~vIatT-n~~~~----------ld~al~R~gRfd~~i~i~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~  211 (256)
T d1lv7a_         144 GFEGNEGIIVIAAT-NRPDV----------LDPALLRPGRFDRQVVVGLPDVRGREQILKVHMRRVPLA-PDIDAAIIAR  211 (256)
T ss_dssp             TCCSSSCEEEEEEE-SCTTT----------SCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHHTTSCBC-TTCCHHHHHH
T ss_pred             CCCCCCCEEEEEeC-CCccc----------CCHhHcCCCCCCEEEECCCcCHHHHHHHHHHhccCCCcC-cccCHHHHHH
Confidence            2  23345555443 33222          22223221 3 3689999999999999999887665544 3445678887


Q ss_pred             HcC----CcHHHHHHHH
Q 005987          367 ASG----GDIRQAITSL  379 (666)
Q Consensus       367 ~s~----GDIR~AIn~L  379 (666)
                      .+.    +||+..++.-
T Consensus       212 ~t~G~s~adi~~l~~~A  228 (256)
T d1lv7a_         212 GTPGFSGADLANLVNEA  228 (256)
T ss_dssp             TCTTCCHHHHHHHHHHH
T ss_pred             hCCCCCHHHHHHHHHHH
Confidence            755    5888777653

>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=99.69  E-value=7.7e-17  Score=162.84  Aligned_cols=227  Identities=14%  Similarity=0.185  Sum_probs=135.0

Q ss_pred             CCccccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCC-CCccEEEEECCCCchHHHHHHHHHHHc---------CCc
Q 005987          136 QQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDK-FSTNVLVITGQAGVGKTATVRQIASHL---------GAR  205 (666)
Q Consensus       136 ~~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~-~~~k~LLL~GPpG~GKTtla~~LAkel---------g~~  205 (666)
                      .++|-++|.|.++   .+++..+++|..++........+. ....+++|+||||||||++++++|+++         .+.
T Consensus         6 ~~~l~~~~~P~~~---~~Re~e~~~l~~~l~~~~~~~~~~~~~~~~l~l~GppGtGKT~l~~~l~~~l~~~~~~~~~~~~   82 (287)
T d1w5sa2           6 RRVFDENYIPPEL---RVRRGEAEALARIYLNRLLSGAGLSDVNMIYGSIGRVGIGKTTLAKFTVKRVSEAAAKEGLTVK   82 (287)
T ss_dssp             GGGGSTTCCCSSC---SSSCHHHHHHHHHHHHHHHTSSCBCCEEEEEECTTCCSSSHHHHHHHHHHHHHHHHHHTTCCEE
T ss_pred             hhhcCCccCCCCC---CCHHHHHHHHHHHHHHHHHcCCCCCCcceEEEeECCCCCCHHHHHHHHHHHHHhhcccccCCce
Confidence            4578899999765   899999999999987655432111 112357889999999999999999997         245


Q ss_pred             EEEEcCCCchhhhhh----hhcccCCccc--cchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhH-H
Q 005987          206 LYEWDTPTPTIWQEY----MHNCKTGLEY--TSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTA-F  278 (666)
Q Consensus       206 viE~nasd~~~~~e~----l~~~~~g~~~--~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~-~  278 (666)
                      ++++++.........    ..........  ......+..+.+......           ...++++||++.+..... .
T Consensus        83 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~-----------~~~~~iide~d~l~~~~~~~  151 (287)
T d1w5sa2          83 QAYVNAFNAPNLYTILSLIVRQTGYPIQVRGAPALDILKALVDNLYVEN-----------HYLLVILDEFQSMLSSPRIA  151 (287)
T ss_dssp             EEEEEGGGCCSHHHHHHHHHHHHTCCCCCTTCCHHHHHHHHHHHHHHHT-----------CEEEEEEESTHHHHSCTTSC
T ss_pred             eeeeccccccchhhHHHHHhhhcccccccccchHHHHHHHHHHHHHhcc-----------CccccceeEEEEeccccccc
Confidence            556665443221111    1111100000  111222233333333222           356889999986532110 0


Q ss_pred             HHHHHHHHHHH-------hcCCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHH
Q 005987          279 ERLRQCLLLLV-------RSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQ  351 (666)
Q Consensus       279 ~~l~~~L~~l~-------~~~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~  351 (666)
                      ......+..+.       .....++|++++...      ...........+..+ .+..+.|.+++..++..+++.++..
T Consensus       152 ~~~~~~l~~l~~~l~~~~~~~~~~~i~i~~~~~------~~~~~~~~~~~~~~r-~~~~i~f~~y~~~el~~Il~~r~~~  224 (287)
T d1w5sa2         152 AEDLYTLLRVHEEIPSRDGVNRIGFLLVASDVR------ALSYMREKIPQVESQ-IGFKLHLPAYKSRELYTILEQRAEL  224 (287)
T ss_dssp             HHHHHHHHTHHHHSCCTTSCCBEEEEEEEEETH------HHHHHHHHCHHHHTT-CSEEEECCCCCHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHhcchhhcccceeEEeecccHH------HHHHHHhhccchhcc-cceeeeccCCcHHHHHHHHhhhHHH
Confidence            11111122221       122334555444321      111111222333333 5789999999999999999999876


Q ss_pred             hC--CCCCHHHHHHHHHHc------CCcHHHHHHHHHHHh
Q 005987          352 EQ--YSLSTEQIDLVAQAS------GGDIRQAITSLQFSS  383 (666)
Q Consensus       352 e~--i~v~~~~l~~Ia~~s------~GDIR~AIn~LQf~~  383 (666)
                      ..  ..+++++++.|++.+      .||+|.|++.|+-+.
T Consensus       225 ~~~~~~~~~~al~~ia~~~~~~~~~~gd~R~ai~~l~~a~  264 (287)
T d1w5sa2         225 GLRDTVWEPRHLELISDVYGEDKGGDGSARRAIVALKMAC  264 (287)
T ss_dssp             HBCTTSCCHHHHHHHHHHHCGGGTSCCCHHHHHHHHHHHH
T ss_pred             hhccCCCCHHHHHHHHHHHhccccCCCCHHHHHHHHHHHH
Confidence            43  458999999999876      699999999998765

>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=99.68  E-value=3e-15  Score=149.98  Aligned_cols=225  Identities=17%  Similarity=0.177  Sum_probs=137.1

Q ss_pred             CCccccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc----CCcEEEEcC
Q 005987          136 QQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL----GARLYEWDT  211 (666)
Q Consensus       136 ~~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel----g~~viE~na  211 (666)
                      ...+...|.|+++   ++++..++.|..+|..++... +..+ +++||+||||||||++++.+|+++    ++.++.+++
T Consensus         6 ~~~l~~~y~p~~l---~~Re~ei~~l~~~l~~~l~~~-~~~~-~~lll~GppGtGKT~l~~~l~~~l~~~~~~~~~~~~~   80 (276)
T d1fnna2           6 DSVFSPSYVPKRL---PHREQQLQQLDILLGNWLRNP-GHHY-PRATLLGRPGTGKTVTLRKLWELYKDKTTARFVYING   80 (276)
T ss_dssp             GGGGSTTCCCSCC---TTCHHHHHHHHHHHHHHHHST-TSSC-CEEEEECCTTSSHHHHHHHHHHHHTTSCCCEEEEEET
T ss_pred             cccCCCCCCCCCC---CCHHHHHHHHHHHHHHHHhCC-CCCC-CceEEECCCCCCHHHHHHHHHHHHhcccCCcEEEecc
Confidence            4567889999765   999999999999999887543 2333 689999999999999999999997    466777776


Q ss_pred             CCchhh----hhhhhcccCCccc--cchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHH
Q 005987          212 PTPTIW----QEYMHNCKTGLEY--TSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCL  285 (666)
Q Consensus       212 sd~~~~----~e~l~~~~~g~~~--~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L  285 (666)
                      ......    .............  ......+..+.......           ....++++|+++....... ..+...+
T Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----------~~~~~~~~~~~d~~~~~~~-~~~~~~~  148 (276)
T d1fnna2          81 FIYRNFTAIIGEIARSLNIPFPRRGLSRDEFLALLVEHLRER-----------DLYMFLVLDDAFNLAPDIL-STFIRLG  148 (276)
T ss_dssp             TTCCSHHHHHHHHHHHTTCCCCSSCCCHHHHHHHHHHHHHHT-----------TCCEEEEEETGGGSCHHHH-HHHHHHT
T ss_pred             hhhhhhhhhhhhhHHhhhhhhhhhccchhHHHHHHHHHHhhc-----------ccccccchhHHHHhhhhhh-hhHHHHH
Confidence            553322    1111111111111  11112223333333222           1245788999987654321 1121112


Q ss_pred             HHHHhcCCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhC--CCCCHHHHHH
Q 005987          286 LLLVRSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQ--YSLSTEQIDL  363 (666)
Q Consensus       286 ~~l~~~~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~--i~v~~~~l~~  363 (666)
                      ..........+++|..... .   +...+....+.+   +.....|.|.+++.+++.++|.+.+....  ..+++++++.
T Consensus       149 ~~~~~~~~~~~~~i~~~~~-~---~~~~~~~~~~~~---r~~~~~i~~~~~~~~e~~~il~~r~~~~~~~~~~~~~~l~~  221 (276)
T d1fnna2         149 QEADKLGAFRIALVIVGHN-D---AVLNNLDPSTRG---IMGKYVIRFSPYTKDQIFDILLDRAKAGLAEGSYSEDILQM  221 (276)
T ss_dssp             TCHHHHSSCCEEEEEEESS-T---HHHHTSCHHHHH---HHTTCEEECCCCBHHHHHHHHHHHHHHHBCTTSSCHHHHHH
T ss_pred             hccccccccceEEeecCCc-h---hhhhhcchhhhh---hhcchhccccchhHHHHHHHHHHHHHHhcccccccHHHHHH
Confidence            2222222333333333211 1   011112222232   22346799999999999999999887643  4589999999


Q ss_pred             HHHH---------cCCcHHHHHHHHHHHhc
Q 005987          364 VAQA---------SGGDIRQAITSLQFSSL  384 (666)
Q Consensus       364 Ia~~---------s~GDIR~AIn~LQf~~~  384 (666)
                      |++.         +.||+|.|++.|+.+..
T Consensus       222 ia~~~~~~~~~~~~~G~~R~a~~ll~~a~~  251 (276)
T d1fnna2         222 IADITGAQTPLDTNRGDARLAIDILYRSAY  251 (276)
T ss_dssp             HHHHHSBSSTTCTTSCCHHHHHHHHHHHHH
T ss_pred             HHHHhhhhhhhhhcCCCHHHHHHHHHHHHH
Confidence            9876         47999999999987643

>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=99.67  E-value=2.9e-16  Score=158.55  Aligned_cols=203  Identities=17%  Similarity=0.249  Sum_probs=130.8

Q ss_pred             CccccccCHHHHHHHHHHHHHhhcC-----CCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCchhhhhhh
Q 005987          147 SLEELAVQRKKVEEVRAWFEERLGD-----SKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTIWQEYM  221 (666)
Q Consensus       147 sl~eLvg~~k~i~el~~wL~~~~~~-----~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~~~~e~l  221 (666)
                      +++||+|.+..+++|++++.-.+..     ..|..+++.+|||||||||||++++++|++++..++.++.++.       
T Consensus         2 ~~~dv~G~~~~k~~l~~~i~~~l~~~~~~~~~g~~~~~giLL~GppGtGKT~l~~ala~~~~~~~~~i~~~~l-------   74 (258)
T d1e32a2           2 GYDDVGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGAFFFLINGPEI-------   74 (258)
T ss_dssp             CGGGCCSCSHHHHHHHHHHHHHHHCHHHHHHCCCCCCCEEEEECCTTSSHHHHHHHHHHHTTCEEEEECHHHH-------
T ss_pred             ChhhhccHHHHHHHHHHHHHHHhcCHHHHHhCCCCCCceeEEecCCCCCchHHHHHHHHHhCCeEEEEEchhh-------
Confidence            6899999999999999986543331     1144445789999999999999999999999999999886531       


Q ss_pred             hcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhH------HHHHHHHHHHHHhcC-CC
Q 005987          222 HNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTA------FERLRQCLLLLVRST-HI  294 (666)
Q Consensus       222 ~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~------~~~l~~~L~~l~~~~-~~  294 (666)
                          ...........++..+..+...            .|.||+|||+|.+.....      ...+...+...+... ..
T Consensus        75 ----~~~~~g~~~~~l~~~f~~A~~~------------~p~il~iDeid~l~~~r~~~~~~~~~~~~~~~~~~~~~~~~~  138 (258)
T d1e32a2          75 ----MSKLAGESESNLRKAFEEAEKN------------APAIIFIDELDAIAPKREKTHGEVERRIVSQLLTLMDGLKQR  138 (258)
T ss_dssp             ----TTSCTTHHHHHHHHHHHHHHHT------------CSEEEEESSGGGTCCHHHHCCCTTHHHHHHHHHHHHHTCCCS
T ss_pred             ----cccccccHHHHHHHHHHHHHhc------------CCeEEEehhhhhhccCCCCCCCchHHHHHHHhcccccccccc
Confidence                1111122344556666666544            378999999998754321      122333333333322 22


Q ss_pred             ceEEEEecCCCCCCccchhhhhhHHHHHHhhc--CeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCC--
Q 005987          295 PTAVVLTECGKADSVDSTAQSFEELQSILVDA--GARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASGG--  370 (666)
Q Consensus       295 PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~--r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~s~G--  370 (666)
                      +-|+++..++.....|          ..+.|+  .-..|.|++|+.++..++|+..+....+. ++..++.|++.+.|  
T Consensus       139 ~~vlvi~tTn~~~~ld----------~al~r~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~G~s  207 (258)
T d1e32a2         139 AHVIVMAATNRPNSID----------PALRRFGRFDREVDIGIPDATGRLEILQIHTKNMKLA-DDVDLEQVANETHGHV  207 (258)
T ss_dssp             SCEEEEEEESCGGGSC----------GGGTSTTSSCEEEECCCCCHHHHHHHHHHTTTTSCBC-TTCCHHHHHHHCTTCC
T ss_pred             CCccEEEeCCCccccc----------hhhhhcccccceeECCCCCHHHHHHHhhhhccCcccc-cccchhhhhhcccCCC
Confidence            3233333333332222          222222  24689999999999999999887654332 22347899999877  


Q ss_pred             --cHHHHHHHHHHHh
Q 005987          371 --DIRQAITSLQFSS  383 (666)
Q Consensus       371 --DIR~AIn~LQf~~  383 (666)
                        ||+.+++.-.+.+
T Consensus       208 ~adl~~lv~~A~~~a  222 (258)
T d1e32a2         208 GADLAALCSEAALQA  222 (258)
T ss_dssp             HHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHH
Confidence              9998887644443

>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=99.60  E-value=3.2e-16  Score=158.85  Aligned_cols=204  Identities=14%  Similarity=0.194  Sum_probs=125.1

Q ss_pred             CC-CccccccCHHHHHHHHHHHHHhhcC-----CCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCchhhh
Q 005987          145 PR-SLEELAVQRKKVEEVRAWFEERLGD-----SKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTIWQ  218 (666)
Q Consensus       145 P~-sl~eLvg~~k~i~el~~wL~~~~~~-----~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~~~~  218 (666)
                      |+ +|+|++|.++.+++|.+++...+..     ..|..+++.+|||||||||||++|+++|++++..++.+++++.    
T Consensus         2 p~~~f~di~G~~~~k~~l~~~i~~~l~~~~~~~~~g~~~~~giLL~Gp~GtGKT~l~~ala~~~~~~~~~~~~~~l----   77 (265)
T d1r7ra3           2 PQVTWEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANECQANFISIKGPEL----   77 (265)
T ss_dssp             CCCSCSSCSSSSCCCCHHHHHTHHHHHCHHHHHHCCCCCCCEEEEBCCTTSSHHHHHHHHHHHTTCEEEEECHHHH----
T ss_pred             CCCCHHHhcCHHHHHHHHHHHHHHHhhCHHHHHhCCCCCCCeEEEECCCCCcchhHHHHHHHHhCCcEEEEEHHHh----
Confidence            54 8999999988888888877543321     1144445789999999999999999999999999999986531    


Q ss_pred             hhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchh---------HHHHHHHHHHHHH
Q 005987          219 EYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRT---------AFERLRQCLLLLV  289 (666)
Q Consensus       219 e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~---------~~~~l~~~L~~l~  289 (666)
                             .+.........++.++..+...            .|.||+|||+|.+....         ...++...|...+
T Consensus        78 -------~~~~~~~~~~~l~~~f~~A~~~------------~p~il~ideid~l~~~~~~~~~~~~~~~~~~~~~ll~~l  138 (265)
T d1r7ra3          78 -------LTMWFGESEANVREIFDKARQA------------APCVLFFDELDSIAKARGGNIGDGGGAADRVINQILTEM  138 (265)
T ss_dssp             -------HTSCTTTHHHHHHHHHHHHHHT------------CSEEEEESSGGGTCCHHHHCCCTTHHHHHHHHHHHHHTC
T ss_pred             -------hhccccchHHHHHHHHHHHHhc------------CCcceeHHhhhhccccCCCcCCCCcHHHHHHHHHHHHHh
Confidence                   1111223345566777777543            36899999999764321         1122333344333


Q ss_pred             hc--CCCceEEEEecCCCCCCccchhhhhhHHHHHHhh--cCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHH
Q 005987          290 RS--THIPTAVVLTECGKADSVDSTAQSFEELQSILVD--AGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVA  365 (666)
Q Consensus       290 ~~--~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r--~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia  365 (666)
                      ..  .+.++++|++. +....          |...+.|  +....|.|++|+.++..++|+..+...... .+..++.|+
T Consensus       139 ~~~~~~~~v~vi~tt-n~~~~----------ld~al~r~gRf~~~i~~~~p~~~~R~~il~~~l~~~~~~-~~~~l~~la  206 (265)
T d1r7ra3         139 DGMSTKKNVFIIGAT-NRPDI----------IDPAILRPGRLDQLIYIPLPDEKSRVAILKANLRKSPVA-KDVDLEFLA  206 (265)
T ss_dssp             C------CCEEEECC-BSCTT----------TSCGGGSSTTSEEEEECCCCCCHHHHHHHHHHTTCC-----CCCCHHHH
T ss_pred             hCcCCCCCEEEEEeC-CCchh----------CCHHHhCCCCccEEEEecchHHHHHHHHHHHHhccCCch-hhhhHHHHH
Confidence            21  22345555543 33322          2222222  135679999999999999998765432211 122356666


Q ss_pred             HH----cCCcHHHHHHHHHHHh
Q 005987          366 QA----SGGDIRQAITSLQFSS  383 (666)
Q Consensus       366 ~~----s~GDIR~AIn~LQf~~  383 (666)
                      ..    +++||...++.....+
T Consensus       207 ~~t~g~s~~di~~lv~~A~~~A  228 (265)
T d1r7ra3         207 KMTNGFSGADLTEICQRACKLA  228 (265)
T ss_dssp             HHHCSSCCHHHHHHHHHHHHHH
T ss_pred             hcCCCCCHHHHHHHHHHHHHHH
Confidence            66    4567877766544444

>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=99.58  E-value=3.3e-14  Score=139.08  Aligned_cols=194  Identities=18%  Similarity=0.232  Sum_probs=122.4

Q ss_pred             Ccccccc---CHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcCCCchhhhhh
Q 005987          147 SLEELAV---QRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL---GARLYEWDTPTPTIWQEY  220 (666)
Q Consensus       147 sl~eLvg---~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~nasd~~~~~e~  220 (666)
                      ||+++++   +....+.++.|++..     +. ..+.++|+||+|||||++++++|+++   +..++.++..+.  ....
T Consensus         8 tFdnF~vg~~N~~a~~~~~~~~~~~-----~~-~~n~l~l~G~~G~GKTHLl~A~~~~~~~~~~~~~~~~~~~~--~~~~   79 (213)
T d1l8qa2           8 TLENFIVGEGNRLAYEVVKEALENL-----GS-LYNPIFIYGSVGTGKTHLLQAAGNEAKKRGYRVIYSSADDF--AQAM   79 (213)
T ss_dssp             CSSSCCCCTTTHHHHHHHHHHHHTT-----TT-SCSSEEEECSSSSSHHHHHHHHHHHHHHTTCCEEEEEHHHH--HHHH
T ss_pred             ChhhccCCCcHHHHHHHHHHHHhCc-----CC-CCCcEEEECCCCCcHHHHHHHHHHHhccCccceEEechHHH--HHHH
Confidence            6777653   666677777777641     22 22469999999999999999999997   566666654321  0000


Q ss_pred             hhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHH-HHHHHHHHHHhcCCCceEEE
Q 005987          221 MHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFE-RLRQCLLLLVRSTHIPTAVV  299 (666)
Q Consensus       221 l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~-~l~~~L~~l~~~~~~PiViI  299 (666)
                      .....        .....++.+....              ..+|+|||++.+.+....+ .+...+..+.+.+ .++ ++
T Consensus        80 ~~~~~--------~~~~~~~~~~~~~--------------~dll~iDDi~~i~~~~~~~~~lf~lin~~~~~~-~~i-ii  135 (213)
T d1l8qa2          80 VEHLK--------KGTINEFRNMYKS--------------VDLLLLDDVQFLSGKERTQIEFFHIFNTLYLLE-KQI-IL  135 (213)
T ss_dssp             HHHHH--------HTCHHHHHHHHHT--------------CSEEEEECGGGGTTCHHHHHHHHHHHHHHHHTT-CEE-EE
T ss_pred             HHHHH--------ccchhhHHHHHhh--------------ccchhhhhhhhhcCchHHHHHHHHHHHHHhhcc-ceE-EE
Confidence            00000        0011223333221              1389999999886543322 2334444444444 334 44


Q ss_pred             EecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCcHH---HHH
Q 005987          300 LTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDLVAQASGGDIR---QAI  376 (666)
Q Consensus       300 it~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~s~GDIR---~AI  376 (666)
                      +++... ..   ....+++|+++|+.  +..+.+. |+.+.+.++|++.+...|+.++++++++|++.+ .|+|   .||
T Consensus       136 ts~~~p-~~---l~~~~~dL~SRL~~--g~~~~i~-p~d~~~~~iL~~~a~~rgl~l~~~v~~yl~~~~-~~~R~L~~~l  207 (213)
T d1l8qa2         136 ASDRHP-QK---LDGVSDRLVSRFEG--GILVEIE-LDNKTRFKIIKEKLKEFNLELRKEVIDYLLENT-KNVREIEGKI  207 (213)
T ss_dssp             EESSCG-GG---CTTSCHHHHHHHHT--SEEEECC-CCHHHHHHHHHHHHHHTTCCCCHHHHHHHHHHC-SSHHHHHHHH
T ss_pred             ecCCcc-hh---ccccchHHHHHhhC--ceEEEEC-CCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHhc-CcHHHHHHHH
Confidence            554332 11   12245678888875  6777885 567889999999999999999999999999998 5677   455


Q ss_pred             HHHH
Q 005987          377 TSLQ  380 (666)
Q Consensus       377 n~LQ  380 (666)
                      +.|+
T Consensus       208 ~~l~  211 (213)
T d1l8qa2         208 KLIK  211 (213)
T ss_dssp             HHHH
T ss_pred             HHhh
Confidence            5554

>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=99.48  E-value=2.6e-13  Score=135.58  Aligned_cols=170  Identities=16%  Similarity=0.238  Sum_probs=104.8

Q ss_pred             CccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCchhhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCCCC
Q 005987          177 STNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSIPG  256 (666)
Q Consensus       177 ~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~  256 (666)
                      |.+.+||+||||||||++|++||+++++.++++++++.          ..|.........++.+++.+.+.         
T Consensus        39 p~~~vLL~GppGtGKT~la~alA~~~~~~~~~i~~~~~----------~~g~~~~~~~~~i~~if~~A~~~---------   99 (246)
T d1d2na_          39 PLVSVLLEGPPHSGKTALAAKIAEESNFPFIKICSPDK----------MIGFSETAKCQAMKKIFDDAYKS---------   99 (246)
T ss_dssp             SEEEEEEECSTTSSHHHHHHHHHHHHTCSEEEEECGGG----------CTTCCHHHHHHHHHHHHHHHHTS---------
T ss_pred             CCeEEEEECcCCCCHHHHHHHHhhcccccccccccccc----------cccccccchhhhhhhhhhhhhhc---------
Confidence            34789999999999999999999999999999988751          11221122234566677777543         


Q ss_pred             CCCCceEEEEeCCCCCcc-----hhHHHHHHHHHHHHHhcCC---CceEEEEecCCCCCCccchhhhhhHHHHH-HhhcC
Q 005987          257 ESKSSAILLIDDLPVTNG-----RTAFERLRQCLLLLVRSTH---IPTAVVLTECGKADSVDSTAQSFEELQSI-LVDAG  327 (666)
Q Consensus       257 ~~~~~~IIlIDEid~l~~-----~~~~~~l~~~L~~l~~~~~---~PiViIit~~~~~~s~d~~~r~l~~L~s~-L~r~r  327 (666)
                         .+.||+|||+|.+..     ....+.+...|..+++...   .++++|+++ +..          ..+... +.++.
T Consensus       100 ---~p~il~iDEid~l~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~v~vi~tT-n~~----------~~ld~~~~~~rF  165 (246)
T d1d2na_         100 ---QLSCVVVDDIERLLDYVPIGPRFSNLVLQALLVLLKKAPPQGRKLLIIGTT-SRK----------DVLQEMEMLNAF  165 (246)
T ss_dssp             ---SEEEEEECCHHHHTTCBTTTTBCCHHHHHHHHHHTTCCCSTTCEEEEEEEE-SCH----------HHHHHTTCTTTS
T ss_pred             ---ccceeehhhhhhHhhhcccccchhHHHHHHHHHHhcCCCccccceeeeecc-CCh----------hhccchhhcCcc
Confidence               368999999985421     1111334445555555432   245555443 211          122222 22222


Q ss_pred             eeEEEeCCCC-HHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCC-----cHHHHHHHHHHHhc
Q 005987          328 ARKVALNPIT-NGSIKRTLSKICRQEQYSLSTEQIDLVAQASGG-----DIRQAITSLQFSSL  384 (666)
Q Consensus       328 ~~~I~F~p~s-~~~i~kiL~~I~~~e~i~v~~~~l~~Ia~~s~G-----DIR~AIn~LQf~~~  384 (666)
                      -..|.|+.+. .+++.++|.+.     ..+++..+..|++.+.|     +++.+++.+++.+.
T Consensus       166 ~~~i~~P~~~~r~~il~~l~~~-----~~~~~~~~~~i~~~~~g~~~~~~ik~ll~~ie~a~~  223 (246)
T d1d2na_         166 STTIHVPNIATGEQLLEALELL-----GNFKDKERTTIAQQVKGKKVWIGIKKLLMLIEMSLQ  223 (246)
T ss_dssp             SEEEECCCEEEHHHHHHHHHHH-----TCSCHHHHHHHHHHHTTSEEEECHHHHHHHHHHHTT
T ss_pred             ceEEecCCchhHHHHHHHHHhc-----cCCChHHHHHHHHHcCCCccchhHHHHHHHHHHHHh
Confidence            3567885443 34555554432     24677788888888777     58999988887653

>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=99.39  E-value=2e-12  Score=129.89  Aligned_cols=210  Identities=16%  Similarity=0.223  Sum_probs=141.9

Q ss_pred             CCccccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc----------CCc
Q 005987          136 QQLWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL----------GAR  205 (666)
Q Consensus       136 ~~~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel----------g~~  205 (666)
                      ...++++-+-..++.++|+++.++++...|.+.      .  ++++||.||||+|||++++.+|+.+          +..
T Consensus         5 ~~dlt~~a~~~~ld~~igRd~Ei~~l~~iL~r~------~--k~n~lLVG~~GvGKTalv~~la~ri~~~~vp~~l~~~~   76 (268)
T d1r6bx2           5 TTNLNQLARVGGIDPLIGREKELERAIQVLCRR------R--KNNPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCT   76 (268)
T ss_dssp             SCBHHHHHHTTCSCCCCSCHHHHHHHHHHHTSS------S--SCEEEEECCTTSSHHHHHHHHHHHHHHTCSCGGGTTCE
T ss_pred             hHHHHHHHHcCCCCcccChHHHHHHHHHHHhcC------c--cCCcEEECCCCCcHHHHHHHHHHHHHhCCcccccccce
Confidence            345666666777888999999999999998642      1  2579999999999999999999975          456


Q ss_pred             EEEEcCCCchhhhhhhhcccCCccccch-hHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcch----hHHHH
Q 005987          206 LYEWDTPTPTIWQEYMHNCKTGLEYTSK-LDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGR----TAFER  280 (666)
Q Consensus       206 viE~nasd~~~~~e~l~~~~~g~~~~s~-~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~----~~~~~  280 (666)
                      +++++...          ...|..|... .+.+..+++.+...            ...|++|||++.+.+.    ..-..
T Consensus        77 i~~l~~~~----------liag~~~~g~~e~r~~~i~~~~~~~------------~~iIlfiDeih~l~~~g~~~g~~~d  134 (268)
T d1r6bx2          77 IYSLDIGS----------LLAGTKYRGDFEKRFKALLKQLEQD------------TNSILFIDEIHTIIGAGAASGGQVD  134 (268)
T ss_dssp             EEECCCC-------------CCCCCSSCHHHHHHHHHHHHSSS------------SCEEEEETTTTTTTTSCCSSSCHHH
T ss_pred             eEEeeech----------HhccCccchhHHHHHHHHHHHhhcc------------CCceEEecchHHHhcCCCCCCcccc
Confidence            77766543          2345555333 33456666666433            2568999999987421    11123


Q ss_pred             HHHHHHHHHhcCCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHH----HhCCCC
Q 005987          281 LRQCLLLLVRSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICR----QEQYSL  356 (666)
Q Consensus       281 l~~~L~~l~~~~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~----~e~i~v  356 (666)
                      +.+.|..++..+...+|..+|.       +.+.+.++. ...|.+ ++..|.+.+|+.++..++|..+..    ..++.+
T Consensus       135 ~a~~Lkp~L~rg~i~vIgatT~-------eey~~~~e~-d~al~r-rF~~I~V~Eps~e~t~~IL~~~~~~~e~~h~v~~  205 (268)
T d1r6bx2         135 AANLIKPLLSSGKIRVIGSTTY-------QEFSNIFEK-DRALAR-RFQKIDITEPSIEETVQIINGLKPKYEAHHDVRY  205 (268)
T ss_dssp             HHHHHSSCSSSCCCEEEEEECH-------HHHHCCCCC-TTSSGG-GEEEEECCCCCHHHHHHHHHHHHHHHHHHHTCCC
T ss_pred             HHHHhhHHHhCCCCeEEEeCCH-------HHHHHHHhh-cHHHHh-hhcccccCCCCHHHHHHHHHHhhHHHhccCCEEe
Confidence            4455666666665433322221       123333332 223333 599999999999999999987654    357999


Q ss_pred             CHHHHHHHHHHcC------CcHHHHHHHHHHHhc
Q 005987          357 STEQIDLVAQASG------GDIRQAITSLQFSSL  384 (666)
Q Consensus       357 ~~~~l~~Ia~~s~------GDIR~AIn~LQf~~~  384 (666)
                      +++++..++..+.      .-..+||..|.-+|.
T Consensus       206 ~~~al~~~v~ls~ryi~~~~~PdKAIdllDea~a  239 (268)
T d1r6bx2         206 TAKAVRAAVELAVKYINDRHLPDKAIDVIDEAGA  239 (268)
T ss_dssp             CHHHHHHHHHHHHHHCTTSCTTHHHHHHHHHHHH
T ss_pred             ChHHHHHHHHHHHhhccCCCCCcHHHHHHHHHHH
Confidence            9999999998753      446789999987764

>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=99.31  E-value=8.9e-12  Score=131.74  Aligned_cols=208  Identities=19%  Similarity=0.193  Sum_probs=133.9

Q ss_pred             cccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc----------CCcEEE
Q 005987          139 WAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL----------GARLYE  208 (666)
Q Consensus       139 W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel----------g~~viE  208 (666)
                      ++++-+--.++.++|+++.++++..+|.+..     +   ++.||.||||+|||++|+.||+.+          +..+++
T Consensus        12 l~~~a~~g~ld~~~gr~~ei~~~~~~L~r~~-----k---~n~llvG~~GvGKtaiv~~la~~i~~~~vp~~l~~~~i~~   83 (387)
T d1qvra2          12 LTRLAAEGKLDPVIGRDEEIRRVIQILLRRT-----K---NNPVLIGEPGVGKTAIVEGLAQRIVKGDVPEGLKGKRIVS   83 (387)
T ss_dssp             HHHHHHTTCSCCCCSCHHHHHHHHHHHHCSS-----C---CCCEEEECTTSCHHHHHHHHHHHHHHTCSCTTSTTCEEEE
T ss_pred             HHHHHHcCCCCCCcCcHHHHHHHHHHHhcCC-----C---CCCeEECCCCCCHHHHHHHHHHHHHhCCCCHHHcCceEEE
Confidence            3444455567788999999999999998521     1   457888999999999999999876          456777


Q ss_pred             EcCCCchhhhhhhhcccCCcccc-chhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHH---HHHHHH
Q 005987          209 WDTPTPTIWQEYMHNCKTGLEYT-SKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAF---ERLRQC  284 (666)
Q Consensus       209 ~nasd~~~~~e~l~~~~~g~~~~-s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~---~~l~~~  284 (666)
                      ++...          ...|..|. .....+..++..+..+.           .+.||+|||++.+.+...-   ..+.+.
T Consensus        84 ld~~~----------l~ag~~~~g~~e~r~~~i~~~~~~~~-----------~~~ilfide~h~l~~~g~~~g~~d~a~~  142 (387)
T d1qvra2          84 LQMGS----------LLAGAKYRGEFEERLKAVIQEVVQSQ-----------GEVILFIDELHTVVGAGKAEGAVDAGNM  142 (387)
T ss_dssp             ECC---------------------CHHHHHHHHHHHHHTTC-----------SSEEEEECCC------------------
T ss_pred             eeHhh----------hhcccCcchhHHHHHHHHHHHhccCC-----------CceEEEeccHHHHhcCCCCCCcccHHHH
Confidence            76542          23455543 23345566666665432           2578999999987542111   133466


Q ss_pred             HHHHHhcCCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHH----hCCCCCHHH
Q 005987          285 LLLLVRSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTLSKICRQ----EQYSLSTEQ  360 (666)
Q Consensus       285 L~~l~~~~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~----e~i~v~~~~  360 (666)
                      |..++..+..-+|..+|.       +.+. .++. ...|.| +++.|.+.+|+.++...+|+.+...    .++.+++++
T Consensus       143 Lkp~L~rg~~~~I~~tT~-------~ey~-~~e~-d~al~r-rF~~v~v~ep~~~~~~~il~~~~~~~e~~h~v~~~~~a  212 (387)
T d1qvra2         143 LKPALARGELRLIGATTL-------DEYR-EIEK-DPALER-RFQPVYVDEPTVEETISILRGLKEKYEVHHGVRISDSA  212 (387)
T ss_dssp             -HHHHHTTCCCEEEEECH-------HHHH-HHTT-CTTTCS-CCCCEEECCCCHHHHHHHHHHHHHHHHHHTTCEECHHH
T ss_pred             HHHHHhCCCcceeeecCH-------HHHH-Hhcc-cHHHHH-hcccccCCCCcHHHHHHHHHHHHHHHHhccCCcccHHH
Confidence            888888887645433332       1232 3444 344555 6999999999999999999987754    478999999


Q ss_pred             HHHHHHHcC------CcHHHHHHHHHHHhcC
Q 005987          361 IDLVAQASG------GDIRQAITSLQFSSLK  385 (666)
Q Consensus       361 l~~Ia~~s~------GDIR~AIn~LQf~~~~  385 (666)
                      +..++..|.      .=..+||..|..+|..
T Consensus       213 i~~~v~ls~ryi~~r~~PdKAidlld~a~a~  243 (387)
T d1qvra2         213 IIAAATLSHRYITERRLPDKAIDLIDEAAAR  243 (387)
T ss_dssp             HHHHHHHHHHHCCSSCTHHHHHHHHHHHHHH
T ss_pred             HHHHHHhcccccccccChhhHHHHHHHHHHH
Confidence            999998753      5678999999988763

>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=99.24  E-value=1.4e-11  Score=117.28  Aligned_cols=169  Identities=20%  Similarity=0.251  Sum_probs=111.3

Q ss_pred             cccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc----------CCcEEE
Q 005987          139 WAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL----------GARLYE  208 (666)
Q Consensus       139 W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel----------g~~viE  208 (666)
                      .+++.+...++.++|+++.++++...|.+..        ++++||.||||+|||++|+.||+.+          +..+++
T Consensus        12 lt~~a~~g~ld~~igRd~Ei~~l~~iL~r~~--------k~n~lLvG~pGVGKTalv~~LA~ri~~~~vp~~L~~~~i~~   83 (195)
T d1jbka_          12 LTERAEQGKLDPVIGRDEEIRRTIQVLQRRT--------KNNPVLIGEPGVGKTAIVEGLAQRIINGEVPEGLKGRRVLA   83 (195)
T ss_dssp             HHHHHHTTCSCCCCSCHHHHHHHHHHHTSSS--------SCEEEEECCTTSCHHHHHHHHHHHHHHTCSCGGGTTCEEEE
T ss_pred             HHHHHHcCCCCCCcCcHHHHHHHHHHHhccC--------CCCeEEEecCCcccHHHHHHHHHHHHhCCCCHHHcCceEEE
Confidence            4455556677889999999999999887521        2579999999999999999999976          466777


Q ss_pred             EcCCCchhhhhhhhcccCCccccc-hhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHH---HHHHH
Q 005987          209 WDTPTPTIWQEYMHNCKTGLEYTS-KLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFE---RLRQC  284 (666)
Q Consensus       209 ~nasd~~~~~e~l~~~~~g~~~~s-~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~---~l~~~  284 (666)
                      ++..          ....|..|.. -.+.+..+++.+..+.           ...||+|||++.+.+...-.   .+.+.
T Consensus        84 ld~~----------~LiAg~~~rG~~E~rl~~il~e~~~~~-----------~~iILfIDeih~l~~~g~~~g~~d~~~~  142 (195)
T d1jbka_          84 LDMG----------ALVAGAKYRGEFEERLKGVLNDLAKQE-----------GNVILFIDELHTMVGAGKADGAMDAGNM  142 (195)
T ss_dssp             ECHH----------HHHTTTCSHHHHHHHHHHHHHHHHHST-----------TTEEEEEETGGGGTT------CCCCHHH
T ss_pred             eeHH----------HHhccCCccHHHHHHHHHHHHHHhcCC-----------CcEEEEcchHHHHhcCCCCCCcccHHHH
Confidence            6632          1234555532 2334666776664432           24799999999875432111   13466


Q ss_pred             HHHHHhcCCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHHHHHHH
Q 005987          285 LLLLVRSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGSIKRTL  345 (666)
Q Consensus       285 L~~l~~~~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~i~kiL  345 (666)
                      |..++..+...+|..++.       +.+.+.++.-+. |.+ +++.|...+|+.++...+|
T Consensus       143 Lkp~L~rg~l~~IgatT~-------eey~~~~e~d~a-L~r-rF~~I~V~Ep~~e~t~~IL  194 (195)
T d1jbka_         143 LKPALARGELHCVGATTL-------DEYRQYIEKDAA-LER-RFQKVFVAEPSVEDTIAIL  194 (195)
T ss_dssp             HHHHHHTTSCCEEEEECH-------HHHHHHTTTCHH-HHT-TEEEEECCCCCHHHHHTTC
T ss_pred             HHHHHhCCCceEEecCCH-------HHHHHHHHcCHH-HHh-cCCEeecCCCCHHHHHHHh
Confidence            888888776544333322       234445554333 444 5999999999999877665

>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=99.23  E-value=1.9e-10  Score=118.50  Aligned_cols=204  Identities=17%  Similarity=0.235  Sum_probs=121.8

Q ss_pred             ccccCHHHHHHHHHHHHHhhcC--CCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCchhhhhhhhcccCC
Q 005987          150 ELAVQRKKVEEVRAWFEERLGD--SKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTIWQEYMHNCKTG  227 (666)
Q Consensus       150 eLvg~~k~i~el~~wL~~~~~~--~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~~~~e~l~~~~~g  227 (666)
                      .++||+.+++.|...+..+...  .+.+ |...+||+||||||||.+|+.||+.++..++.++.+.....  +......|
T Consensus        23 ~viGQ~~a~~~v~~~v~~~~~~l~~~~~-p~~~~lf~Gp~GvGKT~lak~la~~l~~~~i~~d~s~~~~~--~~~~~l~g   99 (315)
T d1r6bx3          23 LVFGQDKAIEALTEAIKMARAGLGHEHK-PVGSFLFAGPTGVGKTEVTVQLSKALGIELLRFDMSEYMER--HTVSRLIG   99 (315)
T ss_dssp             TSCSCHHHHHHHHHHHHHHHTTCSCTTS-CSEEEEEECSTTSSHHHHHHHHHHHHTCEEEEEEGGGCSSS--SCCSSSCC
T ss_pred             eecChHHHHHHHHHHHHHHHccCCCCCC-CceEEEEECCCcchhHHHHHHHHhhccCCeeEeccccccch--hhhhhhcc
Confidence            3689999999999988765542  2222 33579999999999999999999999999999887652211  00000112


Q ss_pred             cc--ccc--hhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcCC----------
Q 005987          228 LE--YTS--KLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTH----------  293 (666)
Q Consensus       228 ~~--~~s--~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~~----------  293 (666)
                      ..  |..  ....+...+   .+            ++..|+++||++..+.     .+++.|+.+++.+.          
T Consensus       100 ~~~gy~g~~~~~~l~~~~---~~------------~~~~vvl~DeieKa~~-----~V~~~lLqild~G~ltd~~Gr~vd  159 (315)
T d1r6bx3         100 APPGYVGFDQGGLLTDAV---IK------------HPHAVLLLDEIEKAHP-----DVFNILLQVMDNGTLTDNNGRKAD  159 (315)
T ss_dssp             CCSCSHHHHHTTHHHHHH---HH------------CSSEEEEEETGGGSCH-----HHHHHHHHHHHHSEEEETTTEEEE
T ss_pred             cCCCccccccCChhhHHH---Hh------------Cccchhhhcccccccc-----hHhhhhHHhhccceecCCCCCccC
Confidence            11  110  011122222   11            1346999999998753     34556666665431          


Q ss_pred             --CceEEEEecCCCCCCccc---------hhhhhhHH-----HHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHh-----
Q 005987          294 --IPTAVVLTECGKADSVDS---------TAQSFEEL-----QSILVDAGARKVALNPITNGSIKRTLSKICRQE-----  352 (666)
Q Consensus       294 --~PiViIit~~~~~~s~d~---------~~r~l~~L-----~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e-----  352 (666)
                        .-++++.++.+.....+.         .....+.+     .+++.| --.+|.|+|++.+++.+++...+...     
T Consensus       160 f~n~iiI~Tsnig~~~i~~~~~~~~~~~~~~~~~~~l~~~f~pEflnR-id~ii~f~~l~~~~~~~I~~~~l~~~~~~l~  238 (315)
T d1r6bx3         160 FRNVVLVMTTNAGVRETERKSIGLIHQDNSTDAMEEIKKIFTPEFRNR-LDNIIWFDHLSTDVIHQVVDKFIVELQVQLD  238 (315)
T ss_dssp             CTTEEEEEEECSSCC-----------------CHHHHHHHSCHHHHTT-CSEEEECCCCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             ccceEEEeccchhhHHHHhhhccchhhhhhHhHHHHHHHhcCHHHHhh-hhhhhcccchhhhHHHHHHHHHHHHHHHHHH
Confidence              123444444332211000         00111111     244444 34689999999999999877665431     


Q ss_pred             ----CCCCCHHHHHHHHHHc------CCcHHHHHH
Q 005987          353 ----QYSLSTEQIDLVAQAS------GGDIRQAIT  377 (666)
Q Consensus       353 ----~i~v~~~~l~~Ia~~s------~GDIR~AIn  377 (666)
                          .+.+++++++.|++.+      ...+|++|.
T Consensus       239 ~~~i~l~~~~~a~~~l~~~~yd~~~GaR~L~r~Ie  273 (315)
T d1r6bx3         239 QKGVSLEVSQEARNWLAEKGYDRAMGARPMARVIQ  273 (315)
T ss_dssp             HTTEEEEECHHHHHHHHHHHCBTTTBTTTHHHHHH
T ss_pred             hcCcchhhHHHHHHHHHHhCCCCCCChhhHHHHHH
Confidence                2457899999999873      247777774

>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=99.23  E-value=2.9e-12  Score=134.62  Aligned_cols=187  Identities=9%  Similarity=-0.039  Sum_probs=102.4

Q ss_pred             HHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCchhhhhhhhcccCCccccchhHHHHHHHH
Q 005987          163 AWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPTIWQEYMHNCKTGLEYTSKLDEFENFVE  242 (666)
Q Consensus       163 ~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~~~~e~l~~~~~g~~~~s~~~~f~~fl~  242 (666)
                      .+|+.++.   |.+.++.+||+||||||||++|+++|+.+|+.++++|+++.+.... +.... ..        +..+++
T Consensus       142 ~~l~~~~~---~~~~~~~~~~~g~~~~gk~~~~~~~~~~~~~~~i~in~s~~rs~~~-l~~~~-~~--------~~~l~d  208 (362)
T d1svma_         142 DFLKCMVY---NIPKKRYWLFKGPIDSGKTTLAAALLELCGGKALNVNLPLDRLNFE-LGVAI-DQ--------FLVVFE  208 (362)
T ss_dssp             HHHHHHHH---CCTTCCEEEEECSTTSSHHHHHHHHHHHHCCEEECCSSCTTTHHHH-HGGGT-TC--------SCEEET
T ss_pred             HHHHHHHh---CCCCcCeEEEECCCCCCHHHHHHHHHHHcCCCEEEEECcchhhHHH-HHhHH-HH--------HHHHHH
Confidence            44444443   5555579999999999999999999999999999999987542110 00000 00        000011


Q ss_pred             HHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHH-HHH----HHHhcCCCceEEEEecCCCCCCccchhhhhh
Q 005987          243 RIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQ-CLL----LLVRSTHIPTAVVLTECGKADSVDSTAQSFE  317 (666)
Q Consensus       243 ~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~-~L~----~l~~~~~~PiViIit~~~~~~s~d~~~r~l~  317 (666)
                      .+..      ........+.++++||+|.+...  +.+... .+.    ........|+|+ +++...       ...  
T Consensus       209 ~~~~------~~~~~~~~~~~~~~DeiD~l~~~--~dg~~~~~~~~~~~~~~~~~~~p~i~-ttN~~~-------~~~--  270 (362)
T d1svma_         209 DVKG------TGGESRDLPSGQGINNLDNLRDY--LDGSVKVNLEKKHLNKRTQIFPPGIV-TMNEYS-------VPK--  270 (362)
T ss_dssp             TCCC------STTTTTTCCCCSHHHHHHTTHHH--HHCSSCEEECCSSSCCEEECCCCEEE-EECSCC-------CCH--
T ss_pred             HHHH------hhhhccCCCCeEEEehHhhcccc--cCCcchhhhhhhhhchhhhccCCcee-eccccc-------ccc--
Confidence            1100      00111223467778888765211  000000 000    000001124444 443111       111  


Q ss_pred             HHHHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHH-HHHHcCCcHHHHHHHHHHHh
Q 005987          318 ELQSILVDAGARKVALNPITNGSIKRTLSKICRQEQYSLSTEQIDL-VAQASGGDIRQAITSLQFSS  383 (666)
Q Consensus       318 ~L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e~i~v~~~~l~~-Ia~~s~GDIR~AIn~LQf~~  383 (666)
                       ++.  .|+++..+.+.|+....+..++..++..+.+.++.+.+.. +...+++|+|++|+.++...
T Consensus       271 -~r~--~Rf~~~i~~~~~~~~~~~~~~l~~i~~~~~l~~~~~~L~~li~~~s~~D~~~~i~~~~~~~  334 (362)
T d1svma_         271 -TLQ--ARFVKQIDFRPKDYLKHCLERSEFLLEKRIIQSGIALLLMLIWYRPVAEFAQSIQSRIVEW  334 (362)
T ss_dssp             -HHH--TTEEEEEECCCCHHHHHHHHTCTHHHHTTCTTCHHHHHHHHHHHSCGGGSCGGGHHHHHHH
T ss_pred             -ccc--ccCceEEeecCCCcHHHHHHHHHHHhcccCCCCCHHHHHHHccCCCHHHHHHHHHHHHHHH
Confidence             121  1333444455555566667788889999998888777755 44667789999999887654

>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=99.21  E-value=6.7e-11  Score=113.75  Aligned_cols=175  Identities=12%  Similarity=0.139  Sum_probs=103.2

Q ss_pred             HHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcC------CcEEEEcCCCchhhhhhhhcccCCcccc
Q 005987          158 VEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLG------ARLYEWDTPTPTIWQEYMHNCKTGLEYT  231 (666)
Q Consensus       158 i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg------~~viE~nasd~~~~~e~l~~~~~g~~~~  231 (666)
                      ++-|++|++.      +..  ..+||+||||+|||++|..+|+.+.      .+++++.+..              .  .
T Consensus         3 ~~~l~~~i~~------~~~--~~~l~~G~~g~gk~~~a~~l~~~i~~~~~~h~D~~~i~~~~--------------~--~   58 (198)
T d2gnoa2           3 LETLKRIIEK------SEG--ISILINGEDLSYPREVSLELPEYVEKFPPKASDVLEIDPEG--------------E--N   58 (198)
T ss_dssp             HHHHHHHHHT------CSS--EEEEEECSSSSHHHHHHHHHHHHHHTSCCCTTTEEEECCSS--------------S--C
T ss_pred             HHHHHHHHhc------CCC--ceEEEECCCCCCHHHHHHHHHHHHhccccCCCCEEEEeCCc--------------C--C
Confidence            4566777764      333  5899999999999999999999772      3566665421              1  1


Q ss_pred             chhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcCCCc-eEEEEecCCCCCCcc
Q 005987          232 SKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHIP-TAVVLTECGKADSVD  310 (666)
Q Consensus       232 s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~~~P-iViIit~~~~~~s~d  310 (666)
                      -..++++++...+...+        ..+..+|++|||+|.++..     .+++|+..++....- ++|++++        
T Consensus        59 I~Id~IR~i~~~~~~~~--------~~~~~KviIId~ad~l~~~-----aqNaLLK~LEEPp~~t~fiLit~--------  117 (198)
T d2gnoa2          59 IGIDDIRTIKDFLNYSP--------ELYTRKYVIVHDCERMTQQ-----AANAFLKALEEPPEYAVIVLNTR--------  117 (198)
T ss_dssp             BCHHHHHHHHHHHTSCC--------SSSSSEEEEETTGGGBCHH-----HHHHTHHHHHSCCTTEEEEEEES--------
T ss_pred             CCHHHHHHHHHHHhhCc--------ccCCCEEEEEeCccccchh-----hhhHHHHHHhCCCCCceeeeccC--------
Confidence            13456666665553221        1124579999999998643     344677777765433 4444444        


Q ss_pred             chhhhhhHHHHHHhhcCeeEEEeCCCCHHH--HHHHHHHHHHHh-----CCCCCHHHHHHHHHHcCCcHHHHHHHHHHHh
Q 005987          311 STAQSFEELQSILVDAGARKVALNPITNGS--IKRTLSKICRQE-----QYSLSTEQIDLVAQASGGDIRQAITSLQFSS  383 (666)
Q Consensus       311 ~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~--i~kiL~~I~~~e-----~i~v~~~~l~~Ia~~s~GDIR~AIn~LQf~~  383 (666)
                      ...+.++.+++     ||+.|.|+++....  +...+..+....     ......+++..++....| +|.+++.|+...
T Consensus       118 ~~~~ll~TI~S-----RC~~i~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~l~~ld~~~  191 (198)
T d2gnoa2         118 RWHYLLPTIKS-----RVFRVVVNVPKEFRDLVKEKIGDLWEELPLLERDFKTALEAYKLGAEKLSG-LMESLKVLETEK  191 (198)
T ss_dssp             CGGGSCHHHHT-----TSEEEECCCCHHHHHHHHHHHTTHHHHCGGGGTCHHHHHHHHHHHHHHHHH-HHHHHHHSCHHH
T ss_pred             ChhhCHHHHhc-----ceEEEeCCCchHHHHHHHHHHHHHHHHHHHHhccccCCHHHHHHHHHHhhC-HHHHHHHHHHHH
Confidence            12345555554     69999998775321  122222122211     111234455666666644 777777665543

>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=99.18  E-value=5.4e-11  Score=122.44  Aligned_cols=63  Identities=19%  Similarity=0.299  Sum_probs=49.0

Q ss_pred             cccCHHHHHHHHHHHHHhhcCC------CCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCC
Q 005987          151 LAVQRKKVEEVRAWFEERLGDS------KDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPT  213 (666)
Q Consensus       151 Lvg~~k~i~el~~wL~~~~~~~------~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd  213 (666)
                      ++||+++++.|...+.......      +...+++.+||+||||||||.+|+++|++++..++.++.+.
T Consensus        16 ViGQd~A~~~l~~av~~~~~r~~~~~~~~~~~~~~~iLl~GPpG~GKT~lAkalA~~~~~~~~~i~~s~   84 (309)
T d1ofha_          16 IIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAKLANAPFIKVEATK   84 (309)
T ss_dssp             CCSCHHHHHHHHHHHHHHHHTTSSCHHHHHHCCCCCEEEECCTTSSHHHHHHHHHHHHTCCEEEEEGGG
T ss_pred             ccChHHHHHHHHHHHHHHHHHhccCCCCccCCCCceEEEECCCCCCHHHHHHHHhhccccchhcccccc
Confidence            5899999999988775322110      01113378999999999999999999999999999998765

>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=99.09  E-value=9e-10  Score=113.30  Aligned_cols=206  Identities=17%  Similarity=0.270  Sum_probs=119.7

Q ss_pred             ccccCHHHHHHHHHHHHHhhcCCC-CCCCccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcCCCchhh---hhhhh
Q 005987          150 ELAVQRKKVEEVRAWFEERLGDSK-DKFSTNVLVITGQAGVGKTATVRQIASHL---GARLYEWDTPTPTIW---QEYMH  222 (666)
Q Consensus       150 eLvg~~k~i~el~~wL~~~~~~~~-g~~~~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~nasd~~~~---~e~l~  222 (666)
                      .++||+..++.|...+..+..... ..-|...+||+||+|+|||.+|+.||+.+   +..++.++.+....-   ...++
T Consensus        24 ~v~GQ~~ai~~v~~~i~~~~~~l~~~~kp~~~~lf~Gp~G~GKt~lak~la~~l~~~~~~~~~~~~~~~~~~~~~~~L~g  103 (315)
T d1qvra3          24 RVVGQDEAIRAVADAIRRARAGLKDPNRPIGSFLFLGPTGVGKTELAKTLAATLFDTEEAMIRIDMTEYMEKHAVSRLIG  103 (315)
T ss_dssp             HSCSCHHHHHHHHHHHHHHGGGCSCSSSCSEEEEEBSCSSSSHHHHHHHHHHHHHSSGGGEEEECTTTCCSSGGGGGC--
T ss_pred             eEeCHHHHHHHHHHHHHHHhcCCCCCCCCceEEEEECCCcchHHHHHHHHHHHhcCCCcceEEEeccccccchhhhhhcC
Confidence            468999999999998886643211 12232478999999999999999999998   667888887653211   11111


Q ss_pred             cccCC-ccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcCCC-------
Q 005987          223 NCKTG-LEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHI-------  294 (666)
Q Consensus       223 ~~~~g-~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~~~-------  294 (666)
                      . ..| ..+. ....+.+.   +++.            +..||++||++.+..     .+++.|..+++.++.       
T Consensus       104 ~-~~gyvG~~-~~~~l~~~---~~~~------------p~~Vvl~DEieK~~~-----~v~~~ll~~l~~g~~~~~~gr~  161 (315)
T d1qvra3         104 A-PPGYVGYE-EGGQLTEA---VRRR------------PYSVILFDEIEKAHP-----DVFNILLQILDDGRLTDSHGRT  161 (315)
T ss_dssp             --------------CHHHH---HHHC------------SSEEEEESSGGGSCH-----HHHHHHHHHHTTTEECCSSSCC
T ss_pred             C-CCCCcCcc-cCChHHHH---HHhC------------CCcEEEEehHhhcCH-----HHHHHHHHHhccCceeCCCCcE
Confidence            1 111 1110 01122222   3222            346999999998753     355566777655311       


Q ss_pred             ----ceEEEEe-cCCCCCCcc------c----hhhhhhH----H-HHHHhhcCeeEEEeCCCCHHHHHHHHHHHHHHh--
Q 005987          295 ----PTAVVLT-ECGKADSVD------S----TAQSFEE----L-QSILVDAGARKVALNPITNGSIKRTLSKICRQE--  352 (666)
Q Consensus       295 ----PiViIit-~~~~~~s~d------~----~~r~l~~----L-~s~L~r~r~~~I~F~p~s~~~i~kiL~~I~~~e--  352 (666)
                          ..++|++ +.+......      .    .......    + .+++.| --.+|.|+|++.+++.+++...+...  
T Consensus       162 v~~~~~i~i~tsnlG~~~i~~~~~~~~~~~~~~~~~~~~l~~~f~pEflnR-id~Ii~F~~L~~~~~~~I~~~~l~~l~~  240 (315)
T d1qvra3         162 VDFRNTVIILTSNLGSPLILEGLQKGWPYERIRDEVFKVLQQHFRPEFLNR-LDEIVVFRPLTKEQIRQIVEIQLSYLRA  240 (315)
T ss_dssp             EECTTEEEEEECCTTHHHHHHHHHTTCCHHHHHHHHHHHHHTTSCHHHHHT-CSBCCBCCCCCHHHHHHHHHHHHHHHHH
T ss_pred             ecCcceEEEEecccChHHHhhhcccccchhhhhHHHHHHHHhhcCHHHHhc-CCeeeeccchhhhhhHHHHHHHHHHHHH
Confidence                2344443 321100000      0    0000000    1 234444 24467899999999999987665532  


Q ss_pred             -------CCCCCHHHHHHHHHHc------CCcHHHHHHH
Q 005987          353 -------QYSLSTEQIDLVAQAS------GGDIRQAITS  378 (666)
Q Consensus       353 -------~i~v~~~~l~~Ia~~s------~GDIR~AIn~  378 (666)
                             .+.+++++++.|++.+      ...+|++|..
T Consensus       241 rl~~~~i~l~i~~~~~~~L~~~~y~~~~GAR~L~r~Ie~  279 (315)
T d1qvra3         241 RLAEKRISLELTEAAKDFLAERGYDPVFGARPLRRVIQR  279 (315)
T ss_dssp             HHHTTTCEEEECHHHHHHHHHHHCBTTTBTSTHHHHHHH
T ss_pred             HHHhccccccccHHHHHHHHHhCCCCCCCcchHHHHHHH
Confidence                   2457899999999873      2578888765

>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=98.89  E-value=3.3e-09  Score=111.03  Aligned_cols=63  Identities=17%  Similarity=0.228  Sum_probs=47.8

Q ss_pred             cccCHHHHHHHHHHHHHhhcC----------------------CCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEE
Q 005987          151 LAVQRKKVEEVRAWFEERLGD----------------------SKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYE  208 (666)
Q Consensus       151 Lvg~~k~i~el~~wL~~~~~~----------------------~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE  208 (666)
                      ++||+++++.|...+.++...                      .....++..+||.||+|||||.+|++||+.++..++.
T Consensus        19 ViGQd~Akkava~Avrn~~rR~~~~~~~r~~~~~~~~~~~~~~~~~~~p~~niLfiGPTGvGKTElAk~LA~~~~~~~ir   98 (364)
T d1um8a_          19 VIGQEQAKKVFSVAVYNHYKRLSFKEKLKKQDNQDSNVELEHLEEVELSKSNILLIGPTGSGKTLMAQTLAKHLDIPIAI   98 (364)
T ss_dssp             CCSCHHHHHHHHHHHHHHHHHHHHHHHHHHHCSHHHHHHHHHHHHTTCCCCCEEEECCTTSSHHHHHHHHHHHTTCCEEE
T ss_pred             ecChHHHHHHHHHHHHHHHHHHHHHHHhhccccccccccccccccccCCCcceeeeCCCCccHHHHHHHHHhhcccceee
Confidence            689999999998777422110                      0012234679999999999999999999999888888


Q ss_pred             EcCCC
Q 005987          209 WDTPT  213 (666)
Q Consensus       209 ~nasd  213 (666)
                      ++++.
T Consensus        99 ~D~s~  103 (364)
T d1um8a_          99 SDATS  103 (364)
T ss_dssp             EEGGG
T ss_pred             hhhhh
Confidence            87764

>d2fnaa2 c.37.1.20 (A:1-283) Archaeal ATPase SSO1545 {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Archaeal ATPase SSO1545
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=98.85  E-value=1.8e-08  Score=99.66  Aligned_cols=203  Identities=14%  Similarity=0.161  Sum_probs=110.9

Q ss_pred             CCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCCch--------hh
Q 005987          146 RSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPTPT--------IW  217 (666)
Q Consensus       146 ~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd~~--------~~  217 (666)
                      .+.++++|+++.++++...    .        .+.++|+||+|+|||++++.++++++.....++.....        ..
T Consensus         9 ~~~~~f~GR~~el~~l~~~----~--------~~~i~i~G~~G~GKTsLl~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~   76 (283)
T d2fnaa2           9 DNRKDFFDREKEIEKLKGL----R--------APITLVLGLRRTGKSSIIKIGINELNLPYIYLDLRKFEERNYISYKDF   76 (283)
T ss_dssp             CSGGGSCCCHHHHHHHHHT----C--------SSEEEEEESTTSSHHHHHHHHHHHHTCCEEEEEGGGGTTCSCCCHHHH
T ss_pred             CChhhCCChHHHHHHHHhc----c--------CCEEEEEcCCCCcHHHHHHHHHHHCCCCeEEEEeccccccccccHHHH
Confidence            5678999999999887542    1        15899999999999999999999998877665432100        00


Q ss_pred             hhhhhcc---------------c-------CCcc-----ccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCC
Q 005987          218 QEYMHNC---------------K-------TGLE-----YTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLP  270 (666)
Q Consensus       218 ~e~l~~~---------------~-------~g~~-----~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid  270 (666)
                      ...+...               .       .+..     .......+.++++.....          .+.+.+|++||++
T Consensus        77 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~----------~~~~~~i~id~~~  146 (283)
T d2fnaa2          77 LLELQKEINKLVKRLPSLLKALKNIQGIVIMGNEIKFNWNRKDRLSFANLLESFEQA----------SKDNVIIVLDEAQ  146 (283)
T ss_dssp             HHHHHHHHHHHHHHCTTHHHHTTTSTTEEECSSSEEEC-----CCCHHHHHHHHHHT----------CSSCEEEEEETGG
T ss_pred             HHHHHHHhhhhhhhhHHHHHHHHhhhcccccccccccccchhhhhHHHHHHHHHHhh----------cccccccccchhh
Confidence            0000000               0       0000     000111222333332221          2356789999998


Q ss_pred             CCcchhHHHHHHHHHHHHHhcCCCceEEEEecCCCCCCccchhhhhhH--HHHHHhhcCeeEEEeCCCCHHHHHHHHHHH
Q 005987          271 VTNGRTAFERLRQCLLLLVRSTHIPTAVVLTECGKADSVDSTAQSFEE--LQSILVDAGARKVALNPITNGSIKRTLSKI  348 (666)
Q Consensus       271 ~l~~~~~~~~l~~~L~~l~~~~~~PiViIit~~~~~~s~d~~~r~l~~--L~s~L~r~r~~~I~F~p~s~~~i~kiL~~I  348 (666)
                      .+..... ..+...|........ ++.+++......    .....+..  ....+.......+.+.|++.+++.++|.+.
T Consensus       147 ~~~~~~~-~~~~~~l~~~~~~~~-~~~~i~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~i~L~~l~~~e~~~~l~~~  220 (283)
T d2fnaa2         147 ELVKLRG-VNLLPALAYAYDNLK-RIKFIMSGSEMG----LLYDYLRVEDPESPLFGRAFSTVELKPFSREEAIEFLRRG  220 (283)
T ss_dssp             GGGGCTT-CCCHHHHHHHHHHCT-TEEEEEEESSHH----HHHHHTTTTCTTSTTTTCCCEEEEECCCCHHHHHHHHHHH
T ss_pred             hhcccch-HHHHHHHHHHHHhhh-hhhhhhccccch----HHHHHHHhhhhcchhcccceeEEeeCCCCHHHHHHHHHhh
Confidence            6533211 112223433333332 233333221100    00000000  000011113678999999999999999999


Q ss_pred             HHHhCCCCCHHHHHHHHHHcCCcHHHHHHHH
Q 005987          349 CRQEQYSLSTEQIDLVAQASGGDIRQAITSL  379 (666)
Q Consensus       349 ~~~e~i~v~~~~l~~Ia~~s~GDIR~AIn~L  379 (666)
                      +...++..+  .++.|.+.++|-.. .++.+
T Consensus       221 ~~~~~~~~~--~~~~i~~~~~G~P~-~L~~~  248 (283)
T d2fnaa2         221 FQEADIDFK--DYEVVYEKIGGIPG-WLTYF  248 (283)
T ss_dssp             HHHHTCCCC--CHHHHHHHHCSCHH-HHHHH
T ss_pred             hhhcCCCHH--HHHHHHHHhCCCHH-HHHHH
Confidence            888776654  46899999999886 44443

>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=98.85  E-value=4.4e-09  Score=107.53  Aligned_cols=73  Identities=19%  Similarity=0.283  Sum_probs=52.0

Q ss_pred             CccEEEEECCCCchHHHHHHHHHHHcC--CcEEEEcCCCchhhhhhhhcccCCccccchhHHHHHHHHHHHhhcCCCCCC
Q 005987          177 STNVLVITGQAGVGKTATVRQIASHLG--ARLYEWDTPTPTIWQEYMHNCKTGLEYTSKLDEFENFVERIRRYGSTSPSI  254 (666)
Q Consensus       177 ~~k~LLL~GPpG~GKTtla~~LAkelg--~~viE~nasd~~~~~e~l~~~~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~  254 (666)
                      +..++||+||||||||.+|++||.+++  ..++.++.++.           .+.........++.+++.++.        
T Consensus       122 ~~g~~l~~G~pG~GKT~la~ala~~~~~~~~~~~~~~~~~-----------~~~~~G~~e~~~~~~f~~a~~--------  182 (321)
T d1w44a_         122 ASGMVIVTGKGNSGKTPLVHALGEALGGKDKYATVRFGEP-----------LSGYNTDFNVFVDDIARAMLQ--------  182 (321)
T ss_dssp             ESEEEEEECSSSSCHHHHHHHHHHHHHTTSCCEEEEBSCS-----------STTCBCCHHHHHHHHHHHHHH--------
T ss_pred             CCceEEEECCCCccHHHHHHHHHHHhcCCCCeEEEEhhHh-----------hhcccchHHHHHHHHHHHHhh--------
Confidence            445788899999999999999999986  45677776652           111223344566777777742        


Q ss_pred             CCCCCCceEEEEeCCCCCcc
Q 005987          255 PGESKSSAILLIDDLPVTNG  274 (666)
Q Consensus       255 ~~~~~~~~IIlIDEid~l~~  274 (666)
                            ++||||||+|.+.+
T Consensus       183 ------~~ilf~DEid~~~~  196 (321)
T d1w44a_         183 ------HRVIVIDSLKNVIG  196 (321)
T ss_dssp             ------CSEEEEECCTTTC-
T ss_pred             ------ccEEEeehhhhhcc
Confidence                  35999999998743

>d1sxja1 a.80.1.1 (A:548-693) Replication factor C1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: post-AAA+ oligomerization domain-like
superfamily: post-AAA+ oligomerization domain-like
family: DNA polymerase III clamp loader subunits, C-terminal domain
domain: Replication factor C1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.83  E-value=6.9e-09  Score=93.62  Aligned_cols=126  Identities=13%  Similarity=0.069  Sum_probs=85.2

Q ss_pred             cchHHHHhHHhhCCCCCCccccccccchhhhhccccCCCCCCChHHHHHhcCCChhHHHHHHHhhcCCCCCc------ch
Q 005987          422 LSLFHALGKFLHNKRETDNLVKMDQDAFVVKDKFSRLPLKMDAPEKVLSQAHGQARPVLDFLHENFLDFISE------DA  495 (666)
Q Consensus       422 l~lFhalGkil~~Kr~~~~~~~~~~~~~~~~~~~~r~pl~~~~pE~vl~~~~~~~~~~~~~LhENy~~f~~d------~~  495 (666)
                      |++|++.+|+|.+.......    .         +++     ...+-++-+..|++.+.+|+||||+++.+.      ..
T Consensus         2 l~pFd~~~kll~~~~~~~~~----~---------~~~-----~i~dk~~lfF~D~~lvpL~vqENYl~~~~~~~~~~~~~   63 (146)
T d1sxja1           2 LKPFDIAHKMLDGQIYSDIG----S---------RNF-----TLNDKIALYFDDFDFTPLMIQENYLSTRPSVLKPGQSH   63 (146)
T ss_dssp             SHHHHHHHHHTBGGGTSTTG----G---------GTS-----CHHHHHHHHTTSTTTHHHHHHHHSSSSEESCCCTTCCH
T ss_pred             CCHHHHHHHHhcccccCccc----c---------ccC-----CHHHHHHHHhcccchhHHHHHhhhcccccccCCCHHHH
Confidence            78999999999875322110    0         011     123445667789999999999999997532      46


Q ss_pred             HHHHHHHHHHhhHhhhccccccCccccccchhHHHHHHHHHHHHHHHhhhCCCCCCCCcccccCCcchhhhhhhHHHH
Q 005987          496 IDDAWAVASYLSDADLLLASFRGRLVRYNEADNVLQSAAASVAARGVLFGNSHPVPPRWHAIRKPKLWRVDQSSLQKK  573 (666)
Q Consensus       496 i~~~~~~~d~LS~aD~l~~~~~~~~~~~~~~~~~l~~~a~sva~RGv~~~n~~p~~~~~~~~~~P~~~~~~~~~~~~~  573 (666)
                      |+.+++|+|.+|++|++.+.+|+..+.|.    ++...+..-|++...+...+. +   ..+++|+|++.+++...++
T Consensus        64 l~~is~aadsis~gDiid~~Ir~~~Q~Ws----Llp~~ai~s~v~P~~~~~g~~-~---~~~~Fp~wLGKnSt~~K~~  133 (146)
T d1sxja1          64 LEAVAEAANCISLGDIVEKKIRSSEQLWS----LLPLHAVLSSVYPASKVAGHM-A---GRINFTAWLGQNSKSAKYY  133 (146)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTTCSSCGG----GHHHHHHHHTHHHHHTTCEEC-S---SCCCCCSHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhHHHHHHHHHccccCCcc----cchhhHHHhhccchHhhcCCC-C---CCCcccHHhhhhhhhhHHH
Confidence            99999999999999999998876534453    455555544454444433221 1   2468999999988765544

>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=98.60  E-value=1.1e-06  Score=86.56  Aligned_cols=204  Identities=16%  Similarity=0.235  Sum_probs=110.8

Q ss_pred             ccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcC---CcEEEEcCCCch--hhhhhhhcc
Q 005987          150 ELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLG---ARLYEWDTPTPT--IWQEYMHNC  224 (666)
Q Consensus       150 eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg---~~viE~nasd~~--~~~e~l~~~  224 (666)
                      |++++...++++.+-++....   .+   .+++|+||+|||||++|+++.....   ..++.+++....  .+...+...
T Consensus         1 ~~v~~S~~~~~~~~~~~~~a~---~~---~pvlI~Ge~GtGK~~~A~~ih~~s~~~~~~~~~~~~~~~~~~~~~~~lfg~   74 (247)
T d1ny5a2           1 EYVFESPKMKEILEKIKKISC---AE---CPVLITGESGVGKEVVARLIHKLSDRSKEPFVALNVASIPRDIFEAELFGY   74 (247)
T ss_dssp             CCCCCSHHHHHHHHHHHHHTT---CC---SCEEEECSTTSSHHHHHHHHHHHSTTTTSCEEEEETTTSCHHHHHHHHHCB
T ss_pred             CeEecCHHHHHHHHHHHHHhC---CC---CCEEEECCCCcCHHHHHHHHHHhcCCcccccccchhhhhhhcccHHHhcCc
Confidence            568888888998888887532   12   3599999999999999999987652   345666654311  111111100


Q ss_pred             cCCccccchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCCCcchhHHHHHHHHHHHHHhcCC-----------
Q 005987          225 KTGLEYTSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPVTNGRTAFERLRQCLLLLVRSTH-----------  293 (666)
Q Consensus       225 ~~g~~~~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~~-----------  293 (666)
                      ..|.. ......-..+++.+               ....|+|||++.++...     +..|..+++...           
T Consensus        75 ~~~~~-~~~~~~~~g~l~~a---------------~gGtL~l~~i~~L~~~~-----Q~~L~~~l~~~~~~~~~~~~~~~  133 (247)
T d1ny5a2          75 EKGAF-TGAVSSKEGFFELA---------------DGGTLFLDEIGELSLEA-----QAKLLRVIESGKFYRLGGRKEIE  133 (247)
T ss_dssp             CTTSS-TTCCSCBCCHHHHT---------------TTSEEEEESGGGCCHHH-----HHHHHHHHHHSEECCBTCCSBEE
T ss_pred             ccCCc-CCcccccCCHHHcc---------------CCCEEEEeChHhCCHHH-----HHHHHHHHHhCCEEECCCCCcee
Confidence            00000 00000000011111               12378999999886432     223444444321           


Q ss_pred             -CceEEEEecCCCCCCccc-hhhhhhHHHHHHhhcCeeEEEeCCCC--HHHHHHHHHH----HHHHhCC---CCCHHHHH
Q 005987          294 -IPTAVVLTECGKADSVDS-TAQSFEELQSILVDAGARKVALNPIT--NGSIKRTLSK----ICRQEQY---SLSTEQID  362 (666)
Q Consensus       294 -~PiViIit~~~~~~s~d~-~~r~l~~L~s~L~r~r~~~I~F~p~s--~~~i~kiL~~----I~~~e~i---~v~~~~l~  362 (666)
                       ...+|.+++....   .. ....+  ...++.+.....|.++|+.  .+++..++..    .+...+.   .+++++++
T Consensus       134 ~~~RlI~~s~~~l~---~l~~~~~f--~~~L~~~l~~~~i~lPpLreR~~Di~~l~~~~l~~~~~~~~~~~~~ls~~al~  208 (247)
T d1ny5a2         134 VNVRILAATNRNIK---ELVKEGKF--REDLYYRLGVIEIEIPPLRERKEDIIPLANHFLKKFSRKYAKEVEGFTKSAQE  208 (247)
T ss_dssp             CCCEEEEEESSCHH---HHHHTTSS--CHHHHHHHTTEEEECCCGGGCHHHHHHHHHHHHHHHHHHTTCCCCEECHHHHH
T ss_pred             cCeEEEEecCCCHH---HHHHcCCC--cHHHHhhcCeeeecCCChhhchhhHhhhhhhhhhhhhhhcCCCCCCCCHHHHH
Confidence             1123333332100   00 00011  1223333345678999985  3566544444    4444443   37899999


Q ss_pred             HHHHHc-CCcHHHHHHHHHHHhcC
Q 005987          363 LVAQAS-GGDIRQAITSLQFSSLK  385 (666)
Q Consensus       363 ~Ia~~s-~GDIR~AIn~LQf~~~~  385 (666)
                      .|.... .|++|...+.++-++..
T Consensus       209 ~L~~~~WPGNl~EL~~~l~~a~~~  232 (247)
T d1ny5a2         209 LLLSYPWYGNVRELKNVIERAVLF  232 (247)
T ss_dssp             HHHHSCCTTHHHHHHHHHHHHHHH
T ss_pred             HHHhCCCCCHHHHHHHHHHHHHHh
Confidence            998875 69999999999877653

>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=98.56  E-value=1.2e-06  Score=93.38  Aligned_cols=63  Identities=19%  Similarity=0.293  Sum_probs=50.7

Q ss_pred             cccCHHHHHHHHHHHHHhhc------CCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCC
Q 005987          151 LAVQRKKVEEVRAWFEERLG------DSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPT  213 (666)
Q Consensus       151 Lvg~~k~i~el~~wL~~~~~------~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd  213 (666)
                      ++||+++.+.|.-.+.++..      ..+....++++||.||||||||.+|+.||+.++..++-..++.
T Consensus        16 VvGQ~~AKk~lsvav~nhyrR~~~~~~~~~ei~ksNILliGPTGvGKTlLAr~LAk~l~VPFv~~daT~   84 (443)
T d1g41a_          16 IIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAKLANAPFIKVEATK   84 (443)
T ss_dssp             CCSCHHHHHHHHHHHHHHHHHHHSCTTTTTTCCCCCEEEECCTTSSHHHHHHHHHHHTTCCEEEEEGGG
T ss_pred             ccCcHHHHHHHHHHHHHHHHHhhcccccccccccccEEEECCCCCCHHHHHHHHHHHhCCCEEEeecce
Confidence            68999999999888765432      1123344578999999999999999999999999999888765

>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=98.41  E-value=1.4e-07  Score=93.35  Aligned_cols=36  Identities=25%  Similarity=0.338  Sum_probs=33.1

Q ss_pred             ccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCCC
Q 005987          178 TNVLVITGQAGVGKTATVRQIASHLGARLYEWDTPT  213 (666)
Q Consensus       178 ~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nasd  213 (666)
                      ++.+||+|||||||||+|++||++++..++.+|+++
T Consensus        32 P~~ilL~GpPGtGKT~la~~la~~~~~~~~~i~~d~   67 (273)
T d1gvnb_          32 PTAFLLGGQPGSGKTSLRSAIFEETQGNVIVIDNDT   67 (273)
T ss_dssp             CEEEEEECCTTSCTHHHHHHHHHHTTTCCEEECTHH
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHhhcceEEEecHH
Confidence            378999999999999999999999999999998754

>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=98.36  E-value=8e-07  Score=81.97  Aligned_cols=26  Identities=50%  Similarity=0.882  Sum_probs=23.7

Q ss_pred             EEEECCCCchHHHHHHHHHHHcCCcE
Q 005987          181 LVITGQAGVGKTATVRQIASHLGARL  206 (666)
Q Consensus       181 LLL~GPpG~GKTtla~~LAkelg~~v  206 (666)
                      ++|+|||||||||++++++..+....
T Consensus         3 i~I~G~~G~GKSTLl~~i~~~l~~~~   28 (178)
T d1ye8a1           3 IIITGEPGVGKTTLVKKIVERLGKRA   28 (178)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHHGGGE
T ss_pred             EEEECCCCcHHHHHHHHHHhcCCCCc
Confidence            89999999999999999999996654

>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=98.26  E-value=5.1e-06  Score=85.06  Aligned_cols=48  Identities=19%  Similarity=0.246  Sum_probs=37.6

Q ss_pred             CccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc
Q 005987          147 SLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       147 sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      -|.+++||+..++.+.-.+-.  .   +   .+++||.||||||||++|+.+|.-|
T Consensus         5 ~f~~I~Gq~~~kral~laa~~--~---~---~h~vLl~G~pG~GKT~lar~~~~iL   52 (333)
T d1g8pa_           5 PFSAIVGQEDMKLALLLTAVD--P---G---IGGVLVFGDRGTGKSTAVRALAALL   52 (333)
T ss_dssp             CGGGSCSCHHHHHHHHHHHHC--G---G---GCCEEEECCGGGCTTHHHHHHHHHS
T ss_pred             ChhhccCcHHHHHHHHHHHhc--c---C---CCeEEEECCCCccHHHHHHHHHHhC
Confidence            589999999887765533321  0   1   1479999999999999999999877

>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=98.11  E-value=2.8e-05  Score=77.48  Aligned_cols=47  Identities=23%  Similarity=0.319  Sum_probs=38.5

Q ss_pred             cccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc
Q 005987          151 LAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       151 Lvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      +.|++..++++..+|....     ....+++.|+|++|+||||+|+.++++.
T Consensus        22 ~~gR~~~~~~i~~~L~~~~-----~~~~~~v~I~GmgGiGKTtLA~~v~~~~   68 (277)
T d2a5yb3          22 CYIREYHVDRVIKKLDEMC-----DLDSFFLFLHGRAGSGKSVIASQALSKS   68 (277)
T ss_dssp             SCCCHHHHHHHHHHHHHHT-----TSSSEEEEEECSTTSSHHHHHHHHHHHC
T ss_pred             eeCcHHHHHHHHHHHHhcc-----CCCceEEEEECCCCCCHHHHHHHHHHhh
Confidence            5799999999999997532     1123689999999999999999998874

>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=98.02  E-value=1.5e-06  Score=78.19  Aligned_cols=30  Identities=30%  Similarity=0.609  Sum_probs=27.7

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEEE
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLYE  208 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~viE  208 (666)
                      +.++|+|||||||||+++.||+++++.++.
T Consensus         3 k~I~l~G~~GsGKSTvak~La~~L~~~~id   32 (169)
T d1kaga_           3 RNIFLVGPMGAGKSTIGRQLAQQLNMEFYD   32 (169)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHHHTTCEEEE
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHhCCCeEe
Confidence            578999999999999999999999998874

>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=98.01  E-value=1.5e-05  Score=74.96  Aligned_cols=50  Identities=16%  Similarity=0.148  Sum_probs=39.1

Q ss_pred             HHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCC
Q 005987          160 EVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDTP  212 (666)
Q Consensus       160 el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nas  212 (666)
                      .+..+|+.++.   |.+..+.++|+|||+||||+++.+|++-++..++.++++
T Consensus        38 ~Fl~~l~~~l~---~~PKkn~i~~~GP~~TGKS~f~~sl~~~l~G~vis~~N~   87 (205)
T d1tuea_          38 TFLGALKSFLK---GTPKKNCLVFCGPANTGKSYFGMSFIHFIQGAVISFVNS   87 (205)
T ss_dssp             HHHHHHHHHHH---TCTTCSEEEEESCGGGCHHHHHHHHHHHHTCEECCCCCS
T ss_pred             HHHHHHHHHHc---CCCCceEEEEECCCCccHHHHHHHHHHHhCCEEEeccCC
Confidence            44455666654   556668999999999999999999999998877766543

>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=97.84  E-value=4.6e-06  Score=76.48  Aligned_cols=31  Identities=19%  Similarity=0.216  Sum_probs=28.2

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEEEE
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLYEW  209 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~viE~  209 (666)
                      +.++|+|||||||||+|++||+.+|..++..
T Consensus         8 K~I~i~G~~GsGKTTla~~La~~~~~~~i~~   38 (192)
T d1lw7a2           8 KTVAILGGESSGKSVLVNKLAAVFNTTSAWE   38 (192)
T ss_dssp             EEEEEECCTTSHHHHHHHHHHHHTTCEEECC
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhCCCeEee
Confidence            7899999999999999999999999877643

>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=97.82  E-value=4.9e-06  Score=75.66  Aligned_cols=30  Identities=33%  Similarity=0.544  Sum_probs=27.1

Q ss_pred             EEEEECCCCchHHHHHHHHHHHcCCcEEEE
Q 005987          180 VLVITGQAGVGKTATVRQIASHLGARLYEW  209 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkelg~~viE~  209 (666)
                      .++|+|||||||||+++.||+.+|+.++..
T Consensus         6 ~I~i~G~pGsGKTTia~~La~~l~~~~i~~   35 (173)
T d1rkba_           6 NILLTGTPGVGKTTLGKELASKSGLKYINV   35 (173)
T ss_dssp             CEEEECSTTSSHHHHHHHHHHHHCCEEEEH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHCCcEEec
Confidence            477999999999999999999999988753

>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=97.79  E-value=5.6e-06  Score=75.10  Aligned_cols=29  Identities=41%  Similarity=0.773  Sum_probs=26.5

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEE
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLY  207 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~vi  207 (666)
                      ++++|+|||||||||+|+.||++++..++
T Consensus         3 klI~i~G~~GsGKTTva~~L~~~~~~~~~   31 (176)
T d2bdta1           3 KLYIITGPAGVGKSTTCKRLAAQLDNSAY   31 (176)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHSSSEEE
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHcCCCEE
Confidence            68999999999999999999999987654

>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=97.78  E-value=4.9e-06  Score=76.05  Aligned_cols=34  Identities=24%  Similarity=0.507  Sum_probs=31.0

Q ss_pred             ccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcC
Q 005987          178 TNVLVITGQAGVGKTATVRQIASHLGARLYEWDT  211 (666)
Q Consensus       178 ~k~LLL~GPpG~GKTtla~~LAkelg~~viE~na  211 (666)
                      +++++|.|||||||||+++.||+++|+.++.++.
T Consensus         4 g~iI~l~G~~GsGKSTia~~La~~lg~~~~~~~~   37 (176)
T d1zp6a1           4 GNILLLSGHPGSGKSTIAEALANLPGVPKVHFHS   37 (176)
T ss_dssp             TEEEEEEECTTSCHHHHHHHHHTCSSSCEEEECT
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhCCCEEEecH
Confidence            3789999999999999999999999999887764

>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=97.75  E-value=7.6e-06  Score=74.51  Aligned_cols=30  Identities=30%  Similarity=0.585  Sum_probs=27.6

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEEE
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLYE  208 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~viE  208 (666)
                      ++++|+|||||||||+++.||+.+++..+.
T Consensus         7 ~iivl~G~~GsGKsT~a~~La~~l~~~~~~   36 (171)
T d1knqa_           7 HIYVLMGVSGSGKSAVASEVAHQLHAAFLD   36 (171)
T ss_dssp             EEEEEECSTTSCHHHHHHHHHHHHTCEEEE
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhCCCeec
Confidence            799999999999999999999999987654

>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=97.72  E-value=1.1e-05  Score=73.48  Aligned_cols=32  Identities=22%  Similarity=0.444  Sum_probs=28.6

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEEEEc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLYEWD  210 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~viE~n  210 (666)
                      ++++|+||||+||||+|+.||++++..++.+.
T Consensus         4 kiI~l~G~~GsGKsTva~~L~~~l~~~~~~~~   35 (178)
T d1qhxa_           4 RMIILNGGSSAGKSGIVRCLQSVLPEPWLAFG   35 (178)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHSSSCEEEEE
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHcCCCeEEee
Confidence            79999999999999999999999987766543

>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=97.69  E-value=1.1e-05  Score=74.17  Aligned_cols=31  Identities=26%  Similarity=0.446  Sum_probs=27.7

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEEEE
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLYEW  209 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~viE~  209 (666)
                      +.++|.|||||||||+++.||+.+|+.++..
T Consensus         3 ~~Iil~G~~GsGKSTia~~LA~~Lg~~~id~   33 (170)
T d1e6ca_           3 EPIFMVGARGCGMTTVGRELARALGYEFVDT   33 (170)
T ss_dssp             CCEEEESCTTSSHHHHHHHHHHHHTCEEEEH
T ss_pred             CCEEEECCCCCCHHHHHHHHHHHhCCCEEeh
Confidence            4577889999999999999999999998853

>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=97.64  E-value=1.3e-05  Score=73.01  Aligned_cols=30  Identities=27%  Similarity=0.407  Sum_probs=27.1

Q ss_pred             EEEEECCCCchHHHHHHHHHHHcCCcEEEE
Q 005987          180 VLVITGQAGVGKTATVRQIASHLGARLYEW  209 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkelg~~viE~  209 (666)
                      .++|.||||+||||+++.||+.+|+.++..
T Consensus         2 ~I~liG~~GsGKsTi~k~La~~l~~~~~d~   31 (161)
T d1viaa_           2 NIVFIGFMGSGKSTLARALAKDLDLVFLDS   31 (161)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHHTCEEEEH
T ss_pred             cEEEECCCCCCHHHHHHHHHHHhCCCEEec
Confidence            477889999999999999999999998854

>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=97.61  E-value=8.2e-05  Score=68.48  Aligned_cols=30  Identities=23%  Similarity=0.328  Sum_probs=26.9

Q ss_pred             ccEEEEECCCCchHHHHHHHHHHHcCCcEE
Q 005987          178 TNVLVITGQAGVGKTATVRQIASHLGARLY  207 (666)
Q Consensus       178 ~k~LLL~GPpG~GKTtla~~LAkelg~~vi  207 (666)
                      +..+||+|+|||||||+++.+++.+++.++
T Consensus        14 p~liil~G~pGsGKST~a~~l~~~~~~~~i   43 (172)
T d1yj5a2          14 PEVVVAVGFPGAGKSTFIQEHLVSAGYVHV   43 (172)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHTGGGTCEEE
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHhcCCEEE
Confidence            469999999999999999999999887655

>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=97.60  E-value=1.7e-05  Score=72.30  Aligned_cols=29  Identities=34%  Similarity=0.547  Sum_probs=25.8

Q ss_pred             EEEECCCCchHHHHHHHHHHHcCCcEEEE
Q 005987          181 LVITGQAGVGKTATVRQIASHLGARLYEW  209 (666)
Q Consensus       181 LLL~GPpG~GKTtla~~LAkelg~~viE~  209 (666)
                      ++|.|+|||||||+++.||+.+|+.++..
T Consensus         4 IvliG~~G~GKSTig~~La~~l~~~fiD~   32 (165)
T d2iyva1           4 AVLVGLPGSGKSTIGRRLAKALGVGLLDT   32 (165)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHTCCEEEH
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCCCeEee
Confidence            55669999999999999999999998854

>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=97.55  E-value=2.6e-05  Score=70.84  Aligned_cols=26  Identities=38%  Similarity=0.570  Sum_probs=23.9

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGA  204 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~  204 (666)
                      -.++|+||||+||||+++.||+.++.
T Consensus         6 ~~I~i~G~~GsGKTT~~~~La~~l~~   31 (174)
T d1y63a_           6 INILITGTPGTGKTSMAEMIAAELDG   31 (174)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHSTT
T ss_pred             CEEEEEeCCCCCHHHHHHHHHHHhCC
Confidence            46999999999999999999999964

>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=97.52  E-value=1.8e-05  Score=72.18  Aligned_cols=24  Identities=33%  Similarity=0.577  Sum_probs=22.9

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      |+++|+|||||||||+++.+++.+
T Consensus         2 k~v~ItG~~GtGKTtl~~~i~~~l   25 (189)
T d2i3ba1           2 RHVFLTGPPGVGKTTLIHKASEVL   25 (189)
T ss_dssp             CCEEEESCCSSCHHHHHHHHHHHH
T ss_pred             cEEEEECCCCCcHHHHHHHHHHHH
Confidence            679999999999999999999998

>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=97.50  E-value=3e-05  Score=72.42  Aligned_cols=30  Identities=27%  Similarity=0.417  Sum_probs=27.5

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEEE
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLYE  208 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~viE  208 (666)
                      ++++|.||||+||||+++.||+++|+..+.
T Consensus         7 ~iI~i~G~pGSGKsT~a~~La~~~g~~~i~   36 (194)
T d1qf9a_           7 NVVFVLGGPGSGKGTQCANIVRDFGWVHLS   36 (194)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHHHCCEEEE
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHHCCceEc
Confidence            689999999999999999999999987664

>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=97.47  E-value=0.00075  Score=63.76  Aligned_cols=35  Identities=31%  Similarity=0.388  Sum_probs=28.9

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcCCC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL---GARLYEWDTPT  213 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel---g~~viE~nasd  213 (666)
                      ++++|.||+|+||||++-.||..+   |.++.-+.+-.
T Consensus        11 ~vi~lvGp~GvGKTTTiaKLA~~~~~~g~kV~lit~Dt   48 (207)
T d1ls1a2          11 NLWFLVGLQGSGKTTTAAKLALYYKGKGRRPLLVAADT   48 (207)
T ss_dssp             EEEEEECCTTTTHHHHHHHHHHHHHHTTCCEEEEECCS
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHHHHCCCcEEEEeccc
Confidence            688999999999999998888876   77777666544

>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=97.43  E-value=0.0019  Score=60.98  Aligned_cols=36  Identities=22%  Similarity=0.319  Sum_probs=24.6

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcCCCc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL---GARLYEWDTPTP  214 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel---g~~viE~nasd~  214 (666)
                      .+++|.||+|+||||++-.||..+   |.++.-+.+-..
T Consensus        13 ~vi~lvGptGvGKTTTiAKLA~~~~~~g~kV~lit~Dt~   51 (211)
T d1j8yf2          13 YVIMLVGVQGTGKATTAGKLAYFYKKKGFKVGLVGADVY   51 (211)
T ss_dssp             EEEEEECSCCC----HHHHHHHHHHHTTCCEEEEECCCS
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHCCCceEEEEeecc
Confidence            789999999999999998888776   666665555443

>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=97.41  E-value=5.1e-05  Score=70.96  Aligned_cols=31  Identities=16%  Similarity=0.292  Sum_probs=28.0

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEEEE
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLYEW  209 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~viE~  209 (666)
                      ++++|.||||+||||.|+.||+.+|+..+..
T Consensus         9 ~iI~i~GppGSGKsT~a~~La~~~g~~~is~   39 (196)
T d1ukza_           9 SVIFVLGGPGAGKGTQCEKLVKDYSFVHLSA   39 (196)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHSSCEEEEH
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHhCCeEEeh
Confidence            5899999999999999999999999877753

>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=97.40  E-value=4.7e-05  Score=71.19  Aligned_cols=31  Identities=19%  Similarity=0.394  Sum_probs=28.4

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEEEE
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLYEW  209 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~viE~  209 (666)
                      ++++|.||||+||||.++.||+.+|+..+..
T Consensus         9 ~iI~l~G~pGSGKsT~a~~La~~~g~~~is~   39 (194)
T d3adka_           9 KIIFVVGGPGSGKGTQCEKIVQKYGYTHLST   39 (194)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHHTCCEEEEH
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHhCCeeEec
Confidence            6899999999999999999999999887754

>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=97.38  E-value=4.4e-05  Score=69.32  Aligned_cols=25  Identities=28%  Similarity=0.409  Sum_probs=23.2

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLG  203 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg  203 (666)
                      .+++|+|+||+||||++++||+.|+
T Consensus         7 ~~I~l~G~~GsGKTTia~~La~~L~   31 (183)
T d1m8pa3           7 FTIFLTGYMNSGKDAIARALQVTLN   31 (183)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHh
Confidence            5788999999999999999999984

>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=97.37  E-value=5.3e-05  Score=69.63  Aligned_cols=29  Identities=28%  Similarity=0.418  Sum_probs=26.6

Q ss_pred             EEEECCCCchHHHHHHHHHHHcCCcEEEE
Q 005987          181 LVITGQAGVGKTATVRQIASHLGARLYEW  209 (666)
Q Consensus       181 LLL~GPpG~GKTtla~~LAkelg~~viE~  209 (666)
                      ++|.||||+||||.++.||+.+|+..+..
T Consensus         3 I~i~G~pGSGKsT~a~~La~~~~~~~i~~   31 (182)
T d1zina1           3 LVLMGLPGAGKGTQAEKIVAAYGIPHIST   31 (182)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHCCCEEEH
T ss_pred             EEEECCCCCCHHHHHHHHHHHHCCceech
Confidence            77999999999999999999999987753

>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=97.35  E-value=5.8e-05  Score=67.10  Aligned_cols=24  Identities=21%  Similarity=0.435  Sum_probs=21.9

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      ++++|+||||+||||+|+.|+++.
T Consensus         3 klIii~G~pGsGKTTla~~L~~~~   26 (152)
T d1ly1a_           3 KIILTIGCPGSGKSTWAREFIAKN   26 (152)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHHHhC
Confidence            689999999999999999988765

>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=97.34  E-value=2e-05  Score=73.13  Aligned_cols=30  Identities=23%  Similarity=0.251  Sum_probs=25.5

Q ss_pred             CccEEEEECCCCchHHHHHHHHHHHcCCcE
Q 005987          177 STNVLVITGQAGVGKTATVRQIASHLGARL  206 (666)
Q Consensus       177 ~~k~LLL~GPpG~GKTtla~~LAkelg~~v  206 (666)
                      .+.+++|+|+||+||||+|+.||+.+++..
T Consensus        18 ~g~vI~L~G~pGSGKTTiAk~La~~l~~~~   47 (195)
T d1x6va3          18 RGCTVWLTGLSGAGKTTVSMALEEYLVCHG   47 (195)
T ss_dssp             CCEEEEEESSCHHHHHHHHHHHHHHHHHTT
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHhcC
Confidence            335788999999999999999999996543

>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=97.32  E-value=7.5e-05  Score=69.38  Aligned_cols=29  Identities=21%  Similarity=0.302  Sum_probs=25.7

Q ss_pred             EEEECCCCchHHHHHHHHHHHcCCcEEEE
Q 005987          181 LVITGQAGVGKTATVRQIASHLGARLYEW  209 (666)
Q Consensus       181 LLL~GPpG~GKTtla~~LAkelg~~viE~  209 (666)
                      ++|.||||+||||.++.||+.+|+..+..
T Consensus         6 iil~G~pGSGKsT~a~~La~~~g~~~i~~   34 (190)
T d1ak2a1           6 AVLLGPPGAGKGTQAPKLAKNFCVCHLAT   34 (190)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHHTCEEEEH
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCCeEEeH
Confidence            55679999999999999999999887764

>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=97.31  E-value=6.3e-05  Score=70.05  Aligned_cols=30  Identities=23%  Similarity=0.382  Sum_probs=27.4

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEEE
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLYE  208 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~viE  208 (666)
                      .+++|.||||+||||.|+.||+.+|+..+.
T Consensus         2 ~iI~i~GppGSGKsT~a~~La~~~g~~~i~   31 (194)
T d1teva_           2 LVVFVLGGPGAGKGTQCARIVEKYGYTHLS   31 (194)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHCCEEEE
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHhCCceEc
Confidence            479999999999999999999999987763

>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=97.27  E-value=8.2e-05  Score=70.38  Aligned_cols=30  Identities=30%  Similarity=0.501  Sum_probs=27.2

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEEE
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLYE  208 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~viE  208 (666)
                      +++.|.||||+||+|.++.||+.+|+..+.
T Consensus         4 piI~I~GppGSGKgT~ak~La~~~gl~~iS   33 (225)
T d1ckea_           4 PVITIDGPSGAGKGTLCKAMAEALQWHLLD   33 (225)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHHTCEEEE
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHhCCcEEC
Confidence            489999999999999999999999987663

>d1p9ra_ c.37.1.11 (A:) Extracellular secretion NTPase EpsE {Vibrio cholerae [TaxId: 666]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Extracellular secretion NTPase EpsE
species: Vibrio cholerae [TaxId: 666]

Probab=97.27  E-value=0.00075  Score=70.39  Aligned_cols=102  Identities=14%  Similarity=0.232  Sum_probs=67.4

Q ss_pred             CCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcCCCchhhhhh
Q 005987          144 KPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL---GARLYEWDTPTPTIWQEY  220 (666)
Q Consensus       144 ~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~nasd~~~~~e~  220 (666)
                      .+.++++|-..+..++.++.++..         +...+||+||+|+||||++.++.+++   +..++.+..|....... 
T Consensus       133 ~~~~l~~LG~~~~~~~~l~~l~~~---------~~GliLvtGpTGSGKSTTl~~~l~~~~~~~~~i~tiEdPiE~~~~~-  202 (401)
T d1p9ra_         133 TRLDLHSLGMTAHNHDNFRRLIKR---------PHGIILVTGPTGSGKSTTLYAGLQELNSSERNILTVEDPIEFDIDG-  202 (401)
T ss_dssp             TCCCGGGSCCCHHHHHHHHHHHTS---------SSEEEEEECSTTSCHHHHHHHHHHHHCCTTSCEEEEESSCCSCCSS-
T ss_pred             cchhhhhhcccHHHHHHHHHHHhh---------hhceEEEEcCCCCCccHHHHHHhhhhcCCCceEEEeccCcccccCC-
Confidence            345788998899988888877653         12589999999999999999999987   35677776664221100 


Q ss_pred             hhcccCCccc-cchhHHHHHHHHHHHhhcCCCCCCCCCCCCceEEEEeCCCC
Q 005987          221 MHNCKTGLEY-TSKLDEFENFVERIRRYGSTSPSIPGESKSSAILLIDDLPV  271 (666)
Q Consensus       221 l~~~~~g~~~-~s~~~~f~~fl~~a~~~~~l~~s~~~~~~~~~IIlIDEid~  271 (666)
                      ...    ..+ ......|...+..+-+.            .|-||+|.|+-.
T Consensus       203 ~~q----~~v~~~~~~~~~~~l~~~lR~------------dPDvi~igEiRd  238 (401)
T d1p9ra_         203 IGQ----TQVNPRVDMTFARGLRAILRQ------------DPDVVMVGEIRD  238 (401)
T ss_dssp             SEE----EECBGGGTBCHHHHHHHHGGG------------CCSEEEESCCCS
T ss_pred             CCe----eeecCCcCCCHHHHHHHHHhh------------cCCEEEecCcCC
Confidence            000    000 11122466666665444            356999999975

>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=97.26  E-value=5.4e-05  Score=70.39  Aligned_cols=29  Identities=17%  Similarity=0.255  Sum_probs=26.2

Q ss_pred             EEEEECCCCchHHHHHHHHHHHcCCcEEE
Q 005987          180 VLVITGQAGVGKTATVRQIASHLGARLYE  208 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkelg~~viE  208 (666)
                      .++|.|||||||||+++.||+.+|+..+.
T Consensus         5 ~I~i~GppGsGKsT~a~~La~~~~~~~is   33 (189)
T d1zaka1           5 KVMISGAPASGKGTQCELIKTKYQLAHIS   33 (189)
T ss_dssp             CEEEEESTTSSHHHHHHHHHHHHCCEECC
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHCCcEEe
Confidence            58899999999999999999999987663

>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=97.26  E-value=0.0016  Score=61.43  Aligned_cols=37  Identities=30%  Similarity=0.425  Sum_probs=29.4

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcCCCch
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL---GARLYEWDTPTPT  215 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel---g~~viE~nasd~~  215 (666)
                      .+++|.||+|+||||++-.||..+   |.+|.-+.+-..|
T Consensus        10 ~vi~lvGptGvGKTTTiAKLA~~~~~~g~kV~lit~Dt~R   49 (211)
T d2qy9a2          10 FVILMVGVNGVGKTTTIGKLARQFEQQGKSVMLAAGDTFR   49 (211)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHHHHTTTCCEEEECCCTTC
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHCCCcEEEEeccccc
Confidence            689999999999999999999766   6666666654433

>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=97.25  E-value=9e-05  Score=68.27  Aligned_cols=29  Identities=24%  Similarity=0.423  Sum_probs=26.5

Q ss_pred             EEEECCCCchHHHHHHHHHHHcCCcEEEE
Q 005987          181 LVITGQAGVGKTATVRQIASHLGARLYEW  209 (666)
Q Consensus       181 LLL~GPpG~GKTtla~~LAkelg~~viE~  209 (666)
                      ++|.||||+||||.++.||+.+|+..+..
T Consensus         3 I~i~G~pGsGKsT~a~~La~~~g~~~i~~   31 (181)
T d2cdna1           3 VLLLGPPGAGKGTQAVKLAEKLGIPQIST   31 (181)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHHTCCEEEH
T ss_pred             EEEECCCCCCHHHHHHHHHHHHCCceEch
Confidence            67789999999999999999999988864

>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=97.22  E-value=0.0027  Score=59.99  Aligned_cols=35  Identities=26%  Similarity=0.406  Sum_probs=27.7

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcCCC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL---GARLYEWDTPT  213 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel---g~~viE~nasd  213 (666)
                      .+++|.||+|+||||++-.||..+   |.+|.-+.+-.
T Consensus        12 ~vi~lvGptGvGKTTTiAKLAa~~~~~~~kV~lit~Dt   49 (213)
T d1vmaa2          12 FVIMVVGVNGTGKTTSCGKLAKMFVDEGKSVVLAAADT   49 (213)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEEEECT
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHCCCceEEEeecc
Confidence            689999999999999998888766   56655555443

>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=97.20  E-value=0.00011  Score=67.82  Aligned_cols=28  Identities=25%  Similarity=0.475  Sum_probs=25.8

Q ss_pred             EEEECCCCchHHHHHHHHHHHcCCcEEE
Q 005987          181 LVITGQAGVGKTATVRQIASHLGARLYE  208 (666)
Q Consensus       181 LLL~GPpG~GKTtla~~LAkelg~~viE  208 (666)
                      ++|.||||+||||.++.||+.+|+..+.
T Consensus         3 I~i~G~pGSGKsT~a~~La~~~g~~~is   30 (182)
T d1s3ga1           3 IVLMGLPGAGKGTQADRIVEKYGTPHIS   30 (182)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHCCCEEE
T ss_pred             EEEECCCCCCHHHHHHHHHHHHCCceee
Confidence            6788999999999999999999998775

>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=97.19  E-value=0.00037  Score=64.97  Aligned_cols=32  Identities=22%  Similarity=0.401  Sum_probs=26.3

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcC---CcEEEEc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLG---ARLYEWD  210 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg---~~viE~n  210 (666)
                      -+++|+|+||+||||+|+.||+.++   ..+..++
T Consensus         3 ~li~l~GlpgsGKSTla~~L~~~l~~~~~~~~~~~   37 (213)
T d1bifa1           3 TLIVMVGLPARGKTYISKKLTRYLNFIGVPTREFN   37 (213)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHhcCCCCeEEc
Confidence            5899999999999999999999874   4444444

>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=97.19  E-value=0.00011  Score=67.87  Aligned_cols=29  Identities=21%  Similarity=0.362  Sum_probs=25.8

Q ss_pred             EEEECCCCchHHHHHHHHHHHcCCcEEEE
Q 005987          181 LVITGQAGVGKTATVRQIASHLGARLYEW  209 (666)
Q Consensus       181 LLL~GPpG~GKTtla~~LAkelg~~viE~  209 (666)
                      ++|.||||+||||.++.||+.+|+..+..
T Consensus         5 Ivl~G~pGSGKtT~a~~La~~~g~~~i~~   33 (180)
T d1akya1           5 MVLIGPPGAGKGTQAPNLQERFHAAHLAT   33 (180)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHHCCEEEEH
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCCceEec
Confidence            56779999999999999999999887764

>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=97.17  E-value=0.00012  Score=68.37  Aligned_cols=30  Identities=23%  Similarity=0.341  Sum_probs=25.8

Q ss_pred             EEEEECCCCchHHHHHHHHHHHcCCcEEEE
Q 005987          180 VLVITGQAGVGKTATVRQIASHLGARLYEW  209 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkelg~~viE~  209 (666)
                      .++|.||||+||||.++.||+.+|+..+..
T Consensus         8 rIiliG~PGSGKtT~a~~La~~~g~~~is~   37 (189)
T d2ak3a1           8 RAAIMGAPGSGKGTVSSRITKHFELKHLSS   37 (189)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHBCCEEEEH
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHCCeEEcH
Confidence            366679999999999999999999887643

>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=97.13  E-value=0.00013  Score=69.17  Aligned_cols=28  Identities=29%  Similarity=0.520  Sum_probs=25.0

Q ss_pred             EEEECCCCchHHHHHHHHHHHcCCcEEE
Q 005987          181 LVITGQAGVGKTATVRQIASHLGARLYE  208 (666)
Q Consensus       181 LLL~GPpG~GKTtla~~LAkelg~~viE  208 (666)
                      +.+.||||+||||.|+.||+++|+..+.
T Consensus         6 IaIdGp~GsGKgT~ak~La~~lg~~~is   33 (223)
T d1q3ta_           6 IAIDGPASSGKSTVAKIIAKDFGFTYLD   33 (223)
T ss_dssp             EEEECSSCSSHHHHHHHHHHHHCCEEEE
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCCcEEC
Confidence            5577999999999999999999988664

>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=97.12  E-value=9.5e-05  Score=67.44  Aligned_cols=25  Identities=36%  Similarity=0.585  Sum_probs=23.5

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLG  203 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg  203 (666)
                      ++++|.||||+||||+++.|++.++
T Consensus         2 kiI~i~G~~GsGKsT~~~~L~~~l~   26 (190)
T d1khta_           2 KVVVVTGVPGVGSTTSSQLAMDNLR   26 (190)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHH
Confidence            6899999999999999999999884

>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=97.10  E-value=0.00014  Score=66.76  Aligned_cols=28  Identities=18%  Similarity=0.312  Sum_probs=25.5

Q ss_pred             EEEECCCCchHHHHHHHHHHHcCCcEEE
Q 005987          181 LVITGQAGVGKTATVRQIASHLGARLYE  208 (666)
Q Consensus       181 LLL~GPpG~GKTtla~~LAkelg~~viE  208 (666)
                      ++|.||||+||||.++.||+.+|+..+.
T Consensus         3 I~i~G~pGSGKsT~~~~La~~~~~~~i~   30 (179)
T d1e4va1           3 IILLGAPVAGKGTQAQFIMEKYGIPQIS   30 (179)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHHCCCEEE
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCCceec
Confidence            6778999999999999999999988775

>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=97.09  E-value=0.0038  Score=58.67  Aligned_cols=35  Identities=29%  Similarity=0.491  Sum_probs=28.1

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcCCC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL---GARLYEWDTPT  213 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel---g~~viE~nasd  213 (666)
                      ++++|.||+|+||||++-.||..+   |.+|.-+++-.
T Consensus         7 ~vi~lvGptGvGKTTTiaKLA~~~~~~g~kV~lit~Dt   44 (207)
T d1okkd2           7 RVVLVVGVNGVGKTTTIAKLGRYYQNLGKKVMFCAGDT   44 (207)
T ss_dssp             SEEEEECSTTSSHHHHHHHHHHHHHTTTCCEEEECCCC
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHCCCcEEEEEecc
Confidence            689999999999999998888876   66666555443

>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=97.07  E-value=0.0017  Score=63.63  Aligned_cols=40  Identities=20%  Similarity=0.148  Sum_probs=31.7

Q ss_pred             CCCCccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcCCC
Q 005987          174 DKFSTNVLVITGQAGVGKTATVRQIASHL---GARLYEWDTPT  213 (666)
Q Consensus       174 g~~~~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~nasd  213 (666)
                      |-+..++..|+||||+|||+++..+|...   |..++.++.-.
T Consensus        50 Gi~~g~itei~G~~gsGKTtl~l~~~~~~q~~g~~~vyidtE~   92 (263)
T d1u94a1          50 GLPMGRIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDAEH   92 (263)
T ss_dssp             SEETTSEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEESSC
T ss_pred             CccCceEEEEecCCCcHHHHHHHHHHHHHHcCCCEEEEEcccc
Confidence            44455799999999999999998887765   77777776543

>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=97.03  E-value=0.00023  Score=64.00  Aligned_cols=31  Identities=26%  Similarity=0.377  Sum_probs=26.2

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc---CCcEEEE
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL---GARLYEW  209 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel---g~~viE~  209 (666)
                      +++.|+|++|+||||+++.|++++   |+.+.-+
T Consensus         3 Pvi~itG~~GSGKTTL~~~L~~~l~~~g~~v~v~   36 (170)
T d1np6a_           3 PLLAFAAWSGTGKTTLLKKLIPALCARGIRPGLI   36 (170)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             CEEEEEcCCCCCHHHHHHHHHHHHHHCCCeEEEe
Confidence            489999999999999999999886   6665543

>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=97.00  E-value=0.0013  Score=57.16  Aligned_cols=34  Identities=18%  Similarity=0.285  Sum_probs=28.5

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLYEWDTP  212 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~viE~nas  212 (666)
                      +..+|.+|+|+|||+++-.++.+.|..++-+-..
T Consensus         9 ~~~ll~apTGsGKT~~~~~~~~~~~~~vli~~P~   42 (136)
T d1a1va1           9 QVAHLHAPTGSGKSTKVPAAYAAQGYKVLVLNPS   42 (136)
T ss_dssp             EEEEEECCTTSCTTTHHHHHHHTTTCCEEEEESC
T ss_pred             CEEEEEeCCCCCHHHHHHHHHHHcCCcEEEEcCh
Confidence            6899999999999999988888888887766543

>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=96.92  E-value=0.0017  Score=62.42  Aligned_cols=25  Identities=44%  Similarity=0.617  Sum_probs=22.8

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLG  203 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg  203 (666)
                      .++-|.||+||||||++++++.-+.
T Consensus        33 e~~~liGpsGaGKSTLl~~i~Gl~~   57 (239)
T d1v43a3          33 EFLVLLGPSGCGKTTTLRMIAGLEE   57 (239)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHTSSC
T ss_pred             CEEEEECCCCChHHHHHHHHHcCCC
Confidence            5899999999999999999998773

>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=96.92  E-value=0.0022  Score=59.28  Aligned_cols=72  Identities=13%  Similarity=0.229  Sum_probs=39.1

Q ss_pred             ceEEEEeCCCCCcchhHHHHHHHHHHHHHhcCCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHHH
Q 005987          261 SAILLIDDLPVTNGRTAFERLRQCLLLLVRSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNGS  340 (666)
Q Consensus       261 ~~IIlIDEid~l~~~~~~~~l~~~L~~l~~~~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~~  340 (666)
                      -.+|++||++.+.........   +..+......|.++.++++...        ....+..++.......|.+..-...+
T Consensus       126 ~~~vIiDE~H~~~~~~~~~~~---~~~~~~~~~~~~~l~~SATp~~--------~~~~~~~~~~~l~~~~i~~~~~~~~~  194 (200)
T d1wp9a1         126 VSLIVFDEAHRAVGNYAYVFI---AREYKRQAKNPLVIGLTASPGS--------TPEKIMEVINNLGIEHIEYRSENSPD  194 (200)
T ss_dssp             CSEEEEETGGGCSTTCHHHHH---HHHHHHHCSSCCEEEEESCSCS--------SHHHHHHHHHHTTCCEEEECCTTSTT
T ss_pred             cceEEEEehhhhhcchhHHHH---HHHHHhcCCCCcEEEEEecCCC--------cHHHHHHHHhcCCceEEEeCCCCChh
Confidence            348999999987554322222   2233334445666666665321        11223444445556778887766555


Q ss_pred             HHH
Q 005987          341 IKR  343 (666)
Q Consensus       341 i~k  343 (666)
                      +++
T Consensus       195 ik~  197 (200)
T d1wp9a1         195 VRP  197 (200)
T ss_dssp             TGG
T ss_pred             hhh
Confidence            444

>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=96.87  E-value=0.00018  Score=65.83  Aligned_cols=32  Identities=22%  Similarity=0.363  Sum_probs=26.4

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcC---CcEEEEc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLG---ARLYEWD  210 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg---~~viE~n  210 (666)
                      ++++|.|+||+||||+++.||+.++   +.+..+.
T Consensus         2 kiivi~G~~GsGKTT~~~~La~~L~~~~~~~~~~~   36 (194)
T d1nksa_           2 KIGIVTGIPGVGKSTVLAKVKEILDNQGINNKIIN   36 (194)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHHHHHTTTCCEEEEE
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHcCCCEEEEE
Confidence            5899999999999999999999984   4444443

>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=96.85  E-value=0.0013  Score=63.12  Aligned_cols=24  Identities=33%  Similarity=0.549  Sum_probs=22.2

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      .++-|.||+||||||++++++.-+
T Consensus        27 ei~~liGpsGsGKSTLl~~i~Gl~   50 (232)
T d2awna2          27 EFVVFVGPSGCGKSTLLRMIAGLE   50 (232)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHTSS
T ss_pred             CEEEEECCCCChHHHHHHHHhcCC
Confidence            589999999999999999998876

>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=96.83  E-value=0.0063  Score=53.30  Aligned_cols=21  Identities=19%  Similarity=0.400  Sum_probs=19.3

Q ss_pred             EEEECCCCchHHHHHHHHHHH
Q 005987          181 LVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       181 LLL~GPpG~GKTtla~~LAke  201 (666)
                      ++|.|+|||||||+++.++..
T Consensus         3 ivlvG~~~vGKSsLi~~l~~~   23 (160)
T d1r8sa_           3 ILMVGLDAAGKTTILYKLKLG   23 (160)
T ss_dssp             EEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            789999999999999998865

>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=96.81  E-value=0.0045  Score=59.34  Aligned_cols=24  Identities=38%  Similarity=0.419  Sum_probs=21.5

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      +.+||+||.++||||++|.+|--.
T Consensus        42 ~~~iiTGpN~~GKSt~lk~i~l~~   65 (234)
T d1wb9a2          42 RMLIITGPNMGGKSTYMRQTALIA   65 (234)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             eEEEEeccCchhhHHHHHHHHHHH
Confidence            689999999999999999987653

>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=96.81  E-value=0.0042  Score=60.79  Aligned_cols=43  Identities=21%  Similarity=0.118  Sum_probs=33.0

Q ss_pred             HHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCC
Q 005987          160 EVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGA  204 (666)
Q Consensus       160 el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~  204 (666)
                      .+..||..|+..  +.+..+.++|+|||++|||+++.+|++-+|-
T Consensus        88 ~f~~~l~~~L~~--~~~k~n~~~l~G~~~tGKS~f~~~i~~~lg~  130 (267)
T d1u0ja_          88 YAASVFLGWATK--KFGKRNTIWLFGPATTGKTNIAEAIAHTVPF  130 (267)
T ss_dssp             HHHHHHHHHHTT--CSTTCCEEEEECSTTSSHHHHHHHHHHHSSC
T ss_pred             HHHHHHHHHHcC--CCCccEEEEEEcCCCCCHHHHHHHHHHHhcc
Confidence            455677777642  2233468999999999999999999999964

>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=96.81  E-value=0.00068  Score=65.36  Aligned_cols=23  Identities=30%  Similarity=0.468  Sum_probs=21.3

Q ss_pred             EEEEECCCCchHHHHHHHHHHHc
Q 005987          180 VLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      .+.|.||+||||||++++++.-+
T Consensus        26 ~~~liGpnGaGKSTll~~i~Gl~   48 (240)
T d2onka1          26 YCVLLGPTGAGKSVFLELIAGIV   48 (240)
T ss_dssp             EEEEECCTTSSHHHHHHHHHTSS
T ss_pred             EEEEECCCCChHHHHHHHHHcCC
Confidence            67788999999999999999987

>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=96.80  E-value=0.00061  Score=62.55  Aligned_cols=24  Identities=38%  Similarity=0.469  Sum_probs=21.1

Q ss_pred             EEEEECCCCchHHHHHHHHHHHcC
Q 005987          180 VLVITGQAGVGKTATVRQIASHLG  203 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkelg  203 (666)
                      ++-|+||+|+||||+|+.|++.++
T Consensus        24 iIgI~G~~GSGKSTla~~L~~~l~   47 (198)
T d1rz3a_          24 VLGIDGLSRSGKTTLANQLSQTLR   47 (198)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhc
Confidence            455999999999999999999774

>d1tf7a2 c.37.1.11 (A:256-497) Circadian clock protein KaiC {Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Circadian clock protein KaiC
species: Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]

Probab=96.72  E-value=0.0041  Score=59.06  Aligned_cols=37  Identities=24%  Similarity=0.396  Sum_probs=29.1

Q ss_pred             CCCccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcC
Q 005987          175 KFSTNVLVITGQAGVGKTATVRQIASHL---GARLYEWDT  211 (666)
Q Consensus       175 ~~~~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~na  211 (666)
                      -++....+|+||||+|||+++..+|...   +..++.+..
T Consensus        23 i~~gsl~li~G~pGsGKT~l~~qia~~~~~~~~~~~~is~   62 (242)
T d1tf7a2          23 FFKDSIILATGATGTGKTLLVSRFVENACANKERAILFAY   62 (242)
T ss_dssp             EESSCEEEEEECTTSSHHHHHHHHHHHHHTTTCCEEEEES
T ss_pred             CcCCeEEEEEeCCCCCHHHHHHHHHHHHHHhccccceeec
Confidence            3445689999999999999999888886   555665544

>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=96.67  E-value=0.0041  Score=55.47  Aligned_cols=22  Identities=23%  Similarity=0.456  Sum_probs=19.4

Q ss_pred             EEEEECCCCchHHHHHHHHHHH
Q 005987          180 VLVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAke  201 (666)
                      -++|.|++|+||||+++.+...
T Consensus         4 ki~ivG~~~~GKTsLi~~l~~~   25 (165)
T d1ksha_           4 RLLMLGLDNAGKTTILKKFNGE   25 (165)
T ss_dssp             EEEEECSTTSSHHHHHHHHTTC
T ss_pred             EEEEECCCCCCHHHHHHHHcCC
Confidence            3889999999999999998664

>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=96.66  E-value=0.0053  Score=57.40  Aligned_cols=48  Identities=15%  Similarity=0.171  Sum_probs=35.3

Q ss_pred             cCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcC
Q 005987          153 VQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDT  211 (666)
Q Consensus       153 g~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~na  211 (666)
                      .++...+.+..|++.           +..+|.+|+|+|||.++-.++++++..++-+..
T Consensus        71 Lr~yQ~eav~~~~~~-----------~~~ll~~~tG~GKT~~a~~~~~~~~~~~Liv~p  118 (206)
T d2fz4a1          71 LRDYQEKALERWLVD-----------KRGCIVLPTGSGKTHVAMAAINELSTPTLIVVP  118 (206)
T ss_dssp             CCHHHHHHHHHHTTT-----------SEEEEEESSSTTHHHHHHHHHHHSCSCEEEEES
T ss_pred             cCHHHHHHHHHHHhC-----------CCcEEEeCCCCCceehHHhHHHHhcCceeEEEc
Confidence            455555556555432           246788999999999999999999888776654

>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=96.64  E-value=0.0077  Score=58.85  Aligned_cols=37  Identities=22%  Similarity=0.160  Sum_probs=30.3

Q ss_pred             CCccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcCC
Q 005987          176 FSTNVLVITGQAGVGKTATVRQIASHL---GARLYEWDTP  212 (666)
Q Consensus       176 ~~~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~nas  212 (666)
                      +..++..|+||+|||||+++..+|...   |..++.++.-
T Consensus        55 p~g~itei~G~~~sGKT~l~l~~~~~aqk~g~~v~yiDtE   94 (268)
T d1xp8a1          55 PRGRITEIYGPESGGKTTLALAIVAQAQKAGGTCAFIDAE   94 (268)
T ss_dssp             ETTSEEEEEESTTSSHHHHHHHHHHHHHHTTCCEEEEESS
T ss_pred             cCceEEEEecCCccchHHHHHHHHHHHHhCCCEEEEEECC
Confidence            455799999999999999998887765   7777777653

>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=96.60  E-value=0.011  Score=57.66  Aligned_cols=90  Identities=14%  Similarity=0.105  Sum_probs=52.0

Q ss_pred             CCCCccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcCCCc--hhhhhhhhcccCCccc--cchhHHHHHHHHHHHh
Q 005987          174 DKFSTNVLVITGQAGVGKTATVRQIASHL---GARLYEWDTPTP--TIWQEYMHNCKTGLEY--TSKLDEFENFVERIRR  246 (666)
Q Consensus       174 g~~~~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~nasd~--~~~~e~l~~~~~g~~~--~s~~~~f~~fl~~a~~  246 (666)
                      |-+..++..|+||||+|||+++..+|...   |..++.++.-..  ..+.+.+.-....+-+  ....++..+.++.+.+
T Consensus        56 G~~~g~i~e~~G~~~~GKT~l~l~~~~~~q~~g~~~vyIDtE~~~~~e~a~~~GvD~d~il~~~~~~~E~~~~~~~~l~~  135 (269)
T d1mo6a1          56 GLPRGRVIEIYGPESSGKTTVALHAVANAQAAGGVAAFIDAEHALDPDYAKKLGVDTDSLLVSQPDTGEQALEIADMLIR  135 (269)
T ss_dssp             SBCSSSEEEEECSSSSSHHHHHHHHHHHHHHTTCEEEEEESSCCCCHHHHHHHTCCGGGCEEECCSSHHHHHHHHHHHHH
T ss_pred             CcccceeEEEecCCCcHHHHHHHHHHHHHhcCCCEEEEEECCccCCHHHHHHhCCCHHHeEEecCCCHHHHHHHHHHHHh
Confidence            55566899999999999999987776654   777777765431  1121221111001101  1223344444444322


Q ss_pred             hcCCCCCCCCCCCCceEEEEeCCCCCcc
Q 005987          247 YGSTSPSIPGESKSSAILLIDDLPVTNG  274 (666)
Q Consensus       247 ~~~l~~s~~~~~~~~~IIlIDEid~l~~  274 (666)
                      -           ++..+||||-+..+..
T Consensus       136 ~-----------~~~~liIiDSi~al~~  152 (269)
T d1mo6a1         136 S-----------GALDIVVIDSVAALVP  152 (269)
T ss_dssp             T-----------TCEEEEEEECSTTCCC
T ss_pred             c-----------CCCCEEEEeccccccc
Confidence            1           2457999999987754

>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=96.53  E-value=0.024  Score=50.40  Aligned_cols=21  Identities=38%  Similarity=0.613  Sum_probs=19.3

Q ss_pred             EEEECCCCchHHHHHHHHHHH
Q 005987          181 LVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       181 LLL~GPpG~GKTtla~~LAke  201 (666)
                      ++|.|++|||||+++..+...
T Consensus         6 i~lvG~~~vGKTsLi~r~~~~   26 (167)
T d1kaoa_           6 VVVLGSGGVGKSALTVQFVTG   26 (167)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            788999999999999999875

>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=96.52  E-value=0.012  Score=52.65  Aligned_cols=22  Identities=32%  Similarity=0.526  Sum_probs=19.5

Q ss_pred             EEEEECCCCchHHHHHHHHHHH
Q 005987          180 VLVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAke  201 (666)
                      -++|.|.+||||||++..+...
T Consensus         6 KivlvG~~~vGKTsli~~~~~~   27 (168)
T d1u8za_           6 KVIMVGSGGVGKSALTLQFMYD   27 (168)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            4889999999999999998764

>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=96.51  E-value=0.011  Score=52.59  Aligned_cols=21  Identities=43%  Similarity=0.691  Sum_probs=19.0

Q ss_pred             EEEECCCCchHHHHHHHHHHH
Q 005987          181 LVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       181 LLL~GPpG~GKTtla~~LAke  201 (666)
                      ++|.|++|||||+++..+...
T Consensus         6 i~viG~~~vGKTsli~~l~~~   26 (166)
T d1ctqa_           6 LVVVGAGGVGKSALTIQLIQN   26 (166)
T ss_dssp             EEEEESTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            788899999999999998874

>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=96.49  E-value=0.0083  Score=53.73  Aligned_cols=22  Identities=27%  Similarity=0.445  Sum_probs=19.3

Q ss_pred             EEEEECCCCchHHHHHHHHHHH
Q 005987          180 VLVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAke  201 (666)
                      -++|.|.|||||||++..+...
T Consensus        17 kI~vvG~~~~GKSsLi~rl~~~   38 (177)
T d1zj6a1          17 KVIIVGLDNAGKTTILYQFSMN   38 (177)
T ss_dssp             EEEEEESTTSSHHHHHHHHHTT
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            4889999999999999988764

>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=96.48  E-value=0.00063  Score=62.93  Aligned_cols=25  Identities=24%  Similarity=0.551  Sum_probs=23.0

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLG  203 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg  203 (666)
                      +.++|+||+|+||||+++.|++++.
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            5699999999999999999999974

>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=96.38  E-value=0.00093  Score=62.02  Aligned_cols=27  Identities=19%  Similarity=0.480  Sum_probs=23.9

Q ss_pred             EEEEECCCCchHHHHHHHHHHHcCCcE
Q 005987          180 VLVITGQAGVGKTATVRQIASHLGARL  206 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkelg~~v  206 (666)
                      +++|.||+|+||||+++.|+++++..+
T Consensus         2 pIvl~GPsGsGK~tl~~~L~~~~~~~~   28 (190)
T d1lvga_           2 PVVLSGPSGAGKSTLLKKLFQEHSSIF   28 (190)
T ss_dssp             CEEEECCTTSSHHHHHHHHHHHHTTTE
T ss_pred             eEEEECCCCCCHHHHHHHHHHhCCCce
Confidence            588999999999999999999986443

>d1g2912 c.37.1.12 (1:1-240) Maltose transport protein MalK, N-terminal domain {Archaeon Thermococcus litoralis [TaxId: 2265]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Maltose transport protein MalK, N-terminal domain
species: Archaeon Thermococcus litoralis [TaxId: 2265]

Probab=96.38  E-value=0.0037  Score=60.12  Aligned_cols=24  Identities=38%  Similarity=0.632  Sum_probs=22.2

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      .++-|.||+||||||++++++.-+
T Consensus        30 e~~~liG~sGaGKSTll~~i~gl~   53 (240)
T d1g2912          30 EFMILLGPSGCGKTTTLRMIAGLE   53 (240)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHTSS
T ss_pred             CEEEEECCCCChHHHHHHHHhcCC
Confidence            589999999999999999999876

>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=96.36  E-value=0.0009  Score=61.41  Aligned_cols=24  Identities=33%  Similarity=0.667  Sum_probs=22.7

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      ++++|.||+|+||||+++.|++++
T Consensus         3 ~iivl~GpsG~GK~tl~~~L~~~~   26 (182)
T d1znwa1           3 RVVVLSGPSAVGKSTVVRCLRERI   26 (182)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHS
T ss_pred             eEEEEECCCCCCHHHHHHHHHhhC
Confidence            689999999999999999999987

>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=96.35  E-value=0.013  Score=55.50  Aligned_cols=24  Identities=33%  Similarity=0.428  Sum_probs=20.8

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      +.++|+||...||||+++.++--.
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            579999999999999999886643

>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=96.33  E-value=0.026  Score=50.16  Aligned_cols=22  Identities=27%  Similarity=0.354  Sum_probs=19.2

Q ss_pred             EEEEECCCCchHHHHHHHHHHH
Q 005987          180 VLVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAke  201 (666)
                      -++|.|++|||||++++.+...
T Consensus         6 Kv~liG~~~vGKTsLl~~~~~~   27 (167)
T d1xtqa1           6 KIAILGYRSVGKSSLTIQFVEG   27 (167)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            4778899999999999998864

>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=96.30  E-value=0.021  Score=49.98  Aligned_cols=21  Identities=29%  Similarity=0.520  Sum_probs=19.4

Q ss_pred             EEEECCCCchHHHHHHHHHHH
Q 005987          181 LVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       181 LLL~GPpG~GKTtla~~LAke  201 (666)
                      ++|.|+|||||||+++.+...
T Consensus         8 I~ivG~~~vGKSSLi~~~~~~   28 (169)
T d1upta_           8 ILILGLDGAGKTTILYRLQVG   28 (169)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            889999999999999998775

>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=96.29  E-value=0.0015  Score=58.73  Aligned_cols=32  Identities=25%  Similarity=0.273  Sum_probs=27.2

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc---CCcEEEEc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL---GARLYEWD  210 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel---g~~viE~n  210 (666)
                      +++-++|++|+||||++..|+++|   |+.+.-+.
T Consensus         2 kii~I~G~~gSGKTTli~~l~~~L~~~g~~v~vik   36 (165)
T d1xjca_           2 NVWQVVGYKHSGKTTLMEKWVAAAVREGWRVGTVK   36 (165)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             cEEEEEeCCCCCHHHHHHHHHHHHHhCCCeEEEEE
Confidence            578899999999999999999876   67776654

>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=96.21  E-value=0.0077  Score=54.20  Aligned_cols=22  Identities=18%  Similarity=0.332  Sum_probs=19.2

Q ss_pred             EEEEECCCCchHHHHHHHHHHH
Q 005987          180 VLVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAke  201 (666)
                      -++|.|+||+||||+++.++..
T Consensus        14 kIvlvG~~~vGKTSli~rl~~~   35 (173)
T d1e0sa_          14 RILMLGLDAAGKTTILYKLKLG   35 (173)
T ss_dssp             EEEEEEETTSSHHHHHHHTTCC
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            3889999999999999988654

>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=96.19  E-value=0.017  Score=51.67  Aligned_cols=21  Identities=43%  Similarity=0.627  Sum_probs=19.1

Q ss_pred             EEEECCCCchHHHHHHHHHHH
Q 005987          181 LVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       181 LLL~GPpG~GKTtla~~LAke  201 (666)
                      ++|.|.+|||||++++.+...
T Consensus         8 i~lvG~~~vGKTsLi~r~~~~   28 (171)
T d2erya1           8 LVVVGGGGVGKSALTIQFIQS   28 (171)
T ss_dssp             EEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            889999999999999988764

>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=96.14  E-value=0.0026  Score=57.15  Aligned_cols=55  Identities=18%  Similarity=0.254  Sum_probs=37.1

Q ss_pred             ccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCc
Q 005987          150 ELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGAR  205 (666)
Q Consensus       150 eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~  205 (666)
                      ..+.++....++-.-|...+.....+ ++-+++|.|+=|+||||+++.+++.+|..
T Consensus         6 ~~l~~e~~t~~lg~~la~~l~~~~~~-~g~ii~L~G~LGaGKTtfvr~~~~~lg~~   60 (158)
T d1htwa_           6 QYIPDEFSMLRFGKKFAEILLKLHTE-KAIMVYLNGDLGAGKTTLTRGMLQGIGHQ   60 (158)
T ss_dssp             EEECSHHHHHHHHHHHHHHHHHHCCS-SCEEEEEECSTTSSHHHHHHHHHHHTTCC
T ss_pred             eeCCCHHHHHHHHHHHHHHHHhccCC-CCeEEEEecCCCccHHHHHHHHHhhcccc
Confidence            33456666666655555433210011 22479999999999999999999999875

>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=96.13  E-value=0.0019  Score=60.84  Aligned_cols=32  Identities=22%  Similarity=0.387  Sum_probs=26.9

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc----CCcEEEEc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL----GARLYEWD  210 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel----g~~viE~n  210 (666)
                      .+++|+|.||+||||+++.|++.+    +..++.++
T Consensus        25 ~vIwltGlsGsGKTTia~~L~~~l~~~~~~~~~~ld   60 (208)
T d1m7ga_          25 LTIWLTGLSASGKSTLAVELEHQLVRDRRVHAYRLD   60 (208)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHHHHHHCCCEEEEC
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHhcCceEEEEc
Confidence            589999999999999999999876    55665554

>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=96.07  E-value=0.018  Score=51.51  Aligned_cols=21  Identities=33%  Similarity=0.588  Sum_probs=18.3

Q ss_pred             EEEECCCCchHHHHHHHHHHH
Q 005987          181 LVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       181 LLL~GPpG~GKTtla~~LAke  201 (666)
                      ++|.|++|+|||++++.+...
T Consensus         4 i~lvG~~~vGKTsLi~~~~~~   24 (168)
T d2gjsa1           4 VLLLGAPGVGKSALARIFGGV   24 (168)
T ss_dssp             EEEECCTTSSHHHHHHHHHTC
T ss_pred             EEEECCCCcCHHHHHHHHhCC
Confidence            678899999999999988653

>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=96.05  E-value=0.015  Score=56.04  Aligned_cols=28  Identities=21%  Similarity=0.343  Sum_probs=23.6

Q ss_pred             CCCccEEEEECCCCchHHHHHHHHHHHc
Q 005987          175 KFSTNVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       175 ~~~~k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      -++....+|+|+||+|||+++..+|..+
T Consensus        26 ~~pg~~~~i~G~~G~GKS~l~l~la~~i   53 (274)
T d1nlfa_          26 MVAGTVGALVSPGGAGKSMLALQLAAQI   53 (274)
T ss_dssp             EETTSEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             ccCCcEEEEEeCCCCCHHHHHHHHHHHH
Confidence            3345789999999999999999888764

>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=96.00  E-value=0.008  Score=51.27  Aligned_cols=34  Identities=24%  Similarity=0.189  Sum_probs=22.6

Q ss_pred             cEEEEECCCCchHHHHHH-HHHHHc---CCcEEEEcCC
Q 005987          179 NVLVITGQAGVGKTATVR-QIASHL---GARLYEWDTP  212 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~-~LAkel---g~~viE~nas  212 (666)
                      +..+|++|+|+|||..+- ++.+.+   +..++-+...
T Consensus         8 ~~~il~~~tGsGKT~~~~~~~~~~~~~~~~~vli~~p~   45 (140)
T d1yksa1           8 MTTVLDFHPGAGKTRRFLPQILAECARRRLRTLVLAPT   45 (140)
T ss_dssp             CEEEECCCTTSSTTTTHHHHHHHHHHHTTCCEEEEESS
T ss_pred             CcEEEEcCCCCChhHHHHHHHHHHhhhcCceeeeeecc
Confidence            579999999999996653 333332   5555555543

>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=95.99  E-value=0.0086  Score=57.53  Aligned_cols=25  Identities=28%  Similarity=0.445  Sum_probs=22.9

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLG  203 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg  203 (666)
                      ..+-|.||+|+||||++++|+..+.
T Consensus        30 e~vaIvG~sGsGKSTLl~ll~gl~~   54 (241)
T d2pmka1          30 EVIGIVGRSGSGKSTLTKLIQRFYI   54 (241)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTTSSC
T ss_pred             CEEEEECCCCCCHHHHHHHHHhcCC
Confidence            5799999999999999999999774

>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=95.93  E-value=0.029  Score=51.45  Aligned_cols=23  Identities=22%  Similarity=0.459  Sum_probs=20.9

Q ss_pred             cEEEEECCCCchHHHHHHHHHHH
Q 005987          179 NVLVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAke  201 (666)
                      +.++|.|+||+||||++.+|..+
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            36899999999999999999875

>d1cr2a_ c.37.1.11 (A:) Gene 4 protein (g4p, DNA primase), helicase domain {Bacteriophage T7 [TaxId: 10760]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Gene 4 protein (g4p, DNA primase), helicase domain
species: Bacteriophage T7 [TaxId: 10760]

Probab=95.91  E-value=0.02  Score=55.38  Aligned_cols=39  Identities=26%  Similarity=0.319  Sum_probs=29.3

Q ss_pred             CCCCccEEEEECCCCchHHHHHHHHHHH----cCCcEEEEcCC
Q 005987          174 DKFSTNVLVITGQAGVGKTATVRQIASH----LGARLYEWDTP  212 (666)
Q Consensus       174 g~~~~k~LLL~GPpG~GKTtla~~LAke----lg~~viE~nas  212 (666)
                      |-.++...+|.|+||+|||+++..+|..    .|..++.+..-
T Consensus        31 G~~~G~l~vi~G~~G~GKT~~~~~la~~~a~~~g~~v~~~s~E   73 (277)
T d1cr2a_          31 GARGGEVIMVTSGSGMGKSTFVRQQALQWGTAMGKKVGLAMLE   73 (277)
T ss_dssp             SBCTTCEEEEECSTTSSHHHHHHHHHHHHHHTSCCCEEEEESS
T ss_pred             CCCCCeEEEEEeCCCCCHHHHHHHHHHhhhhhcccceeEeeec
Confidence            3344469999999999999998777754    37777776543

>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=95.87  E-value=0.032  Score=49.86  Aligned_cols=21  Identities=33%  Similarity=0.637  Sum_probs=18.8

Q ss_pred             EEEECCCCchHHHHHHHHHHH
Q 005987          181 LVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       181 LLL~GPpG~GKTtla~~LAke  201 (666)
                      +++.|+||||||+++..+...
T Consensus         6 ivvvG~~~vGKTsli~r~~~~   26 (173)
T d2a5ja1           6 YIIIGDTGVGKSCLLLQFTDK   26 (173)
T ss_dssp             EEEESSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHhcC
Confidence            778999999999999998765

>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=95.76  E-value=0.013  Score=54.16  Aligned_cols=32  Identities=16%  Similarity=0.166  Sum_probs=21.5

Q ss_pred             cEEEEECCCCchHHHHHHH-HHHHc--CCcEEEEc
Q 005987          179 NVLVITGQAGVGKTATVRQ-IASHL--GARLYEWD  210 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~-LAkel--g~~viE~n  210 (666)
                      +.+++.+|+|+|||+++-. ++..+  +..++.+-
T Consensus        41 ~~~il~apTGsGKT~~a~l~i~~~~~~~~~vl~l~   75 (202)
T d2p6ra3          41 KNLLLAMPTAAGKTLLAEMAMVREAIKGGKSLYVV   75 (202)
T ss_dssp             SCEEEECSSHHHHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             CCEEEEcCCCCchhHHHHHHHHHHhhccCcceeec
Confidence            4589999999999988633 33333  44555443

>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=95.74  E-value=0.0034  Score=64.21  Aligned_cols=49  Identities=24%  Similarity=0.230  Sum_probs=30.6

Q ss_pred             ccccccCCCCccccccCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHH
Q 005987          138 LWAEKYKPRSLEELAVQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       138 ~W~eKY~P~sl~eLvg~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAke  201 (666)
                      .|.+++.|..-    ..+.....+...+.+           +..+|+|||||||||++..+.+.
T Consensus       138 ~~~~~~~~~~~----~~~~Q~~A~~~al~~-----------~~~vI~G~pGTGKTt~i~~~l~~  186 (359)
T d1w36d1         138 QTLDKLFPVSD----EINWQKVAAAVALTR-----------RISVISGGPGTGKTTTVAKLLAA  186 (359)
T ss_dssp             HHHHTTCCCTT----SCCHHHHHHHHHHTB-----------SEEEEECCTTSTHHHHHHHHHHH
T ss_pred             HHHHHhccCcc----cccHHHHHHHHHHcC-----------CeEEEEcCCCCCceehHHHHHHH
Confidence            45666665432    223444445444432           58999999999999998654433

>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=95.70  E-value=0.036  Score=49.36  Aligned_cols=21  Identities=48%  Similarity=0.787  Sum_probs=19.3

Q ss_pred             EEEECCCCchHHHHHHHHHHH
Q 005987          181 LVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       181 LLL~GPpG~GKTtla~~LAke  201 (666)
                      ++|.|++||||||+++.+++.
T Consensus         8 i~lvG~~~vGKTsLi~~l~~~   28 (171)
T d2ew1a1           8 IVLIGNAGVGKTCLVRRFTQG   28 (171)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            789999999999999999874

>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=95.69  E-value=0.0063  Score=59.99  Aligned_cols=45  Identities=27%  Similarity=0.393  Sum_probs=31.7

Q ss_pred             HHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc
Q 005987          156 KKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       156 k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      ..++.+..++..|.... ++.| =++-|.|++||||||++..|.+.+
T Consensus         7 ~~~~~~~~~~~~~~~~~-~~~P-~iIGi~G~qGSGKSTl~~~l~~~L   51 (286)
T d1odfa_           7 YTIEFLDKYIPEWFETG-NKCP-LFIFFSGPQGSGKSFTSIQIYNHL   51 (286)
T ss_dssp             HHHHHHHHHHHHHHTTT-CCSC-EEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhcC-CCCC-EEEEeECCCCCCHHHHHHHHHHHH
Confidence            45666777777776543 2222 255589999999999999887765

>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=95.67  E-value=0.053  Score=48.17  Aligned_cols=21  Identities=48%  Similarity=0.692  Sum_probs=19.2

Q ss_pred             EEEECCCCchHHHHHHHHHHH
Q 005987          181 LVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       181 LLL~GPpG~GKTtla~~LAke  201 (666)
                      ++|.|++|||||++++.+...
T Consensus         5 i~lvG~~~vGKTsli~r~~~~   25 (168)
T d2atva1           5 LAIFGRAGVGKSALVVRFLTK   25 (168)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            788999999999999998874

>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=95.58  E-value=0.0027  Score=58.39  Aligned_cols=29  Identities=17%  Similarity=0.175  Sum_probs=24.2

Q ss_pred             CCCCccEEEEECCCCchHHHHHHHHHHHc
Q 005987          174 DKFSTNVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       174 g~~~~k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      |-++..+.+|+||||+|||+++..+|...
T Consensus        19 Gi~~G~v~~i~G~~GsGKT~l~l~la~~~   47 (242)
T d1n0wa_          19 GIETGSITEMFGEFRTGKTQICHTLAVTC   47 (242)
T ss_dssp             SEETTSEEEEECCTTSSHHHHHHHHHHHT
T ss_pred             CCcCCEEEEEEeCCCCCHHHHHHHHHHHH
Confidence            33455799999999999999999888764

>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=95.57  E-value=0.057  Score=47.76  Aligned_cols=21  Identities=33%  Similarity=0.523  Sum_probs=19.0

Q ss_pred             EEEECCCCchHHHHHHHHHHH
Q 005987          181 LVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       181 LLL~GPpG~GKTtla~~LAke  201 (666)
                      ++|.|.+|||||++++.+...
T Consensus         6 ivlvG~~~vGKTsLi~r~~~~   26 (167)
T d1z08a1           6 VVLLGEGCVGKTSLVLRYCEN   26 (167)
T ss_dssp             EEEECCTTSCHHHHHHHHHHC
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            789999999999999998763

>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=95.57  E-value=0.056  Score=47.79  Aligned_cols=21  Identities=33%  Similarity=0.656  Sum_probs=18.7

Q ss_pred             EEEECCCCchHHHHHHHHHHH
Q 005987          181 LVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       181 LLL~GPpG~GKTtla~~LAke  201 (666)
                      ++|.|.+|+|||++++.+...
T Consensus         7 ivlvG~~~vGKTsli~~~~~~   27 (166)
T d1z0fa1           7 YIIIGDMGVGKSCLLHQFTEK   27 (166)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            678899999999999998864

>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=95.55  E-value=0.0033  Score=58.85  Aligned_cols=25  Identities=24%  Similarity=0.504  Sum_probs=22.5

Q ss_pred             EEEEECCCCchHHHHHHHHHHHcCC
Q 005987          180 VLVITGQAGVGKTATVRQIASHLGA  204 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkelg~  204 (666)
                      ++-|+||+|+||||+++.|++.++.
T Consensus         4 iIgI~G~~gSGKSTla~~L~~~l~~   28 (213)
T d1uj2a_           4 LIGVSGGTASGKSSVCAKIVQLLGQ   28 (213)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHTTG
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhch
Confidence            4569999999999999999999864

>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=95.55  E-value=0.0035  Score=57.42  Aligned_cols=24  Identities=25%  Similarity=0.470  Sum_probs=22.4

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      ++++|.||+|+||||+++.|+++.
T Consensus         4 k~ivl~Gpsg~GK~tl~~~L~~~~   27 (178)
T d1kgda_           4 KTLVLLGAHGVGRRHIKNTLITKH   27 (178)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHC
T ss_pred             CcEEEECCCCCCHHHHHHHHHHhC
Confidence            689999999999999999999876

>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=95.55  E-value=0.0034  Score=58.94  Aligned_cols=25  Identities=12%  Similarity=0.425  Sum_probs=23.0

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLG  203 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg  203 (666)
                      ++++|+||+|+||||+++.|++...
T Consensus         3 ~livi~GPSG~GK~tl~~~L~~~~p   27 (205)
T d1s96a_           3 TLYIVSAPSGAGKSSLIQALLKTQP   27 (205)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHSC
T ss_pred             eEEEEECCCCCCHHHHHHHHHhhCC
Confidence            6899999999999999999999863

>d1uf9a_ c.37.1.1 (A:) Dephospho-CoA kinase {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Dephospho-CoA kinase
species: Thermus thermophilus [TaxId: 274]

Probab=95.49  E-value=0.0042  Score=56.99  Aligned_cols=28  Identities=25%  Similarity=0.485  Sum_probs=24.0

Q ss_pred             EEEEECCCCchHHHHHHHHHHHcCCcEEE
Q 005987          180 VLVITGQAGVGKTATVRQIASHLGARLYE  208 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkelg~~viE  208 (666)
                      ++-|+|++|+||||+|+.| +++|+.++.
T Consensus         5 IIgitG~~gSGKstva~~l-~~~g~~~~~   32 (191)
T d1uf9a_           5 IIGITGNIGSGKSTVAALL-RSWGYPVLD   32 (191)
T ss_dssp             EEEEEECTTSCHHHHHHHH-HHTTCCEEE
T ss_pred             EEEEECCCCCCHHHHHHHH-HHCCCeEEE
Confidence            4559999999999999998 568988874

>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=95.48  E-value=0.051  Score=48.30  Aligned_cols=21  Identities=33%  Similarity=0.569  Sum_probs=19.1

Q ss_pred             EEEECCCCchHHHHHHHHHHH
Q 005987          181 LVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       181 LLL~GPpG~GKTtla~~LAke  201 (666)
                      ++|.|.+|||||++++.+...
T Consensus         9 i~vvG~~~vGKTsLi~~l~~~   29 (170)
T d1r2qa_           9 LVLLGESAVGKSSLVLRFVKG   29 (170)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            788999999999999999865

>d1tf7a1 c.37.1.11 (A:14-255) Circadian clock protein KaiC {Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Circadian clock protein KaiC
species: Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]

Probab=95.47  E-value=0.066  Score=49.52  Aligned_cols=39  Identities=15%  Similarity=0.035  Sum_probs=27.5

Q ss_pred             CCCCccEEEEECCCCchHHHHHHHHHHH----cCCcEEEEcCC
Q 005987          174 DKFSTNVLVITGQAGVGKTATVRQIASH----LGARLYEWDTP  212 (666)
Q Consensus       174 g~~~~k~LLL~GPpG~GKTtla~~LAke----lg~~viE~nas  212 (666)
                      |-+++.+.+|+||||+|||+++.-+|..    .+..+..+...
T Consensus        22 Gi~~G~~~~I~G~~G~GKT~la~~~~~~~~~~~~~~~~~~s~e   64 (242)
T d1tf7a1          22 GLPIGRSTLVSGTSGTGKTLFSIQFLYNGIIEFDEPGVFVTFE   64 (242)
T ss_dssp             SEETTSEEEEEESTTSSHHHHHHHHHHHHHHHHCCCEEEEESS
T ss_pred             CCcCCeEEEEEeCCCCCHHHHHHHHHHHHHHhcCCCccccccc
Confidence            3345579999999999999998665432    25566655543

>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=95.43  E-value=0.045  Score=48.24  Aligned_cols=21  Identities=33%  Similarity=0.545  Sum_probs=18.6

Q ss_pred             EEEECCCCchHHHHHHHHHHH
Q 005987          181 LVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       181 LLL~GPpG~GKTtla~~LAke  201 (666)
                      ++|.|.+|||||++++.+...
T Consensus         3 v~vvG~~~vGKTsLi~r~~~~   23 (164)
T d1yzqa1           3 LVFLGEQSVGKTSLITRFMYD   23 (164)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            678899999999999998764

>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=95.42  E-value=0.029  Score=50.21  Aligned_cols=22  Identities=41%  Similarity=0.573  Sum_probs=19.6

Q ss_pred             EEEEECCCCchHHHHHHHHHHH
Q 005987          180 VLVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAke  201 (666)
                      -++|.|.+|||||++++.+...
T Consensus         8 Kv~lvG~~~vGKTsLi~r~~~~   29 (173)
T d2fn4a1           8 KLVVVGGGGVGKSALTIQFIQS   29 (173)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3889999999999999988764

>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=95.41  E-value=0.04  Score=48.70  Aligned_cols=21  Identities=43%  Similarity=0.425  Sum_probs=18.7

Q ss_pred             EEEECCCCchHHHHHHHHHHH
Q 005987          181 LVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       181 LLL~GPpG~GKTtla~~LAke  201 (666)
                      ++|.|++|+||||+++.+...
T Consensus         5 i~i~G~~~~GKTsLl~~l~~~   25 (164)
T d1zd9a1           5 LTLVGLQYSGKTTFVNVIASG   25 (164)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHcC
Confidence            677899999999999998764

>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=95.40  E-value=0.032  Score=49.33  Aligned_cols=21  Identities=24%  Similarity=0.594  Sum_probs=18.9

Q ss_pred             EEEECCCCchHHHHHHHHHHH
Q 005987          181 LVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       181 LLL~GPpG~GKTtla~~LAke  201 (666)
                      ++|.|+|||||||++..+...
T Consensus         5 v~liG~~~vGKSsLi~rl~~~   25 (164)
T d1z2aa1           5 MVVVGNGAVGKSSMIQRYCKG   25 (164)
T ss_dssp             EEEECSTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            789999999999999988863

>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=95.37  E-value=0.055  Score=51.60  Aligned_cols=24  Identities=33%  Similarity=0.613  Sum_probs=22.3

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      .++-|.||.|+||||++++++--+
T Consensus        33 ei~~liGpnGaGKSTl~~~i~Gl~   56 (240)
T d1ji0a_          33 QIVTLIGANGAGKTTTLSAIAGLV   56 (240)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             CEEEEECCCCCcHHHHHHHHhCCC
Confidence            589999999999999999998876

>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=95.36  E-value=0.062  Score=47.50  Aligned_cols=21  Identities=43%  Similarity=0.627  Sum_probs=19.2

Q ss_pred             EEEECCCCchHHHHHHHHHHH
Q 005987          181 LVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       181 LLL~GPpG~GKTtla~~LAke  201 (666)
                      ++|.|.+|||||++++.+...
T Consensus         6 ivvvG~~~vGKTsli~r~~~~   26 (167)
T d1c1ya_           6 LVVLGSGGVGKSALTVQFVQG   26 (167)
T ss_dssp             EEEECSTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCCCHHHHHHHHHcC
Confidence            788999999999999998875

>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=95.34  E-value=0.018  Score=52.25  Aligned_cols=21  Identities=33%  Similarity=0.574  Sum_probs=18.6

Q ss_pred             EEEECCCCchHHHHHHHHHHH
Q 005987          181 LVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       181 LLL~GPpG~GKTtla~~LAke  201 (666)
                      ++|.|++||||||+++.+.+.
T Consensus         8 i~ivG~~~vGKTsLi~~l~~~   28 (186)
T d2f7sa1           8 LLALGDSGVGKTTFLYRYTDN   28 (186)
T ss_dssp             EEEESCTTSSHHHHHHHHHCS
T ss_pred             EEEECCCCcCHHHHHHHHhcC
Confidence            778899999999999998753

>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=95.30  E-value=0.078  Score=46.97  Aligned_cols=21  Identities=33%  Similarity=0.542  Sum_probs=19.4

Q ss_pred             EEEECCCCchHHHHHHHHHHH
Q 005987          181 LVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       181 LLL~GPpG~GKTtla~~LAke  201 (666)
                      ++|.|++||||||++..++..
T Consensus         8 i~vvG~~~vGKTsLi~~l~~~   28 (169)
T d3raba_           8 ILIIGNSSVGKTSFLFRYADD   28 (169)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHcC
Confidence            889999999999999998865

>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=95.26  E-value=0.003  Score=59.64  Aligned_cols=28  Identities=14%  Similarity=0.188  Sum_probs=22.9

Q ss_pred             CCCCccEEEEECCCCchHHHHHHHHHHH
Q 005987          174 DKFSTNVLVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       174 g~~~~k~LLL~GPpG~GKTtla~~LAke  201 (666)
                      |-++.++.+|+||||+|||+++..+|..
T Consensus        30 Gi~~G~~~li~G~pGsGKT~l~lq~~~~   57 (251)
T d1szpa2          30 GVETGSITELFGEFRTGKSQLCHTLAVT   57 (251)
T ss_dssp             SEESSSEEEEEESTTSSHHHHHHHHTTT
T ss_pred             CCcCCeEEEEEcCCCCCHHHHHHHHHHH
Confidence            3445569999999999999999887654

>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=95.26  E-value=0.024  Score=56.24  Aligned_cols=67  Identities=21%  Similarity=0.293  Sum_probs=39.1

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcC-----CcEEEEcCCCchhhhhhhh----cccCCccccchhHHHHHHHHHHH
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLG-----ARLYEWDTPTPTIWQEYMH----NCKTGLEYTSKLDEFENFVERIR  245 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg-----~~viE~nasd~~~~~e~l~----~~~~g~~~~s~~~~f~~fl~~a~  245 (666)
                      -++-|.||+|+||||+++.|+..+.     ..+.-+..-+.......+.    ....|...+--.+.|.+++..++
T Consensus        81 ~iIGIaG~sgSGKSTla~~L~~lL~~~~~~~~v~~Is~D~F~~~~~~l~~~~~~~~~g~Pes~D~~~L~~~L~~lk  156 (308)
T d1sq5a_          81 YIISIAGSVAVGKSTTARVLQALLSRWPEHRRVELITTDGFLHPNQVLKERGLMKKKGFPESYDMHRLVKFVSDLK  156 (308)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHHHTTSTTCCCEEEEEGGGGBCCHHHHHHHTCTTCTTSGGGBCHHHHHHHHHHHT
T ss_pred             EEEEEeCCCCCCCcHHHHHHHHHHhhhcCCCceEEEeeeeeECCchHHHHhcCCccCCchHhhhHHHHHHHHHHHH
Confidence            5788999999999999999999873     4454443222110011111    11223332334566777777764

>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=95.20  E-value=0.037  Score=49.32  Aligned_cols=21  Identities=33%  Similarity=0.564  Sum_probs=18.7

Q ss_pred             EEEEECCCCchHHHHHHHHHH
Q 005987          180 VLVITGQAGVGKTATVRQIAS  200 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAk  200 (666)
                      -++|.|+||+||||++..+..
T Consensus        18 kI~vvG~~~vGKSsLi~~l~~   38 (176)
T d1fzqa_          18 RILLLGLDNAGKTTLLKQLAS   38 (176)
T ss_dssp             EEEEEESTTSSHHHHHHHHCC
T ss_pred             EEEEECCCCCCHHHHHHHHhc
Confidence            489999999999999998754

>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=95.18  E-value=0.0041  Score=59.18  Aligned_cols=29  Identities=21%  Similarity=0.276  Sum_probs=23.9

Q ss_pred             CCCCccEEEEECCCCchHHHHHHHHHHHc
Q 005987          174 DKFSTNVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       174 g~~~~k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      |-++.+..+|+||||+|||+++..+|...
T Consensus        32 Glp~G~~~li~G~pGsGKT~~~lq~~~~~   60 (254)
T d1pzna2          32 GIETQAITEVFGEFGSGKTQLAHTLAVMV   60 (254)
T ss_dssp             SEESSEEEEEEESTTSSHHHHHHHHHHHT
T ss_pred             CccCCEEEEEEcCCCCCHHHHHHHHHHHh
Confidence            34455699999999999999998887764

>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=95.16  E-value=0.33  Score=42.63  Aligned_cols=22  Identities=23%  Similarity=0.545  Sum_probs=19.1

Q ss_pred             EEEEECCCCchHHHHHHHHHHH
Q 005987          180 VLVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAke  201 (666)
                      .++|.|+||+||||++++|...
T Consensus         2 ~V~liG~~n~GKSsLi~~L~~~   23 (171)
T d1mkya1           2 TVLIVGRPNVGKSTLFNKLVKK   23 (171)
T ss_dssp             EEEEECCTTSSHHHHHHHHHC-
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            4789999999999999999754

>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=95.15  E-value=0.058  Score=48.16  Aligned_cols=21  Identities=33%  Similarity=0.578  Sum_probs=18.7

Q ss_pred             EEEECCCCchHHHHHHHHHHH
Q 005987          181 LVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       181 LLL~GPpG~GKTtla~~LAke  201 (666)
                      ++|.|.+|||||++++.++..
T Consensus         6 v~lvG~~~vGKTsLi~~~~~~   26 (172)
T d2g3ya1           6 VVLIGEQGVGKSTLANIFAGV   26 (172)
T ss_dssp             EEEECCTTSSHHHHHHHHHCC
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            789999999999999988753

>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=95.11  E-value=0.0053  Score=58.30  Aligned_cols=29  Identities=17%  Similarity=0.100  Sum_probs=24.2

Q ss_pred             CCCCccEEEEECCCCchHHHHHHHHHHHc
Q 005987          174 DKFSTNVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       174 g~~~~k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      |-++.+.++|+||||||||+++..+|...
T Consensus        33 Gip~G~~~~i~G~~GsGKT~lalq~~~~~   61 (258)
T d1v5wa_          33 GIESMAITEAFGEFRTGKTQLSHTLCVTA   61 (258)
T ss_dssp             SBCSSEEEEEECCTTCTHHHHHHHHHHHT
T ss_pred             CCcCCEEEEEECCCCCCHHHHHHHHHHHH
Confidence            44455699999999999999999998753

>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=95.08  E-value=0.0047  Score=58.68  Aligned_cols=45  Identities=24%  Similarity=0.469  Sum_probs=31.0

Q ss_pred             HHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcC
Q 005987          156 KKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHLGARLYEWDT  211 (666)
Q Consensus       156 k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkelg~~viE~na  211 (666)
                      .-+++|+.+|+.           +..+|.|++|+||||++.+|..+.....-++..
T Consensus        84 ~g~~~L~~~l~~-----------kt~~~~G~SGVGKSTLiN~L~~~~~~~T~~vs~  128 (225)
T d1u0la2          84 MGIEELKEYLKG-----------KISTMAGLSGVGKSSLLNAINPGLKLRVSEVSE  128 (225)
T ss_dssp             TTHHHHHHHHSS-----------SEEEEECSTTSSHHHHHHHHSTTCCCC------
T ss_pred             hhHhhHHHHhcC-----------CeEEEECCCCCCHHHHHHhhcchhhhhccCccc
Confidence            346677777642           578999999999999999998777666555543

>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=95.06  E-value=0.042  Score=49.04  Aligned_cols=21  Identities=29%  Similarity=0.623  Sum_probs=19.0

Q ss_pred             EEEECCCCchHHHHHHHHHHH
Q 005987          181 LVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       181 LLL~GPpG~GKTtla~~LAke  201 (666)
                      ++|.|.+|+||||+++.+...
T Consensus         8 I~lvG~~~vGKTsll~~~~~~   28 (174)
T d2bmea1           8 FLVIGNAGTGKSCLLHQFIEK   28 (174)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            889999999999999988764

>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=94.91  E-value=0.12  Score=45.49  Aligned_cols=21  Identities=24%  Similarity=0.579  Sum_probs=18.9

Q ss_pred             EEEECCCCchHHHHHHHHHHH
Q 005987          181 LVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       181 LLL~GPpG~GKTtla~~LAke  201 (666)
                      ++|.|.+||||||+++.+.+.
T Consensus         7 i~lvG~~~vGKTsli~rl~~~   27 (167)
T d1z0ja1           7 VCLLGDTGVGKSSIMWRFVED   27 (167)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            778899999999999998864

>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=94.89  E-value=0.01  Score=55.68  Aligned_cols=34  Identities=26%  Similarity=0.451  Sum_probs=28.6

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcCC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL---GARLYEWDTP  212 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel---g~~viE~nas  212 (666)
                      ..+.|.||.|+||||.++.|++.+   |+.++.+..|
T Consensus         4 ~lI~ieG~dGsGKsT~~~~L~~~L~~~g~~v~~~~~p   40 (209)
T d1nn5a_           4 ALIVLEGVDRAGKSTQSRKLVEALCAAGHRAELLRFP   40 (209)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHHHHHHTTCCEEEEESS
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHCCCcEEEEeCC
Confidence            578889999999999999999987   7777766544

>d1yrba1 c.37.1.10 (A:1-244) ATP(GTP)-binding protein PAB0955 {Pyrococcus abyssi [TaxId: 29292]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: ATP(GTP)-binding protein PAB0955
species: Pyrococcus abyssi [TaxId: 29292]

Probab=94.89  E-value=0.0093  Score=56.28  Aligned_cols=31  Identities=26%  Similarity=0.396  Sum_probs=25.2

Q ss_pred             EEEEECCCCchHHHHHHHHHHHc--CCcEEEEc
Q 005987          180 VLVITGQAGVGKTATVRQIASHL--GARLYEWD  210 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkel--g~~viE~n  210 (666)
                      ++++.||+|+||||++..|.+.+  +..+.-+|
T Consensus         2 vi~v~G~~GsGKTTLl~~ll~~~~~~~~~~ivn   34 (244)
T d1yrba1           2 IVVFVGTAGSGKTTLTGEFGRYLEDNYKVAYVN   34 (244)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHTTTSCEEEEE
T ss_pred             EEEEEcCCCCcHHHHHHHHHHHHhhCCeEEEEe
Confidence            58899999999999999998866  44555554

>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=94.82  E-value=0.0063  Score=57.91  Aligned_cols=29  Identities=28%  Similarity=0.413  Sum_probs=25.7

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEE
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLY  207 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~vi  207 (666)
                      +++-|+|+.||||||+|..|++.+|+.++
T Consensus         2 ~iIgiTG~igSGKsTva~~l~e~~g~~~i   30 (241)
T d1deka_           2 KLIFLSGVKRSGKDTTADFIMSNYSAVKY   30 (241)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHSCEEEC
T ss_pred             EEEEEECCCCCCHHHHHHHHHHhCCCeEE
Confidence            57899999999999999999999987544

>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=94.72  E-value=0.013  Score=54.13  Aligned_cols=34  Identities=24%  Similarity=0.484  Sum_probs=28.4

Q ss_pred             EEEEECCCCchHHHHHHHHHHHc---CCcEEEEcCCC
Q 005987          180 VLVITGQAGVGKTATVRQIASHL---GARLYEWDTPT  213 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkel---g~~viE~nasd  213 (666)
                      .+.|.|+.|+||||+++.|++.+   |+.++.+..|+
T Consensus         2 lI~ieG~dGsGKST~~~~L~~~l~~~g~~v~~~~~P~   38 (208)
T d1gsia_           2 LIAIEGVDGAGKRTLVEKLSGAFRAAGRSVATLAFPR   38 (208)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEESSC
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEecCC
Confidence            47889999999999999999976   77887766553

>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=94.68  E-value=0.015  Score=58.36  Aligned_cols=33  Identities=21%  Similarity=0.488  Sum_probs=26.8

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc--CCcEEEEcC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL--GARLYEWDT  211 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel--g~~viE~na  211 (666)
                      +.+|++||+|+||||++++|+..+  +.+++.+..
T Consensus       167 ~nili~G~tgSGKTT~l~al~~~i~~~~rivtiEd  201 (323)
T d1g6oa_         167 KNVIVCGGTGSGKTTYIKSIMEFIPKEERIISIED  201 (323)
T ss_dssp             CCEEEEESTTSSHHHHHHHHGGGSCTTCCEEEEES
T ss_pred             CCEEEEeeccccchHHHHHHhhhcccccceeeccc
Confidence            468999999999999999999987  345555543

>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=94.56  E-value=0.011  Score=55.17  Aligned_cols=28  Identities=29%  Similarity=0.602  Sum_probs=24.6

Q ss_pred             EEEEECCCCchHHHHHHHHHHHcCCcEEE
Q 005987          180 VLVITGQAGVGKTATVRQIASHLGARLYE  208 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkelg~~viE  208 (666)
                      ++-|+|++|+||||+++.+. ++|+.++.
T Consensus         5 iIgitG~igSGKStv~~~l~-~~G~~vid   32 (208)
T d1vhta_           5 IVALTGGIGSGKSTVANAFA-DLGINVID   32 (208)
T ss_dssp             EEEEECCTTSCHHHHHHHHH-HTTCEEEE
T ss_pred             EEEEECCCcCCHHHHHHHHH-HCCCcEEE
Confidence            67799999999999999885 78998774

>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=94.52  E-value=0.0078  Score=55.22  Aligned_cols=29  Identities=21%  Similarity=0.275  Sum_probs=25.3

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEE
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLY  207 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~vi  207 (666)
                      -.+.|.|+.|+||||+++.|++.++...+
T Consensus        10 ~~I~ieG~~GsGKTTl~~~L~~~l~~~~~   38 (197)
T d2vp4a1          10 FTVLIEGNIGSGKTTYLNHFEKYKNDICL   38 (197)
T ss_dssp             EEEEEECSTTSCHHHHHHTTGGGTTTEEE
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhCCcEE
Confidence            47999999999999999999999975443

>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=94.49  E-value=0.035  Score=50.00  Aligned_cols=20  Identities=30%  Similarity=0.552  Sum_probs=18.0

Q ss_pred             EEEEECCCCchHHHHHHHHH
Q 005987          180 VLVITGQAGVGKTATVRQIA  199 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LA  199 (666)
                      -++|.|++|+||||+++.+.
T Consensus        19 KI~lvG~~~vGKTsLi~~l~   38 (182)
T d1moza_          19 RILILGLDGAGKTTILYRLQ   38 (182)
T ss_dssp             EEEEEEETTSSHHHHHHHTC
T ss_pred             EEEEECCCCCCHHHHHHHHh
Confidence            48899999999999998774

>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=94.46  E-value=0.39  Score=42.44  Aligned_cols=23  Identities=22%  Similarity=0.465  Sum_probs=20.7

Q ss_pred             cEEEEECCCCchHHHHHHHHHHH
Q 005987          179 NVLVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAke  201 (666)
                      ..+.|.|.+|+||||++.+|...
T Consensus         6 ~~I~lvG~~~~GKSSLin~l~~~   28 (178)
T d1wf3a1           6 GFVAIVGKPNVGKSTLLNNLLGV   28 (178)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHTS
T ss_pred             cEEEEECCCCCCHHHHHHHHhCC
Confidence            46999999999999999999865

>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=94.42  E-value=0.07  Score=47.63  Aligned_cols=21  Identities=29%  Similarity=0.657  Sum_probs=19.0

Q ss_pred             EEEECCCCchHHHHHHHHHHH
Q 005987          181 LVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       181 LLL~GPpG~GKTtla~~LAke  201 (666)
                      ++|.|++||||||+++.+...
T Consensus         7 i~vvG~~~vGKTsLi~~~~~~   27 (175)
T d2f9la1           7 VVLIGDSGVGKSNLLSRFTRN   27 (175)
T ss_dssp             EEEESSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            889999999999999988764

>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=94.40  E-value=0.0078  Score=56.14  Aligned_cols=24  Identities=38%  Similarity=0.664  Sum_probs=22.2

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      .++.|.||.||||||++++++..+
T Consensus        28 ei~~l~G~NGsGKSTLl~~i~gl~   51 (200)
T d1sgwa_          28 NVVNFHGPNGIGKTTLLKTISTYL   51 (200)
T ss_dssp             CCEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CEEEEECCCCChHHHHHHHHhccc
Confidence            579999999999999999999876

>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=94.39  E-value=0.013  Score=53.39  Aligned_cols=28  Identities=39%  Similarity=0.635  Sum_probs=24.2

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEE
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLY  207 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~vi  207 (666)
                      +.+||.||+|+||||++..+.+. |+.++
T Consensus        15 ~gvl~~G~sG~GKStlal~l~~~-g~~lv   42 (176)
T d1kkma_          15 LGVLITGDSGVGKSETALELVQR-GHRLI   42 (176)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHT-TCEEE
T ss_pred             EEEEEEeCCCCCHHHHHHHHHHc-CCeEE
Confidence            68999999999999999888875 77655

>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=94.29  E-value=0.1  Score=46.21  Aligned_cols=21  Identities=43%  Similarity=0.646  Sum_probs=18.7

Q ss_pred             EEEECCCCchHHHHHHHHHHH
Q 005987          181 LVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       181 LLL~GPpG~GKTtla~~LAke  201 (666)
                      ++|.|.+|||||+++..++..
T Consensus         7 i~lvG~~~vGKTsll~~~~~~   27 (169)
T d1x1ra1           7 LVVVGDGGVGKSALTIQFFQK   27 (169)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            677899999999999998874

>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=94.25  E-value=0.14  Score=45.10  Aligned_cols=21  Identities=43%  Similarity=0.675  Sum_probs=18.7

Q ss_pred             EEEECCCCchHHHHHHHHHHH
Q 005987          181 LVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       181 LLL~GPpG~GKTtla~~LAke  201 (666)
                      ++|.|.+|||||++++.+...
T Consensus         6 i~vvG~~~vGKTsLi~~~~~~   26 (170)
T d1ek0a_           6 LVLLGEAAVGKSSIVLRFVSN   26 (170)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            778899999999999988764

>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=94.18  E-value=0.0086  Score=56.28  Aligned_cols=28  Identities=32%  Similarity=0.318  Sum_probs=24.0

Q ss_pred             CCCccEEEEECCCCchHHHHHHHHHHHc
Q 005987          175 KFSTNVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       175 ~~~~k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      -++..+++|+||||+|||+++..+|..+
T Consensus        31 l~~G~l~~i~G~~G~GKT~~~l~~a~~~   58 (258)
T d2i1qa2          31 LESQSVTEFAGVFGSGKTQIMHQSCVNL   58 (258)
T ss_dssp             EETTEEEEEEESTTSSHHHHHHHHHHHT
T ss_pred             ccCCeEEEEEeCCCCCHHHHHHHHHHHH
Confidence            3345799999999999999999998775

>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=94.14  E-value=0.081  Score=46.82  Aligned_cols=21  Identities=29%  Similarity=0.529  Sum_probs=18.4

Q ss_pred             EEEECCCCchHHHHHHHHHHH
Q 005987          181 LVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       181 LLL~GPpG~GKTtla~~LAke  201 (666)
                      ++|.|.+||||||++..+...
T Consensus         5 i~viG~~~vGKTsLi~r~~~~   25 (171)
T d2erxa1           5 VAVFGAGGVGKSSLVLRFVKG   25 (171)
T ss_dssp             EEEECCTTSSHHHHHHHHHTC
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            678899999999999988763

>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=94.13  E-value=0.12  Score=45.98  Aligned_cols=21  Identities=33%  Similarity=0.670  Sum_probs=8.0

Q ss_pred             EEEECCCCchHHHHHHHHHHH
Q 005987          181 LVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       181 LLL~GPpG~GKTtla~~LAke  201 (666)
                      ++|.|.+||||||+++.+...
T Consensus         9 i~vvG~~~vGKTsLi~~l~~~   29 (173)
T d2fu5c1           9 LLLIGDSGVGKTCVLFRFSED   29 (173)
T ss_dssp             EEEECCCCC------------
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            677899999999999888753

>d1svia_ c.37.1.8 (A:) Probable GTPase EngB {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase EngB
species: Bacillus subtilis [TaxId: 1423]

Probab=94.12  E-value=0.54  Score=42.11  Aligned_cols=21  Identities=19%  Similarity=0.542  Sum_probs=19.2

Q ss_pred             EEEEECCCCchHHHHHHHHHH
Q 005987          180 VLVITGQAGVGKTATVRQIAS  200 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAk  200 (666)
                      .+.|.|+||+||||++.+|..
T Consensus        25 ~I~lvG~~n~GKSTLin~L~g   45 (195)
T d1svia_          25 EIALAGRSNVGKSSFINSLIN   45 (195)
T ss_dssp             EEEEEEBTTSSHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHhcC
Confidence            588999999999999999974

>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=94.03  E-value=0.015  Score=54.03  Aligned_cols=28  Identities=32%  Similarity=0.546  Sum_probs=24.2

Q ss_pred             EEEEECCCCchHHHHHHHHHHHcCCcEEE
Q 005987          180 VLVITGQAGVGKTATVRQIASHLGARLYE  208 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkelg~~viE  208 (666)
                      ++-|+|++||||||+++.+. ++|+.++.
T Consensus         4 iIgITG~igSGKStv~~~l~-~~G~~vid   31 (205)
T d1jjva_           4 IVGLTGGIGSGKTTIANLFT-DLGVPLVD   31 (205)
T ss_dssp             EEEEECSTTSCHHHHHHHHH-TTTCCEEE
T ss_pred             EEEEECCCCCCHHHHHHHHH-HCCCeEEE
Confidence            56689999999999999886 68998874

>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=94.03  E-value=0.2  Score=45.31  Aligned_cols=21  Identities=29%  Similarity=0.651  Sum_probs=18.7

Q ss_pred             EEEECCCCchHHHHHHHHHHH
Q 005987          181 LVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       181 LLL~GPpG~GKTtla~~LAke  201 (666)
                      ++|.|++||||||+++.+...
T Consensus         9 ivvvG~~~vGKTsli~~l~~~   29 (194)
T d2bcgy1           9 LLLIGNSGVGKSCLLLRFSDD   29 (194)
T ss_dssp             EEEEESTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCcCHHHHHHHHhhC
Confidence            778899999999999988764

>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=93.94  E-value=0.11  Score=45.25  Aligned_cols=21  Identities=29%  Similarity=0.602  Sum_probs=19.0

Q ss_pred             EEEECCCCchHHHHHHHHHHH
Q 005987          181 LVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       181 LLL~GPpG~GKTtla~~LAke  201 (666)
                      ++|.|+||+||||++.+|...
T Consensus         4 I~lvG~~nvGKSsLin~l~~~   24 (161)
T d2gj8a1           4 VVIAGRPNAGKSSLLNALAGR   24 (161)
T ss_dssp             EEEEESTTSSHHHHHHHHHTS
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            789999999999999999754

>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=93.92  E-value=0.014  Score=54.26  Aligned_cols=29  Identities=34%  Similarity=0.520  Sum_probs=24.6

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc---CCcEE
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL---GARLY  207 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel---g~~vi  207 (666)
                      +.++|.|+.|+||||.++.|++.+   |+..+
T Consensus         3 kfIviEG~dGsGKsT~~~~L~~~L~~~g~~~~   34 (210)
T d4tmka_           3 KYIVIEGLEGAGKTTARNVVVETLEQLGIRDM   34 (210)
T ss_dssp             CEEEEEECTTSCHHHHHHHHHHHHHHTTCCCE
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHhCCCCeE
Confidence            578999999999999999999877   55433

>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=93.89  E-value=0.012  Score=56.03  Aligned_cols=24  Identities=25%  Similarity=0.397  Sum_probs=22.0

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      .++-|.||+||||||++++++.-.
T Consensus        32 e~~~iiG~sGsGKSTLl~~i~gl~   55 (230)
T d1l2ta_          32 EFVSIMGPSGSGKSTMLNIIGCLD   55 (230)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             CEEEEECCCCCCcchhhHhccCCC
Confidence            589999999999999999998866

>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=93.88  E-value=0.018  Score=54.49  Aligned_cols=30  Identities=23%  Similarity=0.300  Sum_probs=26.3

Q ss_pred             ccEEEEECCCCchHHHHHHHHHHHcCCcEE
Q 005987          178 TNVLVITGQAGVGKTATVRQIASHLGARLY  207 (666)
Q Consensus       178 ~k~LLL~GPpG~GKTtla~~LAkelg~~vi  207 (666)
                      ++.++|-|+-|+||||+++.|++.++...+
T Consensus         2 pk~IviEG~~GsGKST~~~~L~~~l~~~~i   31 (241)
T d2ocpa1           2 PRRLSIEGNIAVGKSTFVKLLTKTYPEWHV   31 (241)
T ss_dssp             CEEEEEEECTTSSHHHHHHHHHHHCTTSEE
T ss_pred             CeEEEEECCCCCcHHHHHHHHHHHHhhcCC
Confidence            378999999999999999999999965544

>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=93.84  E-value=0.014  Score=55.46  Aligned_cols=26  Identities=35%  Similarity=0.423  Sum_probs=23.2

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGA  204 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~  204 (666)
                      .++-|.||+||||||++++++.-+..
T Consensus        27 e~~~liGpsGaGKSTll~~l~Gl~~p   52 (229)
T d3d31a2          27 EYFVILGPTGAGKTLFLELIAGFHVP   52 (229)
T ss_dssp             CEEEEECCCTHHHHHHHHHHHTSSCC
T ss_pred             CEEEEECCCCCcHHHHHHHHhcCcCC
Confidence            58999999999999999999987643

>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=93.79  E-value=0.015  Score=52.96  Aligned_cols=28  Identities=18%  Similarity=0.402  Sum_probs=23.7

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEE
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLY  207 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~vi  207 (666)
                      +.+||.||+|+||||++..+.+. |+.++
T Consensus        16 ~gvli~G~sG~GKS~lal~l~~~-G~~lv   43 (177)
T d1knxa2          16 VGVLLTGRSGIGKSECALDLINK-NHLFV   43 (177)
T ss_dssp             EEEEEEESSSSSHHHHHHHHHTT-TCEEE
T ss_pred             EEEEEEcCCCCCHHHHHHHHHHc-CCcee
Confidence            67999999999999999888764 76654

>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=93.61  E-value=0.18  Score=44.46  Aligned_cols=21  Identities=29%  Similarity=0.593  Sum_probs=19.1

Q ss_pred             EEEECCCCchHHHHHHHHHHH
Q 005987          181 LVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       181 LLL~GPpG~GKTtla~~LAke  201 (666)
                      ++|.|++|||||++++.+...
T Consensus         9 i~vvG~~~vGKTsli~~~~~~   29 (170)
T d2g6ba1           9 VMLVGDSGVGKTCLLVRFKDG   29 (170)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            889999999999999988764

>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=93.57  E-value=0.021  Score=51.63  Aligned_cols=28  Identities=36%  Similarity=0.624  Sum_probs=23.6

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEE
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLY  207 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~vi  207 (666)
                      +.+||.||+|+||||++..+.+. |+.++
T Consensus        16 ~gvli~G~sg~GKS~la~~l~~~-g~~li   43 (169)
T d1ko7a2          16 VGVLITGDSGIGKSETALELIKR-GHRLV   43 (169)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHT-TCEEE
T ss_pred             EEEEEEeCCCCCHHHHHHHHHHc-CCeEE
Confidence            57999999999999999887776 66554

>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=93.53  E-value=0.088  Score=46.99  Aligned_cols=21  Identities=29%  Similarity=0.669  Sum_probs=19.2

Q ss_pred             EEEECCCCchHHHHHHHHHHH
Q 005987          181 LVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       181 LLL~GPpG~GKTtla~~LAke  201 (666)
                      ++|.|.+|||||++++.+...
T Consensus        10 i~vvG~~~vGKTsli~~l~~~   30 (177)
T d1x3sa1          10 ILIIGESGVGKSSLLLRFTDD   30 (177)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            889999999999999998764

>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=93.50  E-value=0.014  Score=55.86  Aligned_cols=24  Identities=21%  Similarity=0.407  Sum_probs=22.0

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      .++-|.||+||||||++++++--+
T Consensus        32 e~~~iiG~sGsGKSTLl~~i~Gl~   55 (240)
T d3dhwc1          32 QIYGVIGASGAGKSTLIRCVNLLE   55 (240)
T ss_dssp             CEEEEEESTTSSHHHHHHHHTTSS
T ss_pred             CEEEEECCCCCCHHHHHHHHcCCc
Confidence            589999999999999999998865

>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=93.42  E-value=0.19  Score=44.38  Aligned_cols=21  Identities=38%  Similarity=0.632  Sum_probs=17.1

Q ss_pred             EEEECCCCchHHHHHHHHHHH
Q 005987          181 LVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       181 LLL~GPpG~GKTtla~~LAke  201 (666)
                      ++|.|++|||||+++..++..
T Consensus         6 i~vvG~~~vGKTsli~~~~~~   26 (170)
T d1i2ma_           6 LVLVGDGGTGKTTFVKRHLTG   26 (170)
T ss_dssp             EEEEECTTSSHHHHHHTTC--
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            677899999999999887654

>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=93.42  E-value=0.042  Score=55.00  Aligned_cols=35  Identities=26%  Similarity=0.402  Sum_probs=26.8

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc---CCc--EEEEcCCC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL---GAR--LYEWDTPT  213 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel---g~~--viE~nasd  213 (666)
                      ..+=|+||||+||||++..|++.+   |.+  ++.++.+.
T Consensus        55 ~~IgitG~pGaGKSTLi~~l~~~~~~~g~~vavlavDpss   94 (327)
T d2p67a1          55 LRLGVTGTPGAGKSTFLEAFGMLLIREGLKVAVIAVDPSS   94 (327)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHHHHHHTTCCEEEEEECCC-
T ss_pred             eEEEeeCCCCCCHHHHHHHHHHHHHhcCCceeeecCCCce
Confidence            478999999999999999999876   433  45555443

>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=93.36  E-value=0.019  Score=56.07  Aligned_cols=22  Identities=32%  Similarity=0.471  Sum_probs=16.6

Q ss_pred             cEEEEECCCCchHHHHH-HHHHH
Q 005987          179 NVLVITGQAGVGKTATV-RQIAS  200 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla-~~LAk  200 (666)
                      .++||.|||||||||++ ..++.
T Consensus        15 ~~~lI~g~aGTGKTt~l~~rv~~   37 (306)
T d1uaaa1          15 GPCLVLAGAGSGKTRVITNKIAH   37 (306)
T ss_dssp             SEEEECCCTTSCHHHHHHHHHHH
T ss_pred             CCEEEEeeCCccHHHHHHHHHHH
Confidence            36889999999999875 43333

>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=93.36  E-value=0.015  Score=55.61  Aligned_cols=24  Identities=38%  Similarity=0.425  Sum_probs=22.2

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      ..+-|.||+||||||++++++.-+
T Consensus        32 e~~~iiG~sGsGKSTll~~i~gl~   55 (242)
T d1oxxk2          32 ERFGILGPSGAGKTTFMRIIAGLD   55 (242)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHTSS
T ss_pred             CEEEEECCCCCcHHHHHHHHHcCc
Confidence            589999999999999999999865

>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=93.35  E-value=0.02  Score=49.80  Aligned_cols=21  Identities=24%  Similarity=0.436  Sum_probs=19.4

Q ss_pred             EEEECCCCchHHHHHHHHHHH
Q 005987          181 LVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       181 LLL~GPpG~GKTtla~~LAke  201 (666)
                      ++|.|+||+||||++..+...
T Consensus         3 I~liG~~nvGKSSLln~l~~~   23 (166)
T d2qtvb1           3 LLFLGLDNAGKTTLLHMLKND   23 (166)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            789999999999999999875

>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=93.25  E-value=0.036  Score=51.81  Aligned_cols=34  Identities=21%  Similarity=0.294  Sum_probs=28.4

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGARLYEWDTP  212 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~viE~nas  212 (666)
                      +.+.|.|+-|+||||.++.|++.+.....-+..+
T Consensus         4 k~I~iEG~DGsGKST~~~~L~~~L~~~~~~~~~p   37 (214)
T d1tmka_           4 KLILIEGLDRTGKTTQCNILYKKLQPNCKLLKFP   37 (214)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHHHTTTSEEEEESS
T ss_pred             EEEEEECCCCCcHHHHHHHHHHHHHhCCEEEEEC
Confidence            5899999999999999999999997665554443

>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=93.19  E-value=0.052  Score=54.18  Aligned_cols=33  Identities=36%  Similarity=0.533  Sum_probs=25.8

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc---CCc--EEEEcC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL---GAR--LYEWDT  211 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel---g~~--viE~na  211 (666)
                      ..+=|+||||+||||++-.|++.+   |.+  |+....
T Consensus        52 ~~igitG~pGaGKSTli~~l~~~~~~~g~~vaViavDp   89 (323)
T d2qm8a1          52 IRVGITGVPGVGKSTTIDALGSLLTAAGHKVAVLAVDP   89 (323)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHHHHHTTCCEEEEEECG
T ss_pred             eEEeeeCCCCCCHHHHHHHHHHHHhhcCCceeeeeccc
Confidence            468899999999999999999875   444  445443

>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=93.16  E-value=0.23  Score=44.17  Aligned_cols=21  Identities=14%  Similarity=0.338  Sum_probs=18.3

Q ss_pred             EEEECCCCchHHHHHHHHHHH
Q 005987          181 LVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       181 LLL~GPpG~GKTtla~~LAke  201 (666)
                      +.|.|.||+||||++.+|...
T Consensus         4 VaivG~~nvGKSTLin~L~~~   24 (180)
T d1udxa2           4 VGLVGYPNAGKSSLLAAMTRA   24 (180)
T ss_dssp             EEEECCGGGCHHHHHHHHCSS
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            677899999999999998654

>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=93.11  E-value=0.024  Score=52.33  Aligned_cols=23  Identities=17%  Similarity=0.302  Sum_probs=20.7

Q ss_pred             cEEEEECCCCchHHHHHHHHHHH
Q 005987          179 NVLVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAke  201 (666)
                      |.++|.|+||+||||++..+...
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            46899999999999999999874

>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=92.96  E-value=0.023  Score=55.66  Aligned_cols=25  Identities=40%  Similarity=0.581  Sum_probs=22.8

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLG  203 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg  203 (666)
                      ..+.|.||+||||||++++++..+.
T Consensus        63 e~vaivG~nGsGKSTLl~~i~Gl~~   87 (281)
T d1r0wa_          63 EMLAITGSTGSGKTSLLMLILGELE   87 (281)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHTSSC
T ss_pred             CEEEEECCCCChHHHHHHHHhCCCc
Confidence            5799999999999999999998773

>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=92.96  E-value=0.17  Score=48.91  Aligned_cols=32  Identities=22%  Similarity=0.312  Sum_probs=21.5

Q ss_pred             cEEEEECCCCchHHHH-HHHHHHH---cCCcEEEEc
Q 005987          179 NVLVITGQAGVGKTAT-VRQIASH---LGARLYEWD  210 (666)
Q Consensus       179 k~LLL~GPpG~GKTtl-a~~LAke---lg~~viE~n  210 (666)
                      +..|+.+|+|+|||+. +-.+.++   -+..++-+.
T Consensus        10 ~~~lv~~~TGsGKT~~~l~~~~~~~~~~~~~~lvi~   45 (305)
T d2bmfa2          10 RLTIMDLHPGAGKTKRYLPAIVREAIKRGLRTLILA   45 (305)
T ss_dssp             CEEEECCCTTSSTTTTHHHHHHHHHHHHTCCEEEEE
T ss_pred             CcEEEEECCCCCHHHHHHHHHHHHHHhcCCEEEEEc
Confidence            6899999999999963 2233332   266666554

>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=92.92  E-value=0.012  Score=55.47  Aligned_cols=26  Identities=19%  Similarity=0.277  Sum_probs=23.9

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGA  204 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~  204 (666)
                      +.+.|-||-||||||+++.|++.+..
T Consensus         3 k~I~ieG~dGsGKST~~~~L~~~l~~   28 (241)
T d1p5zb_           3 KKISIEGNIAAGKSTFVNILKQLCED   28 (241)
T ss_dssp             EEEEEECSTTSSHHHHHTTTGGGCTT
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHhc
Confidence            68999999999999999999999853

>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=92.88  E-value=0.023  Score=54.51  Aligned_cols=24  Identities=17%  Similarity=0.437  Sum_probs=22.2

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      ..+-|.||+|+||||++++++.-+
T Consensus        29 e~vaivG~sGsGKSTLl~ll~gl~   52 (242)
T d1mv5a_          29 SIIAFAGPSGGGKSTIFSLLERFY   52 (242)
T ss_dssp             EEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CEEEEECCCCCCHHHHHHHHHHhh
Confidence            579999999999999999998876

>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=92.84  E-value=0.017  Score=54.79  Aligned_cols=35  Identities=34%  Similarity=0.537  Sum_probs=20.7

Q ss_pred             ccEEEEECCCCchHHHHHHHHHHHcCCcEEEEcCC
Q 005987          178 TNVLVITGQAGVGKTATVRQIASHLGARLYEWDTP  212 (666)
Q Consensus       178 ~k~LLL~GPpG~GKTtla~~LAkelg~~viE~nas  212 (666)
                      .+..+|.|++|+||||++.+|..+....+-++...
T Consensus        97 ~~~~vl~G~SGVGKSSLiN~L~~~~~~~t~~vs~~  131 (231)
T d1t9ha2          97 DKTTVFAGQSGVGKSSLLNAISPELGLRTNEISEH  131 (231)
T ss_dssp             TSEEEEEESHHHHHHHHHHHHCC------------
T ss_pred             cceEEEECCCCccHHHHHHhhccHhHhhhcccccc
Confidence            35788999999999999999987776655555543

>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=92.83  E-value=0.022  Score=54.97  Aligned_cols=25  Identities=20%  Similarity=0.458  Sum_probs=22.6

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLG  203 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg  203 (666)
                      ..+-|.||+||||||++++|+.-+.
T Consensus        42 e~iaivG~sGsGKSTLl~ll~gl~~   66 (253)
T d3b60a1          42 KTVALVGRSGSGKSTIASLITRFYD   66 (253)
T ss_dssp             CEEEEEECTTSSHHHHHHHHTTTTC
T ss_pred             CEEEEECCCCChHHHHHHHHhcccC
Confidence            5799999999999999999988763

>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=92.57  E-value=0.027  Score=54.25  Aligned_cols=25  Identities=20%  Similarity=0.375  Sum_probs=22.8

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLG  203 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg  203 (666)
                      ..+.|.||+||||||++++++.-+.
T Consensus        41 e~vaivG~sGsGKSTLl~li~gl~~   65 (251)
T d1jj7a_          41 EVTALVGPNGSGKSTVAALLQNLYQ   65 (251)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTTSSC
T ss_pred             CEEEEECCCCCcHHHHHHHHhcccC
Confidence            5899999999999999999988774

>d1byia_ c.37.1.10 (A:) Dethiobiotin synthetase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Dethiobiotin synthetase
species: Escherichia coli [TaxId: 562]

Probab=92.50  E-value=0.046  Score=50.22  Aligned_cols=33  Identities=24%  Similarity=0.337  Sum_probs=28.5

Q ss_pred             cEEEEECC-CCchHHHHHHHHHHHc---CCcEEEEcC
Q 005987          179 NVLVITGQ-AGVGKTATVRQIASHL---GARLYEWDT  211 (666)
Q Consensus       179 k~LLL~GP-pG~GKTtla~~LAkel---g~~viE~na  211 (666)
                      |.++++|- +|+||||++-.||..+   |++|.-+.+
T Consensus         2 ~~~~i~gt~~GVGKTtvs~~La~aLa~~G~rVl~id~   38 (224)
T d1byia_           2 KRYFVTGTDTEVGKTVASCALLQAAKAAGYRTAGYKP   38 (224)
T ss_dssp             EEEEEEESSTTSCHHHHHHHHHHHHHHTTCCEEEECS
T ss_pred             ceEEEEECCCCccHHHHHHHHHHHHHHCCCeEEEECc
Confidence            57999999 5999999999998877   899988763

>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=92.42  E-value=0.022  Score=50.80  Aligned_cols=22  Identities=27%  Similarity=0.409  Sum_probs=19.3

Q ss_pred             EEEEECCCCchHHHHHHHHHHH
Q 005987          180 VLVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAke  201 (666)
                      -++|.|+|||||||++..+...
T Consensus        15 kI~lvG~~~vGKTsLl~~l~~~   36 (186)
T d1f6ba_          15 KLVFLGLDNAGKTTLLHMLKDD   36 (186)
T ss_dssp             EEEEEEETTSSHHHHHHHHSCC
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            4889999999999999988654

>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=92.33  E-value=0.029  Score=55.22  Aligned_cols=22  Identities=41%  Similarity=0.502  Sum_probs=16.8

Q ss_pred             EEEEECCCCchHHHHH-HHHHHH
Q 005987          180 VLVITGQAGVGKTATV-RQIASH  201 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla-~~LAke  201 (666)
                      .+|+.|||||||||++ +.+|+-
T Consensus        26 ~~lV~g~aGSGKTt~l~~ri~~l   48 (318)
T d1pjra1          26 PLLIMAGAGSGKTRVLTHRIAYL   48 (318)
T ss_dssp             CEEEEECTTSCHHHHHHHHHHHH
T ss_pred             CEEEEecCCccHHHHHHHHHHHH
Confidence            5889999999999875 444443

>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=92.24  E-value=0.28  Score=42.32  Aligned_cols=35  Identities=23%  Similarity=0.278  Sum_probs=26.1

Q ss_pred             cEEEEECCCCchHHH-HHHHH--HHHcCCcEEEEcCCC
Q 005987          179 NVLVITGQAGVGKTA-TVRQI--ASHLGARLYEWDTPT  213 (666)
Q Consensus       179 k~LLL~GPpG~GKTt-la~~L--Akelg~~viE~nasd  213 (666)
                      .+=+++||=.+|||| +++.+  .+..|.+++-++...
T Consensus         3 ~L~~i~GpMfsGKTteLi~~~~~~~~~~~kv~~ikp~~   40 (139)
T d2b8ta1           3 WIEFITGPMFAGKTAELIRRLHRLEYADVKYLVFKPKI   40 (139)
T ss_dssp             EEEEEECSTTSCHHHHHHHHHHHHHHTTCCEEEEEECC
T ss_pred             EEEEEEccccCHHHHHHHHHHHHHHHCCCcEEEEEEcc
Confidence            466889999999999 55655  334588888887664

>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=92.22  E-value=0.5  Score=44.87  Aligned_cols=23  Identities=35%  Similarity=0.671  Sum_probs=20.1

Q ss_pred             EEEEECCCCchHHHHHHHHHHHc
Q 005987          180 VLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      .++|.|.||+||||++..|..+-
T Consensus        34 ~I~LvG~tg~GKSSliN~ilg~~   56 (257)
T d1h65a_          34 TILVMGKGGVGKSSTVNSIIGER   56 (257)
T ss_dssp             EEEEEESTTSSHHHHHHHHHTSC
T ss_pred             EEEEECCCCCcHHHHHHHHhCCC
Confidence            58889999999999999987653

>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=91.98  E-value=0.033  Score=53.81  Aligned_cols=24  Identities=33%  Similarity=0.477  Sum_probs=21.4

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      .++-|.||+||||||++++++.-+
T Consensus        29 Ei~~iiG~sGsGKSTLl~~i~Gl~   52 (258)
T d1b0ua_          29 DVISIIGSSGSGKSTFLRCINFLE   52 (258)
T ss_dssp             CEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CEEEEECCCCCcHHHHHHHHHcCc
Confidence            589999999999999999998644

>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=91.31  E-value=0.05  Score=48.40  Aligned_cols=21  Identities=33%  Similarity=0.678  Sum_probs=18.9

Q ss_pred             EEEECCCCchHHHHHHHHHHH
Q 005987          181 LVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       181 LLL~GPpG~GKTtla~~LAke  201 (666)
                      ++|.|++||||||+++.+...
T Consensus         5 i~~vG~~~vGKSsLi~~~~~~   25 (175)
T d1ky3a_           5 VIILGDSGVGKTSLMHRYVND   25 (175)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHcC
Confidence            789999999999999998764

>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=91.28  E-value=0.046  Score=48.34  Aligned_cols=21  Identities=24%  Similarity=0.618  Sum_probs=19.3

Q ss_pred             EEEECCCCchHHHHHHHHHHH
Q 005987          181 LVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       181 LLL~GPpG~GKTtla~~LAke  201 (666)
                      +++.|++|+||||+++.++..
T Consensus         5 i~vvG~~~vGKTSli~~l~~~   25 (166)
T d1g16a_           5 ILLIGDSGVGKSCLLVRFVED   25 (166)
T ss_dssp             EEEEESTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            789999999999999998875

>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=91.26  E-value=0.083  Score=51.01  Aligned_cols=33  Identities=39%  Similarity=0.491  Sum_probs=28.9

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL---GARLYEWDT  211 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel---g~~viE~na  211 (666)
                      ++++++|.-|+||||++-.+|..+   |.+++-+.+
T Consensus         9 ~~i~~sGKGGVGKTTvaa~lA~~lA~~G~rVLlvD~   44 (296)
T d1ihua1           9 PYLFFTGKGGVGKTSISCATAIRLAEQGKRVLLVST   44 (296)
T ss_dssp             SEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEEC
T ss_pred             eEEEEECCCcChHHHHHHHHHHHHHHCCCCEEEEeC
Confidence            799999999999999998888877   888877664

>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=91.10  E-value=0.03  Score=53.99  Aligned_cols=25  Identities=20%  Similarity=0.405  Sum_probs=22.5

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLG  203 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg  203 (666)
                      ..+.|.||+||||||++++|+..+.
T Consensus        45 e~vaivG~sGsGKSTLl~ll~gl~~   69 (255)
T d2hyda1          45 ETVAFVGMSGGGKSTLINLIPRFYD   69 (255)
T ss_dssp             CEEEEECSTTSSHHHHHTTTTTSSC
T ss_pred             CEEEEECCCCCcHHHHHHHHHhcCC
Confidence            5799999999999999999988764

>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=90.94  E-value=0.052  Score=51.74  Aligned_cols=26  Identities=31%  Similarity=0.570  Sum_probs=23.2

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGA  204 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~  204 (666)
                      .++-|.||.|+||||++++|+..+..
T Consensus        29 ei~glvG~nGaGKSTLl~~l~G~~~p   54 (238)
T d1vpla_          29 EIFGLIGPNGAGKTTTLRIISTLIKP   54 (238)
T ss_dssp             CEEEEECCTTSSHHHHHHHHTTSSCC
T ss_pred             CEEEEECCCCCCHHHHHHHHhcCCCC
Confidence            58889999999999999999988743

>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=90.84  E-value=0.1  Score=50.05  Aligned_cols=33  Identities=30%  Similarity=0.484  Sum_probs=28.1

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL---GARLYEWDT  211 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel---g~~viE~na  211 (666)
                      ++++++|.-|+||||++-.||..+   |.+|+-+.+
T Consensus        21 ~iii~sGKGGVGKTT~a~nLA~~lA~~G~rVllvD~   56 (279)
T d1ihua2          21 GLIMLMGKGGVGKTTMAAAIAVRLADMGFDVHLTTS   56 (279)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEES
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHCCCcEEEEeC
Confidence            799999999999999977777665   888887765

>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=90.81  E-value=0.059  Score=48.49  Aligned_cols=21  Identities=38%  Similarity=0.695  Sum_probs=19.1

Q ss_pred             EEEECCCCchHHHHHHHHHHH
Q 005987          181 LVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       181 LLL~GPpG~GKTtla~~LAke  201 (666)
                      ++|.|.+||||||++..+...
T Consensus         5 v~vvG~~~vGKSSLi~~l~~~   25 (184)
T d1vg8a_           5 VIILGDSGVGKTSLMNQYVNK   25 (184)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            789999999999999998864

>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=90.77  E-value=0.061  Score=47.29  Aligned_cols=21  Identities=24%  Similarity=0.528  Sum_probs=19.1

Q ss_pred             EEEECCCCchHHHHHHHHHHH
Q 005987          181 LVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       181 LLL~GPpG~GKTtla~~LAke  201 (666)
                      ++|.|++|+|||++++.+...
T Consensus         5 v~liG~~~vGKTsLl~~~~~~   25 (165)
T d1z06a1           5 IIVIGDSNVGKTCLTYRFCAG   25 (165)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            789999999999999998864

>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=90.74  E-value=0.054  Score=52.13  Aligned_cols=25  Identities=32%  Similarity=0.554  Sum_probs=22.7

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLG  203 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg  203 (666)
                      .++-|.||.|+||||++++++-.+.
T Consensus        31 ei~~liG~nGaGKSTLl~~i~Gl~~   55 (254)
T d1g6ha_          31 DVTLIIGPNGSGKSTLINVITGFLK   55 (254)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTTSSC
T ss_pred             CEEEEECCCCCcHHHHHHHHHCCCc
Confidence            5899999999999999999988763

>d1wmsa_ c.37.1.8 (A:) Rab9a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab9a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.68  E-value=0.063  Score=47.85  Aligned_cols=21  Identities=24%  Similarity=0.651  Sum_probs=19.2

Q ss_pred             EEEECCCCchHHHHHHHHHHH
Q 005987          181 LVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       181 LLL~GPpG~GKTtla~~LAke  201 (666)
                      ++|.|++||||||++..+...
T Consensus         9 I~vvG~~~vGKSSli~~~~~~   29 (174)
T d1wmsa_           9 VILLGDGGVGKSSLMNRYVTN   29 (174)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            889999999999999888764

>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=90.47  E-value=0.06  Score=48.14  Aligned_cols=23  Identities=30%  Similarity=0.361  Sum_probs=19.6

Q ss_pred             EEEEECCCCchHHHHHHHHHHHc
Q 005987          180 VLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      -++|.|++|||||+++..+...-
T Consensus         4 KivvvG~~~vGKTsLi~~~~~~~   26 (177)
T d1kmqa_           4 KLVIVGDGACGKTCLLIVNSKDQ   26 (177)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCcCHHHHHHHHHhCC
Confidence            36778999999999999988753

>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=90.39  E-value=0.054  Score=48.43  Aligned_cols=22  Identities=18%  Similarity=0.581  Sum_probs=19.6

Q ss_pred             EEEEECCCCchHHHHHHHHHHH
Q 005987          180 VLVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAke  201 (666)
                      .++|.|+||+||||++.+|..+
T Consensus         2 ~I~lvG~~nvGKSsLin~l~~~   23 (184)
T d2cxxa1           2 TIIFAGRSNVGKSTLIYRLTGK   23 (184)
T ss_dssp             EEEEEEBTTSSHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            4789999999999999999754

>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=90.25  E-value=0.86  Score=43.79  Aligned_cols=25  Identities=28%  Similarity=0.329  Sum_probs=22.4

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLG  203 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg  203 (666)
                      |.+-|.|..|+||||++.++....|
T Consensus         7 Rni~i~gh~~~GKTtL~e~ll~~~g   31 (276)
T d2bv3a2           7 RNIGIAAHIDAGKTTTTERILYYTG   31 (276)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHHHHT
T ss_pred             eEEEEEeCCCCCHHHHHHHHHHhcC
Confidence            5799999999999999999987765

>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=90.15  E-value=0.059  Score=51.06  Aligned_cols=22  Identities=27%  Similarity=0.610  Sum_probs=20.5

Q ss_pred             cEEEEECCCCchHHHHHHHHHH
Q 005987          179 NVLVITGQAGVGKTATVRQIAS  200 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAk  200 (666)
                      .++-|.||.|+||||++++++.
T Consensus        26 ei~~iiG~nGaGKSTLl~~l~G   47 (231)
T d1l7vc_          26 EILHLVGPNGAGKSTLLARMAG   47 (231)
T ss_dssp             CEEECBCCTTSSHHHHHHHHHT
T ss_pred             CEEEEECCCCCcHHHHHHHHhC
Confidence            5899999999999999999987

>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=90.11  E-value=0.045  Score=53.58  Aligned_cols=24  Identities=17%  Similarity=0.454  Sum_probs=19.2

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      .++-++|++|+||||++++|++.+
T Consensus         5 pIIgIaG~SGSGKTTva~~l~~i~   28 (288)
T d1a7ja_           5 PIISVTGSSGAGTSTVKHTFDQIF   28 (288)
T ss_dssp             CEEEEESCC---CCTHHHHHHHHH
T ss_pred             CEEEEECCCCCcHHHHHHHHHHHH
Confidence            389999999999999999998877

>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=89.69  E-value=0.083  Score=47.48  Aligned_cols=22  Identities=27%  Similarity=0.439  Sum_probs=19.7

Q ss_pred             EEEEECCCCchHHHHHHHHHHH
Q 005987          180 VLVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAke  201 (666)
                      -++|.|.+|||||+++..+...
T Consensus         7 KivviG~~~vGKTsli~~~~~~   28 (183)
T d1mh1a_           7 KCVVVGDGAVGKTCLLISYTTN   28 (183)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            3899999999999999988875

>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=89.62  E-value=0.24  Score=42.38  Aligned_cols=35  Identities=14%  Similarity=0.141  Sum_probs=25.7

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcCCC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL---GARLYEWDTPT  213 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel---g~~viE~nasd  213 (666)
                      .+-|++||=.+||||-.-..++.+   |..++-+++..
T Consensus         3 ~L~li~GpMfsGKTt~Li~~~~~~~~~g~~v~~ikp~~   40 (133)
T d1xbta1           3 QIQVILGPMFSGKSTELMRRVRRFQIAQYKCLVIKYAK   40 (133)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHHHHTTTCCEEEEEETT
T ss_pred             EEEEEEecccCHHHHHHHHHHHHHHHcCCcEEEEeccc
Confidence            467889999999999765555443   77777777553

>d1qhla_ c.37.1.12 (A:) Cell division protein MukB {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Cell division protein MukB
species: Escherichia coli [TaxId: 562]

Probab=89.36  E-value=0.039  Score=49.49  Aligned_cols=25  Identities=28%  Similarity=0.426  Sum_probs=22.2

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLG  203 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg  203 (666)
                      .+-+|+||.|+||||++.+|.--++
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            4678999999999999999998774

>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=89.29  E-value=0.084  Score=47.42  Aligned_cols=21  Identities=33%  Similarity=0.558  Sum_probs=19.1

Q ss_pred             EEEECCCCchHHHHHHHHHHH
Q 005987          181 LVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       181 LLL~GPpG~GKTtla~~LAke  201 (666)
                      ++|.|.+|||||++++.+...
T Consensus         5 ivliG~~~vGKTsli~r~~~~   25 (179)
T d1m7ba_           5 IVVVGDSQCGKTALLHVFAKD   25 (179)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            789999999999999988874

>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=89.25  E-value=0.067  Score=50.25  Aligned_cols=28  Identities=36%  Similarity=0.597  Sum_probs=23.4

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc-CCcE
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL-GARL  206 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel-g~~v  206 (666)
                      ++.||+|.-|+||||+++.+.++. +.++
T Consensus         4 Pv~iitGFLGaGKTTll~~lL~~~~~~ri   32 (222)
T d1nija1           4 AVTLLTGFLGAGKTTLLRHILNEQHGYKI   32 (222)
T ss_dssp             EEEEEEESSSSSCHHHHHHHHHSCCCCCE
T ss_pred             CEEEEeeCCCCCHHHHHHHHHhcCCCCcE
Confidence            489999999999999999998865 3444

>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=89.01  E-value=0.092  Score=47.34  Aligned_cols=21  Identities=33%  Similarity=0.504  Sum_probs=19.2

Q ss_pred             EEEECCCCchHHHHHHHHHHH
Q 005987          181 LVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       181 LLL~GPpG~GKTtla~~LAke  201 (666)
                      ++|.|.+|||||++++.+.+.
T Consensus        12 i~lvG~~~vGKTsLi~r~~~~   32 (185)
T d2atxa1          12 CVVVGDGAVGKTCLLMSYAND   32 (185)
T ss_dssp             EEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHhhC
Confidence            789999999999999998764

>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=88.68  E-value=0.098  Score=47.37  Aligned_cols=21  Identities=29%  Similarity=0.487  Sum_probs=18.7

Q ss_pred             EEEECCCCchHHHHHHHHHHH
Q 005987          181 LVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       181 LLL~GPpG~GKTtla~~LAke  201 (666)
                      ++|.|++|||||+++..+...
T Consensus         6 vvllG~~~vGKTSli~r~~~~   26 (191)
T d2ngra_           6 CVVVGDGAVGKTCLLISYTTN   26 (191)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            778899999999999888765

>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=87.99  E-value=0.35  Score=45.48  Aligned_cols=51  Identities=16%  Similarity=0.066  Sum_probs=36.9

Q ss_pred             cCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcC
Q 005987          153 VQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL---GARLYEWDT  211 (666)
Q Consensus       153 g~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~na  211 (666)
                      .+.+.++++...+..      +.+  -..||+|.+|+|||.++-..+...   |..++-+-+
T Consensus        59 ~Q~~~~~~i~~~~~~------~~~--~~~LL~GdvGsGKT~V~~~a~~~~~~~g~qv~~l~P  112 (233)
T d2eyqa3          59 DQAQAINAVLSDMCQ------PLA--MDRLVCGDVGFGKTEVAMRAAFLAVDNHKQVAVLVP  112 (233)
T ss_dssp             HHHHHHHHHHHHHHS------SSC--CEEEEECCCCTTTHHHHHHHHHHHHTTTCEEEEECS
T ss_pred             hHHHHHHHHHHHHhc------cCc--cCeEEEcCCCCCcHHHHHHHHHHHHHcCCceEEEcc
Confidence            466777777777764      332  368999999999999986665543   777776653

>d1xzpa2 c.37.1.8 (A:212-371) TrmE GTPase domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: TrmE GTPase domain
species: Thermotoga maritima [TaxId: 2336]

Probab=87.96  E-value=0.059  Score=47.00  Aligned_cols=21  Identities=29%  Similarity=0.627  Sum_probs=19.4

Q ss_pred             EEEECCCCchHHHHHHHHHHH
Q 005987          181 LVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       181 LLL~GPpG~GKTtla~~LAke  201 (666)
                      +.|.|.||+||||++.+|..+
T Consensus         3 I~liG~~n~GKSSLin~l~g~   23 (160)
T d1xzpa2           3 MVIVGKPNVGKSTLLNRLLNE   23 (160)
T ss_dssp             EEEECCHHHHTCHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            789999999999999999876

>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=87.62  E-value=0.1  Score=50.66  Aligned_cols=26  Identities=31%  Similarity=0.489  Sum_probs=22.5

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGA  204 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~  204 (666)
                      +.-+|+||.|+|||+++.||+--+|.
T Consensus        25 ~lnvlvG~NgsGKS~iL~Ai~~~lg~   50 (308)
T d1e69a_          25 RVTAIVGPNGSGKSNIIDAIKWVFGE   50 (308)
T ss_dssp             SEEEEECCTTTCSTHHHHHHHHTSCC
T ss_pred             CeEEEECCCCCcHHHHHHHHHHHhCC
Confidence            57899999999999999999776653

>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=87.54  E-value=0.13  Score=45.55  Aligned_cols=23  Identities=22%  Similarity=0.537  Sum_probs=20.3

Q ss_pred             cEEEEECCCCchHHHHHHHHHHH
Q 005987          179 NVLVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAke  201 (666)
                      ..++|.|.||+||||++.+|.+.
T Consensus         6 ~~I~iiG~~nvGKSSLin~L~~~   28 (179)
T d1egaa1           6 GFIAIVGRPNVGKSTLLNKLLGQ   28 (179)
T ss_dssp             EEEEEECSSSSSHHHHHHHHHTC
T ss_pred             cEEEEECCCCCCHHHHHHHHhCC
Confidence            36889999999999999999754

>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=87.22  E-value=0.18  Score=51.51  Aligned_cols=32  Identities=31%  Similarity=0.525  Sum_probs=25.2

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc---CCcEEEEc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL---GARLYEWD  210 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel---g~~viE~n  210 (666)
                      +++++.|++|+|||+++..+..++   |..++-++
T Consensus        51 ~H~~I~G~tGsGKT~~l~~li~~~~~~g~~~iiiD   85 (433)
T d1e9ra_          51 RHLLVNGATGTGKSVLLRELAYTGLLRGDRMVIVD   85 (433)
T ss_dssp             GCEEEEECTTSSHHHHHHHHHHHHHHTTCEEEEEE
T ss_pred             ceEEEEeCCCCcHHHHHHHHHHHHHhCCCCEEEEe
Confidence            689999999999999998776654   55665554

>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=86.24  E-value=0.17  Score=45.07  Aligned_cols=21  Identities=29%  Similarity=0.528  Sum_probs=18.6

Q ss_pred             EEEECCCCchHHHHHHHHHHH
Q 005987          181 LVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       181 LLL~GPpG~GKTtla~~LAke  201 (666)
                      +.|.|.+|+||||++.+|...
T Consensus        11 V~iiG~~~~GKSTLin~l~~~   31 (186)
T d1mkya2          11 VAIVGRPNVGKSTLFNAILNK   31 (186)
T ss_dssp             EEEECSTTSSHHHHHHHHHTS
T ss_pred             EEEECCCCCCHHHHHHHHHCC
Confidence            678899999999999998764

>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=85.95  E-value=3.3  Score=39.20  Aligned_cols=25  Identities=28%  Similarity=0.510  Sum_probs=21.7

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLG  203 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg  203 (666)
                      |.+.|.|..|+||||++.+|....|
T Consensus         3 RNv~iiGh~~~GKTtL~e~ll~~~g   27 (267)
T d2dy1a2           3 RTVALVGHAGSGKTTLTEALLYKTG   27 (267)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHHTT
T ss_pred             eEEEEEcCCCCcHHHHHHHHHHHcC
Confidence            5788899999999999999976654

>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=85.92  E-value=0.41  Score=45.86  Aligned_cols=52  Identities=19%  Similarity=0.173  Sum_probs=37.4

Q ss_pred             cCHHHHHHHHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcCC
Q 005987          153 VQRKKVEEVRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL---GARLYEWDTP  212 (666)
Q Consensus       153 g~~k~i~el~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel---g~~viE~nas  212 (666)
                      .|.++++++..-+..      +.+  -.-||+|..|+|||.++-..+...   |+.++-+-..
T Consensus        87 ~Q~~ai~ei~~d~~~------~~~--m~rLL~GdvGSGKT~Va~~a~~~~~~~g~q~~~m~Pt  141 (264)
T d1gm5a3          87 AQKRAHQEIRNDMIS------EKP--MNRLLQGDVGSGKTVVAQLAILDNYEAGFQTAFMVPT  141 (264)
T ss_dssp             HHHHHHHHHHHHHHS------SSC--CCCEEECCSSSSHHHHHHHHHHHHHHHTSCEEEECSC
T ss_pred             hHHHHHHHHHHHhhc------cCc--ceeeeeccccccccHHHHHHHHHHHhcccceeEEeeh
Confidence            377778888777764      332  257999999999999986665543   8887766543

>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=85.75  E-value=0.18  Score=45.40  Aligned_cols=18  Identities=22%  Similarity=0.567  Sum_probs=17.2

Q ss_pred             EEEECCCCchHHHHHHHH
Q 005987          181 LVITGQAGVGKTATVRQI  198 (666)
Q Consensus       181 LLL~GPpG~GKTtla~~L  198 (666)
                      ++|-|.+|+|||++++.+
T Consensus         5 ivllG~~~vGKTsll~r~   22 (200)
T d1zcba2           5 ILLLGAGESGKSTFLKQM   22 (200)
T ss_dssp             EEEECSTTSSHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHH
Confidence            789999999999999988

>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=85.56  E-value=0.15  Score=45.61  Aligned_cols=20  Identities=25%  Similarity=0.443  Sum_probs=17.9

Q ss_pred             EEEECCCCchHHHHHHHHHH
Q 005987          181 LVITGQAGVGKTATVRQIAS  200 (666)
Q Consensus       181 LLL~GPpG~GKTtla~~LAk  200 (666)
                      +-|.|+||+||||++.+|.+
T Consensus         4 VaiiG~~nvGKSSLin~L~~   23 (185)
T d1lnza2           4 VGLVGFPSVGKSTLLSVVSS   23 (185)
T ss_dssp             EEEESSTTSSHHHHHHHSEE
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            67999999999999998854

>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=85.19  E-value=0.11  Score=46.01  Aligned_cols=22  Identities=14%  Similarity=0.424  Sum_probs=19.1

Q ss_pred             cEEEEECCCCchHHHHHHHHHH
Q 005987          179 NVLVITGQAGVGKTATVRQIAS  200 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAk  200 (666)
                      .-+.|.|+|++||||++.+|..
T Consensus        17 ~~I~lvG~~NvGKSSL~n~L~~   38 (188)
T d1puia_          17 IEVAFAGRSNAGKSSALNTLTN   38 (188)
T ss_dssp             EEEEEEECTTSSHHHHHTTTCC
T ss_pred             CEEEEECCCCCCHHHHHHHHhC
Confidence            3589999999999999988854

>d1wb1a4 c.37.1.8 (A:1-179) Elongation factor SelB, N-terminal domain {Methanococcus maripaludis [TaxId: 39152]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Elongation factor SelB, N-terminal domain
species: Methanococcus maripaludis [TaxId: 39152]

Probab=85.05  E-value=1.7  Score=38.24  Aligned_cols=22  Identities=27%  Similarity=0.283  Sum_probs=19.4

Q ss_pred             EEEEECCCCchHHHHHHHHHHH
Q 005987          180 VLVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAke  201 (666)
                      .+-|.|.|++||||++.+|.+.
T Consensus         7 nIaiiG~~naGKSTL~n~L~~~   28 (179)
T d1wb1a4           7 NLGIFGHIDHGKTTLSKVLTEI   28 (179)
T ss_dssp             EEEEEECTTSSHHHHHHHHHTT
T ss_pred             EEEEEeCCCCcHHHHHHHHHHh
Confidence            3778999999999999999854

>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=84.94  E-value=0.24  Score=44.17  Aligned_cols=22  Identities=23%  Similarity=0.374  Sum_probs=19.6

Q ss_pred             EEEEECCCCchHHHHHHHHHHH
Q 005987          180 VLVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAke  201 (666)
                      -+++.|++|+|||+++..+...
T Consensus         7 ki~vlG~~~vGKTsLi~~~~~~   28 (175)
T d2bmja1           7 RLGVLGDARSGKSSLIHRFLTG   28 (175)
T ss_dssp             EEEEECCTTTTHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            3889999999999999988775

>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=84.61  E-value=0.22  Score=44.53  Aligned_cols=22  Identities=23%  Similarity=0.407  Sum_probs=19.9

Q ss_pred             EEEECCCCchHHHHHHHHHHHc
Q 005987          181 LVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       181 LLL~GPpG~GKTtla~~LAkel  202 (666)
                      ++|-|..|+|||++++.+...-
T Consensus         5 iv~lG~~~vGKTsll~r~~~~~   26 (200)
T d2bcjq2           5 LLLLGTGESGKSTFIKQMRIIH   26 (200)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHT
T ss_pred             EEEECCCCCCHHHHHHHHhCCC
Confidence            8899999999999999997764

>d1lkxa_ c.37.1.9 (A:) Myosin S1, motor domain {Dictyostelium discoideum, class-I myosin MyoE [TaxId: 44689]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Myosin S1, motor domain
species: Dictyostelium discoideum, class-I myosin MyoE [TaxId: 44689]

Probab=84.59  E-value=0.42  Score=52.17  Aligned_cols=60  Identities=20%  Similarity=0.331  Sum_probs=44.9

Q ss_pred             CCCccccccCCCCccccccCHHHHHH--HHHHHHHhhcCCCCCCCccEEEEECCCCchHHHHHHHHHHHc
Q 005987          135 TQQLWAEKYKPRSLEELAVQRKKVEE--VRAWFEERLGDSKDKFSTNVLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       135 ~~~~W~eKY~P~sl~eLvg~~k~i~e--l~~wL~~~~~~~~g~~~~k~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      .+..++.+|+-+...++.-|--.+.+  .+.++..      ++  ...+|++|.+|+|||+.++.+-+.+
T Consensus        49 y~~~~~~~y~~~~~~~~~PHif~iA~~Ay~~l~~~------~~--~QsIiisGeSGsGKTe~~k~il~yL  110 (684)
T d1lkxa_          49 YKESDIKAYNGRYKYEMPPHMYALANDAYRSMRQS------QE--NQCVIISGESGAGKTEASKKIMQFL  110 (684)
T ss_dssp             CSHHHHHHHSSCCGGGSCCCHHHHHHHHHHHHHHH------CC--CEEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CCHHHHHHHcCCCCCCCCChHHHHHHHHHHHHHHc------CC--CeEEEEEcCCCCCHHHHHHHHHHHH
Confidence            45678999998888888877666544  2233332      22  2589999999999999999998876

>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=84.24  E-value=0.2  Score=49.86  Aligned_cols=33  Identities=27%  Similarity=0.414  Sum_probs=26.0

Q ss_pred             EEEEECCCCchHHHHHHHHHHHcCC--cEEEEcCC
Q 005987          180 VLVITGQAGVGKTATVRQIASHLGA--RLYEWDTP  212 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkelg~--~viE~nas  212 (666)
                      .+.|-|+-|+||||+++.|++.++.  .++.+..|
T Consensus         8 rI~iEG~iGsGKSTl~~~L~~~l~~~~~v~~~~EP   42 (333)
T d1p6xa_           8 RIYLDGVYGIGKSTTGRVMASAASGGSPTLYFPEP   42 (333)
T ss_dssp             EEEEECSTTSSHHHHHHHHHSGGGCSSCEEEECCC
T ss_pred             EEEEECCccCCHHHHHHHHHHHhccCCCeEEEeCc
Confidence            4889999999999999999999843  44444433

>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=83.95  E-value=0.24  Score=46.03  Aligned_cols=22  Identities=27%  Similarity=0.436  Sum_probs=19.2

Q ss_pred             EEEEECCCCchHHHHHHHHHHH
Q 005987          180 VLVITGQAGVGKTATVRQIASH  201 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAke  201 (666)
                      -+||-|++|+||||+++.+...
T Consensus         8 KilllG~~~vGKTsll~~~~~~   29 (221)
T d1azta2           8 RLLLLGAGESGKSTIVKQMRIL   29 (221)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            4899999999999999988644

>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=83.20  E-value=0.38  Score=45.67  Aligned_cols=33  Identities=27%  Similarity=0.502  Sum_probs=27.1

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL---GARLYEWDT  211 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel---g~~viE~na  211 (666)
                      +.+.++|.=||||||++-.||..+   |.+|+-+.+
T Consensus         2 r~Iai~gKGGvGKTT~a~nLA~~LA~~G~rVllID~   37 (269)
T d1cp2a_           2 RQVAIYGKGGIGKSTTTQNLTSGLHAMGKTIMVVGC   37 (269)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHHHHTTTCCEEEEEE
T ss_pred             CEEEEECCCcCCHHHHHHHHHHHHHhCCCcEEEEec
Confidence            356679999999999998887776   888887765

>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=82.80  E-value=2.6  Score=38.68  Aligned_cols=23  Identities=22%  Similarity=0.413  Sum_probs=20.5

Q ss_pred             EEEEECCCCchHHHHHHHHHHHc
Q 005987          180 VLVITGQAGVGKTATVRQIASHL  202 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkel  202 (666)
                      ++-+.|.|++||||++.+|....
T Consensus         7 ~IaIiGh~d~GKSTL~~~L~~~~   29 (227)
T d1g7sa4           7 IVSVLGHVDHGKTTLLDHIRGSA   29 (227)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEEEeCCCccHHHHHHHHHhhc
Confidence            58889999999999999998764

>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=82.40  E-value=0.29  Score=48.64  Aligned_cols=33  Identities=24%  Similarity=0.505  Sum_probs=26.6

Q ss_pred             EEEEECCCCchHHHHHHHHHHHcCC---cEEEEcCC
Q 005987          180 VLVITGQAGVGKTATVRQIASHLGA---RLYEWDTP  212 (666)
Q Consensus       180 ~LLL~GPpG~GKTtla~~LAkelg~---~viE~nas  212 (666)
                      .+.|-|+-|+||||+++.|++.++.   .++.+..|
T Consensus         7 rI~IEG~iGsGKSTl~~~L~~~l~~~g~~v~~~~EP   42 (331)
T d1osna_           7 RIYLDGAYGIGKTTAAEEFLHHFAITPNRILLIGEP   42 (331)
T ss_dssp             EEEEEESSSSCTTHHHHHHHHTTTTSGGGEEEECCC
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHhhcCCceEEEeCc
Confidence            3789999999999999999999853   45555544

>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=82.00  E-value=0.41  Score=48.06  Aligned_cols=27  Identities=37%  Similarity=0.543  Sum_probs=22.6

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHcCCc
Q 005987          179 NVLVITGQAGVGKTATVRQIASHLGAR  205 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkelg~~  205 (666)
                      +.-+|+||.|+|||+++.+|+=.||..
T Consensus        26 ~l~~i~G~NGsGKS~ileAi~~~lg~~   52 (427)
T d1w1wa_          26 NFTSIIGPNGSGKSNMMDAISFVLGVR   52 (427)
T ss_dssp             SEEEEECSTTSSHHHHHHHHHHHTTC-
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHhCCC
Confidence            467899999999999999998767643

>d1ys7a2 c.23.1.1 (A:7-127) Transcriptional regulatory protein PrrA, N-terminal domain {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Transcriptional regulatory protein PrrA, N-terminal domain
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=81.74  E-value=9.8  Score=30.83  Aligned_cols=75  Identities=17%  Similarity=0.376  Sum_probs=44.4

Q ss_pred             ceEEEEe-CCCCCcchhHHHHHHHHHHHHHhcCCCceEEEEecCCCCCCccchhhhhhHHHHHHhhcCeeEEEeCCCCHH
Q 005987          261 SAILLID-DLPVTNGRTAFERLRQCLLLLVRSTHIPTAVVLTECGKADSVDSTAQSFEELQSILVDAGARKVALNPITNG  339 (666)
Q Consensus       261 ~~IIlID-Eid~l~~~~~~~~l~~~L~~l~~~~~~PiViIit~~~~~~s~d~~~r~l~~L~s~L~r~r~~~I~F~p~s~~  339 (666)
                      +-++|+| .+|.+++-+....    +..  .....|+|++.+......    ..+.+        ..++.-+-.+|++.+
T Consensus        46 ~dlvl~D~~mP~~~G~el~~~----ir~--~~~~~piI~lt~~~~~~~----~~~a~--------~~Ga~dyl~KP~~~~  107 (121)
T d1ys7a2          46 PDAIVLDINMPVLDGVSVVTA----LRA--MDNDVPVCVLSARSSVDD----RVAGL--------EAGADDYLVKPFVLA  107 (121)
T ss_dssp             CSEEEEESSCSSSCHHHHHHH----HHH--TTCCCCEEEEECCCTTTC----CCTTT--------TTTCSEEEESSCCHH
T ss_pred             CCEEEEEeeccCcccHHHHHH----HHh--cCCCCEEEEEEeeCCHHH----HHHHH--------HCCCCEEEECCCCHH
Confidence            4588898 4576655332222    222  123467776655422211    11111        126777888999999


Q ss_pred             HHHHHHHHHHHHhC
Q 005987          340 SIKRTLSKICRQEQ  353 (666)
Q Consensus       340 ~i~kiL~~I~~~e~  353 (666)
                      ++...+++++++.|
T Consensus       108 ~L~~~i~~~l~rrG  121 (121)
T d1ys7a2         108 ELVARVKALLRRRG  121 (121)
T ss_dssp             HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCC
Confidence            99999998887653

>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=80.76  E-value=0.58  Score=44.89  Aligned_cols=33  Identities=24%  Similarity=0.470  Sum_probs=25.8

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL---GARLYEWDT  211 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel---g~~viE~na  211 (666)
                      +.+.++|.=|+||||++--||..|   |.+|+-+..
T Consensus         3 r~IaisgKGGVGKTT~a~NLA~~LA~~G~rVLlID~   38 (289)
T d2afhe1           3 RQCAIYGKGGIGKSTTTQNLVAALAEMGKKVMIVGC   38 (289)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHHHHHTTCCEEEEEE
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEec
Confidence            345679999999999877766655   889887764

>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=80.66  E-value=0.57  Score=43.57  Aligned_cols=33  Identities=30%  Similarity=0.351  Sum_probs=24.2

Q ss_pred             cEEEEECCCCchHHHHHHHHHHHc---CCcEEEEcC
Q 005987          179 NVLVITGQAGVGKTATVRQIASHL---GARLYEWDT  211 (666)
Q Consensus       179 k~LLL~GPpG~GKTtla~~LAkel---g~~viE~na  211 (666)
                      +.+++.+|+|+|||+++-..+..+   |..++-+-.
T Consensus        59 ~~~~i~apTGsGKT~~~~~~~~~~~~~~~rvliv~P   94 (237)
T d1gkub1          59 ESFAATAPTGVGKTSFGLAMSLFLALKGKRCYVIFP   94 (237)
T ss_dssp             CCEECCCCBTSCSHHHHHHHHHHHHTTSCCEEEEES
T ss_pred             CCEEEEecCCChHHHHHHHHHHHHHHhcCeEEEEec
Confidence            469999999999998876665543   556665554

>d1mvoa_ c.23.1.1 (A:) PhoP receiver domain {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: PhoP receiver domain
species: Bacillus subtilis [TaxId: 1423]

Probab=80.52  E-value=13  Score=29.97  Aligned_cols=25  Identities=20%  Similarity=0.383  Sum_probs=21.5

Q ss_pred             CeeEEEeCCCCHHHHHHHHHHHHHH
Q 005987          327 GARKVALNPITNGSIKRTLSKICRQ  351 (666)
Q Consensus       327 r~~~I~F~p~s~~~i~kiL~~I~~~  351 (666)
                      ++..+-.+|++.+++...++.++++
T Consensus        96 Ga~~yl~KP~~~~~L~~~i~~~lrR  120 (121)
T d1mvoa_          96 GADDYMTKPFSPREVNARVKAILRR  120 (121)
T ss_dssp             TCCEEEESSCCHHHHHHHHHHHHHT
T ss_pred             CCCEEEECCCCHHHHHHHHHHHHcc
Confidence            7888899999999999999887653